From 32a43edbc3c248d7fd5b7197ab3c2f7df8779099 Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Wed, 11 Feb 2026 11:52:26 -0500 Subject: [PATCH 01/10] Nexus: Update Quantum ESPRESSO density functional lists for QE 7.5 --- nexus/nexus/pwscf.py | 118 +++++++++++++++++++++++++++---------------- 1 file changed, 75 insertions(+), 43 deletions(-) diff --git a/nexus/nexus/pwscf.py b/nexus/nexus/pwscf.py index ddef6c1dd6..33f85ef505 100644 --- a/nexus/nexus/pwscf.py +++ b/nexus/nexus/pwscf.py @@ -27,53 +27,85 @@ from .execute import execute +# From q-e/Modules/funct.f90, QE 7.5, 2/11/26 unique_vdw_functionals = [ - 'optb86b-vdw', - 'vdw-df3', # optB88+vdW - 'vdw-df', - 'vdw-df2', - 'rev-vdw-df2', - 'vdw-df-c09', - 'vdw-df2-c09', - 'rvv10', - ] -repeat_vdw_functionals = [ - 'vdw-df4', # 'optB86b-vdW' - ] + "vdw-df", + "vdw-df2", + "vdw-df-c09", + "vdw-df2-c09", + "vdw-df-obk8", + "vdw-df-ob86", + "vdw-df2-b86r", + "vdw-df-cx", + "vdw-df-cx0", + "vdw-df2-0", + "vdw-df2-br0", + "vdw-df-c090", + "vdw-df3-opt1", + "vdw-df3-opt2", + "vdw-df3-mc", + "vdw-df-C6", + "rvv10", +] + +# From q-e/XClib/qe_dft_list.f90, QE 7.5, 2/11/26 unique_functionals = [ - 'revpbe', - 'pw86pbe', - 'b86bpbe', - 'pbe0', - 'hse', - 'gaup', - 'pbesol', - 'pbeq2d', - 'optbk88', - 'optb86b', - 'pbe', - 'wc', - 'b3lyp', - 'pbc', - 'bp', - 'pw91', - 'hcth', - 'olyp', - 'tpss', - 'oep', - 'hf', - 'blyp', - 'lda', - 'sogga', - 'm06l', - 'ev93', - ]+unique_vdw_functionals + "pz", + "lda", + "pw", + "vwn-rpa", + "oep", + "kli", + "hf", + "pbe", + "b88", + "bp", + "pw91", + "revpbe", + "pbesol", + "blyp", + "optbk88", + "optb86b", + "pbc", + "hcth", + "olyp", + "wc", + "pw86pbe", + "b86bpbe", + "pbeq2d", + "q2d", + "sogga", + "ev93", + "rpbe", + "pbe0", + "b86bpbex", + "bhahlyp", + "bhandhlyp", + "hse", + "gaup", + "b3lyp", + "b3lyp-v1r", + "x3lyp", + "tpss", + "m06l", + "tb09", + "scan", + "scan0", + "r2scan", + "pbe-ah", + "pbesol-ah", + "rscan", +] + unique_vdw_functionals + +# From q-e/XClib/qe_dft_list.f90, QE 7.5, 2/11/26 repeat_functionals = [ - 'q2d', # pbeq2d - 'pz', # lda - ]+repeat_vdw_functionals + "lda", # "pz" + "q2d", # "pbeq2d" + "bhandhlyp", # "bhahlyp" + "gaupbe", # "gaup" +] -vdw_functionals = set(unique_vdw_functionals+repeat_vdw_functionals) +vdw_functionals = set(unique_vdw_functionals) allowed_functionals = set(unique_functionals+repeat_functionals) From c124b43f7d36cdef691079d301faef7bfadefc0f Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Wed, 18 Feb 2026 17:46:35 -0500 Subject: [PATCH 02/10] Nexus: Begin rework of `pwscf_input.py` --- nexus/nexus/pwscf_input_new.py | 154 +++++++++++++++++++++++++++++++++ nexus/nxs_pw_inp_arrays.txt | 24 +++++ nexus/nxs_pw_inp_bools.txt | 43 +++++++++ nexus/nxs_pw_inp_floats.txt | 138 +++++++++++++++++++++++++++++ nexus/nxs_pw_inp_ints.txt | 70 +++++++++++++++ nexus/nxs_pw_inp_strs.txt | 45 ++++++++++ 6 files changed, 474 insertions(+) create mode 100644 nexus/nexus/pwscf_input_new.py create mode 100644 nexus/nxs_pw_inp_arrays.txt create mode 100644 nexus/nxs_pw_inp_bools.txt create mode 100644 nexus/nxs_pw_inp_floats.txt create mode 100644 nexus/nxs_pw_inp_ints.txt create mode 100644 nexus/nxs_pw_inp_strs.txt diff --git a/nexus/nexus/pwscf_input_new.py b/nexus/nexus/pwscf_input_new.py new file mode 100644 index 0000000000..581a583a91 --- /dev/null +++ b/nexus/nexus/pwscf_input_new.py @@ -0,0 +1,154 @@ +from __future__ import annotations +import os +import numpy as np +import numpy.typing as npt +import builtins +from abc import ABC +from enum import Enum + + +type PwscfInputType = ( + str + | bool + | int + | float + | list +) + + +class NamelistVariableBase(ABC): + """Abstract base class for all namelist variables.""" + + def __init__( + self, + name: str, + datatype: PwscfInputType, + default: PwscfInputType | None, + allowed_values: tuple[PwscfInputType] | None = None, + dependencies: tuple[NamelistVariableBase] | None = None, + ): + self.name = name + self.datatype = datatype + self.default = default + self.required = self.default is None + self.allowed_values = allowed_values + self.dependencies = dependencies + + + @property + def value(self) -> PwscfInputType: + return self._value + + + @value.setter + def value(self, val: PwscfInputType): + if val is None and self.required: + raise ValueError( + f"Can not set {self.name} to None, it is required!" + ) + elif not isinstance(val, self.datatype): + return TypeError( + f"Expected a value of type {self.datatype} for {self.name} but got {type(val)} instead!" + ) + else: + self._value = val + + + def write_value(self) -> str: + match self.datatype: + case builtins.bool: + if self._value: + return f" {self.name:<15} = .true." + else: + return f" {self.name:<15} = .false." + + case builtins.str: + return f" {self.name:<15} = '{self.value}'" + + case builtins.int: + return f" {self.name:<15} = {self.value}" + + case builtins.float: + return f" {self.name:<15} = {self.value}" + + case builtins.list: + string = "" + if isinstance(self.value[0], str): + for index, val in enumerate(self.value): + string += f" {self.name+f'({index+1})':<15} = '{val}'" + else: + for index, val in enumerate(self.value): + string += f" {self.name+f'({index+1})':<15} = {val}" + return string + case _: + raise TypeError("Value is not a valid Pwscf Input Type!") + #end def write_value +#end class InputCard + + +class ControlVariable(NamelistVariableBase, Enum): + """Class representing a single variable that belongs to the + &CONTROL input namelist for ``pw.x``. + """ + + def __new__(cls, datatype, default, allowed_values, dependencies): ... + + calculation = str, "scf", ["scf", "nscf", "bands", "relax", "md"], None + + + +class SystemVariable(NamelistVariableBase): + """Class representing a single variable that belongs to the + &SYSTEM input namelist for ``pw.x``. + """ + + def __init__(self, **kwargs): + super().__init__(**kwargs) + + +class ElectronsVariable(NamelistVariableBase): + """Class representing a single variable that belongs to the + &ELECTRONS input namelist for ``pw.x``. + """ + + def __init__(self, **kwargs): + super().__init__(**kwargs) + + +class IonsVariable(NamelistVariableBase): + """Class representing a single variable that belongs to the + &IONS input namelist for ``pw.x``. + """ + + def __init__(self, **kwargs): + super().__init__(**kwargs) + + +class CellVariable(NamelistVariableBase): + """Class representing a single variable that belongs to the + &CELL input namelist for ``pw.x``. + """ + + def __init__(self, **kwargs): + super().__init__(**kwargs) + + +class FCPVariable(NamelistVariableBase): + """Class representing a single variable that belongs to the + &FCP input namelist for ``pw.x``. + """ + + def __init__(self, **kwargs): + super().__init__(**kwargs) + + +class RismVariable(NamelistVariableBase): + """Class representing a single variable that belongs to the + &RISM input namelist for ``pw.x``. + """ + + def __init__(self, **kwargs): + super().__init__(**kwargs) + + + diff --git a/nexus/nxs_pw_inp_arrays.txt b/nexus/nxs_pw_inp_arrays.txt new file mode 100644 index 0000000000..9a95d88414 --- /dev/null +++ b/nexus/nxs_pw_inp_arrays.txt @@ -0,0 +1,24 @@ +"celldm", +!"starting_magnetization", +!"hubbard_alpha", # Removed? +!"hubbard_u", # Removed? +!"hubbard_j0", # Removed? +!"hubbard_beta", +!"hubbard_j", # Removed? +"starting_ns_eigenvalue", +!"angle1", +!"angle2", +"fixed_magnetization", +"fe_step", # Removed? +"efield_cart", +!"london_c6", +!"london_rvdw", +!"starting_charge" + + +fnhscl -start 1 -end ntyp REAL +solute_epsilon -start 1 -end ntyp REAL +solute_sigma -start 1 -end ntyp REAL +Hubbard_occ -start 1,1 -end ntyp,3 -indexes ityp,i REAL +nhgrp -start 1 -end ntyp INTEGER +solute_lj -start 1 -end ntyp CHARACTER \ No newline at end of file diff --git a/nexus/nxs_pw_inp_bools.txt b/nexus/nxs_pw_inp_bools.txt new file mode 100644 index 0000000000..ba67a43093 --- /dev/null +++ b/nexus/nxs_pw_inp_bools.txt @@ -0,0 +1,43 @@ +"wf_collect", +"tstress", +"tprnfor", +"lkpoint_dir", +"tefield", +"dipfield", +"lelfield", +"lberry", +"nosym", +"nosym_evc", +"noinv", +"force_symmorphic", +"noncolin", # Removed? +"lda_plus_u", # Removed? +"lspinorb", +"do_ee", # Removed? +"london", +"diago_full_acc", +"tqr", +"remove_rigid_rot", +"refold_pos", +"first_last_opt", # Removed? +"use_masses", # Removed? +"use_freezing", # Removed? +"la2F", # Removed? +"lorbm", +"lfcpopt", # Removed? +"scf_must_converge", +"adaptive_thr", +"no_t_rev", +"use_all_frac", +"one_atom_occupations", +"starting_spin_angle", +"x_gamma_extrapolation", +"xdm", +"uniqueb", +"rhombohedral", +"gate", +"block", +"relaxz", +"dftd3_threebody", +"ts_vdw_isolated", # Removed? +"lforcet", diff --git a/nexus/nxs_pw_inp_floats.txt b/nexus/nxs_pw_inp_floats.txt new file mode 100644 index 0000000000..54e6525445 --- /dev/null +++ b/nexus/nxs_pw_inp_floats.txt @@ -0,0 +1,138 @@ +"dt", +"max_seconds", +"etot_conv_thr", +"forc_conv_thr", +"celldm", +"A", +"B", +"C", +"cosAB", +"cosAC", +"cosBC", +"nelec", # Removed? +"ecutwfc", +"ecutrho", +"degauss", +"tot_charge", +"tot_magnetization", +"starting_magnetization", +"nelup", # Removed? +"neldw", # Removed? +"ecfixed", +"qcutz", +"q2sigma", +"Hubbard_alpha", # Removed? +"Hubbard_U", # Removed? +"Hubbard_J", # Removed? +"starting_ns_eigenvalue", +"emaxpos", +"eopreg", +"eamp", +"angle1", +"angle2", +"fixed_magnetization", +"lambda", +"london_s6", +"london_rcut", +"conv_thr", +"mixing_beta", +"diago_thr_init", +"efield", +"tempw", +"tolp", +"delta_t", +"upscale", +"trust_radius_max", +"trust_radius_min", +"trust_radius_ini", +"w_1", +"w_2", +"temp_req", # Removed? +"ds", # Removed? +"k_max", # Removed? +"k_min", # Removed? +"path_thr", # Removed? +"fe_step", # Removed? +"g_amplitude", # Removed? +"press", +"wmass", +"cell_factor", +"press_conv_thr", +"xqq", # Removed? +"ecutcoarse", # Removed? +"mixing_charge_compensation", # Removed? +"comp_thr", # Removed? +"exx_fraction", +"ecutfock", +"conv_thr_init", +"conv_thr_multi", +"efield_cart", +"screening_parameter", +"ecutvcut", +"Hubbard_J0", # Removed? +"Hubbard_beta", +"Hubbard_J", # Removed? +"esm_w", +"esm_efield", +"fcp_mu", +"london_c6", +"london_rvdw", +"xdm_a1", +"xdm_a2", +"block_1", +"block_2", +"block_height", +"zgate", +"ts_vdw_econv_thr", +"starting_charge" + + + +"degauss_cond", # New? +"nelec_cond", # New? +"sic_gamma", # New? +"sci_vb", # New? +"sci_cb", # New? +"localization_thr", # New? +"gcscf_mu", # New? +"gcscf_conv_thr", # New? +"gcscf_beta", # New? +"fnosep", # New? +"fire_alpha_init", # New? +"fire_falpha", # New? +"fire_f_inc", # New? +"fire_f_dec", # New? +"fire_dtmax", # New? +"fcp_conv_thr", # New? +"fcp_mass", # New? +"fcp_velocity", # New? +"fcp_tempw", # New? +"fcp_tolp", # New? +"fcp_delta_t", # New? +"tempv", # New? +"ecutsolv", # New? +"smear1d", # New? +"smear3d", # New? +"rism1d_conv_thr", # New? +"rism3d_conv_thr", # New? +"mdiis1d_step", # New? +"mdiis3d_step", # New? +"rism1d_bond_width", # New? +"rism1d_dielectric", # New? +"rism1d_molesize", # New? +"rism3d_conv_level", # New? +"laue_expand_right", # New? +"laue_expand_left", # New? +"laue_starting_right", # New? +"laue_starting_left", # New? +"laue_buffer_right", # New? +"laue_buffer_left", # New? +"laue_wall_z", # New? +"laue_wall_rho", # New? +"laue_wall_epsilon", # New? +"laue_wall_sigma", # New? +"constr_tol", # New? +"Hubbard_occ", # New? +"fnhscl", # New? +"solute_epsilon", # New? +"solute_sigma", # New? \ No newline at end of file diff --git a/nexus/nxs_pw_inp_ints.txt b/nexus/nxs_pw_inp_ints.txt new file mode 100644 index 0000000000..75215d2bea --- /dev/null +++ b/nexus/nxs_pw_inp_ints.txt @@ -0,0 +1,70 @@ +"nstep" +"iprint" +"gdir" +"nppstr" +"nberrycyc" +"ibrav" +"nat" +"ntyp" +"nbnd" +"nr1" +"nr2" +"nr3" +"nr1s" +"nr2s" +"nr3s" +"nspin" +"multiplicity" # Removed? +"edir" +"report" +"electron_maxstep" +"mixing_ndim" +"mixing_fixed_ns" +"ortho_para" # Removed? +"diago_cg_maxiter" +"diago_david_ndim" +"nraise" +"bfgs_ndim" +"num_of_images" # Removed? +"fe_nstep" # Removed? +"sw_nstep" # Removed? +"modenum" # Removed? +"n_charge_compensation" # Removed? +"nlev" # Removed? +"lda_plus_u_kind" # Removed? +"nqx1" +"nqx2" +"nqx3" +"esm_nfit" +"space_group" +"origin_choice" +"dftd3_version" + + +"nextffield", # New? +"exx_maxstep", # New? +"diago_rmm_ndim", # New? +"diago_gs_nblock", # New? +"nhpcl", # New? +"nhptyp", # New? +"ndega", # New? +"fire_nmin", # New? +"fcp_ndiis", # New? +"fcp_nraise", # New? +"nsolv", # New? +"rism1d_maxstep", # New? +"rism3d_maxstep", # New? +"mdiis1d_size", # New? +"mdiis3d_size", # New? +"rism1d_nproc", # New? +"laue_nfit", # New? +"nks", # New? +"nks_add", # New? +"nconstr", # New? +"nbnd_cond", # New? +"nk1", # New? +"nk2", # New? +"nk3", # New? +"sk1", # New? +"sk2", # New? +"sk3", # New? \ No newline at end of file diff --git a/nexus/nxs_pw_inp_strs.txt b/nexus/nxs_pw_inp_strs.txt new file mode 100644 index 0000000000..25bc23c0ff --- /dev/null +++ b/nexus/nxs_pw_inp_strs.txt @@ -0,0 +1,45 @@ +"calculation", +"title", +"verbosity", +"restart_mode", +"outdir", +"wfcdir", +"prefix", +"disk_io", +"pseudo_dir", +"occupations", +"smearing", +"input_dft", +"U_projection_type", # Removed? +"constrained_magnetization", +"mixing_mode", +"diagonalization", +"startingpot", +"startingwfc", +"ion_dynamics", +"ion_positions", +"phase_space", # Removed? +"pot_extrapolation", +"wfc_extrapolation", +"ion_temperature", +"opt_scheme", # Removed? +"CI_scheme", # Removed? +"cell_dynamics", +"cell_dofree", +"which_compensation", # Removed? +"assume_isolated", +"exxdiv_treatment", +"esm_bc", +"vdw_corr", +"efield_phase", + + +"pol_type", # New? +"dmft_prefix", # New? +"ion_velocities", # New? +"fcp_dynamics", # New? +"fcp_temperature", # New? +"closure", # New? +"starting1d", # New? +"starting3d", # New? +"laue_wall", # New? \ No newline at end of file From 2192c93f8d64defb111238494b442ccd29d543e1 Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Wed, 18 Feb 2026 23:23:27 -0500 Subject: [PATCH 03/10] Nexus: Continue reworking `pwscf_input.py` Signed-off-by: brockdyer03 --- nexus/nexus/pwscf_input_new.py | 197 +++++++++++++++++---------------- 1 file changed, 101 insertions(+), 96 deletions(-) diff --git a/nexus/nexus/pwscf_input_new.py b/nexus/nexus/pwscf_input_new.py index 581a583a91..a4bb40b1fb 100644 --- a/nexus/nexus/pwscf_input_new.py +++ b/nexus/nexus/pwscf_input_new.py @@ -3,7 +3,8 @@ import numpy as np import numpy.typing as npt import builtins -from abc import ABC +from dataclasses import dataclass +from abc import ABC, abstractmethod from enum import Enum @@ -15,140 +16,144 @@ | list ) - -class NamelistVariableBase(ABC): - """Abstract base class for all namelist variables.""" - - def __init__( - self, - name: str, - datatype: PwscfInputType, - default: PwscfInputType | None, - allowed_values: tuple[PwscfInputType] | None = None, - dependencies: tuple[NamelistVariableBase] | None = None, - ): - self.name = name - self.datatype = datatype - self.default = default - self.required = self.default is None - self.allowed_values = allowed_values - self.dependencies = dependencies - - - @property - def value(self) -> PwscfInputType: - return self._value - - - @value.setter - def value(self, val: PwscfInputType): - if val is None and self.required: - raise ValueError( - f"Can not set {self.name} to None, it is required!" - ) - elif not isinstance(val, self.datatype): - return TypeError( - f"Expected a value of type {self.datatype} for {self.name} but got {type(val)} instead!" - ) - else: - self._value = val - - - def write_value(self) -> str: - match self.datatype: - case builtins.bool: - if self._value: - return f" {self.name:<15} = .true." - else: - return f" {self.name:<15} = .false." - - case builtins.str: - return f" {self.name:<15} = '{self.value}'" - - case builtins.int: - return f" {self.name:<15} = {self.value}" - - case builtins.float: - return f" {self.name:<15} = {self.value}" - - case builtins.list: - string = "" - if isinstance(self.value[0], str): - for index, val in enumerate(self.value): - string += f" {self.name+f'({index+1})':<15} = '{val}'" - else: - for index, val in enumerate(self.value): - string += f" {self.name+f'({index+1})':<15} = {val}" - return string - case _: - raise TypeError("Value is not a valid Pwscf Input Type!") - #end def write_value +@dataclass +class NamelistDefinition: + """Base class for all namelist variables.""" + + name: str + datatype: PwscfInputType + default: PwscfInputType | None + allowed_values: tuple[PwscfInputType] | None = None + dependencies: tuple[NamelistDefinition] | None = None +#end class NamelistDefinition + + + # @property + # def value(self) -> PwscfInputType: + # return self._value + + + # @value.setter + # def value(self, val: PwscfInputType): + # if val is None and self.required: + # raise ValueError( + # f"Can not set {self.name} to None, it is required!" + # ) + # elif not isinstance(val, self.datatype): + # return TypeError( + # f"Expected a value of type {self.datatype} for {self.name} but got {type(val)} instead!" + # ) + # else: + # self._value = val + + + # def write_value(self) -> str: + # match self.datatype: + # case builtins.bool: + # if self._value: + # return f" {self.name:<15} = .true." + # else: + # return f" {self.name:<15} = .false." + + # case builtins.str: + # return f" {self.name:<15} = '{self.value}'" + + # case builtins.int: + # return f" {self.name:<15} = {self.value}" + + # case builtins.float: + # return f" {self.name:<15} = {self.value}" + + # case builtins.list: + # string = "" + # if isinstance(self.value[0], str): + # for index, val in enumerate(self.value): + # string += f" {self.name+f'({index+1})':<15} = '{val}'" + # else: + # for index, val in enumerate(self.value): + # string += f" {self.name+f'({index+1})':<15} = {val}" + # return string + # case _: + # raise TypeError("Value is not a valid Pwscf Input Type!") + # #end def write_value #end class InputCard -class ControlVariable(NamelistVariableBase, Enum): - """Class representing a single variable that belongs to the +class ControlDefinitions(NamelistDefinition, Enum): + """Class representing all variables that belongs to the &CONTROL input namelist for ``pw.x``. """ def __new__(cls, datatype, default, allowed_values, dependencies): ... - calculation = str, "scf", ["scf", "nscf", "bands", "relax", "md"], None - + calculation = str, "scf", ("scf", "nscf", "bands", "relax", "md", "vc-md", "vc-relax"), None + title = str, "", None, None + verbosity = str, "low", ("high", "low"), None + restart_mode = str, "from_scratch", ("from_scratch", "restart"), None + nstep = int, (1, 50), None, (calculation, ("scf, nscf, bands")) + iprint = int, 10, None, None + tstress = bool, (True, False), None, (calculation, ("vc-md", "vc-relax")) + tprnfor = bool, (True, False), None, (calculation, ("relax", "md", "vc-md")) + dt = float, 20.0, None, (calculation, ("md")) + outdir = str, "./", None, None + -class SystemVariable(NamelistVariableBase): + +class SystemVariables(NamelistDefinition, Enum): """Class representing a single variable that belongs to the &SYSTEM input namelist for ``pw.x``. """ - - def __init__(self, **kwargs): - super().__init__(**kwargs) + ... -class ElectronsVariable(NamelistVariableBase): +class ElectronsVariables(NamelistDefinition, Enum): """Class representing a single variable that belongs to the &ELECTRONS input namelist for ``pw.x``. """ - - def __init__(self, **kwargs): - super().__init__(**kwargs) + ... -class IonsVariable(NamelistVariableBase): +class IonsVariables(NamelistDefinition, Enum): """Class representing a single variable that belongs to the &IONS input namelist for ``pw.x``. """ + ... - def __init__(self, **kwargs): - super().__init__(**kwargs) - -class CellVariable(NamelistVariableBase): +class CellVariables(NamelistDefinition, Enum): """Class representing a single variable that belongs to the &CELL input namelist for ``pw.x``. """ - - def __init__(self, **kwargs): - super().__init__(**kwargs) + ... -class FCPVariable(NamelistVariableBase): +class FCPVariables(NamelistDefinition, Enum): """Class representing a single variable that belongs to the &FCP input namelist for ``pw.x``. """ - - def __init__(self, **kwargs): - super().__init__(**kwargs) + ... -class RismVariable(NamelistVariableBase): +class RismVariables(NamelistDefinition, Enum): """Class representing a single variable that belongs to the &RISM input namelist for ``pw.x``. """ + ... + + +class PWscfNamelist(ABC): + """Abstract base class for all PWscf namelists.""" - def __init__(self, **kwargs): - super().__init__(**kwargs) + @abstractmethod + def write_card(self) -> str: + pass + @abstractmethod + def meets_requirements(self) -> bool: + pass + @abstractmethod + def __setattr__(self, name, value): + pass From 27df14af46c3a5be6908760ff303327bb19fb835 Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Thu, 19 Feb 2026 17:21:47 -0500 Subject: [PATCH 04/10] Nexus: Continue work on `pwscf_input.py` --- nexus/nexus/pwscf_input_new.py | 244 ++++++++++++++++++++++----------- 1 file changed, 162 insertions(+), 82 deletions(-) diff --git a/nexus/nexus/pwscf_input_new.py b/nexus/nexus/pwscf_input_new.py index a4bb40b1fb..fcdb1cc1cc 100644 --- a/nexus/nexus/pwscf_input_new.py +++ b/nexus/nexus/pwscf_input_new.py @@ -6,6 +6,7 @@ from dataclasses import dataclass from abc import ABC, abstractmethod from enum import Enum +from collections.abc import Sequence type PwscfInputType = ( @@ -13,129 +14,159 @@ | bool | int | float - | list + | Sequence ) -@dataclass -class NamelistDefinition: +@dataclass(frozen=True) # We generally don't want any of these to be modified +class NamelistParamDefinition: """Base class for all namelist variables.""" - name: str - datatype: PwscfInputType - default: PwscfInputType | None - allowed_values: tuple[PwscfInputType] | None = None - dependencies: tuple[NamelistDefinition] | None = None + datatype: PwscfInputType + default: PwscfInputType | None = None + required: bool + allowed_values: tuple[PwscfInputType] | None + dependencies: tuple[NamelistParamDefinition] | None + version_added: tuple[float] | None + version_removed: tuple[float] | None #end class NamelistDefinition - # @property - # def value(self) -> PwscfInputType: - # return self._value - - - # @value.setter - # def value(self, val: PwscfInputType): - # if val is None and self.required: - # raise ValueError( - # f"Can not set {self.name} to None, it is required!" - # ) - # elif not isinstance(val, self.datatype): - # return TypeError( - # f"Expected a value of type {self.datatype} for {self.name} but got {type(val)} instead!" - # ) - # else: - # self._value = val - - - # def write_value(self) -> str: - # match self.datatype: - # case builtins.bool: - # if self._value: - # return f" {self.name:<15} = .true." - # else: - # return f" {self.name:<15} = .false." - - # case builtins.str: - # return f" {self.name:<15} = '{self.value}'" - - # case builtins.int: - # return f" {self.name:<15} = {self.value}" - - # case builtins.float: - # return f" {self.name:<15} = {self.value}" - - # case builtins.list: - # string = "" - # if isinstance(self.value[0], str): - # for index, val in enumerate(self.value): - # string += f" {self.name+f'({index+1})':<15} = '{val}'" - # else: - # for index, val in enumerate(self.value): - # string += f" {self.name+f'({index+1})':<15} = {val}" - # return string - # case _: - # raise TypeError("Value is not a valid Pwscf Input Type!") - # #end def write_value -#end class InputCard - - -class ControlDefinitions(NamelistDefinition, Enum): +class ControlDefinitions(NamelistParamDefinition, Enum): """Class representing all variables that belongs to the &CONTROL input namelist for ``pw.x``. - """ - - def __new__(cls, datatype, default, allowed_values, dependencies): ... - - calculation = str, "scf", ("scf", "nscf", "bands", "relax", "md", "vc-md", "vc-relax"), None - title = str, "", None, None - verbosity = str, "low", ("high", "low"), None - restart_mode = str, "from_scratch", ("from_scratch", "restart"), None - nstep = int, (1, 50), None, (calculation, ("scf, nscf, bands")) - iprint = int, 10, None, None - tstress = bool, (True, False), None, (calculation, ("vc-md", "vc-relax")) - tprnfor = bool, (True, False), None, (calculation, ("relax", "md", "vc-md")) - dt = float, 20.0, None, (calculation, ("md")) - outdir = str, "./", None, None - - + Notes + ----- + If you wish to add a new variable to the &CONTROL namelist, you + can simply append the variable to the end of the definitions. + The only required attributes that you must define are ``datatype`` + and ``default``, however it is ***strongly encouraged*** to specify + the remaining information so that the various checks present + throughout the rest of the code base can be utilized properly. + """ -class SystemVariables(NamelistDefinition, Enum): + def __new__( + cls, + datatype: PwscfInputType, + default: PwscfInputType | None = None, + allowed_values: tuple[PwscfInputType] | None = None, + dependencies: tuple[NamelistParamDefinition] | None = None, + version_added: tuple[float] | None = None, + version_removed: tuple[float] | None = None, + ): + definition = NamelistParamDefinition.__new__(cls) + required = default is None + definition._value_ = NamelistParamDefinition( + datatype, + default, + required, + allowed_values, + dependencies, + version_added, + version_removed, + ) + return definition + + + calculation = ( + str, + "scf", + ("scf", "nscf", "bands", "relax", "md", "vc-md", "vc-relax"), + None, + ) + title = ( + str, + "", + None, + None + ) + verbosity = ( + str, + "low", + ("high", "low"), + None + ) + restart_mode = ( + str, + "from_scratch", + ("from_scratch", "restart"), + None + ) + nstep = ( + int, + (1, 50), + None, + (calculation, ("scf, nscf, bands")) + ) + iprint = ( + int, + 10, + None, + None + ) + tstress = ( + bool, + (True, False), + None, + (calculation, ("vc-md", "vc-relax")) + ) + tprnfor = ( + bool, + (True, False), + None, + (calculation, ("relax", "md", "vc-md")) + ) + dt = ( + float, + 20.0, + None, + (calculation, ("md")) + ) + outdir = ( + str, + "./", + None, + None, + ) + + + +class SystemVariables(NamelistParamDefinition, Enum): """Class representing a single variable that belongs to the &SYSTEM input namelist for ``pw.x``. """ ... -class ElectronsVariables(NamelistDefinition, Enum): +class ElectronsVariables(NamelistParamDefinition, Enum): """Class representing a single variable that belongs to the &ELECTRONS input namelist for ``pw.x``. """ ... -class IonsVariables(NamelistDefinition, Enum): +class IonsVariables(NamelistParamDefinition, Enum): """Class representing a single variable that belongs to the &IONS input namelist for ``pw.x``. """ ... -class CellVariables(NamelistDefinition, Enum): +class CellVariables(NamelistParamDefinition, Enum): """Class representing a single variable that belongs to the &CELL input namelist for ``pw.x``. """ ... -class FCPVariables(NamelistDefinition, Enum): +class FCPVariables(NamelistParamDefinition, Enum): """Class representing a single variable that belongs to the &FCP input namelist for ``pw.x``. """ ... -class RismVariables(NamelistDefinition, Enum): +class RismVariables(NamelistParamDefinition, Enum): """Class representing a single variable that belongs to the &RISM input namelist for ``pw.x``. """ @@ -157,3 +188,52 @@ def meets_requirements(self) -> bool: def __setattr__(self, name, value): pass + + @property + def value(self) -> PwscfInputType: + return self._value + + + @value.setter + def value(self, val: PwscfInputType): + if val is None and self.required: + raise ValueError( + f"Can not set {self.name} to None, it is required!" + ) + elif not isinstance(val, self.datatype): + return TypeError( + f"Expected a value of type {self.datatype} for {self.name} but got {type(val)} instead!" + ) + else: + self._value = val + + + def write_value(self) -> str: + match self.datatype: + case builtins.bool: + if self._value: + return f" {self.name:<15} = .true." + else: + return f" {self.name:<15} = .false." + + case builtins.str: + return f" {self.name:<15} = '{self.value}'" + + case builtins.int: + return f" {self.name:<15} = {self.value}" + + case builtins.float: + return f" {self.name:<15} = {self.value}" + + case builtins.list: + string = "" + if isinstance(self.value[0], str): + for index, val in enumerate(self.value): + string += f" {self.name+f'({index+1})':<15} = '{val}'" + else: + for index, val in enumerate(self.value): + string += f" {self.name+f'({index+1})':<15} = {val}" + return string + case _: + raise TypeError("Value is not a valid Pwscf Input Type!") + #end def write_value From df831ab6a0502b0eabbd1c8779a6cf48c5d2f829 Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Fri, 20 Feb 2026 14:05:50 -0500 Subject: [PATCH 05/10] Nexus: Add first pass at defining INPUT_PW variables in enums with automatic generation --- nexus/nexus/pwscf_input_new.py | 473 +++++++++++++++++++++++++-------- 1 file changed, 365 insertions(+), 108 deletions(-) diff --git a/nexus/nexus/pwscf_input_new.py b/nexus/nexus/pwscf_input_new.py index fcdb1cc1cc..7c29d6f684 100644 --- a/nexus/nexus/pwscf_input_new.py +++ b/nexus/nexus/pwscf_input_new.py @@ -17,48 +17,37 @@ | Sequence ) + @dataclass(frozen=True) # We generally don't want any of these to be modified class NamelistParamDefinition: """Base class for all namelist variables.""" - datatype: PwscfInputType - default: PwscfInputType | None = None + datatype: tuple[PwscfInputType] required: bool - allowed_values: tuple[PwscfInputType] | None - dependencies: tuple[NamelistParamDefinition] | None - version_added: tuple[float] | None - version_removed: tuple[float] | None + shape: tuple + allowed_values: tuple[PwscfInputType] | None = None + dependencies: tuple[NamelistParamDefinition] | None = None + version_added: tuple[float] | None = None + version_removed: tuple[float] | None = None #end class NamelistDefinition -class ControlDefinitions(NamelistParamDefinition, Enum): - """Class representing all variables that belongs to the - &CONTROL input namelist for ``pw.x``. - - Notes - ----- - If you wish to add a new variable to the &CONTROL namelist, you - can simply append the variable to the end of the definitions. - The only required attributes that you must define are ``datatype`` - and ``default``, however it is ***strongly encouraged*** to specify - the remaining information so that the various checks present - throughout the rest of the code base can be utilized properly. +class NamelistEnumBase(Enum, ABC): + """Abstract base class for the namelist enumerations. + Provides the ``__new__`` method for the enums. """ - def __new__( cls, datatype: PwscfInputType, - default: PwscfInputType | None = None, + required: bool, allowed_values: tuple[PwscfInputType] | None = None, dependencies: tuple[NamelistParamDefinition] | None = None, version_added: tuple[float] | None = None, version_removed: tuple[float] | None = None, ): definition = NamelistParamDefinition.__new__(cls) - required = default is None definition._value_ = NamelistParamDefinition( datatype, - default, required, allowed_values, dependencies, @@ -66,115 +55,382 @@ def __new__( version_removed, ) return definition +#end class NamelistEnumBase - calculation = ( - str, - "scf", - ("scf", "nscf", "bands", "relax", "md", "vc-md", "vc-relax"), - None, - ) - title = ( - str, - "", - None, - None - ) - verbosity = ( - str, - "low", - ("high", "low"), - None - ) - restart_mode = ( - str, - "from_scratch", - ("from_scratch", "restart"), - None - ) - nstep = ( - int, - (1, 50), - None, - (calculation, ("scf, nscf, bands")) - ) - iprint = ( - int, - 10, - None, - None - ) - tstress = ( - bool, - (True, False), - None, - (calculation, ("vc-md", "vc-relax")) - ) - tprnfor = ( - bool, - (True, False), - None, - (calculation, ("relax", "md", "vc-md")) - ) - dt = ( - float, - 20.0, - None, - (calculation, ("md")) - ) - outdir = ( - str, - "./", - None, - None, - ) - - - -class SystemVariables(NamelistParamDefinition, Enum): - """Class representing a single variable that belongs to the - &SYSTEM input namelist for ``pw.x``. +class ControlDefinitions(NamelistParamDefinition, NamelistEnumBase): + """Class representing all variables that belongs to the + &CONTROL input namelist for ``pw.x``. + + Notes + ----- + If you wish to add a new variable to the &CONTROL namelist, you + can simply append the variable to the end of the definitions. + The only required attributes that you must define are ``datatype`` + and ``default``, however it is ***strongly encouraged*** to specify + the remaining information so that the various checks present + throughout the rest of the code base can be utilized properly. """ - ... + calculation = str, False, (1,), ('scf', 'nscf', 'bands', 'relax', 'md', 'vc-relax', 'vc-md') + title = str, False, (1,), None + verbosity = str, False, (1,), ('high', 'low') + restart_mode = str, False, (1,), ('from_scratch', 'restart') + wf_collect = bool, False, (1,), None + nstep = int, False, (1,), None + iprint = int, False, (1,), None + tstress = bool, False, (1,), None + tprnfor = bool, False, (1,), None + dt = float, False, (1,), None + outdir = str, False, (1,), None + wfcdir = str, False, (1,), None + prefix = str, False, (1,), None + lkpoint_dir = bool, False, (1,), None + max_seconds = float, False, (1,), None + etot_conv_thr = float, False, (1,), None + forc_conv_thr = float, False, (1,), None + disk_io = str, False, (1,), ('high', 'medium', 'low', 'nowf', 'minimal', 'none') + pseudo_dir = str, False, (1,), None + tefield = bool, False, (1,), None + dipfield = bool, False, (1,), None + lelfield = bool, False, (1,), None + nberrycyc = int, False, (1,), None + lorbm = bool, False, (1,), None + lberry = bool, False, (1,), None + gdir = int, False, (1,), None + nppstr = int, False, (1,), None + gate = bool, False, (1,), None + twochem = bool, False, (1,), None + lfcp = bool, False, (1,), None + trism = bool, False, (1,), None +#end class ControlDefinitions + +class SystemVariables(NamelistParamDefinition, NamelistEnumBase): + """Class representing all variables that belongs to the + &SYSTEM input namelist for ``pw.x``. -class ElectronsVariables(NamelistParamDefinition, Enum): - """Class representing a single variable that belongs to the - &ELECTRONS input namelist for ``pw.x``. + Notes + ----- + If you wish to add a new variable to the &CONTROL namelist, you + can simply append the variable to the end of the definitions. + The only required attributes that you must define are ``datatype`` + and ``default``, however it is ***strongly encouraged*** to specify + the remaining information so that the various checks present + throughout the rest of the code base can be utilized properly. """ - ... + ibrav = int, True, (1,), None + nat = int, True, (1,), None + ntyp = int, True, (1,), None + nbnd = int, False, (1,), None + nbnd_cond = int, False, (1,), None + tot_charge = float, False, (1,), None + tot_magnetization = float, False, (1,), None + ecutwfc = float, True, (1,), None + ecutrho = float, False, (1,), None + ecutfock = float, False, (1,), None + nosym = bool, False, (1,), None + nosym_evc = bool, False, (1,), None + noinv = bool, False, (1,), None + no_t_rev = bool, False, (1,), None + force_symmorphic = bool, False, (1,), None + use_all_frac = bool, False, (1,), None + occupations = str, False, (1,), ('smearing', 'tetrahedra', 'tetrahedra_lin', 'tetrahedra_opt', 'fixed', 'from_input') + one_atom_occupations = bool, False, (1,), None + starting_spin_angle = bool, False, (1,), None + degauss_cond = float, False, (1,), None + nelec_cond = float, False, (1,), None + degauss = float, False, (1,), None + smearing = str, False, (1,), ('gaussian', 'gauss', 'methfessel-paxton', 'm-p', 'mp', 'marzari-vanderbilt', 'cold', 'm-v', 'mv', 'fermi-dirac', 'f-d', 'fd') + nspin = int, False, (1,), None + sic_gamma = float, False, (1,), None + pol_type = str, False, (1,), ('e', 'h') + sic_energy = bool, False, (1,), None + sci_vb = float, False, (1,), None + sci_cb = float, False, (1,), None + noncolin = bool, False, (1,), None + ecfixed = float, False, (1,), None + qcutz = float, False, (1,), None + q2sigma = float, False, (1,), None + input_dft = str, False, (1,), None + ace = bool, False, (1,), None + exx_fraction = float, False, (1,), None + screening_parameter = float, False, (1,), None + exxdiv_treatment = str, False, (1,), ('gygi-baldereschi', 'vcut_spherical', 'vcut_ws', 'none') + x_gamma_extrapolation = bool, False, (1,), None + ecutvcut = float, False, (1,), None + localization_thr = float, False, (1,), None + dmft = bool, False, (1,), None + dmft_prefix = str, False, (1,), None + ensemble_energies = bool, False, (1,), None + edir = int, False, (1,), None + emaxpos = float, False, (1,), None + eopreg = float, False, (1,), None + eamp = float, False, (1,), None + lforcet = bool, False, (1,), None + constrained_magnetization = str, False, (1,), ('none', 'total', 'atomic', 'total direction', 'atomic direction') + # Lambda is reserved by Python, so it gets an underscore. + # Will need to handle the underscore at some point. + lambda_ = float, False, (1,), None + report = int, False, (1,), None + lspinorb = bool, False, (1,), None + assume_isolated = str, False, (1,), ('none', 'makov-payne', 'm-p', 'mp', 'martyna-tuckerman', 'm-t', 'mt', 'esm', '2D') + esm_bc = str, False, (1,), ('pbc', 'bc1', 'bc2', 'bc3') + esm_w = float, False, (1,), None + esm_efield = float, False, (1,), None + esm_nfit = int, False, (1,), None + lgcscf = bool, False, (1,), None + gcscf_mu = float, True, (1,), None + gcscf_conv_thr = float, False, (1,), None + gcscf_beta = float, False, (1,), None + vdw_corr = str, False, (1,), ('grimme-d2', 'Grimme-D2', 'DFT-D', 'dft-d', 'grimme-d3', 'Grimme-D3', 'DFT-D3', 'dft-d3', 'TS', 'ts', 'ts-vdw', 'ts-vdW', 'tkatchenko-scheffler', 'MBD', 'mbd', 'many-body-dispersion', 'mbd_vdw', 'XDM', 'xdm') + london = bool, False, (1,), None + london_s6 = float, False, (1,), None + london_rcut = float, False, (1,), None + dftd3_version = int, False, (1,), None + dftd3_threebody = bool, False, (1,), None + ts_vdw_econv_thr = float, False, (1,), None + ts_vdw_isolated = bool, False, (1,), None + xdm = bool, False, (1,), None + xdm_a1 = float, False, (1,), None + xdm_a2 = float, False, (1,), None + space_group = int, False, (1,), None + uniqueb = bool, False, (1,), None + origin_choice = int, False, (1,), None + rhombohedral = bool, False, (1,), None + nextffield = int, False, (1,), None + celldm = float, False, ((1,), (6,)), None + A = float, False, (1,), None + B = float, False, (1,), None + C = float, False, (1,), None + cosAB = float, False, (1,), None + cosAC = float, False, (1,), None + cosBC = float, False, (1,), None + zgate = float, False, (1,), None + relaxz = bool, False, (1,), None + block = bool, False, (1,), None + block_1 = float, False, (1,), None + block_2 = float, False, (1,), None + block_height = float, False, (1,), None + starting_charge = float, False, ((1,), ('ntyp',)), None + starting_magnetization = float, False, ((1,), ('ntyp',)), None + Hubbard_beta = float, False, ((1,), ('ntyp',)), None + angle1 = float, False, ((1,), ('ntyp',)), None + angle2 = float, False, ((1,), ('ntyp',)), None + fixed_magnetization = float, False, ((1,), (3,)), None + london_c6 = float, False, ((1,), ('ntyp',)), None + london_rvdw = float, False, ((1,), ('ntyp',)), None + nr1 = int, False, (1,), None + nr2 = int, False, (1,), None + nr3 = int, False, (1,), None + nr1s = int, False, (1,), None + nr2s = int, False, (1,), None + nr3s = int, False, (1,), None + nqx1 = int, False, (1,), None + nqx2 = int, False, (1,), None + nqx3 = int, False, (1,), None + Hubbard_occ = float, False, ((1,), ('ntyp,3',)), None + starting_ns_eigenvalue = float, False, ((1,), ('2*lmax+1,nspin or npol,ntyp',)), None +#end class SystemVariables + +class ElectronsVariables(NamelistParamDefinition, NamelistEnumBase): + """Class representing all variables that belongs to the + &ELECTRONS input namelist for ``pw.x``. -class IonsVariables(NamelistParamDefinition, Enum): - """Class representing a single variable that belongs to the - &IONS input namelist for ``pw.x``. + Notes + ----- + If you wish to add a new variable to the &CONTROL namelist, you + can simply append the variable to the end of the definitions. + The only required attributes that you must define are ``datatype`` + and ``default``, however it is ***strongly encouraged*** to specify + the remaining information so that the various checks present + throughout the rest of the code base can be utilized properly. """ - ... + electron_maxstep = int, False, (1,), None + exx_maxstep = int, False, (1,), None + scf_must_converge = bool, False, (1,), None + conv_thr = float, False, (1,), None + adaptive_thr = bool, False, (1,), None + conv_thr_init = float, False, (1,), None + conv_thr_multi = float, False, (1,), None + mixing_mode = str, False, (1,), ('plain', 'TF', 'local-TF') + mixing_beta = float, False, (1,), None + mixing_ndim = int, False, (1,), None + mixing_fixed_ns = int, False, (1,), None + diagonalization = str, False, (1,), ('david', 'cg', 'ppcg', 'paro', 'ParO', 'rmm-davidson', 'rmm-paro') + diago_thr_init = float, False, (1,), None + diago_cg_maxiter = int, False, (1,), None + diago_david_ndim = int, False, (1,), None + diago_rmm_ndim = int, False, (1,), None + diago_rmm_conv = bool, False, (1,), None + diago_gs_nblock = int, False, (1,), None + diago_full_acc = bool, False, (1,), None + efield = float, False, (1,), None + efield_phase = str, False, (1,), ('read', 'write', 'none') + startingpot = str, False, (1,), ('atomic', 'file') + startingwfc = str, False, (1,), ('atomic', 'atomic+random', 'random', 'file') + tqr = bool, False, (1,), None + real_space = bool, False, (1,), None + efield_cart = float, False, ((1,), (3,)), None +#end class ElectronsVariables + +class IonsVariables(NamelistParamDefinition, NamelistEnumBase): + """Class representing all variables that belongs to the + &IONS input namelist for ``pw.x``. -class CellVariables(NamelistParamDefinition, Enum): - """Class representing a single variable that belongs to the + Notes + ----- + If you wish to add a new variable to the &CONTROL namelist, you + can simply append the variable to the end of the definitions. + The only required attributes that you must define are ``datatype`` + and ``default``, however it is ***strongly encouraged*** to specify + the remaining information so that the various checks present + throughout the rest of the code base can be utilized properly. + """ + + ion_positions = str, False, (1,), ('default', 'from_input') + ion_velocities = str, False, (1,), ('default', 'from_input') + ion_dynamics = str, False, (1,), ('bfgs', 'damp', 'fire', 'verlet', 'velocity-verlet', 'langevin', 'langevin-smc', 'bfgs', 'damp', 'beeman') + pot_extrapolation = str, False, (1,), ('none', 'atomic', 'first_order', 'second_order') + wfc_extrapolation = str, False, (1,), ('none', 'first_order', 'second_order') + remove_rigid_rot = bool, False, (1,), None + ion_temperature = str, False, (1,), ('rescaling', 'rescale-v', 'rescale-T', 'reduce-T', 'nose', 'berendsen', 'andersen', 'svr', 'initial', 'not_controlled') + tempw = float, False, (1,), None + fnosep = float, False, (1,), None + nhpcl = int, False, (1,), None + nhptyp = int, False, (1,), None + ndega = int, False, (1,), None + tolp = float, False, (1,), None + delta_t = float, False, (1,), None + nraise = int, False, (1,), None + refold_pos = bool, False, (1,), None + nhgrp = int, False, ((1,), ('ntyp',)), None + fnhscl = float, False, ((1,), ('ntyp',)), None + upscale = float, False, (1,), None + bfgs_ndim = int, False, (1,), None + tgdiis_step = bool, False, (1,), None + trust_radius_max = float, False, (1,), None + trust_radius_min = float, False, (1,), None + trust_radius_ini = float, False, (1,), None + w_1 = float, False, (1,), None + w_2 = float, False, (1,), None + fire_alpha_init = float, False, (1,), None + fire_falpha = float, False, (1,), None + fire_nmin = int, False, (1,), None + fire_f_inc = float, False, (1,), None + fire_f_dec = float, False, (1,), None + fire_dtmax = float, False, (1,), None +#end class IonsVariables + +class CellVariables(NamelistParamDefinition, NamelistEnumBase): + """Class representing all variables that belongs to the &CELL input namelist for ``pw.x``. + + Notes + ----- + If you wish to add a new variable to the &CONTROL namelist, you + can simply append the variable to the end of the definitions. + The only required attributes that you must define are ``datatype`` + and ``default``, however it is ***strongly encouraged*** to specify + the remaining information so that the various checks present + throughout the rest of the code base can be utilized properly. """ - ... + cell_dynamics = str, False, (1,), ('none', 'sd', 'damp-pr', 'damp-w', 'bfgs', 'none', 'pr', 'w') + press = float, False, (1,), None + wmass = float, False, (1,), None + cell_factor = float, False, (1,), None + press_conv_thr = float, False, (1,), None + cell_dofree = str, False, (1,), ('all', 'ibrav', 'a', 'b', 'c', 'fixa', 'fixb', 'fixc', 'x', 'y', 'z', 'xy', 'xz', 'yz', 'xyz', 'shape', 'volume', '2Dxy', '2Dshape', 'epitaxial_ab', 'epitaxial_ac', 'epitaxial_bc') +#end class CellVariables -class FCPVariables(NamelistParamDefinition, Enum): - """Class representing a single variable that belongs to the +class FCPVariables(NamelistParamDefinition, NamelistEnumBase): + """Class representing all variables that belongs to the &FCP input namelist for ``pw.x``. - """ - ... + Notes + ----- + If you wish to add a new variable to the &CONTROL namelist, you + can simply append the variable to the end of the definitions. + The only required attributes that you must define are ``datatype`` + and ``default``, however it is ***strongly encouraged*** to specify + the remaining information so that the various checks present + throughout the rest of the code base can be utilized properly. + """ -class RismVariables(NamelistParamDefinition, Enum): - """Class representing a single variable that belongs to the + fcp_mu = float, True, (1,), None + fcp_dynamics = str, False, (1,), ('bfgs', 'newton', 'damp', 'lm', 'velocity-verlet', 'verlet') + fcp_conv_thr = float, False, (1,), None + fcp_ndiis = int, False, (1,), None + freeze_all_atoms = bool, False, (1,), None + fcp_mass = float, False, (1,), None + fcp_velocity = float, False, (1,), None + fcp_temperature = str, False, (1,), ('rescaling', 'rescale-v', 'rescale-T', 'reduce-T', 'berendsen', 'andersen', 'initial', 'not_controlled') + fcp_tempw = float, False, (1,), None + fcp_tolp = float, False, (1,), None + fcp_delta_t = float, False, (1,), None + fcp_nraise = int, False, (1,), None +#end class FCPVariables + +class RismVariables(NamelistParamDefinition, NamelistEnumBase): + """Class representing all variables that belongs to the &RISM input namelist for ``pw.x``. + + Notes + ----- + If you wish to add a new variable to the &CONTROL namelist, you + can simply append the variable to the end of the definitions. + The only required attributes that you must define are ``datatype`` + and ``default``, however it is ***strongly encouraged*** to specify + the remaining information so that the various checks present + throughout the rest of the code base can be utilized properly. """ - ... + + nsolv = int, True, (1,), None + closure = str, False, (1,), ('kh', 'hnc') + tempv = float, False, (1,), None + ecutsolv = float, False, (1,), None + starting1d = str, False, (1,), ('zero', 'file', 'fix') + starting3d = str, False, (1,), ('zero', 'file') + smear1d = float, False, (1,), None + smear3d = float, False, (1,), None + rism1d_maxstep = int, False, (1,), None + rism3d_maxstep = int, False, (1,), None + rism1d_conv_thr = float, False, (1,), None + rism3d_conv_thr = float, False, (1,), None + mdiis1d_size = int, False, (1,), None + mdiis3d_size = int, False, (1,), None + mdiis1d_step = float, False, (1,), None + mdiis3d_step = float, False, (1,), None + rism1d_bond_width = float, False, (1,), None + rism1d_dielectric = float, False, (1,), None + rism1d_molesize = float, False, (1,), None + rism1d_nproc = int, False, (1,), None + rism3d_conv_level = float, False, (1,), None + rism3d_planar_average = bool, False, (1,), None + laue_nfit = int, False, (1,), None + laue_expand_right = float, False, (1,), None + laue_expand_left = float, False, (1,), None + laue_starting_right = float, False, (1,), None + laue_starting_left = float, False, (1,), None + laue_buffer_right = float, False, (1,), None + laue_buffer_left = float, False, (1,), None + laue_both_hands = bool, False, (1,), None + laue_wall = str, False, (1,), ('none', 'auto', 'manual') + laue_wall_z = float, False, (1,), None + laue_wall_rho = float, False, (1,), None + laue_wall_epsilon = float, False, (1,), None + laue_wall_sigma = float, False, (1,), None + laue_wall_lj6 = bool, False, (1,), None + solute_lj = str, False, ((1,), ('ntyp',)), None + solute_epsilon = float, False, ((1,), ('ntyp',)), None + solute_sigma = float, False, ((1,), ('ntyp',)), None +#end class RismVariables class PWscfNamelist(ABC): - """Abstract base class for all PWscf namelists.""" + """Abstract base class for real instances of PWscf namelists.""" @abstractmethod def write_card(self) -> str: @@ -237,3 +493,4 @@ def write_value(self) -> str: case _: raise TypeError("Value is not a valid Pwscf Input Type!") #end def write_value +#end class PWscfNamelist From a50b560e8a311a6905bf63097a7d288ea90c05c4 Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Fri, 20 Feb 2026 14:14:50 -0500 Subject: [PATCH 06/10] Nexus: Remove excess spacing in some namelists --- nexus/nexus/pwscf_input_new.py | 292 ++++++++++++++++----------------- 1 file changed, 146 insertions(+), 146 deletions(-) diff --git a/nexus/nexus/pwscf_input_new.py b/nexus/nexus/pwscf_input_new.py index 7c29d6f684..ff9fd48531 100644 --- a/nexus/nexus/pwscf_input_new.py +++ b/nexus/nexus/pwscf_input_new.py @@ -72,37 +72,37 @@ class ControlDefinitions(NamelistParamDefinition, NamelistEnumBase): throughout the rest of the code base can be utilized properly. """ - calculation = str, False, (1,), ('scf', 'nscf', 'bands', 'relax', 'md', 'vc-relax', 'vc-md') - title = str, False, (1,), None - verbosity = str, False, (1,), ('high', 'low') - restart_mode = str, False, (1,), ('from_scratch', 'restart') - wf_collect = bool, False, (1,), None - nstep = int, False, (1,), None - iprint = int, False, (1,), None - tstress = bool, False, (1,), None - tprnfor = bool, False, (1,), None - dt = float, False, (1,), None - outdir = str, False, (1,), None - wfcdir = str, False, (1,), None - prefix = str, False, (1,), None - lkpoint_dir = bool, False, (1,), None - max_seconds = float, False, (1,), None - etot_conv_thr = float, False, (1,), None - forc_conv_thr = float, False, (1,), None - disk_io = str, False, (1,), ('high', 'medium', 'low', 'nowf', 'minimal', 'none') - pseudo_dir = str, False, (1,), None - tefield = bool, False, (1,), None - dipfield = bool, False, (1,), None - lelfield = bool, False, (1,), None - nberrycyc = int, False, (1,), None - lorbm = bool, False, (1,), None - lberry = bool, False, (1,), None - gdir = int, False, (1,), None - nppstr = int, False, (1,), None - gate = bool, False, (1,), None - twochem = bool, False, (1,), None - lfcp = bool, False, (1,), None - trism = bool, False, (1,), None + calculation = str, False, (1,), ('scf', 'nscf', 'bands', 'relax', 'md', 'vc-relax', 'vc-md') + title = str, False, (1,), None + verbosity = str, False, (1,), ('high', 'low') + restart_mode = str, False, (1,), ('from_scratch', 'restart') + wf_collect = bool, False, (1,), None + nstep = int, False, (1,), None + iprint = int, False, (1,), None + tstress = bool, False, (1,), None + tprnfor = bool, False, (1,), None + dt = float, False, (1,), None + outdir = str, False, (1,), None + wfcdir = str, False, (1,), None + prefix = str, False, (1,), None + lkpoint_dir = bool, False, (1,), None + max_seconds = float, False, (1,), None + etot_conv_thr = float, False, (1,), None + forc_conv_thr = float, False, (1,), None + disk_io = str, False, (1,), ('high', 'medium', 'low', 'nowf', 'minimal', 'none') + pseudo_dir = str, False, (1,), None + tefield = bool, False, (1,), None + dipfield = bool, False, (1,), None + lelfield = bool, False, (1,), None + nberrycyc = int, False, (1,), None + lorbm = bool, False, (1,), None + lberry = bool, False, (1,), None + gdir = int, False, (1,), None + nppstr = int, False, (1,), None + gate = bool, False, (1,), None + twochem = bool, False, (1,), None + lfcp = bool, False, (1,), None + trism = bool, False, (1,), None #end class ControlDefinitions class SystemVariables(NamelistParamDefinition, NamelistEnumBase): @@ -247,32 +247,32 @@ class ElectronsVariables(NamelistParamDefinition, NamelistEnumBase): throughout the rest of the code base can be utilized properly. """ - electron_maxstep = int, False, (1,), None - exx_maxstep = int, False, (1,), None - scf_must_converge = bool, False, (1,), None - conv_thr = float, False, (1,), None - adaptive_thr = bool, False, (1,), None - conv_thr_init = float, False, (1,), None - conv_thr_multi = float, False, (1,), None - mixing_mode = str, False, (1,), ('plain', 'TF', 'local-TF') - mixing_beta = float, False, (1,), None - mixing_ndim = int, False, (1,), None - mixing_fixed_ns = int, False, (1,), None - diagonalization = str, False, (1,), ('david', 'cg', 'ppcg', 'paro', 'ParO', 'rmm-davidson', 'rmm-paro') - diago_thr_init = float, False, (1,), None - diago_cg_maxiter = int, False, (1,), None - diago_david_ndim = int, False, (1,), None - diago_rmm_ndim = int, False, (1,), None - diago_rmm_conv = bool, False, (1,), None - diago_gs_nblock = int, False, (1,), None - diago_full_acc = bool, False, (1,), None - efield = float, False, (1,), None - efield_phase = str, False, (1,), ('read', 'write', 'none') - startingpot = str, False, (1,), ('atomic', 'file') - startingwfc = str, False, (1,), ('atomic', 'atomic+random', 'random', 'file') - tqr = bool, False, (1,), None - real_space = bool, False, (1,), None - efield_cart = float, False, ((1,), (3,)), None + electron_maxstep = int, False, (1,), None + exx_maxstep = int, False, (1,), None + scf_must_converge = bool, False, (1,), None + conv_thr = float, False, (1,), None + adaptive_thr = bool, False, (1,), None + conv_thr_init = float, False, (1,), None + conv_thr_multi = float, False, (1,), None + mixing_mode = str, False, (1,), ('plain', 'TF', 'local-TF') + mixing_beta = float, False, (1,), None + mixing_ndim = int, False, (1,), None + mixing_fixed_ns = int, False, (1,), None + diagonalization = str, False, (1,), ('david', 'cg', 'ppcg', 'paro', 'ParO', 'rmm-davidson', 'rmm-paro') + diago_thr_init = float, False, (1,), None + diago_cg_maxiter = int, False, (1,), None + diago_david_ndim = int, False, (1,), None + diago_rmm_ndim = int, False, (1,), None + diago_rmm_conv = bool, False, (1,), None + diago_gs_nblock = int, False, (1,), None + diago_full_acc = bool, False, (1,), None + efield = float, False, (1,), None + efield_phase = str, False, (1,), ('read', 'write', 'none') + startingpot = str, False, (1,), ('atomic', 'file') + startingwfc = str, False, (1,), ('atomic', 'atomic+random', 'random', 'file') + tqr = bool, False, (1,), None + real_space = bool, False, (1,), None + efield_cart = float, False, ((1,), (3,)), None #end class ElectronsVariables class IonsVariables(NamelistParamDefinition, NamelistEnumBase): @@ -289,38 +289,38 @@ class IonsVariables(NamelistParamDefinition, NamelistEnumBase): throughout the rest of the code base can be utilized properly. """ - ion_positions = str, False, (1,), ('default', 'from_input') - ion_velocities = str, False, (1,), ('default', 'from_input') - ion_dynamics = str, False, (1,), ('bfgs', 'damp', 'fire', 'verlet', 'velocity-verlet', 'langevin', 'langevin-smc', 'bfgs', 'damp', 'beeman') - pot_extrapolation = str, False, (1,), ('none', 'atomic', 'first_order', 'second_order') - wfc_extrapolation = str, False, (1,), ('none', 'first_order', 'second_order') - remove_rigid_rot = bool, False, (1,), None - ion_temperature = str, False, (1,), ('rescaling', 'rescale-v', 'rescale-T', 'reduce-T', 'nose', 'berendsen', 'andersen', 'svr', 'initial', 'not_controlled') - tempw = float, False, (1,), None - fnosep = float, False, (1,), None - nhpcl = int, False, (1,), None - nhptyp = int, False, (1,), None - ndega = int, False, (1,), None - tolp = float, False, (1,), None - delta_t = float, False, (1,), None - nraise = int, False, (1,), None - refold_pos = bool, False, (1,), None - nhgrp = int, False, ((1,), ('ntyp',)), None - fnhscl = float, False, ((1,), ('ntyp',)), None - upscale = float, False, (1,), None - bfgs_ndim = int, False, (1,), None - tgdiis_step = bool, False, (1,), None - trust_radius_max = float, False, (1,), None - trust_radius_min = float, False, (1,), None - trust_radius_ini = float, False, (1,), None - w_1 = float, False, (1,), None - w_2 = float, False, (1,), None - fire_alpha_init = float, False, (1,), None - fire_falpha = float, False, (1,), None - fire_nmin = int, False, (1,), None - fire_f_inc = float, False, (1,), None - fire_f_dec = float, False, (1,), None - fire_dtmax = float, False, (1,), None + ion_positions = str, False, (1,), ('default', 'from_input') + ion_velocities = str, False, (1,), ('default', 'from_input') + ion_dynamics = str, False, (1,), ('bfgs', 'damp', 'fire', 'verlet', 'velocity-verlet', 'langevin', 'langevin-smc', 'bfgs', 'damp', 'beeman') + pot_extrapolation = str, False, (1,), ('none', 'atomic', 'first_order', 'second_order') + wfc_extrapolation = str, False, (1,), ('none', 'first_order', 'second_order') + remove_rigid_rot = bool, False, (1,), None + ion_temperature = str, False, (1,), ('rescaling', 'rescale-v', 'rescale-T', 'reduce-T', 'nose', 'berendsen', 'andersen', 'svr', 'initial', 'not_controlled') + tempw = float, False, (1,), None + fnosep = float, False, (1,), None + nhpcl = int, False, (1,), None + nhptyp = int, False, (1,), None + ndega = int, False, (1,), None + tolp = float, False, (1,), None + delta_t = float, False, (1,), None + nraise = int, False, (1,), None + refold_pos = bool, False, (1,), None + nhgrp = int, False, ((1,), ('ntyp',)), None + fnhscl = float, False, ((1,), ('ntyp',)), None + upscale = float, False, (1,), None + bfgs_ndim = int, False, (1,), None + tgdiis_step = bool, False, (1,), None + trust_radius_max = float, False, (1,), None + trust_radius_min = float, False, (1,), None + trust_radius_ini = float, False, (1,), None + w_1 = float, False, (1,), None + w_2 = float, False, (1,), None + fire_alpha_init = float, False, (1,), None + fire_falpha = float, False, (1,), None + fire_nmin = int, False, (1,), None + fire_f_inc = float, False, (1,), None + fire_f_dec = float, False, (1,), None + fire_dtmax = float, False, (1,), None #end class IonsVariables class CellVariables(NamelistParamDefinition, NamelistEnumBase): @@ -337,12 +337,12 @@ class CellVariables(NamelistParamDefinition, NamelistEnumBase): throughout the rest of the code base can be utilized properly. """ - cell_dynamics = str, False, (1,), ('none', 'sd', 'damp-pr', 'damp-w', 'bfgs', 'none', 'pr', 'w') - press = float, False, (1,), None - wmass = float, False, (1,), None - cell_factor = float, False, (1,), None - press_conv_thr = float, False, (1,), None - cell_dofree = str, False, (1,), ('all', 'ibrav', 'a', 'b', 'c', 'fixa', 'fixb', 'fixc', 'x', 'y', 'z', 'xy', 'xz', 'yz', 'xyz', 'shape', 'volume', '2Dxy', '2Dshape', 'epitaxial_ab', 'epitaxial_ac', 'epitaxial_bc') + cell_dynamics = str, False, (1,), ('none', 'sd', 'damp-pr', 'damp-w', 'bfgs', 'none', 'pr', 'w') + press = float, False, (1,), None + wmass = float, False, (1,), None + cell_factor = float, False, (1,), None + press_conv_thr = float, False, (1,), None + cell_dofree = str, False, (1,), ('all', 'ibrav', 'a', 'b', 'c', 'fixa', 'fixb', 'fixc', 'x', 'y', 'z', 'xy', 'xz', 'yz', 'xyz', 'shape', 'volume', '2Dxy', '2Dshape', 'epitaxial_ab', 'epitaxial_ac', 'epitaxial_bc') #end class CellVariables class FCPVariables(NamelistParamDefinition, NamelistEnumBase): @@ -359,18 +359,18 @@ class FCPVariables(NamelistParamDefinition, NamelistEnumBase): throughout the rest of the code base can be utilized properly. """ - fcp_mu = float, True, (1,), None - fcp_dynamics = str, False, (1,), ('bfgs', 'newton', 'damp', 'lm', 'velocity-verlet', 'verlet') - fcp_conv_thr = float, False, (1,), None - fcp_ndiis = int, False, (1,), None - freeze_all_atoms = bool, False, (1,), None - fcp_mass = float, False, (1,), None - fcp_velocity = float, False, (1,), None - fcp_temperature = str, False, (1,), ('rescaling', 'rescale-v', 'rescale-T', 'reduce-T', 'berendsen', 'andersen', 'initial', 'not_controlled') - fcp_tempw = float, False, (1,), None - fcp_tolp = float, False, (1,), None - fcp_delta_t = float, False, (1,), None - fcp_nraise = int, False, (1,), None + fcp_mu = float, True, (1,), None + fcp_dynamics = str, False, (1,), ('bfgs', 'newton', 'damp', 'lm', 'velocity-verlet', 'verlet') + fcp_conv_thr = float, False, (1,), None + fcp_ndiis = int, False, (1,), None + freeze_all_atoms = bool, False, (1,), None + fcp_mass = float, False, (1,), None + fcp_velocity = float, False, (1,), None + fcp_temperature = str, False, (1,), ('rescaling', 'rescale-v', 'rescale-T', 'reduce-T', 'berendsen', 'andersen', 'initial', 'not_controlled') + fcp_tempw = float, False, (1,), None + fcp_tolp = float, False, (1,), None + fcp_delta_t = float, False, (1,), None + fcp_nraise = int, False, (1,), None #end class FCPVariables class RismVariables(NamelistParamDefinition, NamelistEnumBase): @@ -387,45 +387,45 @@ class RismVariables(NamelistParamDefinition, NamelistEnumBase): throughout the rest of the code base can be utilized properly. """ - nsolv = int, True, (1,), None - closure = str, False, (1,), ('kh', 'hnc') - tempv = float, False, (1,), None - ecutsolv = float, False, (1,), None - starting1d = str, False, (1,), ('zero', 'file', 'fix') - starting3d = str, False, (1,), ('zero', 'file') - smear1d = float, False, (1,), None - smear3d = float, False, (1,), None - rism1d_maxstep = int, False, (1,), None - rism3d_maxstep = int, False, (1,), None - rism1d_conv_thr = float, False, (1,), None - rism3d_conv_thr = float, False, (1,), None - mdiis1d_size = int, False, (1,), None - mdiis3d_size = int, False, (1,), None - mdiis1d_step = float, False, (1,), None - mdiis3d_step = float, False, (1,), None - rism1d_bond_width = float, False, (1,), None - rism1d_dielectric = float, False, (1,), None - rism1d_molesize = float, False, (1,), None - rism1d_nproc = int, False, (1,), None - rism3d_conv_level = float, False, (1,), None - rism3d_planar_average = bool, False, (1,), None - laue_nfit = int, False, (1,), None - laue_expand_right = float, False, (1,), None - laue_expand_left = float, False, (1,), None - laue_starting_right = float, False, (1,), None - laue_starting_left = float, False, (1,), None - laue_buffer_right = float, False, (1,), None - laue_buffer_left = float, False, (1,), None - laue_both_hands = bool, False, (1,), None - laue_wall = str, False, (1,), ('none', 'auto', 'manual') - laue_wall_z = float, False, (1,), None - laue_wall_rho = float, False, (1,), None - laue_wall_epsilon = float, False, (1,), None - laue_wall_sigma = float, False, (1,), None - laue_wall_lj6 = bool, False, (1,), None - solute_lj = str, False, ((1,), ('ntyp',)), None - solute_epsilon = float, False, ((1,), ('ntyp',)), None - solute_sigma = float, False, ((1,), ('ntyp',)), None + nsolv = int, True, (1,), None + closure = str, False, (1,), ('kh', 'hnc') + tempv = float, False, (1,), None + ecutsolv = float, False, (1,), None + starting1d = str, False, (1,), ('zero', 'file', 'fix') + starting3d = str, False, (1,), ('zero', 'file') + smear1d = float, False, (1,), None + smear3d = float, False, (1,), None + rism1d_maxstep = int, False, (1,), None + rism3d_maxstep = int, False, (1,), None + rism1d_conv_thr = float, False, (1,), None + rism3d_conv_thr = float, False, (1,), None + mdiis1d_size = int, False, (1,), None + mdiis3d_size = int, False, (1,), None + mdiis1d_step = float, False, (1,), None + mdiis3d_step = float, False, (1,), None + rism1d_bond_width = float, False, (1,), None + rism1d_dielectric = float, False, (1,), None + rism1d_molesize = float, False, (1,), None + rism1d_nproc = int, False, (1,), None + rism3d_conv_level = float, False, (1,), None + rism3d_planar_average = bool, False, (1,), None + laue_nfit = int, False, (1,), None + laue_expand_right = float, False, (1,), None + laue_expand_left = float, False, (1,), None + laue_starting_right = float, False, (1,), None + laue_starting_left = float, False, (1,), None + laue_buffer_right = float, False, (1,), None + laue_buffer_left = float, False, (1,), None + laue_both_hands = bool, False, (1,), None + laue_wall = str, False, (1,), ('none', 'auto', 'manual') + laue_wall_z = float, False, (1,), None + laue_wall_rho = float, False, (1,), None + laue_wall_epsilon = float, False, (1,), None + laue_wall_sigma = float, False, (1,), None + laue_wall_lj6 = bool, False, (1,), None + solute_lj = str, False, ((1,), ('ntyp',)), None + solute_epsilon = float, False, ((1,), ('ntyp',)), None + solute_sigma = float, False, ((1,), ('ntyp',)), None #end class RismVariables From 3a5c703825234a5bb1530bcdd1defa42e67b2b09 Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Tue, 24 Feb 2026 16:46:25 -0500 Subject: [PATCH 07/10] Nexus: WIP on Cards for `pwscf_input_new.py` --- nexus/nexus/pwscf_input_new.py | 76 ++++++++++++++++++++++++++-------- 1 file changed, 59 insertions(+), 17 deletions(-) diff --git a/nexus/nexus/pwscf_input_new.py b/nexus/nexus/pwscf_input_new.py index ff9fd48531..c134b1a583 100644 --- a/nexus/nexus/pwscf_input_new.py +++ b/nexus/nexus/pwscf_input_new.py @@ -1,12 +1,18 @@ from __future__ import annotations import os -import numpy as np -import numpy.typing as npt -import builtins -from dataclasses import dataclass +from os import PathLike +from collections.abc import Sequence from abc import ABC, abstractmethod +from dataclasses import dataclass +from pathlib import Path +from typing import Self from enum import Enum -from collections.abc import Sequence +import builtins + +import numpy as np +import numpy.typing as npt + +from .physical_system import PhysicalSystem type PwscfInputType = ( @@ -31,7 +37,6 @@ class NamelistParamDefinition: version_removed: tuple[float] | None = None #end class NamelistDefinition - class NamelistEnumBase(Enum, ABC): """Abstract base class for the namelist enumerations. Provides the ``__new__`` method for the enums. @@ -57,7 +62,6 @@ def __new__( return definition #end class NamelistEnumBase - class ControlDefinitions(NamelistParamDefinition, NamelistEnumBase): """Class representing all variables that belongs to the &CONTROL input namelist for ``pw.x``. @@ -429,27 +433,22 @@ class RismVariables(NamelistParamDefinition, NamelistEnumBase): #end class RismVariables -class PWscfNamelist(ABC): +class PWscfNamelistBase(ABC): """Abstract base class for real instances of PWscf namelists.""" @abstractmethod - def write_card(self) -> str: - pass + def write(self) -> str: ... @abstractmethod - def meets_requirements(self) -> bool: - pass + def meets_requirements(self) -> bool: ... @abstractmethod - def __setattr__(self, name, value): - pass - + def __setattr__(self, name, value): ... @property def value(self) -> PwscfInputType: return self._value - @value.setter def value(self, val: PwscfInputType): if val is None and self.required: @@ -493,4 +492,47 @@ def write_value(self) -> str: case _: raise TypeError("Value is not a valid Pwscf Input Type!") #end def write_value -#end class PWscfNamelist +#end class PWscfNamelistBase + + +class PWscfCardBase(ABC): + """Abstract base class for PWscf cards.""" + + @abstractmethod + def write(self) -> str: ... + + @classmethod + @abstractmethod + def read(cls, card: str): ... + +#end class PWscfCardBase + + +class AtomicSpecies(PWscfCardBase): + """Class for the ATOMIC_SPECIES card.""" + + def __init__( + self, + elements: Sequence[str], + pseudos: Sequence[str | PathLike], + ): + self.elements = list(elements) + self.pseudos = [Path(ps) for ps in pseudos] + #+ Will need to add masses, contingent on PR #5832 + self.masses = None + + + @classmethod + def from_physical_system(cls, system: PhysicalSystem, pseudos: str) -> Self: + """Generate the information for the ATOMIC_SPECIES card from a + Nexus ``PhysicalSystem``. Must have elements and be pseudized. + """ + ... + + + + + + + + From 4b4dca3a25f9346288465d940b3a76104ab2b3b3 Mon Sep 17 00:00:00 2001 From: kayahans Date: Thu, 26 Feb 2026 17:00:39 -0500 Subject: [PATCH 08/10] hubbard and kpoints cards --- nexus/nexus/pwscf_input_new.py | 600 ++++++++++++++++++++++++++++++++- 1 file changed, 591 insertions(+), 9 deletions(-) diff --git a/nexus/nexus/pwscf_input_new.py b/nexus/nexus/pwscf_input_new.py index c134b1a583..e7b42fa19a 100644 --- a/nexus/nexus/pwscf_input_new.py +++ b/nexus/nexus/pwscf_input_new.py @@ -5,23 +5,21 @@ from abc import ABC, abstractmethod from dataclasses import dataclass from pathlib import Path -from typing import Self +from typing import ClassVar, Self, TypeVar from enum import Enum import builtins import numpy as np import numpy.typing as npt +from numpy.linalg import inv from .physical_system import PhysicalSystem +from .structure import kmesh -type PwscfInputType = ( - str - | bool - | int - | float - | Sequence -) +PwscfInputType = str | bool | int | float | Sequence +# For structured array inputs (k-points, weights, reciprocal lattice, etc.) +PwscfArrayInput = npt.NDArray[np.floating] | Sequence[Sequence[float]] | Sequence[float] @dataclass(frozen=True) # We generally don't want any of these to be modified @@ -495,8 +493,25 @@ def write_value(self) -> str: #end class PWscfNamelistBase + +class PWscfCardBaseIO(ABC): + """Abstract base for PWscf card read/write IO.""" + + @abstractmethod + def write(self, card: PWscfCardBase) -> str: + """Write the card body (excluding header line).""" + ... + + @abstractmethod + def read(self, body: str, **kwargs) -> PWscfCardBase: + """Read the card body (excluding header line). Returns the card instance.""" + ... + + class PWscfCardBase(ABC): """Abstract base class for PWscf cards.""" + allowed_specifiers: frozenset[str] = frozenset() + _io: dict[str, 'PWscfCardBaseIO'] = {} @abstractmethod def write(self) -> str: ... @@ -528,11 +543,578 @@ def from_physical_system(cls, system: PhysicalSystem, pseudos: str) -> Self: Nexus ``PhysicalSystem``. Must have elements and be pseudized. """ ... - +_PWSCF_ARRAY_FORMAT = '{0:16.8f}' # could be imported from somewhere else to be more general + + +def _array_to_string( + a: PwscfArrayInput, + pad: str = ' ', + fmt: str = _PWSCF_ARRAY_FORMAT, + rowsep: str = '\n', +) -> str: + """Format a numpy array for QE card output.""" + a = np.asarray(a) + if a.ndim == 1: + return pad + ' '.join(fmt.format(v) for v in a) + rowsep + return rowsep.join( + pad + ' '.join(fmt.format(v) for v in row) for row in a + ) + +# Kpoints Card +class KPointsGammaIO(PWscfCardBaseIO): + """IO for K_POINTS {gamma} - no additional lines.""" + + def write(self, card: KPoints) -> str: + return '' + @staticmethod + def read(lines: list[str]) -> KPoints: + return KPoints(specifier='gamma') + +class KPointsAutomaticIO(PWscfCardBaseIO): + """IO for K_POINTS {automatic} - Monkhorst-Pack grid.""" + + def write(self, card: KPoints) -> str: + grid = np.asarray(card.grid, dtype=int) + shift = np.asarray(card.shift, dtype=int) + s = ' ' + s += ' '.join(str(g) for g in grid) + s += ' ' + s += ' '.join(str(sv) for sv in shift) + return s + + def read(self, lines: list[str]) -> KPoints: + a = np.fromstring(lines[0], sep=' ') + grid = a[0:3] + shift = a[3:] + return KPoints(specifier='automatic', grid=grid, shift=shift) + + +class KPointsExplicitIO(PWscfCardBaseIO): + """IO for K_POINTS {tpiba,crystal,tpiba_b,crystal_b,tpiba_c,crystal_c}. + + The card must store kpoints in the coordinate system matching the specifier: + - tpiba*: Cartesian coordinates in 2π/alat units + - crystal*: Crystal (reciprocal lattice) coordinates + The writer outputs the stored values as-is; no unit conversion is performed. + """ + + def write(self, card: KPoints) -> str: + kpoints = np.asarray(card.kpoints) + weights = np.asarray(card.weights) + nkpoints = len(kpoints) + a = np.empty((nkpoints, 4)) + a[:, 0:3] = kpoints + a[:, 3] = weights + return f' {nkpoints}\n' + _array_to_string(a) + + def read(self, lines: list[str], specifier: str = 'crystal', **kwargs) -> KPoints: + nkpoints = int(lines[0].strip()) + if len(lines) < 1 + nkpoints: + raise ValueError( + f"K_POINTS explicit: expected {nkpoints} data rows, got {len(lines) - 1}" + ) + arr = np.loadtxt(lines[1:1 + nkpoints]) + if arr.ndim == 1: + arr = arr.reshape(1, -1) + kpoints = arr[:, :3] + weights = arr[:, 3] if arr.shape[1] > 3 else np.ones(len(kpoints)) + return KPoints(specifier=specifier, kpoints=kpoints, weights=weights) + +class KPoints(PWscfCardBase): + """K_POINTS card with strategy-pattern writers for specifier-dependent formats. + + Specifiers: + - gamma: Gamma-point only + - automatic: Monkhorst-Pack grid (nk1 nk2 nk3 sk1 sk2 sk3) + - tpiba, crystal, tpiba_b, crystal_b, tpiba_c, crystal_c: require explicit list + + For explicit specifiers, kpoints must be in the matching coordinate system, no unit conversion is performed. + - tpiba*: Cartesian, 2pi/alat units + - crystal*: Crystal (reciprocal lattice) coordinates + + Use change_specifier() to convert between explicit specifiers + Use from_physical_system() to create to inherit kpoints from a Nexus PhysicalSystem + """ + + _allowed_specifiers = frozenset({ + 'gamma', 'automatic', + 'tpiba', 'crystal', 'tpiba_b', 'crystal_b', 'tpiba_c', 'crystal_c', + }) + _explicit_specifiers = frozenset({ + 'tpiba', 'crystal', 'tpiba_b', 'crystal_b', 'tpiba_c', 'crystal_c', + }) + _io: dict[str, PWscfCardBaseIO] = { + 'gamma': KPointsGammaIO(), + 'automatic': KPointsAutomaticIO(), + 'tpiba': KPointsExplicitIO(), + 'crystal': KPointsExplicitIO(), + 'tpiba_b': KPointsExplicitIO(), + 'crystal_b': KPointsExplicitIO(), + 'tpiba_c': KPointsExplicitIO(), + 'crystal_c': KPointsExplicitIO(), + } + def __init__( + self, + specifier: str = 'gamma', + grid: tuple[int, int, int] | None = None, + shift: tuple[int, int, int] | None = None, + kpoints: PwscfArrayInput | None = None, + weights: PwscfArrayInput | None = None, + ): + spec = specifier.lower() if specifier else 'gamma' + if spec not in self._allowed_specifiers: + raise ValueError( + f"K_POINTS specifier '{specifier}' not recognized. " + f"Allowed: {sorted(self._allowed_specifiers)}" + ) + self.specifier = spec + + if spec == 'gamma': + self.grid = None + self.shift = None + self.kpoints = np.empty((0, 3)) + self.weights = np.empty((0,)) + elif spec == 'automatic': + if grid is None or shift is None: + raise ValueError("grid and shift required for specifier 'automatic'") + self.grid = tuple(int(g) for g in grid) + self.shift = tuple(int(sv) for sv in shift) + self.kpoints = np.empty((0, 3)) + self.weights = np.empty((0,)) + else: + if kpoints is None or weights is None: + raise ValueError( + f"kpoints and weights required for specifier '{spec}'" + ) + kpoints = np.asarray(kpoints) + weights = np.asarray(weights) + if len(kpoints) != len(weights): + raise ValueError( + f"kpoints and weights length mismatch: {len(kpoints)} vs {len(weights)}" + ) + self.grid = None + self.shift = None + self.kpoints = kpoints + self.weights = weights + + def write(self) -> str: + header = f"K_POINTS {self.specifier}\n" + body = self._io[self.specifier].write(self) + return header + body + ('\n' if body else '') + + @classmethod + def read(cls, lines: list[str], specifier: str = 'crystal') -> Self: + if specifier in cls._explicit_specifiers: + return cls._io[specifier].read(lines, specifier=specifier.lower()) + else: + return cls._io[specifier].read(lines) + + def change_specifier( + self, + new_specifier: str, + scale: float, + kaxes: PwscfArrayInput, + ) -> None: + """Convert k-points to a different coordinate specifier. + + Reuses the legacy logic. Converts via cartesian reciprocal space as intermediate. + + Parameters + ---------- + new_specifier : str + One of: gamma, automatic, tpiba, crystal (tpiba_b, crystal_b not yet implemented). + scale : float + Lattice parameter alat (e.g. celldm(1) in Bohr). + kaxes : ndarray + Reciprocal lattice vectors, shape (3,3). kaxes = 2π * inv(axes).T + for axes in Bohr. + """ + pi = np.pi + spec = self.specifier + new_spec = new_specifier.lower() + # Convert from current specifier to Cartesian reciprocal + if spec in ('tpiba', ''): + kpoints = self.kpoints * (2 * pi) / scale + elif spec == 'gamma': + kpoints = np.array([[0.0, 0.0, 0.0]]) + elif spec == 'crystal': + kpoints = np.dot(self.kpoints, kaxes) + elif spec == 'automatic': + grid = np.array(self.grid, dtype=int) + shift = 0.5 * np.array(self.shift) + kpoints = kmesh(kaxes, grid, shift) + # automatic -> explicit: need weights (uniform for MP mesh) + nk = len(kpoints) + self.weights = np.full(nk, 1.0 / nk) + elif spec in ('tpiba_b', 'crystal_b', 'tpiba_c', 'crystal_c'): + raise NotImplementedError( + f"change_specifier from '{spec}' not yet implemented" + ) + else: + raise ValueError( + f"Invalid current specifier '{spec}'. " + f"Valid: tpiba, gamma, crystal, automatic, tpiba_b, crystal_b" + ) + + # Convert from Cartesian to new specifier + if new_spec in ('tpiba', 'tpiba_b', 'tpiba_c'): + kpoints = kpoints / ((2 * pi) / scale) + elif new_spec == 'gamma': + kpoints = np.array([[0.0, 0.0, 0.0]]) + elif new_spec in ('crystal', 'crystal_b', 'crystal_c'): + kpoints = np.dot(kpoints, inv(kaxes)) + elif new_spec == 'automatic': + if spec != 'automatic': + raise ValueError( + "cannot map arbitrary k-points into a Monkhorst-Pack mesh" + ) + else: + raise ValueError( + f"Invalid new specifier '{new_specifier}'. " + f"Valid: {sorted(self._explicit_specifiers)}" + ) + + self.kpoints = np.asarray(kpoints) + self.specifier = new_spec + + @classmethod + def from_gamma(cls) -> Self: + """Create K_POINTS for Gamma-point-only calculation.""" + return cls(specifier='gamma') + + @classmethod + def from_automatic( + cls, + kgrid: Sequence[int], + kshift: Sequence[int] = (0, 0, 0), + ) -> Self: + """Create K_POINTS using uniform grid and shift.""" + kgrid = tuple(kgrid) + kshift = tuple(kshift) + if len(kgrid) != 3 or len(kshift) != 3: + raise ValueError("kgrid and kshift must have 3 elements each") + return cls(specifier='automatic', grid=kgrid, shift=kshift) + @classmethod + def from_explicit( + cls, + kpoints: PwscfArrayInput, + weights: PwscfArrayInput, + specifier: str = 'crystal', + ) -> Self: + """Create K_POINTS from an explicit k-point list.""" + spec = specifier.lower() + if spec not in cls._explicit_specifiers: + raise ValueError(f"Specifier '{spec}' must be one of {sorted(cls.explicit_specifiers)}") + kpoints = np.asarray(kpoints) + weights = np.asarray(weights) + return cls( + specifier=spec, + kpoints=kpoints, + weights=weights, + ) + + @classmethod + def from_physical_system( + cls, + system: PhysicalSystem, + specifier: str = 'crystal', + ) -> Self: + """Create K_POINTS from a Nexus PhysicalSystem. + + Uses structure.kpoints (Cartesian reciprocal) and structure.kweights. + Builds in crystal coordinates first, then uses change_specifier to convert + if the requested specifier is tpiba or another format. + """ + structure = system.structure + kpoints = structure.kpoints + kweights = structure.kweights + + if len(kpoints) == 0 or len(kweights) == 0: + raise ValueError("PhysicalSystem has no k-points or k-weights") + + spec = specifier.lower() + if spec not in cls._explicit_specifiers: + raise ValueError(f"Specifier '{spec}' must be one of {sorted(cls._explicit_specifiers)}") + + # Build in crystal coordinates (from structure.kpoints_unit) + card = cls.from_explicit( + kpoints=structure.kpoints_unit(), + weights=kweights, + specifier='crystal', + ) + if spec in ('tpiba', 'tpiba_b', 'tpiba_c'): + scale = structure.scale + kaxes = structure.kaxes + card.change_specifier('tpiba', scale, kaxes) + card.specifier = spec # preserve tpiba_b, tpiba_c if requested + elif spec in ('crystal_b', 'crystal_c'): + card.specifier = spec # same coords as crystal, different specifier + return card + +# Hubbard Card +@dataclass(frozen=True) +class HubbardOnSite: + """On site Hubbard parameters. + Format: param label value + """ + _allowed_params: ClassVar[frozenset[str]] = frozenset({'U', 'ALPHA', 'J0', 'J', 'B', 'E2', 'E3'}) + param: str + label: str # e.g. "Ni-3d" + value: float + + def __post_init__(self): + if self.param not in self._allowed_params: + raise ValueError(f"Invalid on-site parameter: {self.param}") + +@dataclass(frozen=True) +class HubbardOrbitalResolved(HubbardOnSite): + """On site Hubbard parameters for orbital-resolved calculations. + Format: param label value orb1 orb2 ... orbn, n should be in the range [1, 2*l+1] + """ + param: str + orbitals: tuple[int, ...] # orbital indices in manifold + +@dataclass(frozen=True) +class HubbardInterSite: + """Inter-site Hubbard parameters. + Format: V label1 label2 ind1 ind2 value + """ + _allowed_params: ClassVar[frozenset[str]] = frozenset({'V'}) + param: str + label1: str # e.g. "Co-3d" + label2: str # e.g. "O-2p" + ind1: int # atom index (1-based, ATOMIC_POSITIONS order) + ind2: int + value: float + + def __post_init__(self): + if self.param not in self._allowed_params: + raise ValueError(f"Invalid inter-site parameter: {self.param}") + + +HubbardEntry = HubbardOnSite | HubbardInterSite | HubbardOrbitalResolved + + +class HubbardIO(PWscfCardBaseIO): + """IO for HUBBARD card. Body format is the same for all specifiers.""" + + _param_width = 5 + _label_width = 5 + _value_fmt = '.3f' + + def write(self, card: 'Hubbard') -> str: + entries = card.entries + on_site = [e for e in entries if isinstance(e, HubbardOnSite) and not isinstance(e, HubbardOrbitalResolved)] + orbital = [e for e in entries if isinstance(e, HubbardOrbitalResolved)] + inter_site = [e for e in entries if isinstance(e, HubbardInterSite)] + ordered = on_site + orbital + inter_site + + parts = [] + for e in ordered: + p = f"{e.param:<{self._param_width}}" + v = format(e.value, self._value_fmt) + if isinstance(e, HubbardOrbitalResolved): + lb = f"{e.label:<{self._label_width}}" + orb_str = ' '.join(str(o) for o in e.orbitals) + parts.append(f"{p} {lb} {v} {orb_str}") + elif isinstance(e, HubbardOnSite): + lb = f"{e.label:<{self._label_width}}" + parts.append(f"{p} {lb} {v}") + elif isinstance(e, HubbardInterSite): + l1 = f"{e.label1:<{self._label_width}}" + l2 = f"{e.label2:<{self._label_width}}" + parts.append(f"{p} {l1} {l2} {e.ind1} {e.ind2} {v}") + return '\n'.join(parts) + + def read(self, lines: list[str], specifier: str = 'atomic', **kwargs) -> Hubbard: + entries: list[HubbardEntry] = [] + on_site_params = HubbardOnSite._allowed_params + for line in lines: + tokens = line.split() + if len(tokens) == 3: + param, label, val = tokens[0], tokens[1], float(tokens[2]) + if param in on_site_params: + entries.append(HubbardOnSite(param, label, val)) + elif len(tokens) == 6 and tokens[0].upper() == 'V': + entries.append(HubbardInterSite( + tokens[0], tokens[1], tokens[2], + int(tokens[3]), int(tokens[4]), float(tokens[5]), + )) + elif len(tokens) >= 4 and tokens[0] in on_site_params: + param, label, val = tokens[0], tokens[1], float(tokens[2]) + orbitals = tuple(int(t) for t in tokens[3:]) + entries.append(HubbardOrbitalResolved(param, label, val, orbitals)) + return Hubbard(entries=entries, specifier=specifier) + + +class Hubbard(PWscfCardBase): + """HUBBARD card with strategy-pattern writers for line types 1, 2, 3. + + Specifiers (projection type): atomic, ortho-atomic, norm-atomic, wf, pseudo. + Line types: + 1: param label value (on-site shell-averaged) + 2: V label1 label2 ind1 ind2 value (inter-site) + 3: param label value orb1 orb2 ... (on-site orbital-resolved) + """ + + allowed_specifiers = frozenset({ + 'atomic', 'ortho-atomic', 'norm-atomic', 'wf', 'pseudo', + }) + default_specifier = 'atomic' + _io = HubbardIO() + + def __init__( + self, + entries: Sequence[HubbardEntry], + specifier: str = 'atomic', + ): + spec = specifier.lower() if specifier else self.default_specifier + if spec not in self.allowed_specifiers: + raise ValueError( + f"HUBBARD specifier '{specifier}' not recognized. " + f"Allowed: {sorted(self.allowed_specifiers)}" + ) + self.specifier = spec + self.entries = list(entries) + + def check_compatible(self, physical_system: PhysicalSystem) -> bool: + """Check if the HUBBARD card is compatible with the PhysicalSystem. + + Validates that: + - Species in Hubbard labels (e.g. 'Ni' from 'Ni-3d') exist in structure.elem + - Inter-site indices are not checked, as these are typically provided by hp.x + """ + if len(self.entries) == 0: + return True + + valid_species = set(physical_system.structure.elem) + def _extract_species(label: str) -> str: + """Extract species from Hubbard label (e.g. 'Ni-3d' -> 'Ni').""" + return label.split('-')[0] if '-' in label else label + + for e in self.entries: + if isinstance(e, (HubbardOnSite, HubbardOrbitalResolved)): + sp = _extract_species(e.label) + if sp not in valid_species: + raise ValueError( + f"Hubbard label '{e.label}' references unknown species '{sp}'. " + f"Valid species: {sorted(valid_species)}" + ) + elif isinstance(e, HubbardInterSite): + for lbl in (e.label1, e.label2): + sp = _extract_species(lbl) + if sp not in valid_species: + raise ValueError( + f"Hubbard inter-site label '{lbl}' references unknown species '{sp}'. " + f"Valid species: {sorted(valid_species)}" + ) + return True + + def write(self) -> str: + header = f"HUBBARD {self.specifier}\n" + body = self._io.write(self) + return header + body + '\n' + + @classmethod + def read(cls, lines: list[str], specifier: str = 'atomic') -> Self: + return cls._io.read(lines, specifier=specifier) + + @classmethod + def from_entries( + cls, + entries: Sequence[HubbardEntry], + specifier: str = 'atomic', + ) -> Self: + """Create HUBBARD card from a sequence of HubbardEntry objects.""" + return cls(entries=entries, specifier=specifier) + + @classmethod + def from_records( + cls, + records: Sequence[dict], + specifier: str = 'atomic', + ) -> Self: + """Create HUBBARD card from a list of dicts. + + Options: + 1. on_site: {type: 'on_site', param, label, value} + 2. orbital: {type: 'orbital', param, label, value, orbitals: tuple|list} + 3. inter_site: {type: 'inter_site', param, label1, label2, ind1, ind2, value} + """ + entries: list[HubbardEntry] = [] + for r in records: + kind = r.get('type') + if kind == 'on_site': + entries.append(HubbardOnSite( + r['param'], r['label'], float(r['value']) + )) + elif kind == 'orbital': + orb = r['orbitals'] + entries.append(HubbardOrbitalResolved( + r['param'], r['label'], float(r['value']), + tuple(orb) if not isinstance(orb, tuple) else orb, + )) + elif kind == 'inter_site': + entries.append(HubbardInterSite( + r['param'], + r['label1'], r['label2'], + int(r['ind1']), int(r['ind2']), + float(r['value']), + )) + else: + raise ValueError( + f"Hubbard record type '{kind}' not recognized. " + "Use 'on_site', 'orbital', or 'inter_site'." + ) + return cls(entries=entries, specifier=specifier) + + @classmethod + def from_hp_output(cls, text: str) -> Self: + """Create HUBBARD card from hp.x HUBBARD.dat output. + + Parses the block after '# Copy this data in the pw.x input file...' + """ + lines = [ln.strip() for ln in text.splitlines() if ln.strip()] + specifier = cls.default_specifier + entries: list[HubbardEntry] = [] + on_site_params = HubbardOnSite._allowed_params + for line in lines: + if line.startswith('#'): + continue + tokens = line.split() + if not tokens: + continue + if tokens[0].upper() == 'HUBBARD': + for t in tokens[1:]: + s = t.strip('{}()') + if s and s.lower() in cls.allowed_specifiers: + specifier = s.lower() + break + continue + if len(tokens) == 3: + param, label, val = tokens[0], tokens[1], float(tokens[2]) + if param in on_site_params: + entries.append(HubbardOnSite(param, label, val)) + elif len(tokens) == 6 and tokens[0].upper() == 'V': + entries.append(HubbardInterSite( + tokens[0], + tokens[1], tokens[2], + int(tokens[3]), int(tokens[4]), + float(tokens[5]), + )) + elif len(tokens) >= 4 and tokens[0] in on_site_params: + param, label, val = tokens[0], tokens[1], float(tokens[2]) + orbitals = tuple(int(t) for t in tokens[3:]) + entries.append(HubbardOrbitalResolved(param, label, val, orbitals)) + return cls(entries=entries, specifier=specifier) + def from_hubbard_dat_file(self, file: PathLike) -> Self: + """Create HUBBARD card from a hubbard.dat file.""" + with Path(file).open() as f: + return self.from_hp_output(f.read()) \ No newline at end of file From c409aa87eb4683c753e745812653722ce3166abf Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Sun, 14 Jun 2026 10:34:20 -0400 Subject: [PATCH 09/10] Squashed merge of develop --- .github/pull_request_template.md | 46 +- .../workflows/ci-github-actions-nexus.yaml | 83 + .../ci-github-actions-self-hosted.yaml | 32 +- .../workflows/ci-github-actions-static.yaml | 2 +- .github/workflows/ci-github-actions.yaml | 24 +- .../workflows/close-inactive-issues-prs.yaml | 22 + .github/workflows/ghcr-develop.yaml | 8 +- .../update-ghcr-ci-image-centos10.yaml | 8 +- .../update-ghcr-ci-image-ubuntu22-clang.yaml | 8 +- ...update-ghcr-ci-image-ubuntu22-openmpi.yaml | 8 +- .../update-ghcr-ci-image-ubuntu22-serial.yaml | 8 +- ...update-ghcr-ci-image-ubuntu24-openmpi.yaml | 45 + .gitignore | 1 - CHANGELOG.md | 56 +- CMake/python.cmake | 40 +- CMake/unit_test.cmake | 14 +- CMakeLists.txt | 12 +- .../docker/dependencies/centos10/Dockerfile | 1 + .../dependencies/ubuntu22/clang/Dockerfile | 1 + .../dependencies/ubuntu22/openmpi/Dockerfile | 2 + .../dependencies/ubuntu22/serial/Dockerfile | 2 + .../dependencies/ubuntu24/openmpi/Dockerfile | 61 + docs/LCAO.rst | 10 +- docs/additional_tools.rst | 42 +- docs/afqmc.rst | 8 +- docs/analyzing.rst | 2 +- docs/appendices.rst | 1 + docs/citing.rst | 8 + docs/developing.rst | 139 +- docs/hamiltonianobservable.rst | 68 +- docs/index.rst | 1 + docs/input_overview.rst | 6 +- docs/installation.rst | 35 +- docs/intro_wavefunction.rst | 56 +- docs/lab_advanced_molecules.rst | 14 +- docs/lab_condensed_matter.rst | 8 +- docs/lab_excited.rst | 38 +- docs/lab_qmc_basics.rst | 50 +- docs/lab_qmc_statistics.rst | 2 +- docs/methods.rst | 64 +- docs/performance_portable.rst | 2 +- docs/requirements.txt | 6 +- docs/simulationcell.rst | 10 +- docs/spin_orbit.rst | 12 +- docs/unit_testing.rst | 4 +- examples/molecules/H2O/simple-H2O.xml | 9 +- examples/molecules/He/he_bspline_jastrow.xml | 4 +- examples/molecules/He/he_example_wf.xml | 7 +- examples/molecules/He/he_from_gamess.xml | 5 +- examples/molecules/He/he_simple.xml | 4 +- examples/molecules/He/he_simple_dmc.xml | 2 +- examples/molecules/He/he_simple_opt.xml | 7 +- examples/solids/simple-LiH.xml | 9 +- labs/lab1_qmc_statistics/average/average.py | 2 +- labs/lab1_qmc_statistics/average/stddev.py | 2 +- labs/lab1_qmc_statistics/average/stddev2.py | 2 +- nexus/README.md | 12 +- nexus/docs/code-style.rst | 33 + nexus/docs/examples.rst | 27 +- nexus/docs/installation.rst | 383 ++- nexus/docs/overview.rst | 7 +- nexus/docs/requirements.txt | 20 +- nexus/manual_install | 151 + nexus/nexus/__init__.py | 110 +- nexus/nexus/basisset.py | 40 +- nexus/nexus/bin/eshdf | 10 + nexus/nexus/bin/nxs-redo | 11 + nexus/nexus/bin/nxs-sim | 11 + nexus/nexus/bin/nxs-test | 2610 +---------------- nexus/nexus/bin/qdens | 11 + nexus/nexus/bin/qdens-radial | 11 + nexus/nexus/bin/qmc-fit | 10 + nexus/nexus/bin/qmca | 9 + nexus/nexus/developer.py | 8 +- .../01_basic_dependencies/dyn_basic_dep.py | 133 + .../02_energy_convergence/dyn_energy_conv.py | 225 ++ .../dyn_energy_conv_brief.py | 146 + .../examples/dynamic_workflows/README.rst | 36 + nexus/nexus/fileio.py | 27 +- nexus/nexus/gamess.py | 3 +- nexus/nexus/gamess_analyzer.py | 5 + nexus/nexus/gamess_input.py | 8 +- nexus/nexus/gaussian_process.py | 2253 -------------- nexus/nexus/generic.py | 147 +- nexus/nexus/hdfreader.py | 3 +- nexus/nexus/machines.py | 36 +- nexus/nexus/nexus_base.py | 32 +- nexus/nexus/nexus_version.py | 2 +- nexus/nexus/numerics.py | 7 +- nexus/nexus/periodic_table.py | 2396 ++++----------- nexus/nexus/physical_system.py | 55 +- nexus/nexus/project_manager.py | 134 +- nexus/nexus/pseudopotential.py | 78 +- nexus/nexus/pwscf.py | 133 +- nexus/nexus/pwscf_analyzer.py | 15 +- nexus/nexus/pwscf_data_reader.py | 3 +- nexus/nexus/pwscf_input.py | 14 +- nexus/nexus/pwscf_postprocessors.py | 3 +- nexus/nexus/qmcpack.py | 172 ++ nexus/nexus/qmcpack_analyzer.py | 5 +- nexus/nexus/qmcpack_converters.py | 71 +- nexus/nexus/qmcpack_input.py | 1011 ++++--- nexus/nexus/quantum_package.py | 7 +- nexus/nexus/quantum_package_input.py | 4 +- nexus/nexus/simulation.py | 422 ++- nexus/nexus/structure.py | 332 ++- nexus/nexus/template_simulation.py | 7 +- nexus/nexus/testing.py | 379 --- nexus/nexus/tests/CMakeLists.txt | 89 +- nexus/nexus/tests/__init__.py | 261 ++ .../qmcpack/rsqmc_misc/H2O/runs/dmc.in.xml | 4 +- .../qmcpack/rsqmc_misc/H2O/runs/opt.in.xml | 4 +- .../qmcpack/rsqmc_misc/H2O/runs/scf.in | 2 +- .../qmcpack/rsqmc_misc/LiH/runs/dmc.in.xml | 8 +- .../qmcpack/rsqmc_misc/LiH/runs/nscf.in | 4 +- .../qmcpack/rsqmc_misc/LiH/runs/opt.in.xml | 8 +- .../qmcpack/rsqmc_misc/LiH/runs/scf.in | 4 +- .../runs/relax/kgrid_111/relax.in | 2 +- .../runs/relax/kgrid_222/relax.in | 2 +- .../runs/relax/kgrid_444/relax.in | 2 +- .../runs/relax/kgrid_666/relax.in | 2 +- nexus/nexus/tests/test_basisset.py | 156 +- nexus/nexus/tests/test_bundle.py | 14 +- nexus/nexus/tests/test_developer.py | 16 +- nexus/nexus/tests/test_execute.py | 10 +- nexus/nexus/tests/test_fileio.py | 106 +- nexus/nexus/tests/test_gamess_analyzer.py | 34 +- nexus/nexus/tests/test_gamess_input.py | 104 +- nexus/nexus/tests/test_gamess_simulation.py | 73 +- nexus/nexus/tests/test_generic.py | 168 +- .../test_generic_files/old_nxs_pwscf_input.p | Bin 0 -> 1698 bytes .../old_nxs_pwscf_input_numpy_1.p | Bin 0 -> 1697 bytes .../tests/test_generic_files/old_nxs_sim.p | Bin 0 -> 745 bytes .../test_generic_files/old_nxs_sim_numpy_1.p | Bin 0 -> 745 bytes nexus/nexus/tests/test_grid_functions.py | 19 +- nexus/nexus/tests/test_hdfreader.py | 156 +- nexus/nexus/tests/test_machines.py | 48 +- nexus/nexus/tests/test_memory.py | 10 +- nexus/nexus/tests/test_nexus_base.py | 39 +- nexus/nexus/tests/test_nexus_imports.py | 88 - nexus/nexus/tests/test_numerics.py | 356 ++- nexus/nexus/tests/test_nxs_redo.py | 39 +- nexus/nexus/tests/test_nxs_sim.py | 26 +- nexus/nexus/tests/test_observables.py | 17 +- .../nexus/tests/test_optional_dependencies.py | 42 - nexus/nexus/tests/test_periodic_table.py | 375 ++- nexus/nexus/tests/test_physical_system.py | 35 +- nexus/nexus/tests/test_project_manager.py | 46 +- nexus/nexus/tests/test_pseudopotential.py | 95 +- nexus/nexus/tests/test_pwscf_analyzer.py | 29 +- nexus/nexus/tests/test_pwscf_input.py | 131 +- .../test_pwscf_postprocessor_analyzers.py | 43 +- .../tests/test_pwscf_postprocessor_input.py | 40 +- .../test_pwscf_postprocessor_simulations.py | 21 +- nexus/nexus/tests/test_pwscf_simulation.py | 111 +- nexus/nexus/tests/test_pyscf_analyzer.py | 9 +- nexus/nexus/tests/test_pyscf_input.py | 62 +- nexus/nexus/tests/test_pyscf_simulation.py | 40 +- nexus/nexus/tests/test_qdens.py | 346 ++- nexus/nexus/tests/test_qdens_radial.py | 211 +- nexus/nexus/tests/test_qmc_fit.py | 60 +- nexus/nexus/tests/test_qmca.py | 163 +- nexus/nexus/tests/test_qmcpack_analyzer.py | 126 +- .../tests/test_qmcpack_converter_analyzers.py | 12 +- .../tests/test_qmcpack_converter_input.py | 42 +- .../test_qmcpack_converter_simulations.py | 153 +- nexus/nexus/tests/test_qmcpack_input.py | 205 +- .../VO2_M1_afm.in.xml | 4 +- nexus/nexus/tests/test_qmcpack_simulation.py | 157 +- .../tests/test_quantum_package_analyzer.py | 9 +- .../nexus/tests/test_quantum_package_input.py | 35 +- .../tests/test_quantum_package_simulation.py | 46 +- .../nexus/tests/test_required_dependencies.py | 14 - nexus/nexus/tests/test_rmg_analyzer.py | 12 +- nexus/nexus/tests/test_rmg_input.py | 152 +- nexus/nexus/tests/test_rmg_simulation.py | 15 +- nexus/nexus/tests/test_settings.py | 43 +- nexus/nexus/tests/test_simulation_module.py | 537 ++-- nexus/nexus/tests/test_structure.py | 1118 ++++--- nexus/nexus/tests/test_testing.py | 12 +- nexus/nexus/tests/test_unit_converter.py | 9 +- nexus/nexus/tests/test_user_examples.py | 447 +++ nexus/nexus/tests/test_utilities.py | 298 ++ nexus/nexus/tests/test_vasp_analyzer.py | 77 +- nexus/nexus/tests/test_vasp_input.py | 108 +- nexus/nexus/tests/test_vasp_simulation.py | 154 +- nexus/nexus/tests/test_versions.py | 134 - nexus/nexus/tests/test_xmlreader.py | 40 +- nexus/nexus/utilities.py | 109 +- nexus/nexus/vasp.py | 3 +- nexus/nexus/vasp_analyzer.py | 3 +- nexus/nexus/vasp_input.py | 22 +- nexus/nexus/versions.py | 920 ------ nexus/nexus/xmlreader.py | 11 +- nexus/pyproject.toml | 94 +- nexus/requirements.txt | 12 - nexus/requirements_minimal.txt | 5 - nexus/uv.lock | 1962 +++++++++++++ src/Estimators/EnergyDensityEstimator.cpp | 7 +- src/Estimators/tests/CMakeLists.txt | 2 + .../EDenEstimatorManagerIntegrationTest.cpp | 7 +- .../tests/test_EnergyDensityEstimator.cpp | 16 +- ...test_EnergyDensityEstimatorIntegration.cpp | 18 +- .../test_EnergyDensityEstimatorIntegration.h | 296 +- .../tests/test_EstimatorManagerCrowd.cpp | 2 +- src/Message/Communicate.cpp | 12 +- src/Message/Communicate.h | 9 +- src/Message/tests/CMakeLists.txt | 5 +- src/Message/tests/test_communciate.cpp | 15 + src/Numerics/codegen/gen_cartesian_tensor.py | 17 +- src/Numerics/codegen/read_order.py | 20 +- src/Numerics/tests/gen_gto.py | 38 +- src/Numerics/tests/gen_ylm.py | 4 +- src/Particle/ParticleSetPool.cpp | 5 + src/Particle/ParticleSetPool.h | 12 +- src/Particle/SimulationCell.h | 2 +- .../LMYE_QMCCostFunction.cpp | 22 +- .../LMYE_QMCCostFunctionBatched.cpp | 22 +- src/QMCDrivers/WFOpt/QMCCostFunction.cpp | 10 +- src/QMCDrivers/WFOpt/QMCCostFunction.h | 4 +- src/QMCDrivers/WFOpt/QMCCostFunctionBase.cpp | 19 +- src/QMCDrivers/WFOpt/QMCCostFunctionBase.h | 6 +- .../WFOpt/QMCCostFunctionBatched.cpp | 12 +- src/QMCDrivers/WFOpt/QMCCostFunctionBatched.h | 4 +- .../WFOpt/QMCFixedSampleLinearOptimize.cpp | 122 +- .../WFOpt/QMCFixedSampleLinearOptimize.h | 4 +- .../QMCFixedSampleLinearOptimizeBatched.cpp | 109 +- .../QMCFixedSampleLinearOptimizeBatched.h | 4 +- src/QMCDrivers/tests/CMakeLists.txt | 2 + src/QMCDrivers/tests/diffuse.py | 8 +- src/QMCHamiltonians/CoulombPBCAA.cpp | 134 +- src/QMCHamiltonians/CoulombPBCAA.h | 10 + .../CoulombPotentialFactory.cpp | 8 + .../tests/MinimalHamiltonianPool.cpp | 14 + .../tests/MinimalHamiltonianPool.h | 13 + .../tests/test_QMCHamiltonian.cpp | 215 +- .../tests/test_RotatedSPOs_NLPP.cpp | 3 +- .../tests/test_coulomb_pbcAA.cpp | 464 ++- src/QMCTools/ppconvert/src/common/IOASCII.cc | 2 +- .../BsplineFactory/BsplineReader.cpp | 10 +- .../BsplineFactory/BsplineReader.h | 11 +- .../BsplineFactory/EinsplineSetBuilder.h | 6 + .../EinsplineSetBuilder_createSPOs.cpp | 51 +- .../EinsplineSpinorSetBuilder.cpp | 4 +- .../BsplineFactory/HybridRepSetReader.cpp | 16 +- .../BsplineFactory/HybridRepSetReader.h | 1 + .../BsplineFactory/SplineC2C.cpp | 94 +- .../BsplineFactory/SplineC2C.h | 16 +- .../BsplineFactory/SplineC2COMPTarget.cpp | 19 +- .../BsplineFactory/SplineC2R.cpp | 93 +- .../BsplineFactory/SplineC2R.h | 16 +- .../BsplineFactory/SplineC2ROMPTarget.cpp | 21 +- .../BsplineFactory/SplineR2R.cpp | 85 +- .../BsplineFactory/SplineR2R.h | 3 - .../BsplineFactory/SplineSetReader.cpp | 86 +- .../BsplineFactory/SplineSetReader.h | 8 +- .../BsplineFactory/contraction_helper.hpp | 6 +- .../Fermion/SlaterDetBuilder.cpp | 13 +- src/QMCWaveFunctions/tests/CMakeLists.txt | 2 +- .../tests/test_RotatedSPOs.cpp | 6 +- .../tests/test_TrialWaveFunction.cpp | 2 +- .../test_TrialWaveFunction_diamondC_2x1x1.cpp | 4 +- .../tests/test_einset_LiH.cpp | 2 +- .../tests/test_einset_NiO_a16.cpp | 2 +- .../tests/test_einset_diamondC.cpp | 28 +- .../tests/test_einset_spinor.cpp | 6 +- src/QMCWaveFunctions/tests/test_hybridrep.cpp | 4 +- src/QMCWaveFunctions/tests/test_pw.cpp | 4 +- .../tests/test_spline_applyrotation.cpp | 8 +- .../test_spo_collection_input_spline.cpp | 2 +- src/Sandbox/diff_distancetables.cpp | 3 +- src/Sandbox/einspline_spo.cpp | 8 +- src/Sandbox/einspline_spo_nested.cpp | 8 +- src/Sandbox/input/graphite.hpp | 4 +- src/Sandbox/restart.cpp | 6 +- .../for_testing/NativeInitializerPrint.hpp | 5 +- .../MockGoldWalkerElements.cpp | 9 + .../MockGoldWalkerElements.h | 4 + src/spline2/CMakeLists.txt | 2 +- src/spline2/MultiBsplineBase.hpp | 18 +- src/spline2/MultiBsplineEval.hpp | 30 +- src/spline2/MultiBsplineMPIShared.hpp | 35 +- src/spline2/MultiBsplineOffloadMapper.cpp | 151 + src/spline2/MultiBsplineOffloadMapper.hpp | 66 + src/spline2/MultiBsplineVGLH_OMPoffload.hpp | 3 +- src/spline2/MultiBsplineValue_OMPoffload.hpp | 3 +- src/spline2/SplineUtils.cpp | 40 +- src/spline2/SplineUtils.h | 13 +- src/spline2/tests/CMakeLists.txt | 3 + src/spline2/tests/bspline_funcs.py | 177 +- src/spline2/tests/gen_bspline_values.py | 133 +- src/spline2/tests/gen_prefactor.py | 30 +- src/spline2/tests/gen_trace.py | 64 +- src/spline2/tests/test_multi_spline.cpp | 36 +- .../tests/test_multi_spline_MPI_shared.cpp | 59 +- .../UNR_timestep_comparison/E_DMC_vs_tau.py | 88 +- .../solids/LiH_solid_1x1x1_pp/CMakeLists.txt | 4 +- tests/solids/NiO_a4_e48_pp/CMakeLists.txt | 2 +- tests/solids/bccH_1x1x1_ae/CMakeLists.txt | 2 +- .../dft-inputs/diamondC_1x1x1_pp.py | 2 +- tests/solids/diamondC_1x1x1_pp/CMakeLists.txt | 4 +- .../diamondC_2x1x1-Gaussian_pp/CMakeLists.txt | 6 +- .../dft-inputs/diamondC_2x1x1_pp.py | 2 +- .../Dockerfile_gcc_mpi_develop_complete | 13 +- .../github-actions/ci/run_step.sh | 17 +- .../ci/run_step_ornl-sulfur-1.sh | 1 + .../nightly_test_scripts/nightly_ornl.sh | 88 +- .../nightly_test_scripts/ornl_setup.sh | 188 +- .../ornl_setup_environments.sh | 530 ++-- .../nightly_test_scripts/ornl_versions.sh | 46 +- utils/ncjf_gen.py | 15 +- 311 files changed, 13382 insertions(+), 14594 deletions(-) create mode 100644 .github/workflows/ci-github-actions-nexus.yaml create mode 100644 .github/workflows/close-inactive-issues-prs.yaml create mode 100644 .github/workflows/update-ghcr-ci-image-ubuntu24-openmpi.yaml create mode 100644 config/docker/dependencies/ubuntu24/openmpi/Dockerfile create mode 100644 docs/citing.rst create mode 100755 nexus/manual_install create mode 100755 nexus/nexus/examples/dynamic_workflows/01_basic_dependencies/dyn_basic_dep.py create mode 100755 nexus/nexus/examples/dynamic_workflows/02_energy_convergence/dyn_energy_conv.py create mode 100755 nexus/nexus/examples/dynamic_workflows/02_energy_convergence/dyn_energy_conv_brief.py create mode 100644 nexus/nexus/examples/dynamic_workflows/README.rst delete mode 100644 nexus/nexus/gaussian_process.py create mode 100644 nexus/nexus/tests/test_generic_files/old_nxs_pwscf_input.p create mode 100644 nexus/nexus/tests/test_generic_files/old_nxs_pwscf_input_numpy_1.p create mode 100644 nexus/nexus/tests/test_generic_files/old_nxs_sim.p create mode 100644 nexus/nexus/tests/test_generic_files/old_nxs_sim_numpy_1.p delete mode 100644 nexus/nexus/tests/test_nexus_imports.py delete mode 100644 nexus/nexus/tests/test_optional_dependencies.py delete mode 100644 nexus/nexus/tests/test_required_dependencies.py create mode 100644 nexus/nexus/tests/test_user_examples.py create mode 100644 nexus/nexus/tests/test_utilities.py delete mode 100644 nexus/nexus/tests/test_versions.py delete mode 100644 nexus/nexus/versions.py delete mode 100644 nexus/requirements.txt delete mode 100644 nexus/requirements_minimal.txt create mode 100644 nexus/uv.lock mode change 100644 => 100755 src/Numerics/codegen/gen_cartesian_tensor.py mode change 100644 => 100755 src/Numerics/codegen/read_order.py create mode 100644 src/spline2/MultiBsplineOffloadMapper.cpp create mode 100644 src/spline2/MultiBsplineOffloadMapper.hpp diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index fbf12576ac..9f57c491af 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,15 +1,28 @@ -Please review the [developer documentation](https://github.com/QMCPACK/qmcpack/wiki/Development-workflow) -on the wiki of this project that contains help and requirements. + +## Proposed changes + + + ## What type(s) of changes does this code introduce? -_Delete the items that do not apply_ + - Bugfix - New feature @@ -21,16 +34,29 @@ _Delete the items that do not apply_ - Other (please describe): ### Does this introduce a breaking change? - + - Yes - No ## What systems has this change been tested on? + -_Update the following with an [x] where the items apply. If you're unsure about any of them, don't hesitate to ask. This is -simply a reminder of what we are going to look for before merging your code._ + + +## Checklist + * * [ ] I have read the pull request guidance and develop docs * * [ ] This PR is up to date with the current state of 'develop' diff --git a/.github/workflows/ci-github-actions-nexus.yaml b/.github/workflows/ci-github-actions-nexus.yaml new file mode 100644 index 0000000000..e427f07dbf --- /dev/null +++ b/.github/workflows/ci-github-actions-nexus.yaml @@ -0,0 +1,83 @@ +name: Nexus Testing + +on: + push: + branches: + - develop + - main + pull_request: + branches: + - develop + - main + +jobs: + linux: + strategy: + fail-fast: false + matrix: + python-version: ["3.10", "3.14"] + + runs-on: ubuntu-latest + + steps: + - name: Checkout Action + uses: actions/checkout@v6 + + - name: Setup Graphviz + run: sudo apt-get install graphviz + + - name: Install uv and Setup Python ${{ matrix.python-version }} + uses: astral-sh/setup-uv@v7 + with: + version: "0.11.11" + python-version: ${{ matrix.python-version }} + + - name: Install Project and All Dependencies + run: uv sync --locked --all-extras --dev + working-directory: ./nexus + + - name: Downgrade to Minimum Versions (Python 3.10 only) + if: contains(matrix.python-version, '3.10') + run: uv pip install numpy==1.22.0 scipy==1.8.0 h5py==3.6.0 matplotlib==3.3.0 spglib==1.16.0 cif2cell==2.1.0 pydot==2.0.0 seekpath==2.0.0 + working-directory: ./nexus + + - name: Run Nexus Tests + run: | + source .venv/bin/activate + pytest nexus/tests/ + working-directory: ./nexus + + macos: + strategy: + fail-fast: false + matrix: + python-version: ["3.10", "3.14"] + runs-on: macos-latest + + steps: + - name: Checkout Action + uses: actions/checkout@v6 + + - name: Setup Graphviz + run: brew install graphviz + + - name: Install uv and Setup Python ${{ matrix.python-version }} + uses: astral-sh/setup-uv@v7 + with: + version: "0.11.11" + python-version: ${{ matrix.python-version }} + + - name: Install Project and All Dependencies + run: uv sync --locked --all-extras --dev + working-directory: ./nexus + + - name: Downgrade to Minimum Versions (Python 3.10 only) + if: contains(matrix.python-version, '3.10') + run: uv pip install numpy==1.22.0 scipy==1.8.0 spglib==1.16.0 cif2cell==2.1.0 pydot==2.0.0 seekpath==2.0.0 + working-directory: ./nexus + + - name: Run Nexus Tests + run: | + source .venv/bin/activate + pytest nexus/tests/ + working-directory: ./nexus diff --git a/.github/workflows/ci-github-actions-self-hosted.yaml b/.github/workflows/ci-github-actions-self-hosted.yaml index 9b12e38f33..e7ac00d8ac 100644 --- a/.github/workflows/ci-github-actions-self-hosted.yaml +++ b/.github/workflows/ci-github-actions-self-hosted.yaml @@ -42,7 +42,7 @@ jobs: - name: GitHub API Request if: steps.check.outputs.triggered == 'true' id: request - uses: octokit/request-action@v2.4.0 + uses: octokit/request-action@v3.0.0 with: route: ${{github.event.issue.pull_request.url}} env: @@ -52,7 +52,7 @@ jobs: # just like any other third-party service - name: Create PR status if: steps.check.outputs.triggered == 'true' - uses: guibranco/github-status-action-v2@v1.1.14 + uses: guibranco/github-status-action-v2@v1.2.0 with: authToken: ${{secrets.GITHUB_TOKEN}} context: "ornl-sulfur CI ${{ matrix.jobname }}" @@ -71,7 +71,7 @@ jobs: - name: Checkout PR branch if: steps.check.outputs.triggered == 'true' - uses: actions/checkout@v4 + uses: actions/checkout@v6 with: token: ${{secrets.GITHUB_TOKEN}} repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}} @@ -91,7 +91,7 @@ jobs: - name: Report PR status if: always() && steps.check.outputs.triggered == 'true' - uses: guibranco/github-status-action-v2@v1.1.14 + uses: guibranco/github-status-action-v2@v1.2.0 with: authToken: ${{secrets.GITHUB_TOKEN}} context: "ornl-sulfur CI ${{matrix.jobname}}" @@ -141,7 +141,7 @@ jobs: - name: GitHub API Request if: steps.check.outputs.triggered == 'true' id: request - uses: octokit/request-action@v2.4.0 + uses: octokit/request-action@v3.0.0 with: route: ${{github.event.issue.pull_request.url}} env: @@ -151,7 +151,7 @@ jobs: # just like any other third-party service - name: Create PR status if: steps.check.outputs.triggered == 'true' - uses: guibranco/github-status-action-v2@v1.1.14 + uses: guibranco/github-status-action-v2@v1.2.0 with: authToken: ${{secrets.GITHUB_TOKEN}} context: "ornl-sulfur CI ${{ matrix.jobname }}" @@ -170,7 +170,7 @@ jobs: - name: Checkout PR branch if: steps.check.outputs.triggered == 'true' - uses: actions/checkout@v4 + uses: actions/checkout@v6 with: token: ${{secrets.GITHUB_TOKEN}} repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}} @@ -190,7 +190,7 @@ jobs: - name: Report PR status if: always() && steps.check.outputs.triggered == 'true' - uses: guibranco/github-status-action-v2@v1.1.14 + uses: guibranco/github-status-action-v2@v1.2.0 with: authToken: ${{secrets.GITHUB_TOKEN}} context: "ornl-sulfur CI ${{matrix.jobname}}" @@ -237,7 +237,7 @@ jobs: - name: GitHub API Request if: steps.check.outputs.triggered == 'true' id: request - uses: octokit/request-action@v2.4.0 + uses: octokit/request-action@v3.0.0 with: route: ${{github.event.issue.pull_request.url}} env: @@ -247,7 +247,7 @@ jobs: # just like any other third-party service - name: Create PR status if: steps.check.outputs.triggered == 'true' - uses: guibranco/github-status-action-v2@v1.1.14 + uses: guibranco/github-status-action-v2@v1.2.0 with: authToken: ${{secrets.GITHUB_TOKEN}} context: "ornl-nitrogen CI ${{matrix.jobname}}" @@ -266,7 +266,7 @@ jobs: - name: Checkout PR branch if: steps.check.outputs.triggered == 'true' - uses: actions/checkout@v4 + uses: actions/checkout@v6 with: token: ${{secrets.GITHUB_TOKEN}} repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}} @@ -286,7 +286,7 @@ jobs: - name: Report PR status if: always() && steps.check.outputs.triggered == 'true' - uses: guibranco/github-status-action-v2@v1.1.14 + uses: guibranco/github-status-action-v2@v1.2.0 with: authToken: ${{secrets.GITHUB_TOKEN}} context: "ornl-nitrogen CI ${{matrix.jobname}}" @@ -333,7 +333,7 @@ jobs: - name: GitHub API Request if: steps.check.outputs.triggered == 'true' id: request - uses: octokit/request-action@v2.4.0 + uses: octokit/request-action@v3.0.0 with: route: ${{github.event.issue.pull_request.url}} env: @@ -343,7 +343,7 @@ jobs: # just like any other third-party service - name: Create PR status if: steps.check.outputs.triggered == 'true' - uses: guibranco/github-status-action-v2@v1.1.14 + uses: guibranco/github-status-action-v2@v1.2.0 with: authToken: ${{secrets.GITHUB_TOKEN}} context: "ornl-nitrogen2 CI ${{matrix.jobname}}" @@ -362,7 +362,7 @@ jobs: - name: Checkout PR branch if: steps.check.outputs.triggered == 'true' - uses: actions/checkout@v4 + uses: actions/checkout@v6 with: token: ${{secrets.GITHUB_TOKEN}} repository: ${{fromJson(steps.request.outputs.data).head.repo.full_name}} @@ -382,7 +382,7 @@ jobs: - name: Report PR status if: always() && steps.check.outputs.triggered == 'true' - uses: guibranco/github-status-action-v2@v1.1.14 + uses: guibranco/github-status-action-v2@v1.2.0 with: authToken: ${{secrets.GITHUB_TOKEN}} context: "ornl-nitrogen2 CI ${{matrix.jobname}}" diff --git a/.github/workflows/ci-github-actions-static.yaml b/.github/workflows/ci-github-actions-static.yaml index a915f04ab5..7eac9f1f3e 100644 --- a/.github/workflows/ci-github-actions-static.yaml +++ b/.github/workflows/ci-github-actions-static.yaml @@ -30,7 +30,7 @@ jobs: steps: - name: Checkout Action - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Configure run: tests/test_automation/github-actions/ci/run_step_static.sh configure diff --git a/.github/workflows/ci-github-actions.yaml b/.github/workflows/ci-github-actions.yaml index 8329c807d5..08fa81062b 100644 --- a/.github/workflows/ci-github-actions.yaml +++ b/.github/workflows/ci-github-actions.yaml @@ -27,8 +27,8 @@ jobs: GCC9-NoMPI-NoOMP-Complex, GCC9-MPI-Sandbox-Real, GCC9-NoMPI-Sandbox-Complex, - GCC9-MPI-Debug-Gcov-Real, - GCC9-MPI-Debug-Gcov-Complex, + GCC13-MPI-Debug-Gcov-Real, + GCC13-MPI-Debug-Gcov-Complex, GCC12-NoMPI-Werror-Real, GCC12-NoMPI-Werror-Complex, GCC12-NoMPI-Werror-Real-Mixed, @@ -65,14 +65,14 @@ jobs: image: ghcr.io/qmcpack/ubuntu22-serial:latest options: -u 1001 - - jobname: GCC9-MPI-Debug-Gcov-Real + - jobname: GCC13-MPI-Debug-Gcov-Real container: - image: ghcr.io/qmcpack/ubuntu22-openmpi:latest + image: ghcr.io/qmcpack/ubuntu24-openmpi:latest options: -u 1001 - - jobname: GCC9-MPI-Debug-Gcov-Complex + - jobname: GCC13-MPI-Debug-Gcov-Complex container: - image: ghcr.io/qmcpack/ubuntu22-openmpi:latest + image: ghcr.io/qmcpack/ubuntu24-openmpi:latest options: -u 1001 - jobname: GCC12-NoMPI-Werror-Real @@ -122,7 +122,7 @@ jobs: steps: - name: Checkout Action - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Configure run: tests/test_automation/github-actions/ci/run_step.sh configure @@ -139,7 +139,7 @@ jobs: - name: Upload Coverage if: contains(matrix.jobname, 'Gcov') && github.repository_owner == 'QMCPACK' - uses: codecov/codecov-action@v5 + uses: codecov/codecov-action@v6 with: files: ../qmcpack-build/coverage.xml,../qmcpack-build/python_coverage.xml flags: tests-deterministic # optional @@ -161,10 +161,10 @@ jobs: steps: - name: Checkout Action - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Set Python Version - uses: actions/setup-python@v4 + uses: actions/setup-python@v6 with: python-version: "3.12" @@ -172,7 +172,7 @@ jobs: run: | brew upgrade || brew link --overwrite python@3.12 brew install gcc@14 ninja hdf5 fftw boost - python3 -m pip install numpy h5py + python3 -m pip install numpy h5py pytest pytest-cov pytest-order - name: Configure run: tests/test_automation/github-actions/ci/run_step.sh configure @@ -223,7 +223,7 @@ jobs: steps: - name: Checkout Action - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Echo Debug run: | diff --git a/.github/workflows/close-inactive-issues-prs.yaml b/.github/workflows/close-inactive-issues-prs.yaml new file mode 100644 index 0000000000..6f05fb2003 --- /dev/null +++ b/.github/workflows/close-inactive-issues-prs.yaml @@ -0,0 +1,22 @@ +name: Close inactive issues +on: + schedule: + - cron: "45 13 * * 3" + timezone: "America/New_York" +jobs: + close-issues: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@v10 + with: + days-before-issue-stale: 2920 + days-before-issue-close: 28 + stale-issue-label: "stale" + stale-issue-message: "This issue is stale because it has been open for 2920 days with no activity. It will be closed in 28 days if there is no fresh activity. Please comment within 28 days if this issue is still important to you and it should be kept open." + close-issue-message: "This issue was closed because it has been inactive for 28 days since being marked as stale." + days-before-pr-stale: -1 + days-before-pr-close: -1 + repo-token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/ghcr-develop.yaml b/.github/workflows/ghcr-develop.yaml index fd175fb8b3..9af6f3d9fa 100644 --- a/.github/workflows/ghcr-develop.yaml +++ b/.github/workflows/ghcr-develop.yaml @@ -19,20 +19,20 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Log in to the Container registry - uses: docker/login-action@v3 + uses: docker/login-action@v4 with: registry: ${{ env.REGISTRY }} username: ${{ github.actor }} password: ${{ secrets.GITHUB_TOKEN }} - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v3 + uses: docker/setup-buildx-action@v4 - name: Build and push Docker image - uses: docker/build-push-action@v6 + uses: docker/build-push-action@v7 with: context: . file: tests/test_automation/containers/Dockerfile_gcc_mpi_develop_complete diff --git a/.github/workflows/update-ghcr-ci-image-centos10.yaml b/.github/workflows/update-ghcr-ci-image-centos10.yaml index afe69daba6..4b9355a368 100644 --- a/.github/workflows/update-ghcr-ci-image-centos10.yaml +++ b/.github/workflows/update-ghcr-ci-image-centos10.yaml @@ -21,20 +21,20 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Log in to the Container registry - uses: docker/login-action@v3 + uses: docker/login-action@v4 with: registry: ${{ env.REGISTRY }} username: ${{ github.actor }} password: ${{ secrets.GITHUB_TOKEN }} - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v3 + uses: docker/setup-buildx-action@v4 - name: Build and push Docker image - uses: docker/build-push-action@v6 + uses: docker/build-push-action@v7 with: context: . file: config/docker/dependencies/centos10/Dockerfile diff --git a/.github/workflows/update-ghcr-ci-image-ubuntu22-clang.yaml b/.github/workflows/update-ghcr-ci-image-ubuntu22-clang.yaml index ea2e9f167f..9df7757504 100644 --- a/.github/workflows/update-ghcr-ci-image-ubuntu22-clang.yaml +++ b/.github/workflows/update-ghcr-ci-image-ubuntu22-clang.yaml @@ -21,20 +21,20 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Log in to the Container registry - uses: docker/login-action@v3 + uses: docker/login-action@v4 with: registry: ${{ env.REGISTRY }} username: ${{ github.actor }} password: ${{ secrets.GITHUB_TOKEN }} - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v3 + uses: docker/setup-buildx-action@v4 - name: Build and push Docker image - uses: docker/build-push-action@v6 + uses: docker/build-push-action@v7 with: context: . file: config/docker/dependencies/ubuntu22/clang/Dockerfile diff --git a/.github/workflows/update-ghcr-ci-image-ubuntu22-openmpi.yaml b/.github/workflows/update-ghcr-ci-image-ubuntu22-openmpi.yaml index 60c9e4ffae..97e59da7a6 100644 --- a/.github/workflows/update-ghcr-ci-image-ubuntu22-openmpi.yaml +++ b/.github/workflows/update-ghcr-ci-image-ubuntu22-openmpi.yaml @@ -21,20 +21,20 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Log in to the Container registry - uses: docker/login-action@v3 + uses: docker/login-action@v4 with: registry: ${{ env.REGISTRY }} username: ${{ github.actor }} password: ${{ secrets.GITHUB_TOKEN }} - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v3 + uses: docker/setup-buildx-action@v4 - name: Build and push Docker image - uses: docker/build-push-action@v6 + uses: docker/build-push-action@v7 with: context: . file: config/docker/dependencies/ubuntu22/openmpi/Dockerfile diff --git a/.github/workflows/update-ghcr-ci-image-ubuntu22-serial.yaml b/.github/workflows/update-ghcr-ci-image-ubuntu22-serial.yaml index 68398879de..5b6bd1f3c8 100644 --- a/.github/workflows/update-ghcr-ci-image-ubuntu22-serial.yaml +++ b/.github/workflows/update-ghcr-ci-image-ubuntu22-serial.yaml @@ -21,20 +21,20 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v4 + uses: actions/checkout@v6 - name: Log in to the Container registry - uses: docker/login-action@v3 + uses: docker/login-action@v4 with: registry: ${{ env.REGISTRY }} username: ${{ github.actor }} password: ${{ secrets.GITHUB_TOKEN }} - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v3 + uses: docker/setup-buildx-action@v4 - name: Build and push Docker image - uses: docker/build-push-action@v6 + uses: docker/build-push-action@v7 with: context: . file: config/docker/dependencies/ubuntu22/serial/Dockerfile diff --git a/.github/workflows/update-ghcr-ci-image-ubuntu24-openmpi.yaml b/.github/workflows/update-ghcr-ci-image-ubuntu24-openmpi.yaml new file mode 100644 index 0000000000..b3e1cb04af --- /dev/null +++ b/.github/workflows/update-ghcr-ci-image-ubuntu24-openmpi.yaml @@ -0,0 +1,45 @@ +name: Build and Push Ubuntu24 OpenMPI build CI Image to GHCR + +on: + push: + paths: + - 'config/docker/dependencies/ubuntu24/openmpi/**' + branches: + - develop + +env: + REGISTRY: ghcr.io + IMAGE_NAME: ${{ github.repository }} + +jobs: + build-and-push-image: + if: github.repository == 'qmcpack/qmcpack' + runs-on: ubuntu-latest + permissions: + contents: read + packages: write + + steps: + - name: Checkout repository + uses: actions/checkout@v6 + + - name: Log in to the Container registry + uses: docker/login-action@v4 + with: + registry: ${{ env.REGISTRY }} + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v4 + + - name: Build and push Docker image + uses: docker/build-push-action@v7 + with: + context: . + file: config/docker/dependencies/ubuntu24/openmpi/Dockerfile + push: true + tags: | + ghcr.io/qmcpack/ubuntu24-openmpi:latest + platforms: linux/amd64 + diff --git a/.gitignore b/.gitignore index 6e5230f5f9..3085682940 100644 --- a/.gitignore +++ b/.gitignore @@ -2,7 +2,6 @@ *.aux .python-version .coverage -uv.lock .venv .DS_Store /build_*/ diff --git a/CHANGELOG.md b/CHANGELOG.md index f8d9c5d138..eb019d7833 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,58 @@ Notable changes to QMCPACK are documented in this file. +## [4.3.0] - 2026-06-09 + +This release contains two new QMC features and numerous "behind the scenes" updates to improve both QMCPACK and Nexus. As detailed +in the Nexus section, most notably, Nexus is now fully installable as a Python package and the Python-based testing now uses pytest. +The QMCPACK CMake has been updated consistently. Tests will be created provided the necessary packages are available otherwise a +message is printed and the tests are skipped. Feedback is welcomed. + +* Upcoming breaking change: Classic/non-batched drivers will be removed in a future release. See + https://qmcpack.readthedocs.io/en/develop/performance_portable.html for instructions on using the batched/performance portable + drivers. We recommend that all new projects should only use the batched drivers. For compatibility with future QMCPACK versions, + verify that all new QMCPACK input XML and Nexus scripts explicitly request batched drivers. +* Energy density supported in batched code (CPU only) [#5865](https://github.com/QMCPACK/qmcpack/pull/5865) +* New developmental features to share splines between processes to reduce memory usage. This feature (spline distributed_ranks, + shared_ranks) allows the large spline data buffers to be shared between MPI processes within a node, potentially significantly + reducing overall CPU memory usage. This CPU feature will be expanded in future versions to support more complex sharing + arrangements. Shared splines between GPUs is also under development. While these features are being enhanced, please contact + developers for more information on how to best use them. [#5908](https://github.com/QMCPACK/qmcpack/pull/5908), + [#5889](https://github.com/QMCPACK/qmcpack/pull/5889) +* Citations for table method and delayed update are now included in the output. Please advise where any additional references would + be useful. [#5938](https://github.com/QMCPACK/qmcpack/pull/5938) +* CUDA minimum version updated 12.3 [#5876](https://github.com/QMCPACK/qmcpack/pull/5876) +* Several Python helper and testing scripts have been updated to modern Python 3 and package versions. Please report any files that + still need updates. +* Development container updated to include PySCF 2.13.0 [#5956](https://github.com/QMCPACK/qmcpack/pull/5956) +* Fix bounds error in MPC spline evaluation [#5830](https://github.com/QMCPACK/qmcpack/pull/5830) +* Various documentation and build recipe updates, minor bug fixes and quality of life improvements. + +### NEXUS [2.3.0] + +Nexus is updated to be a standard Python package for easier use and installation. e.g. Nexus and all dependencies are now +straightforwardly installable with uv or pip. See e.g. [Installing Nexus with +uv](https://nexus-workflows.readthedocs.io/en/latest/installation.html#installation-using-the-uv-package-manager). Existing use and +installation methods will continue to be supported. The test infrastructure has also been fully updated to use the standard pytest +and coverage.py packages. + +* Python >= 3.10 is a minimum requirement. Use e.g. uv, spack, or a system package manager to get a newer Python if needed. +* Installable as a Python package [#5742](https://github.com/QMCPACK/qmcpack/pull/5742) +* Nexus "executables" (qmca, qdens, nxs-sim etc.) are directly usable via the installed package. + [#5851](https://github.com/QMCPACK/qmcpack/pull/5851) +* Testing moved to pytest [#5894](https://github.com/QMCPACK/qmcpack/pull/5894), + [#5924](https://github.com/QMCPACK/qmcpack/pull/5924). This included many updates to files handling throughout, e.g. + [#5943](https://github.com/QMCPACK/qmcpack/pull/5943). +* Improved error handling and messaging, e.g. [#5985](https://github.com/QMCPACK/qmcpack/pull/5985), + [#5981](https://github.com/QMCPACK/qmcpack/pull/5981) +* Several edge case bug fixes and refinements, e.g. [#5960](https://github.com/QMCPACK/qmcpack/pull/5960), + [#5972](https://github.com/QMCPACK/qmcpack/pull/5972) +* Checkpoint setting supported in generate_qmcpack [#5869](https://github.com/QMCPACK/qmcpack/pull/5869) +* Updated manual install script [#5870](https://github.com/QMCPACK/qmcpack/pull/5870) +* Added `pathlib.Path` support throughout, e.g. [#5937](https://github.com/QMCPACK/qmcpack/pull/5937) +* `uv.lock` file for developers [#5885](https://github.com/QMCPACK/qmcpack/pull/5885) +* Refactoring and cleanup throughout. + ## [4.2.0] - 2026-02-12 This release is recommended for all users and includes several new features, improved GPU support, a broad range of other useful @@ -9,8 +61,8 @@ improvements, and compatibility and bug fixes. NEXUS also receives significant u function as a conventional Python package (requiring an update PYTHONPATH). * Upcoming breaking change: Classic/non-batched drivers will be removed in a future release. See - https://qmcpack.readthedocs.io/en/develop/performance_portable.html for instructions on using the batched/performance portable drivers. - New projects should only use the batched drivers. + https://qmcpack.readthedocs.io/en/develop/performance_portable.html for instructions on using the batched/performance portable + drivers. New projects should only use the batched drivers. * Added new variable period for estimator measurements feature, input parameter estimator_period, and Nexus support [#5574](https://github.com/QMCPACK/qmcpack/pull/5574), [#5577](https://github.com/QMCPACK/qmcpack/pull/5577). Substantial speed and efficiency improvements are possible for properties with a long autocorrelation period. diff --git a/CMake/python.cmake b/CMake/python.cmake index 6ad15f9334..a0e3143c92 100644 --- a/CMake/python.cmake +++ b/CMake/python.cmake @@ -14,6 +14,33 @@ function(TEST_PYTHON_MODULE MODULE_NAME MODULE_PRESENT) CACHE BOOL "" FORCE) endfunction() +# Ensure we have a compatible version of Pytest for Nexus's testing. +function(CHECK_PYTEST_VERSION pytest_version_ok) + execute_process(COMMAND ${Python3_EXECUTABLE} -m pytest --version + RESULT_VARIABLE PYTEST_VERSION_RESULT + OUTPUT_VARIABLE PYTEST_VERSION + ERROR_VARIABLE PYTEST_VERSION_ERROR + OUTPUT_STRIP_TRAILING_WHITESPACE + ERROR_STRIP_TRAILING_WHITESPACE) + if(PYTEST_VERSION) + string(REPLACE "pytest " "" PYTEST_VERSION ${PYTEST_VERSION}) + else() + # Old versions of pytest put the version output in stderr for some reason + string(REPLACE "pytest " "" PYTEST_VERSION ${PYTEST_VERSION_ERROR}) + endif() + if(PYTEST_VERSION VERSION_GREATER_EQUAL "6.2.4") + message(STATUS "Found compatible Pytest version ${PYTEST_VERSION}") + set(${pytest_version_ok} + TRUE + CACHE BOOL "" FORCE) + else() + message(STATUS "Incompatible Pytest version ${PYTEST_VERSION} found, tests will not be added. Required version >= 6.2.4 ") + set(${pytest_version_ok} + FALSE + CACHE BOOL "" FORCE) + endif() +endfunction() + # Test python module prerequisites for a particular test script # module_list - input - list of module names, for example "numpy;h5py" (including the quotation marks) # test_name - input - name of test (used for missing module message) @@ -35,11 +62,22 @@ function(CHECK_PYTHON_REQS module_list test_name add_test) endif() if(NOT ${cached_variable_name}) if(test_name) - message("Missing python module ${python_module}, not adding test ${test_name}") + message("Skipping ${test_name} tests because valid module ${python_module} is not found.") endif() set(${add_test} false PARENT_SCOPE) + else() + if(${python_module} STREQUAL "pytest") + check_pytest_version(pytest_version_ok) + if(NOT ${pytest_version_ok}) + message("Pytest version < 6.2.4 found, will not add Nexus tests") + set(${add_test} + false + PARENT_SCOPE) + endif() + endif() endif() endforeach() endfunction() + diff --git a/CMake/unit_test.cmake b/CMake/unit_test.cmake index cecf4f8e1c..aa8cdf7376 100644 --- a/CMake/unit_test.cmake +++ b/CMake/unit_test.cmake @@ -40,14 +40,14 @@ function(ADD_UNIT_TEST TESTNAME PROCS THREADS TEST_BINARY) APPEND PROPERTY ENVIRONMENT "OMP_TARGET_OFFLOAD=mandatory") endif() - endif() - set(TEST_LABELS_TEMP "") - add_test_labels(${TESTNAME} TEST_LABELS_TEMP) - set_property( - TEST ${TESTNAME} - APPEND - PROPERTY LABELS "unit") + set(TEST_LABELS_TEMP "") + add_test_labels(${TESTNAME} TEST_LABELS_TEMP) + set_property( + TEST ${TESTNAME} + APPEND + PROPERTY LABELS "unit") + endif() endfunction() # Add a test to see if the target output exists in the desired location in the build directory. diff --git a/CMakeLists.txt b/CMakeLists.txt index 4358823c46..2d6ce58ea1 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -18,7 +18,7 @@ endif() ###################################################################### project( qmcpack - VERSION 4.2.9 + VERSION 4.3.9 LANGUAGES C CXX) #-------------------------------------------------------------------- @@ -164,6 +164,7 @@ set(VALID_SANITIZERS "asan" "ubsan" "tsan" "msan" "typesan") set(ENABLE_SANITIZER "" CACHE STRING "Valid input: ${VALID_SANITIZERS} or left empty") option(QMC_INSTALL_NEXUS "Install Nexus alongside QMCPACK" ON) +option(QMC_DOXYGEN "Enable use of Doxygen documentation generator tool" ON) ###################################################################### # Set compiler specific options/flags @@ -291,7 +292,7 @@ if(ENABLE_GCOV) endif(ENABLE_GCOV) if(ENABLE_PYCOV) - find_program(PYTHON_COVERAGE_EXECUTABLE NAMES python3-coverage coverage.py REQUIRED) + find_program(PYTHON_COVERAGE_EXECUTABLE NAMES python3-coverage coverage.py coverage3 coverage REQUIRED) message(STATUS "Python coverage is enabled. Using ${PYTHON_COVERAGE_EXECUTABLE}") endif(ENABLE_PYCOV) @@ -684,7 +685,7 @@ if(ENABLE_CUDA AND NOT QMC_CUDA2HIP) if(ENABLE_CUDA) include(TestCUDAHostCompatibility) endif() - find_package(CUDAToolkit 11.0 REQUIRED) + find_package(CUDAToolkit 12.3 REQUIRED) if(NOT TARGET CUDA::cublas) message( FATAL_ERROR @@ -1059,7 +1060,9 @@ message(STATUS "Ready to parse QMCPACK source tree") add_subdirectory(external_codes) add_subdirectory(src) -add_subdirectory(doxygen) +if(QMC_DOXYGEN) + add_subdirectory(doxygen) +endif(QMC_DOXYGEN) if(NOT QMC_BUILD_SANDBOX_ONLY) if(NOT QMC_NO_SLOW_CUSTOM_TESTING_COMMANDS) @@ -1076,5 +1079,6 @@ if(NOT QMC_BUILD_SANDBOX_ONLY) foreach(NEXUS_SCRIPT IN LISTS QMCPACK_NEXUS_SCRIPTS) install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink ../lib/nexus/bin/${NEXUS_SCRIPT} ${CMAKE_INSTALL_PREFIX}/bin/${NEXUS_SCRIPT})") endforeach() + install(PROGRAMS ${qmcpack_SOURCE_DIR}/nexus/manual_install DESTINATION ${CMAKE_INSTALL_PREFIX}/lib RENAME nexus-setup-env) endif() endif() diff --git a/config/docker/dependencies/centos10/Dockerfile b/config/docker/dependencies/centos10/Dockerfile index 4c7945f4fa..ee0cc35e74 100644 --- a/config/docker/dependencies/centos10/Dockerfile +++ b/config/docker/dependencies/centos10/Dockerfile @@ -11,6 +11,7 @@ RUN dnf install -y ninja-build RUN dnf install -y rsync # Nexus hard requirement RUN dnf install -y python3-numpy RUN dnf install -y python3-h5py +#RUN dnf install -y python3-pytest # Ensure build works without pytest available. ## Add a user different from root for OpenMPI RUN adduser -u 1000 -d /home/user -s /bin/bash user diff --git a/config/docker/dependencies/ubuntu22/clang/Dockerfile b/config/docker/dependencies/ubuntu22/clang/Dockerfile index 4ff7888999..c4fa84446e 100644 --- a/config/docker/dependencies/ubuntu22/clang/Dockerfile +++ b/config/docker/dependencies/ubuntu22/clang/Dockerfile @@ -24,6 +24,7 @@ RUN export DEBIAN_FRONTEND=noninteractive &&\ sudo \ curl \ rsync \ + python3-numpy python3-pytest python3-pytest-cov python3-pytest-order \ wget \ software-properties-common \ vim \ diff --git a/config/docker/dependencies/ubuntu22/openmpi/Dockerfile b/config/docker/dependencies/ubuntu22/openmpi/Dockerfile index 6370af0fbf..be73c00f4f 100644 --- a/config/docker/dependencies/ubuntu22/openmpi/Dockerfile +++ b/config/docker/dependencies/ubuntu22/openmpi/Dockerfile @@ -45,6 +45,8 @@ RUN export DEBIAN_FRONTEND=noninteractive &&\ python3-pandas \ python3-coverage \ python3-pytest \ + python3-pytest-cov \ + python3-pytest-order \ python3-pip \ -y diff --git a/config/docker/dependencies/ubuntu22/serial/Dockerfile b/config/docker/dependencies/ubuntu22/serial/Dockerfile index 05f0cb2c72..5d875add19 100644 --- a/config/docker/dependencies/ubuntu22/serial/Dockerfile +++ b/config/docker/dependencies/ubuntu22/serial/Dockerfile @@ -43,6 +43,8 @@ RUN export DEBIAN_FRONTEND=noninteractive &&\ python3-pandas \ python3-coverage \ python3-pytest \ + python3-pytest-cov \ + python3-pytest-order \ python3-pip \ -y diff --git a/config/docker/dependencies/ubuntu24/openmpi/Dockerfile b/config/docker/dependencies/ubuntu24/openmpi/Dockerfile new file mode 100644 index 0000000000..173ded075d --- /dev/null +++ b/config/docker/dependencies/ubuntu24/openmpi/Dockerfile @@ -0,0 +1,61 @@ +FROM ubuntu:24.04 + +RUN export DEBIAN_FRONTEND=noninteractive &&\ + apt-get clean &&\ + apt-get update -y &&\ + apt-get upgrade -y apt-utils &&\ + apt-get install -y gpg wget + +RUN export DEBIAN_FRONTEND=noninteractive &&\ + apt-get install gcc g++ \ + clang clang-format clang-tidy \ + libomp-dev \ + gcovr \ + python3 \ + cmake \ + ninja-build \ + libboost-all-dev \ + git \ + libopenmpi-dev \ + libhdf5-openmpi-dev \ + libhdf5-serial-dev \ + hdf5-tools \ + libfftw3-dev \ + libopenblas-openmp-dev \ + libxml2-dev \ + sudo \ + curl \ + rsync \ + wget \ + software-properties-common \ + vim \ + numdiff \ + -y + +# Python packages for tests +RUN export DEBIAN_FRONTEND=noninteractive &&\ + apt-get install python3-numpy \ + python3-h5py \ + python3-pandas \ + python3-coverage \ + python3-pytest \ + python3-pytest-cov \ + python3-pytest-order \ + python3-cif2cell \ + python3-spglib \ + python3-pip \ + -y + +# Install gcovr from pip since the Ubuntu 24.04 apt version doesn't support files >9999 lines +# https://github.com/gcovr/gcovr/pull/883 +RUN export DEBIAN_FRONTEND=noninteractive &&\ + sudo pip3 install --break-system-packages gcovr==8.6 + +# must add a user different from root to run MPI executables +RUN useradd -ms /bin/bash user +# allow in sudoers to install packages +RUN adduser user sudo +RUN echo "user:user" | chpasswd + +USER user +WORKDIR /home/user diff --git a/docs/LCAO.rst b/docs/LCAO.rst index d10633c591..d40d0a3969 100644 --- a/docs/LCAO.rst +++ b/docs/LCAO.rst @@ -75,7 +75,7 @@ wavefunction can be generated according to the following example for a supertwist shifted away from :math:`\Gamma`, leading to a complex wavefunction. -.. code-block:: +.. code-block:: python :caption: Example PySCF input for single k-point calculation for a :math:`2 \times 1 \times 1` carbon supercell. :name: Listing 48 @@ -127,7 +127,7 @@ wavefunction. Note that the last three lines of the file -:: +.. code-block:: python title="C_diamond-tiled-cplx" from PyscfToQmcpack import savetoqmcpack @@ -153,7 +153,7 @@ https://github.com/QMCPACK/qmcpack_workshop_2019 under For the converter in the script to be called properly, you need to specify the path to the file in your PYTHONPATH such as -:: +.. code-block:: bash export PYTHONPATH=QMCPACK_PATH/src/QMCTools:$PYTHONPATH @@ -171,7 +171,7 @@ further modification. Running convert4qmc will generate 3 input files: -.. code-block:: +.. code-block:: xml :caption: C_diamond-tiled-cplx.structure.xml. This file contains the geometry of the system. :name: Listing 49 @@ -216,7 +216,7 @@ As one can see, for both examples, the two-atom primitive cell has been expanded to contain four atoms in a :math:`2 \times 1 \times 1` carbon cell. -.. code-block:: +.. code-block:: xml :caption: C_diamond-tiled-cplx.wfj.xml. This file contains the trial wavefunction. :name: Listing 50 diff --git a/docs/additional_tools.rst b/docs/additional_tools.rst index c6c05b3ea8..22c7ab1dd9 100644 --- a/docs/additional_tools.rst +++ b/docs/additional_tools.rst @@ -177,7 +177,7 @@ prefix ``Mysim`` and output files will be the user to modify the ECP name to match the one used to generate the wavefunction. - :: + .. code-block:: xml @@ -211,7 +211,7 @@ prefix ``Mysim`` and output files will be minimum number of blocks to reproduce the HF/DFT energy used to generate the trial wavefunction. - :: + .. code-block:: xml @@ -230,7 +230,7 @@ prefix ``Mysim`` and output files will be system; however, they need to be updated and optimized for each system. The initial values might only be suitable for a small molecule. - :: + .. code-block:: xml @@ -270,7 +270,7 @@ prefix ``Mysim`` and output files will be Production VMC and DMC: Examine the results of the optimization before running these blocks. - For example, choose the best optimized jastrow from all obtained, put in the + For example, choose the best optimized Jastrow from all obtained, put in the wavefunction file, and do not reoptimize. --> @@ -369,7 +369,7 @@ Command line options This option is to be used when a multideterminant expansion (mainly a CI expansion) is present in an HDF5 file. The trial wavefunction file will not display the full list of multideterminants and will add a path to the HDF5 file as follows (full example for the C2 molecule in qmcpack/tests/molecules/C2_pp). - :: + .. code-block:: xml @@ -404,7 +404,7 @@ Command line options This option generates the ``*.orbs.h5`` HDF5 file containing the basis set and the orbital coefficients. If the wavefunction contains a multideterminant expansion from QP2, it will also be stored in this file. This option minimizes the size of the ``*.wfj.xml`` file, which points to the HDF file, as in the following example: - :: + .. code-block:: xml @@ -451,7 +451,7 @@ Command line options et al. :cite:`Ma2005` When this option is present, the wavefunction file has a new set of tags: - :: + .. code-block:: xml qmcsystem> @@ -465,7 +465,7 @@ Command line options In the “orbitals“ section of the wavefunction file, a new tag “cuspInfo” will be added for orbitals spin-up and orbitals spin-down: - :: + .. code-block:: xml @@ -505,7 +505,7 @@ Command line options Although similar to **-psi_tag**, this is used for the type of ions. - :: + .. code-block:: xml @@ -609,7 +609,7 @@ Supported codes PySCF script, this path must be added to the PYTHONPATH environment variable. For the bash shell, this can be done as follows: - :: + .. code-block:: bash export PYTHONPATH=/PATH_TO_QMCPACK/qmcpack/src/QMCTools:\$PYTHONPATH @@ -617,7 +617,7 @@ Supported codes Copy and paste the following code in a file named LiH.py. - :: + .. code-block:: python #! /usr/bin/env python3 from pyscf import gto, scf, df @@ -989,7 +989,7 @@ The QMC code CASINO also makes available its pseudopotentials available at the w QMCPACK can directly read in the CASINO-formated pseudopotential (``pp.data``), but four parameters found in the pseudopotential summary file must be specified in the pseudo element (``l-local``, ``lmax``, ``nrule``, ``cutoff``)[see :ref:`nlpp` for details]: -.. code-block:: +.. code-block:: xml :caption: XML syntax to use CASINO-formatted pseudopotentials in QMCPACK :name: Listing 73 @@ -1018,7 +1018,7 @@ into optimization, VMC, or DMC runs, as it is a valid block. As an example, the following code generates a random walker configuration and compares the trial wave function ratio computed in two different ways: -.. code-block:: +.. code-block:: xml :caption: The following executes the wavefunction ratio test in "wftester" :name: Listing 74 @@ -1030,7 +1030,7 @@ Here's a summary of some of the tests provided: - Ratio Test. Invoked with - :: + .. code-block:: xml yes @@ -1039,7 +1039,7 @@ Here's a summary of some of the tests provided: - Clone Test. Invoked with - :: + .. code-block:: xml yes @@ -1048,7 +1048,7 @@ Here's a summary of some of the tests provided: - Elocal Test. Invoked with - :: + .. code-block:: xml yes @@ -1058,9 +1058,9 @@ Here's a summary of some of the tests provided: - Derivative Test. Invoked with - :: + .. code-block:: xml - deriv} + deriv Computes electron gradients, laplacians, and wave function parameter derivatives using implemented calls and compares them to @@ -1068,7 +1068,7 @@ Here's a summary of some of the tests provided: - Ion Gradient Test. Invoked with - :: + .. code-block:: xml ion0 @@ -1077,7 +1077,7 @@ Here's a summary of some of the tests provided: - “Basic Test". Invoked with - :: + .. code-block:: xml yes diff --git a/docs/afqmc.rst b/docs/afqmc.rst index 98d3aae6d2..4733afbaa5 100644 --- a/docs/afqmc.rst +++ b/docs/afqmc.rst @@ -28,7 +28,7 @@ For example, in the example, multiple Hamiltonian objects with different names can be defined. The one actually used in the calculation is the one passed to “execute” as ham. -.. code-block:: +.. code-block:: xml :caption: Sample input file for AFQMC. :name: Listing 51 @@ -290,7 +290,7 @@ The back_propagation estimator has the following parameters: - **nsteps**. Maximum number of back-propagation steps. Default: 10 - **naverages**. Number of back propagation calculations to perform. - The number of steps will be chosed equally distributed in the range + The number of steps will be chosen equally distributed in the range 0,nsteps. Default: 1 - **block_size**. Number of blocks to use in the internal average of @@ -340,7 +340,7 @@ this form of factorization QMCPACK allows for the integrals to be stored in either dense or sparse format. The dense case is the simplest and is only implemented for Hamiltonians -with *real* integrals (and basis functions, i.e. not the homegeneous +with *real* integrals (and basis functions, i.e. not the homogeneous electron gas which has complex orbitals but real integrals). The file format is given as follows: @@ -820,7 +820,7 @@ The following is a growing list of useful advice for new users, followed by a sa parallel implementation. For large calculations, values between 6–12 for both quantities should be reasonable, depending on architecture. -.. code-block:: +.. code-block:: xml :caption: Example of sections of an AFQMC input file for a large calculation. :name: Listing 56 diff --git a/docs/analyzing.rst b/docs/analyzing.rst index 5100a507fc..ea810219dd 100644 --- a/docs/analyzing.rst +++ b/docs/analyzing.rst @@ -170,7 +170,7 @@ can get an estimate of the autocorrelation time in the following way: >qmca -q e -e 100 qmc.s000.scalar.dat --sac qmc series 0 LocalEnergy = -45.877363 +/- 0.017432 4.8 -The flag ``–sac`` stands for (s)how (a)uto(c)orrelation. In this case, +The flag ``–sac`` stands for show autocorrelation. In this case, the autocorrelation estimate is :math:`4.8\approx 5` samples. Since the total run contained 800 samples and we have excluded 100 of them, we can estimate the number of independent samples as :math:`(800-100)/5=140`. diff --git a/docs/appendices.rst b/docs/appendices.rst index f15a60e25b..c013cce11e 100644 --- a/docs/appendices.rst +++ b/docs/appendices.rst @@ -1,3 +1,4 @@ + .. _appendices: Appendices diff --git a/docs/citing.rst b/docs/citing.rst new file mode 100644 index 0000000000..fbb769a124 --- /dev/null +++ b/docs/citing.rst @@ -0,0 +1,8 @@ +.. _chap:citing: + +Citing QMCPACK +============== + +The citation papers for QMCPACK are J. Kim *et al.* J. Phys. Cond. Mat. **30** 195901 (2018), +https://doi.org/10.1088/1361-648X/aab9c3, and if space allows, P. Kent *et al.* J. Chem. Phys. **152** 174105 (2020), +https://doi.org/10.1063/5.0004860 . These papers are both open access. diff --git a/docs/developing.rst b/docs/developing.rst index 6802fd0e5a..f60b101df8 100644 --- a/docs/developing.rst +++ b/docs/developing.rst @@ -153,9 +153,10 @@ Type and class names Type and class names should start with a capital letter and have a capital letter for each new word. Underscores (``_``) are not allowed. It's redundant to end these names with ``Type`` or ``_t``. -.. code:: c++ - \\no +.. code:: cpp + + // no using ValueMatrix_t = Matrix; using RealType = double; @@ -185,7 +186,7 @@ Lambda expressions Named lambda expressions follow the naming convention for functions: -:: +.. code:: cpp auto myWhatever = [](int i) { return i + 4; }; @@ -199,7 +200,7 @@ Test case and test names Test code files should be named as follows: -:: +.. code:: cpp class DiracMatrix; //leads to @@ -219,7 +220,7 @@ Use the ``// Comment`` syntax for actual comments. Use -:: +.. code:: cpp /** base class for Single-particle orbital sets * @@ -230,7 +231,7 @@ Use or -:: +.. code:: cpp ///index in the builder list of sposets int builder_index; @@ -245,7 +246,7 @@ File docs Do not put the file name after the ``\file`` Doxygen command. Doxygen will fill it in for the file the tag appears in. -:: +.. code:: cpp /** \file * File level documentation @@ -266,7 +267,7 @@ For function parameters whose type is non-const reference or pointer to non-cons Example: -:: +.. code:: cpp /** Updates foo and computes bar using in_1 .. in_5. * \param[in] in_3 @@ -306,7 +307,7 @@ particularly large changes, commit the formatting changes in a separate pull req Disable the use of clang-format for sections of code that would be more readable when formatted differently, e.g., for matrices or for code blocks where a particular alignment would clearly help readability. -:: +.. code:: cpp // clang-format off Matrix my_matrix = { {1, 2, 3}, @@ -357,7 +358,7 @@ Pointers and references Pointer or reference operators should go with the type. But understand the compiler reads them from right to left. -:: +.. code:: cpp Type* var; Type& var; @@ -370,7 +371,7 @@ Templates The angle brackets of templates should not have any external or internal padding. -:: +.. code:: cpp template class Class1; @@ -389,7 +390,7 @@ Variable declarations and definitions - Avoid declaring multiple variables in the same declaration, especially if they are not fundamental types: - :: + .. code:: cpp int x, y; // Not recommended Matrix a("my-matrix"), b(size); // Not allowed @@ -402,7 +403,7 @@ Variable declarations and definitions - Use the following order for keywords and modifiers in variable declarations: - :: + .. code:: cpp // General type [static] [const/constexpr] Type variable_name; @@ -429,7 +430,7 @@ on it, in which case one parameter per line aligned with the first parameter sho Also include the parameter names in the declaration of a function, that is, -:: +.. code:: cpp // calculates a*b+c double function(double a, double b, double c); @@ -451,7 +452,7 @@ Conditionals Examples: -:: +.. code:: cpp if (condition) statement; @@ -478,7 +479,7 @@ Switch statements should always have a default case. Example: -:: +.. code:: cpp switch (var) { @@ -502,7 +503,7 @@ Loops Examples: -:: +.. code:: cpp for (statement; condition; statement) statement; @@ -537,7 +538,7 @@ Class format Example: -:: +.. code:: cpp class Foo : public Bar { @@ -569,7 +570,7 @@ Constructor initializer lists Examples: -:: +.. code:: cpp // When everything fits on one line: Foo::Foo(int var) : var_(var) @@ -691,7 +692,7 @@ Pre-increment and pre-decrement Use the pre-increment (pre-decrement) operator when a variable is incremented (decremented) and the value of the expression is not used. In particular, use the pre-increment (pre-decrement) operator for loop counters where i is not used: -:: +.. code:: cpp for (int i = 0; i < N; ++i) { @@ -721,7 +722,7 @@ Use of const - Member functions should be specified const whenever possible. - :: + .. code:: cpp // Declaration int computeFoo(int bar, const Matrix& m) @@ -798,7 +799,7 @@ Adding and using timers In your class header file, add ```#include ```. Add a timer enumeration and define the timer names in the header file or preferably cpp file. For example, put the following under "protected/private" -:: +.. code:: cpp enum PSTimers { @@ -812,7 +813,7 @@ header file or preferably cpp file. For example, put the following under "protec Initialize timers in the constructor: -:: +.. code:: cpp # if you have many timers; const TimerNameList_t @@ -827,7 +828,7 @@ Initialize timers in the constructor: Finally, there are two ways of using the timers. Using the ScopedTimer is required when possible. -:: +.. code:: cpp // RAII pattern { @@ -976,7 +977,7 @@ interface may change to use functions to set and retrieve positions so the SoA transformation of the particle data can happen automatically. For now, it is crucial to call ``P.update()`` to populate ``RSoA`` anytime ``P.R`` is changed. Otherwise, the distance tables associated with ``R`` will be uninitialized or out-of-date. -:: +.. code:: cpp const SimulationCell sc; ParticleSet elec(sc), ions(sc); @@ -1037,7 +1038,7 @@ Looping over particles Some sample code on how to loop over all the particles in an electron-ion distance table: -:: +.. code:: cpp // d_table is an electron-ion distance table @@ -1057,7 +1058,7 @@ out of the loop. An example of the first approach is -:: +.. code:: cpp // P is a ParticleSet @@ -1069,7 +1070,7 @@ An example of the first approach is An example of the second approach is -:: +.. code:: cpp // P is a ParticleSet assert(P.IsGrouped == true); // ensure particles are grouped @@ -1227,7 +1228,7 @@ For particle-by-particle moves, each timestep advance The following example shows part of an input block for VMC with all-electron moves and drift. -:: +.. code:: xml yes @@ -1244,7 +1245,7 @@ To get the electron-ion distances, add the ion ``ParticleSet`` using ``addTable`` and save the returned index. Use that index to get the ion-electron distance table. -:: +.. code:: cpp const int ei_id = elecs.addTable(ions); // in the constructor only const auto& ei_table = elecs.getDistTable(ei_id); // when consuming a distance table @@ -1491,7 +1492,7 @@ value of the determinant is stored during the inversion of the matrix :math:`M` (``cgetrf``\ :math:`\rightarrow`\ ``cgetri``). Suppose :math:`M=LU`, then :math:`S=\prod\limits_{i=1}^N L_{ii} U_{ii}`. -:: +.. code:: cpp // In DiracDeterminantWithBackflow::evaluateLog(P,G,L) Phi->evaluate(BFTrans->QP, FirstIndex, LastIndex, psiM,dpsiM,grad_grad_psiM); @@ -1557,7 +1558,7 @@ from the notations of ref. :cite:`Kwon1993backflow`. This name change is intended to help the reader associate M with the QMCPACK variable ``psiM``. -:: +.. code:: cpp // In DiracDeterminantWithBackflow::evaluateLog(P,G,L) for(int i=0; i @@ -1943,7 +1944,7 @@ Notice that a local reference ``tpset`` to the target particle set ``P`` is save Now, head over to HamiltonianFactory and instantiate this observable if an XML node is found requesting it. Look for "gofr" in HamiltonianFactory.cpp, for example, and follow the if block. -:: +.. code:: cpp // In HamiltonianFactory.cpp #include @@ -1961,7 +1962,7 @@ Evaluate The evaluate() method is where we perform the calculation of the desired observable. In a first iteration, we will simply hard-code the name and mass of the particles. -:: +.. code:: cpp // In SpeciesKineticEnergy.cpp #include // laplaician() defined here @@ -1998,7 +1999,7 @@ kinetic energy of the up electron (group=“u") or the down electron (group=“d"). This is easily achievable using the OhmmsAttributeSet class, -:: +.. code:: cpp // In SpeciesKineticEnergy.cpp #include @@ -2020,7 +2021,7 @@ class, where we may keep "group" and "minus\_over\_2m" as local variables to our specific class. -:: +.. code:: cpp // In SpeciesKineticEnergy.h private: @@ -2039,7 +2040,7 @@ Make sure the sum of the “ukinetic" and “dkinetic" columns is For easy reference, a summary of the complete list of changes follows: -:: +.. code:: cpp // In HamiltonianFactory.cpp #include "QMCHamiltonians/SpeciesKineticEnergy.h" @@ -2050,7 +2051,7 @@ For easy reference, a summary of the complete list of changes follows: targetH->addOperator(apot,potName,false); } -:: +.. code:: cpp // In SpeciesKineticEnergy.h #include @@ -2092,7 +2093,7 @@ For easy reference, a summary of the complete list of changes follows: } // namespace qmcplusplus #endif -:: +.. code:: cpp // In SpeciesKineticEnergy.cpp #include @@ -2148,7 +2149,7 @@ Multiple scalars It is fairly straightforward to create more than one column in the ``scalar.dat`` file with a single observable class. For example, if we want a single SpeciesKineticEnergy estimator to simultaneously record the kinetic energies of all species in the target particle set, we only have to write two new methods: addObservables() and setObservables(), then tweak the behavior of evaluate(). First, we will have to override the default behavior of addObservables() to make room for more than one column in the ``scalar.dat`` file as follows, -:: +.. code:: cpp // In SpeciesKineticEnergy.cpp void SpeciesKineticEnergy::addObservables(PropertySetType& plist, BufferType& collectables) @@ -2164,7 +2165,7 @@ where “num_species” and “species_name” can be local variables initialized in the constructor. We should also initialize some local arrays to hold temporary data. -:: +.. code:: cpp // In SpeciesKineticEnergy.h private: @@ -2191,7 +2192,7 @@ arrays to hold temporary data. Next, we need to override the default behavior of ``setObservables()`` to transfer multiple values to the property list kept by the main particle set, which eventually goes into the ``scalar.dat`` file. -:: +.. code:: cpp // In SpeciesKineticEnergy.cpp void SpeciesKineticEnergy::setObservables(PropertySetType& plist) @@ -2202,7 +2203,7 @@ Next, we need to override the default behavior of ``setObservables()`` to transf Finally, we need to change the behavior of evaluate() to fill the local vector “species_kinetic” with appropriate observable values. -:: +.. code:: cpp SpeciesKineticEnergy::Return_t SpeciesKineticEnergy::evaluate(ParticleSet& P) { @@ -2226,7 +2227,7 @@ HDF5 output If we desire an observable that will output hundreds of scalars per simulation step (e.g., SkEstimator), then it is preferred to output to the ``stat.h5`` file instead of the ``scalar.dat`` file for better organization. A large chunk of data to be registered in the ``stat.h5`` file is called a "Collectable" in QMCPACK. In particular, if a OperatorBase object is initialized with ``UpdateMode.set(COLLECTABLE,1)``, then the "Collectables" object carried by the main particle set will be processed and written to the ``stat.h5`` file, where "UpdateMode" is a bit set (i.e., a collection of flags) with the following enumeration: -:: +.. code:: cpp // In OperatorBase.h ///enum for UpdateMode @@ -2241,7 +2242,7 @@ If we desire an observable that will output hundreds of scalars per simulation s As a simple example, to put the two columns we produced in the previous section into the ``stat.h5`` file, we will first need to declare that our observable uses "Collectables." -:: +.. code:: cpp // In constructor add: hdf5_out = true; @@ -2249,7 +2250,7 @@ As a simple example, to put the two columns we produced in the previous section Then make some room in the "Collectables" object carried by the target particle set. -:: +.. code:: cpp // In addObservables(PropertySetType& plist, BufferType& collectables) add: if (hdf5_out) @@ -2261,7 +2262,7 @@ Then make some room in the "Collectables" object carried by the target particle Next, make some room in the ``stat.h5`` file by overriding the registerCollectables() method. -:: +.. code:: cpp // In SpeciesKineticEnergy.cpp void SpeciesKineticEnergy::registerCollectables(std::vector& h5desc, hid_t gid) const @@ -2278,7 +2279,7 @@ Next, make some room in the ``stat.h5`` file by overriding the registerCollectab Finally, edit evaluate() to use the space in the "Collectables" object. -:: +.. code:: cpp // In SpeciesKineticEnergy.cpp SpeciesKineticEnergy::Return_t SpeciesKineticEnergy::evaluate(ParticleSet& P) @@ -2393,7 +2394,7 @@ Collect stage File output is performed by the master ``EstimatorManager`` owned by ``QMCDriver``. The first 8+ entries in ``EstimatorManagerBase::AverageCache`` will be written to ``scalar.dat``. The remaining entries in ``AverageCache`` will be written to ``stat.h5``. File writing is triggered by ``EstimatorManagerBase`` ``::collectBlockAverages`` inside ``EstimatorManagerBase::stopBlock``. -:: +.. code:: cpp // In EstimatorManagerBase.cpp::collectBlockAverages if(Archive) @@ -2412,7 +2413,7 @@ File output is performed by the master ``EstimatorManager`` owned by ``QMCDriver ``EstimatorManagerBase::collectBlockAverages`` is triggered from the master-thread estimator via either ``stopBlock(std::vector)`` or ``stopBlock(RealType, true)``. Notice that file writing is NOT triggered by the slave-thread estimator method ``stopBlock(RealType, false)``. -:: +.. code:: cpp // In EstimatorManagerBase.cpp void EstimatorManagerBase::stopBlock(RealType accept, bool collectall) @@ -2431,7 +2432,7 @@ File output is performed by the master ``EstimatorManager`` owned by ``QMCDriver collectBlockAverages(1); } -:: +.. code:: cpp // In ScalarEstimatorBase.h template @@ -2466,7 +2467,7 @@ should unload a subset of walkers. Thus, the slave estimator should call ``SimpleFixedNodeBranch::myEstimator``, should unload data from the entire walker ensemble. This is achieved by calling ``accumulate(W)``. -:: +.. code:: cpp void EstimatorManagerBase::accumulate(MCWalkerConfiguration& W) { // intended to be called by master estimator only @@ -2478,7 +2479,7 @@ entire walker ensemble. This is achieved by calling ``accumulate(W)``. Collectables->accumulate_all(W.Collectables,1.0); } -:: +.. code:: cpp void EstimatorManagerBase::accumulate(MCWalkerConfiguration& W , MCWalkerConfiguration::iterator it @@ -2492,7 +2493,7 @@ entire walker ensemble. This is achieved by calling ``accumulate(W)``. Collectables->accumulate_all(W.Collectables,1.0); } -:: +.. code:: cpp // In LocalEnergyEstimator.h inline void accumulate(const Walker_t& awalker, RealType wgt) @@ -2507,7 +2508,7 @@ entire walker ensemble. This is achieved by calling ``accumulate(W)``. scalars[target](ePtr[source],wwght); } -:: +.. code:: cpp // In CollectablesEstimator.h inline void accumulate_all(const MCWalkerConfiguration::Buffer_t& data, RealType wgt) @@ -2528,7 +2529,7 @@ Load ensemble stage ``::KineticEnergy``, and ``::Observables`` must be properly populated at the end of the evaluate stage. -:: +.. code:: cpp // In QMCHamiltonian.h template @@ -2552,7 +2553,7 @@ Evaluate stage ``QMCHamiltonian::evaluate`` and ``QMCHamiltonian::`` | ``auxHevaluate``. -:: +.. code:: cpp // In QMCHamiltonian.cpp QMCHamiltonian::Return_t @@ -2577,7 +2578,7 @@ Evaluate stage return LocalEnergy; } -:: +.. code:: cpp // In QMCHamiltonian.cpp void QMCHamiltonian::auxHevaluate(ParticleSet& P, Walker_t& ThisWalker) @@ -2603,7 +2604,7 @@ Estimator use cases VMCSingleOMP pseudo code ^^^^^^^^^^^^^^^^^^^^^^^^ -:: +.. code:: cpp bool VMCSingleOMP::run() { @@ -2634,7 +2635,7 @@ VMCSingleOMP pseudo code DMCOMP pseudo code ^^^^^^^^^^^^^^^^^^^ -:: +.. code:: cpp bool DMCOMP::run() { diff --git a/docs/hamiltonianobservable.rst b/docs/hamiltonianobservable.rst index 601afcf161..eba6e6e0b1 100644 --- a/docs/hamiltonianobservable.rst +++ b/docs/hamiltonianobservable.rst @@ -68,7 +68,7 @@ Additional information: one hamiltonian component or observable requires the detailed knowledge of the wavefunction that it operates on. If the specified value is not an empty string, it must match the ``name`` attribute of a ``wavefunction`` xml node. -.. code-block:: +.. code-block:: xml :caption: All electron Hamiltonian XML element. :name: Listing 14 @@ -79,7 +79,7 @@ Additional information: -.. code-block:: +.. code-block:: xml :caption: Pseudopotential Hamiltonian XML element. :name: Listing 15 @@ -230,19 +230,19 @@ Additional information: - **gpu**: When not specified, use the ``gpu`` attribute of ``particleset``. -.. code-block:: +.. code-block:: xml :caption: QMCPXML element for Coulomb interaction between electrons. :name: Listing 16 -.. code-block:: +.. code-block:: xml :caption: QMCPXML element for Coulomb interaction between electrons and ions (all-electron only). :name: Listing 17 -.. code-block:: +.. code-block:: xml :caption: QMCPXML element for Coulomb interaction between ions. :name: Listing 18 @@ -380,13 +380,13 @@ Additional information: the structure of the Slater-Jastrow wave function in order to analytically perform the spin integral. -.. code-block:: +.. code-block:: xml :caption: QMCPXML element for pseudopotential electron-ion interaction (psf files). :name: Listing 19 -.. code-block:: +.. code-block:: xml :caption: QMCPXML element for pseudopotential electron-ion interaction (xml files). If SOC terms present in xml, they are added to local energy :name: Listing 20 @@ -395,7 +395,7 @@ Additional information: -.. code-block:: +.. code-block:: xml :caption: QMCPXML element for pseudopotential to accumulate the spin-orbit energy, but do not include in local energy :name: Listing 21 @@ -436,7 +436,7 @@ attributes: | ``l-local``:math:`^o` | integer | | | Override local channel | +-----------------------------------+--------------+-----------------+-------------+---------------------------+ -.. code-block:: +.. code-block:: xml :caption: QMCPXML element for pseudopotential of single ionic species. :name: Listing 21b @@ -491,7 +491,7 @@ Remarks: - **Developer note:** Currently the ``name`` attribute for the MPC interaction is ignored. The name is always reset to ``MPC``. -.. code-block:: +.. code-block:: xml :caption: MPC for finite-size postcorrection. :name: Listing 22 @@ -597,7 +597,7 @@ attributes: | ``source``:math:`^o` | text | ``particleset.name`` | e | Identify quantum particles | +-----------------------+--------------+------------------------+-------------+----------------------------+ -.. code-block:: +.. code-block:: xml :caption: "Chiesa" kinetic energy finite-size postcorrection. :name: Listing 23 @@ -692,7 +692,7 @@ Additional information: the cell, and hence the density grid, is defined from :math:`0` to :math:`L`). -.. code-block:: +.. code-block:: xml :caption: QMCPXML,caption=Density estimator (uniform grid). :name: Listing 24 @@ -781,7 +781,7 @@ Additional information: not specified. Simultaneous use of ``corner`` and ``center`` will cause QMCPACK to abort. -.. code-block:: +.. code-block:: xml :caption: Spin density estimator (uniform grid). :name: Listing 25 @@ -789,7 +789,7 @@ Additional information: 40 40 40 -.. code-block:: +.. code-block:: xml :caption: Spin density estimator (uniform grid centered about origin). :name: Listing 26 @@ -911,7 +911,7 @@ Additional information: Post-processing tools are provided in Nexus. -.. code-block:: +.. code-block:: xml :caption: Magnetization density estimator (uniform grid). :name: Listing 27 @@ -1011,13 +1011,13 @@ Additional information: ``gofr_e_0_0``, ``gofr_e_0_1``, and ``gofr_e_1_1`` for up-up, up-down, and down-down correlations, respectively. -.. code-block:: +.. code-block:: xml :caption: Pair correlation function estimator element. :name: Listing 28 -.. code-block:: +.. code-block:: xml :caption: Pair correlation function estimator element with additional electron-ion correlations. :name: Listing 29 @@ -1108,13 +1108,13 @@ Additional information: ``gofr_e_0_0``, ``gofr_e_0_1``, and ``gofr_e_1_1`` for up-up, up-down, and down-down correlations, respectively. -.. code-block:: +.. code-block:: xml :caption: Pair correlation function estimator element. :name: Listing PCorr 1 -.. code-block:: +.. code-block:: xml :caption: Pair correlation function estimator element with additional electron-ion correlations. :name: Listing PCorr 2 @@ -1181,7 +1181,7 @@ Additional information: electronic density, thus meaning it will not accurately measure the electron-electron density response. -.. code-block:: +.. code-block:: xml :caption: Static structure factor estimator element. :name: Listing 30 @@ -1241,7 +1241,7 @@ Additional information: electronic density, thus meaning it wil not accurately measure the electron-electron density response. -.. code-block:: +.. code-block:: xml :caption: SkAll estimator element. :name: Listing 31 @@ -1276,7 +1276,7 @@ attributes: | ``hdf5``:math:`^o` | boolean | yes/no | no | Output to ``stat.h5`` (yes) | +---------------------+--------------+----------------+-------------+-----------------------------+ -.. code-block:: +.. code-block:: xml :caption: Species kinetic energy estimator element. :name: Listing 32 @@ -1337,7 +1337,7 @@ Additional information: - ``hdf5``: Used to record particle-resolved distances in the h5 file if ``gdf5=yes``. -.. code-block:: +.. code-block:: xml :caption: Lattice deviation estimator element. :name: Listing 33 @@ -1442,7 +1442,7 @@ Additional information: ``name``. - **Important:** in order for the estimator to work, a traces XML input element () must appear following the element and prior to any element. -.. code-block:: +.. code-block:: xml :caption: Energy density estimator accumulated on a :math:`20 \times 10 \times 10` grid over the simulation cell. :name: Listing 34 @@ -1455,7 +1455,7 @@ Additional information: -.. code-block:: +.. code-block:: xml :caption: Energy density estimator accumulated within spheres of radius 6.9 Bohr centered on the first and second atoms in the ion0 particleset. :name: Listing 35 @@ -1479,7 +1479,7 @@ Additional information: -.. code-block:: +.. code-block:: xml :caption: Energy density estimator accumulated within Voronoi polyhedra centered on the ions. :name: Listing 36 @@ -1855,7 +1855,7 @@ Additional information: any detail here; the interested reader is referred to :cite:`Krogel2014`. -.. code-block:: +.. code-block:: xml :caption: One body density matrix with uniform grid integration. :name: Listing 37 @@ -1868,7 +1868,7 @@ Additional information: 0 0 0 -.. code-block:: +.. code-block:: xml :caption: One body density matrix with uniform sampling. :name: Listing 38 @@ -1881,7 +1881,7 @@ Additional information: 0 0 0 -.. code-block:: +.. code-block:: xml :caption: One body density matrix with density sampling. :name: Listing 39 @@ -1894,7 +1894,7 @@ Additional information: no -.. code-block:: +.. code-block:: xml :caption: Example ``sposet`` initialization for density matrix use. Occupied and virtual orbital sets are created separately, then joined (``basis="spo_u spo_uv"``). :name: Listing 40 @@ -1904,7 +1904,7 @@ Additional information: -.. code-block:: +.. code-block:: xml :caption: Example ``sposet`` initialization for density matrix use. Density matrix orbital basis created separately (``basis="dm_basis"``). :name: Listing 41 @@ -2019,7 +2019,7 @@ Additional information: The following is an example use case. -:: +.. code-block:: xml ... @@ -2168,7 +2168,7 @@ Additional information: The following is an example use case. -:: +.. code-block:: xml @@ -2216,7 +2216,7 @@ Additional information: The following is an example use case. -:: +.. code-block:: xml ... diff --git a/docs/index.rst b/docs/index.rst index d6111877c3..0f50c6675c 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -18,6 +18,7 @@ User's Guide and Developer's Manual introduction features + citing performance_portable installation running diff --git a/docs/input_overview.rst b/docs/input_overview.rst index 17e77bd883..107ac76e22 100644 --- a/docs/input_overview.rst +++ b/docs/input_overview.rst @@ -23,7 +23,7 @@ QMCPACK uses XML to represent structured data in its input file. Instead of tex QMCPACK input looks like -:: +.. code-block:: xml @@ -38,7 +38,7 @@ XML elements start with ````, end with ``}``, and c The overall structure of the input file reflects different aspects of the QMC simulation: the simulation cell, particles, trial wavefunction, Hamiltonian, and QMC run parameters. A condensed version of the actual input file is shown as follows: -:: +.. code-block:: xml @@ -131,7 +131,7 @@ Random number initialization The random number generator state is initialized from the ``random`` element using the ``seed`` attribute: -:: +.. code-block:: xml diff --git a/docs/installation.rst b/docs/installation.rst index fe3760554c..5b553348e8 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -145,30 +145,34 @@ unsupported and untested by the developers although they may still work. Many of the utilities provided with QMCPACK require Python (v3). The numpy and matplotlib libraries are required for full functionality. +.. note:: + + We additionally recommend installing ``pytest`` for testing Python code, such as that in Nexus, however this is not a requirement for QMCPACK. + Nightly testing currently includes at least the following software versions: * Compilers - * Clang/LLVM 20.1.4 - * GCC 14.2.0, 12.4.0 + * Clang/LLVM 22.1.1 + * GCC 15.2.0, 13.4.0 * OneAPI 2025.3 -* Boost 1.88.0, 1.82.0 +* Boost 1.90.0, 1.84.0 * HDF5 1.14.5 * FFTW 3.3.10 -* CMake 3.31.6 -* OpenMPI 5.0.6 -* CUDA 12.6 -* ROCm 6.4.0 -* Python 3.13.2 -* NumPy 2.2.5 +* CMake 4.2.3, 3.27.9 +* OpenMPI 5.0.10 +* CUDA 12.9 +* ROCm 7.0.1 +* Python 3.14.2 +* NumPy 2.3.5 For GPU acceleration on NVIDIA GPUs we test LLVM with CUDA using the above versions. On AMD GPUs we support using the latest ROCm version and its matching amdclang compiler, as listed above. On Intel GPUs we test the up-to-date OneAPI release. GitHub Actions-based tests include additional version combinations from within our two-year support window. -Workflow tests are currently performed with Quantum ESPRESSO v7.4.1 and PySCF v2.9.0. These check trial wavefunction generation and +Workflow tests are currently performed with Quantum ESPRESSO v7.5 and PySCF v2.13.0. These check trial wavefunction generation and conversion through to actual QMC runs. C++ 17 standard library @@ -351,7 +355,6 @@ the path to the source directory. Also supported: CMAKE_CXX_FLAGS_DEBUG, CMAKE_CXX_FLAGS_RELEASE, and CMAKE_CXX_FLAGS_RELWITHDEBINFO CMAKE_INSTALL_PREFIX Set the install location (if using the optional install step) - QMC_INSTALL_NEXUS Install Nexus alongside QMCPACK (if using the optional install step) - Additional QMCPACK build options @@ -377,6 +380,8 @@ the path to the source directory. ENABLE_PPCONVERT ON/OFF. Enable the ppconvert tool. If requirements are met, it is ON by default. USE_OBJECT_TARGET ON/OFF(default). Use CMake object library targets to workaround linker not being able to handle hybrid binary archives which contain both host and device codes. + QMC_INSTALL_NEXUS ON(default)/OFF. Install Nexus alongside QMCPACK (if using the optional install step). + QMC_DOXYGEN ON(default)/OFF. Enable use of Doxygen documentation generator tool. - Expert performance fine tuning options @@ -449,7 +454,7 @@ See :ref:`Sanitizer-Libraries` for more information. :: ENABLE_GCOV OFF(default)/ON, build with C++ source code line coverage measurement using gcov - ENABLE_PYCOV OFF(default)/ON, build with Python source code line coverage measurement using coverage.py + ENABLE_PYCOV OFF(default)/ON, build with Python source code line coverage measurement using coverage.py and/or pytest Installation from CMake @@ -895,7 +900,7 @@ Job script example with one MPI rank per GPU. Frontier is configured in low oper cores are not available on each node by default. i.e. We use 7 OpenMP CPU threads per MPI rank. The part of the job script that makes specific modules available is copied directly from the build script used above. -:: +.. code-block:: bash #!/bin/bash #SBATCH -A MAT151 @@ -947,7 +952,7 @@ Installing on systems with ARMv8-based processors The following build recipe was verified using the 'Arm Compiler for HPC' on the ANL JLSE Comanche system with Cavium ThunderX2 processors on November 6, 2018. -:: +.. code-block:: bash # load armclang compiler module load Generic-AArch64/RHEL/7/arm-hpc-compiler/18.4 @@ -959,7 +964,7 @@ The following build recipe was verified using the 'Arm Compiler for HPC' on the Then using the following command: -:: +.. code-block:: bash mkdir build_armclang cd build_armclang diff --git a/docs/intro_wavefunction.rst b/docs/intro_wavefunction.rst index 84d218c81f..907304591e 100644 --- a/docs/intro_wavefunction.rst +++ b/docs/intro_wavefunction.rst @@ -39,7 +39,7 @@ where :math:`\textit{A}(\vec{r})` is one of the antisymmetric functions: (1) Slater determinant, (2) multislater determinant, or (3) pfaffian and :math:`\textit{J}_k` is any of the Jastrow functions (described in :ref:`jastrow`). The antisymmetric functions are built from a set of single particle orbitals (SPO) ``(sposet)``. QMCPACK implements four different types of ``sposet``, described in the following section. Each ``sposet`` is designed for a different type of calculation, so their definition and generation varies accordingly. -.. code-block:: +.. code-block:: xml :caption: wavefunction XML element skeleton. :name: wavefunction.skeleton.xml @@ -78,7 +78,7 @@ QMCPACK supports a range of SPOSet types: sposet_collection input style ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -.. code-block:: +.. code-block:: xml :caption: SPO XML element framework. :name: spo.collection.xml @@ -120,7 +120,7 @@ SPOSet construction related details out of ``determinantset``. This revised specification keeps the basis set details separate from information about the determinants. -.. code-block:: +.. code-block:: xml :caption: Deprecated input style. :name: spo.singledet.old.xml @@ -137,7 +137,7 @@ determinants. After updating the input style. -.. code-block:: +.. code-block:: xml :caption: Updated input style. :name: spo.singledet.xml @@ -216,7 +216,7 @@ OpenMP/MPI hybrid QMC. The input XML block for the spline SPOs is given in :ref:`spline.spo.xml`. A list of options is given in :numref:`table3`. -.. code-block:: +.. code-block:: xml :caption: Spline SPO XML element :name: spline.spo.xml @@ -344,7 +344,7 @@ In this section we describe the input sections of ``sposet_collection`` for the Here is an :ref:`example ` of single determinant with LCAO. The input sections for multideterminant trial wavefunctions are described in :ref:`multideterminants`. -.. code-block:: +.. code-block:: xml :caption: ``slaterdeterminant`` with an LCAO ``sposet_collection`` example :name: spo.singledet.lcao.xml @@ -373,7 +373,7 @@ The input sections for multideterminant trial wavefunctions are described in :re Here is the :ref:`basic structure ` for LCAO ``sposet_collection`` input block. A list of options for ``sposet_collection`` is given in :numref:`table4`. -.. code-block:: +.. code-block:: xml :caption: Basic input block for ``sposet_collection`` for LCAO. :name: spo.lcao.xml @@ -439,7 +439,7 @@ Attribute: - cuspCorrection Enable (disable) use of the cusp correction algorithm (CASINO REFERENCE) for a ``basisset`` built with GTO functions. The algorithm is implemented as described in (CASINO REFERENCE) and works only with transform="yes" and an input GTO basis set. No further input is needed. -.. code-block:: +.. code-block:: xml :caption: Basic input block for ``basisset``. :name: Listing 4 @@ -608,7 +608,7 @@ Orbitals in region C are computed as the regular B-spline basis described in :re To enable hybrid orbital representation, the input XML needs to see the tag ``hybridrep="yes"`` shown in :ref:`Listing 6 `. -.. code-block:: +.. code-block:: xml :caption: Hybrid orbital representation input example. :name: Listing 6 @@ -620,7 +620,7 @@ To enable hybrid orbital representation, the input XML needs to see the tag ``hy Second, the information describing the atomic regions is required in the particle set, shown in :ref:`Listing 7 `. -.. code-block:: +.. code-block:: xml :caption: particleset elements for ions with information needed by hybrid orbital representation. :name: Listing 7 @@ -682,7 +682,7 @@ The lowest-energy plane-wave states compatible with the boundary condition are o This following example can also be used for Helium simulations by specifying the proper pair interaction in the Hamiltonian section and using a bosonic wavefunction. -.. code-block:: +.. code-block:: xml :caption: 2D Fermi liquid example: particle specification :name: Listing 8 @@ -702,7 +702,7 @@ proper pair interaction in the Hamiltonian section and using a bosonic wavefunct -.. code-block:: +.. code-block:: xml :caption: 2D Fermi liquid example (Slater Jastrow wavefunction) :name: Listing 9 @@ -766,7 +766,7 @@ Attribute: .. centered:: Table 2 Options for the ``slaterdeterminant`` XML-block. -.. code-block:: +.. code-block:: xml :caption: Slaterdeterminant set XML element. :name: Listing 1 @@ -855,7 +855,7 @@ Additional information: - When the multideterminant wavefunction is read from an HDF5 file in the ``detlist`` child, the HDF5 dataset must use 64 bit unsigned integers to represent the determinants. The ``utils/determinants_tools.py`` script described in further detail below will check that the determinants are stored using the correct type and correct files that are storing signed 64 bit integers. -.. code-block:: +.. code-block:: xml :caption: multideterminant set XML element. :name: multideterminant.xml @@ -951,7 +951,7 @@ Attribute: | ``name`` | Text | | | Name of rotated SPOSet | +-----------------+----------+----------------+---------+------------------------------------+ -.. code-block:: +.. code-block:: xml :caption: Orbital Rotation XML element. :name: Listing 1R @@ -1072,7 +1072,7 @@ Example Use Case Having specified the general form, we present a general example of one-body and two-body backflow transformations in a hydrogen-helium mixture. The hydrogen and helium ions have independent backflow transformations, as do the like and unlike-spin two-body terms. One caveat is in order: ionic backflow transformations must be listed in the order they appear in the particle set. If in our example, helium is listed first and hydrogen is listed second, the following example would be correct. However, switching backflow declaration to hydrogen first then helium, will result in an error. Outside of this, declaration of one-body blocks and two-body blocks are not sensitive to ordering. -:: +.. code-block:: xml @@ -1106,7 +1106,7 @@ Having specified the general form, we present a general example of one-body and Currently, backflow works only with single-Slater determinant wavefunctions. When a backflow transformation has been declared, it should be placed within the ```` block, but outside of the ```` blocks, like so: -:: +.. code-block:: xml @@ -1410,7 +1410,7 @@ specified, the default cutoff of the Wigner Seitz cell radius is used; this Jastrow must be used with a 3D periodic system such as a bulk solid. The name of the particleset holding the ionic positions is "i." -:: +.. code-block:: xml @@ -1424,7 +1424,7 @@ the ions is labeled as ion0 rather than "i," as in the other example. Also in t the ion is lithium with a coulomb potential, so the cusp condition is satisfied by setting cusp="d." -:: +.. code-block:: xml @@ -1517,7 +1517,7 @@ Example use case Specify a spin-independent function with independent Jastrow factors for two different species (Li and H). The name of the particleset holding the ionic positions is "i." -:: +.. code-block:: xml @@ -1572,7 +1572,7 @@ will typically be fixed as the desired cusp condition is known. To specify this one-body Jastrow factor, use an input section like the following. -:: +.. code-block:: xml @@ -1762,7 +1762,7 @@ Specify a spin-dependent function with four parameters for each channel. In thi a radius of 4.0 bohr (rather than to the default of the Wigner Seitz cell radius). Also, in this example, the coefficients are set to not be optimized during an optimization step. -:: +.. code-block:: xml @@ -1976,7 +1976,7 @@ Additional information: - ``symmetry=none``: Impose no symmetry on the coefficients. -.. code-block:: +.. code-block:: xml :caption: k-space Jastrow with one- and two-body terms. :name: Listing 10 @@ -1991,7 +1991,7 @@ Additional information: -.. code-block:: +.. code-block:: xml :caption: k-space Jastrow with one-body term only. :name: Listing 11 @@ -2002,7 +2002,7 @@ Additional information: -.. code-block:: +.. code-block:: xml :caption: k-space Jastrow with two-body term only. :name: Listing 12 @@ -2127,7 +2127,7 @@ For both the Yukawa and Gaskell RPA Jastrows, the default value for :math:`r_s` | ``kc``:math:`^o` | kc | :math:`k_c>0` | :math:`2\left(\tfrac{9\pi}{4}\right)^{1/3}\tfrac{4\pi N_e}{3\Omega}` | k-space cutoff | +-------------------+--------------+----------------+----------------------------------------------------------------------+-------------------------+ -.. code-block:: +.. code-block:: xml :caption: Two body RPA Jastrow with long- and short-ranged parts. :name: Listing 13 @@ -2173,7 +2173,7 @@ Example use case Here is an example of H2O molecule. After optimizing one and two body Jastrow factors, add the following block in the wavefunction. The coefficients will be filled zero automatically if not given. -:: +.. code-block:: xml @@ -2248,7 +2248,7 @@ Additional information: Example Use Case ~~~~~~~~~~~~~~~~ -:: +.. code-block:: xml diff --git a/docs/lab_advanced_molecules.rst b/docs/lab_advanced_molecules.rst index 41b2253157..b4638be89e 100644 --- a/docs/lab_advanced_molecules.rst +++ b/docs/lab_advanced_molecules.rst @@ -147,7 +147,7 @@ favorite text editor and modify the name of the files that contain the ``wavefunction`` and ``particleset`` XML blocks. These files are included with the commands: -:: +.. code-block:: xml @@ -861,7 +861,7 @@ Useful notes Appendix C: Wavefunction optimization XML block ----------------------------------------------- -.. code-block:: +.. code-block:: xml :caption: Sample XML optimization block. :name: Listing 60 @@ -943,7 +943,7 @@ Recommendations: Appendix D: VMC and DMC XML block --------------------------------- -.. code-block:: +.. code-block:: xml :caption: Sample XML blocks for VMC and DMC calculations. :name: Listing 61 @@ -1018,7 +1018,7 @@ Options unique to DMC: Appendix E: Wavefunction XML block ---------------------------------- -.. code-block:: +.. code-block:: xml :caption: Basic framework for a single-determinant determinantset XML block. :name: Listing 62 @@ -1076,7 +1076,7 @@ in the determinant block refers to the number of SPOs present while the “size” parameter in the coefficient block refers to the number of atomic basis functions per SPO. -.. code-block:: +.. code-block:: xml :caption: Sample XML block for the single Slater determinant case. :name: Listing 63 @@ -1109,7 +1109,7 @@ that two sposet sets must be defined, one for each electron spin. The name of ea is required in the definition of the multideterminant block. The determinants are defined in terms of occupation numbers based on these orbitals. -.. code-block:: +.. code-block:: xml :caption: Basic framework for a multideterminant determinantset XML block. :name: Listing 64 @@ -1184,7 +1184,7 @@ Optimization of individual radial functions can be turned on/off using the “op parameter. It can be added to any coefficients block, even though it is currently not present in the J1 and J2 blocks. -.. code-block:: +.. code-block:: xml :caption: Sample Jastrow XML block. :name: Listing 65 diff --git a/docs/lab_condensed_matter.rst b/docs/lab_condensed_matter.rst index 1913bef112..c67500b89d 100644 --- a/docs/lab_condensed_matter.rst +++ b/docs/lab_condensed_matter.rst @@ -165,7 +165,7 @@ We will now use Nexus to generate the trial wavefunction for this BCC beryllium. Fortunately, the Nexus will handle determination of the proper k-vectors given the tiling matrix. All that is needed is to place the tiling matrix in the ``Be-2at-setup.py`` file. Now the definition of the physical system is -:: +.. code-block:: python bcc_Be = generate_physical_system( lattice = 'cubic', @@ -228,13 +228,13 @@ finite-size effects. To fix this, delete the directory ``bcc-beryllium/opt-2at``, change the line near the top of ``Be-2at-setup.py`` from -:: +.. code-block:: python qmcpack = '/soft/applications/qmcpack/Binaries/qmcpack' to -:: +.. code-block:: python qmcpack = '/soft/applications/qmcpack/Binaries/qmcpack_comp' @@ -370,7 +370,7 @@ variance. Finally, edit the file ``graphene-final.py``, which will perform two DMC calculations. In the first, (qmc1) replace the following lines: -:: +.. code-block:: python meshfactor = xxx, precision = '---', diff --git a/docs/lab_excited.rst b/docs/lab_excited.rst index 1c3931d9b7..47613b7e05 100644 --- a/docs/lab_excited.rst +++ b/docs/lab_excited.rst @@ -203,7 +203,7 @@ In the ``band.py`` script, identification of high-symmetry k-points and band str In the script, where the ``dia`` PhysicalSystem object is used as the input structure, ``dia2_structure`` is the standardized primitive cell and ``dia2_kpath`` is the respective k-path around the iBZ. ``dia2_kpath`` has a dictionary of the k-path in various coordinate systems; please make sure you are using the right one. -:: +.. code-block:: python from structure import get_primitive_cell, get_kpath dia2_structure = get_primitive_cell(structure=dia.structure)['structure'] @@ -235,11 +235,11 @@ denote the CBM wavevector in the rest of this document. In ``band.py`` script, once the band structure calculation is finished, you can use the following lines to get the exact location of VBM and CBM using -:: +.. code-block:: python p = band.load_analyzer_image() - print "VBM:\n{0}".format(p.bands.vbm) - print "CBM:\n{0}".format(p.bands.cbm) + print("VBM:\n{0}".format(p.bands.vbm)) + print("CBM:\n{0}".format(p.bands.cbm)) Output must be the following: @@ -300,11 +300,11 @@ denote the CBM wavevector in the rest of this document. In script, once the band structure calculation is finished, you can use the following lines to get the exact location of VBM and CBM using -:: +.. code-block:: python p = band.load_analyzer_image() - print "VBM:\n{0}".format(p.bands.vbm) - print "CBM:\n{0}".format(p.bands.cbm) + print("VBM:\n{0}".format(p.bands.vbm)) + print("CBM:\n{0}".format(p.bands.cbm)) Output must be the following: @@ -382,7 +382,7 @@ we use :math:`\Delta'=[1/3, 0., 1/3]`, we could use a :math:`\Delta'` can be a good approximation. We can compare the eigenvalues using their index numbers: -:: +.. code-block:: python >>> print p.bands.up[51] ## CBM, $\Delta$ ## eigs = [-3.2076 4.9221 7.5433 7.5433 17.1545 19.7598 28.3242 28.3242] @@ -454,15 +454,15 @@ transition can be defined as from (0,3) to (4,4). Alternatively, we can also read the band and twist indexes using PwscfAnalyzer and determine the band/twist indexes on the go: -:: +.. code-block:: python p = nscf.load_analyzer_image() - print 'band information' - print p.bands.up - print 'twist 0 k-point:',p.bands.up[0].kpoint_rel - print 'twist 4 k-point:',p.bands.up[4].kpoint_rel - print 'twist 0 band 3 eigenvalue:',p.bands.up[0].eigs[3] - print 'twist 4 band 4 eigenvalue:',p.bands.up[4].eigs[4] + print('band information') + print(p.bands.up) + print('twist 0 k-point:',p.bands.up[0].kpoint_rel) + print('twist 4 k-point:',p.bands.up[4].kpoint_rel) + print('twist 0 band 3 eigenvalue:',p.bands.up[0].eigs[3]) + print('twist 4 band 4 eigenvalue:',p.bands.up[4].eigs[4]) Giving output: @@ -560,7 +560,7 @@ A typical workflow for a quasiparticle calculation includes the following: #. Check the convergence of the quasiparticle gap with respect to the simulation cell size. -:: +.. code-block:: xml ##Change size to 35 @@ -584,7 +584,7 @@ Going back to :eq:`eq77`, we can see that it is essential to include VBM and CBM Therefore, the added electron will sit at CBM while the subtracted electron will be removed from VBM. However, for the charged cell calculations, we may need to make changes in the input files for the fourth step. Alternatively, in the quasiparticle.py file, the changes in the QMC input are shown for a negatively charged system: -:: +.. code-block:: python qmc.input.simulation.qmcsystem.particlesets.e.groups.u.size +=1 (qmc.input.simulation.qmcsystem.wavefunction.determinantset @@ -611,7 +611,7 @@ gap calculations. Here, the modified input file is given for the :math:`\Gamma\rightarrow\Delta'` transition, which can be compared with the ground state input file in the previous section. -:: +.. code-block:: xml @@ -652,7 +652,7 @@ And the ``updet.tile_300010003.spin_0.tw_0.g0.bandinfo.dat`` file must be change Alternatively, the excitations within Nexus can be defined as shown in the ``optical.py`` file: -:: +.. code-block:: python qmc = generate_qmcpack( ... diff --git a/docs/lab_qmc_basics.rst b/docs/lab_qmc_basics.rst index e72a194a99..f59e138b48 100644 --- a/docs/lab_qmc_basics.rst +++ b/docs/lab_qmc_basics.rst @@ -271,7 +271,7 @@ For this exercise, we will focus on minimizing the variance. First, we need to update the template particle and wavefunction information in ``O.q0.ptcl.xml`` and ``O.q0.wfs.xml``. We want to simulate the O atom in open boundary conditions (the default is periodic). To do this, open ```O.q0.ptcl.xml`` with your favorite text editor (e.g., ``emacs`` or ``vi``) and replace -:: +.. code-block:: xml p p p @@ -282,7 +282,7 @@ First, we need to update the template particle and wavefunction information in ` with -:: +.. code-block:: xml n n n @@ -290,7 +290,7 @@ with Next we will select Jastrow factors appropriate for an atom. In open boundary conditions, the B-spline Jastrow correlation functions should cut off to zero at some distance away from the atom. Open ``O.q0.wfs.xml`` and add the following cutoffs (``rcut`` in Bohr radii) to the correlation factors: -:: +.. code-block:: xml ... @@ -310,7 +310,7 @@ parameters, which are just the values of :math:`u` on a uniformly spaced grid up to ``rcut``. Initially the parameters (``coefficients``) are set to zero: -:: +.. code-block:: xml @@ -320,7 +320,7 @@ to zero: Finally, we need to assemble particle, wavefunction, and pseudopotential information into the main QMCPACK input file (``O.q0.opt.in.xml``) and specify inputs for the Jastrow optimization process. Open ``O.q0.opt.in.xml`` and write in the location of the particle, wavefunction, and pseudopotential files ("````" are comments): -:: +.. code-block:: xml ... @@ -335,7 +335,7 @@ Finally, we need to assemble particle, wavefunction, and pseudopotential informa The relevant portion of the input describing the linear optimization process is -:: +.. code-block:: xml @@ -527,7 +527,7 @@ The DMC algorithm contains two biases in addition to the fixed node and pseudopo In the same directory you used to perform wavefunction optimization (``oxygen_atom``) you will find a sample DMC input file for the neutral oxygen atom named ``O.q0.dmc.in.xml``. Open this file in a text editor and note the differences from the optimization case. Wavefunction information is no longer included from ``pw2qmcpack`` but instead should come from the optimization run: -:: +.. code-block:: xml @@ -609,7 +609,7 @@ is sufficient for this system. Choose an initial DMC time step and create a sequence of :math:`N` time steps according to :eq:`eq69`. Make :math:`N` copies of the DMC XML block in the input file. -:: +.. code-block:: xml DWARMUP @@ -728,7 +728,7 @@ convenience, the necessary steps are summarized as follows. (a) Copy the optimization input (``O.q0.opt.in.xml``) to ``O.q1.opt.in.xml`` (b) Edit ``O.q1.opt.in.xml`` to match the file prefix used in DFT. - :: + .. code-block:: xml ... @@ -740,7 +740,7 @@ convenience, the necessary steps are summarized as follows. (c) Edit the particle XML file (``O.q1.ptcl.xml``) to have open boundary conditions. - :: + .. code-block:: xml n n n @@ -748,7 +748,7 @@ convenience, the necessary steps are summarized as follows. (d) Add cutoffs to the Jastrow factors in the wavefunction XML file (``O.q1.wfs.xml``) - :: + .. code-block:: xml ... @@ -766,7 +766,7 @@ convenience, the necessary steps are summarized as follows. (a) Copy the DMC input (``O.q0.dmc.in.xml``) to ``O.q1.dmc.in.xml`` (b) Edit ``O.q1.dmc.in.xml`` to use the DFT prefix and the optimal Jastrow. - :: + .. code-block:: xml ... @@ -826,7 +826,7 @@ The set of automation tools we will be using is known as Nexus :cite:`Krogel2016 Nexus is driven by simple user-defined scripts that resemble keyword-driven input files. An example Nexus input file that performs a single VMC calculation (with pregenerated orbitals) follows. Take a moment to read it over and especially note the comments (prefixed with "``\#``") explaining most of the contents. If the input syntax is unclear you may want to consult portions of :ref:`python-basics`, which gives a condensed summary of Python constructs. An additional example and details about the inner workings of Nexus can be found in the reference publication :cite:`Krogel2016nexus`. -:: +.. code-block:: python #! /usr/bin/env python3 @@ -897,7 +897,7 @@ Enter the ``oxygen_dimer`` directory. Copy your BFD pseudopotential from the at As in the example in the last section, the oxygen dimer is generated with the ``generate_physical_ system`` function: -:: +.. code-block:: python dimer = generate_physical_system( type = 'dimer', @@ -913,7 +913,7 @@ Similar syntax can be used to generate crystal structures or to specify systems Next, objects representing a QE (PWSCF) run and subsequent orbital conversion step are constructed with respective ``generate_*`` functions: -:: +.. code-block:: python dft = generate_pwscf( identifier = 'dft', @@ -935,7 +935,7 @@ Note the ``dependencies`` keyword. This keyword is used to construct workflows Objects representing QMCPACK simulations are then constructed with the ``generate_qmcpack`` function: -:: +.. code-block:: python opt = generate_qmcpack( identifier = 'opt', @@ -1000,7 +1000,7 @@ Objects representing QMCPACK simulations are then constructed with the ``generat Shared details such as the run directory, job, pseudopotentials, and orbital file have been omitted (``...``). The "``opt``" run will optimize a 1-body B-spline Jastrow with 8 knots having a cutoff of 5.0 Bohr and a B-spline Jastrow (for up-up and up-down correlations) with 8 knots and cutoffs of 10.0 Bohr. The Jastrow list for the DMC run is empty, and the previous use of ``dependencies`` indicates that the DMC run depends on the optimization run for the Jastrow factor. Nexus will submit the "``opt``" run first, and upon completion it will scan the output, select the optimal set of parameters, pass the Jastrow information to the "``qmc``" run, and then submit the DMC job. Independent job workflows are submitted in parallel when permitted. No input files are written or job submissions made until the "``run_project``" function is reached: -:: +.. code-block:: python run_project(sims) @@ -1008,7 +1008,7 @@ All of the simulation objects have been collected into a list (``sims``) for sub As written, ``O_dimer.py`` will perform calculations only at the equilibrium separation distance of 1.2074 {\AA} since the list of scaling factors (representing stretching or compressing the dimer) contains only one value (``scales = [1.00]``). Modify the file now to perform DMC calculations across a range of separation distances with each DMC run using the Jastrow factor optimized at the equilibrium separation distance. Specifically, you will want to change the list of scaling factors to include both compression (``scale<1.0``) and stretch (``scale>1.0``): -:: +.. code-block:: python scales = [1.00,0.90,0.95,1.05,1.10] @@ -1257,7 +1257,7 @@ Before performing production calculations (more than just the initial setup in t Beyond PPs, all that is required to get started are the atomic positions and the dimensions/shape of the simulation cell. The Nexus file ``example.py`` illustrates how to set up PWSCF and QMCPACK input files by providing minimal information regarding the physical system (an 8-atom cubic cell of diamond in the example). Most of the contents should be familiar from your experience with the automated calculations of the oxygen dimer binding curve in :ref:`dimer-automation` (if you have skipped ahead you may want to skim that section for relevant information). The most important change is the expanded description of the physical system: -:: +.. code-block:: python # details of your physical system (diamond conventional cell below) my_project_name = 'diamond_vmc' # directory to perform runs @@ -1335,7 +1335,7 @@ Basic Python data types (``int``, ``float``, ``str``, ``tuple``, ``list``, ``arr Intrinsic types: ``int, float, str`` ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -:: +.. code-block:: python #this is a comment i=5 # integer @@ -1353,7 +1353,7 @@ Intrinsic types: ``int, float, str`` Container types: ``tuple, list, array, dict, obj`` ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -:: +.. code-block:: python from numpy import array # get array from numpy module from developer import obj # get obj from Nexus' developer module @@ -1412,7 +1412,7 @@ Container types: ``tuple, list, array, dict, obj`` An important feature of Python to be aware of is that assignment is most often by reference, that is, new values are not always created. This point is illustrated with an ``obj`` instance in the following example, but it also holds for ``list``, ``array``, ``dict``, and others. -:: +.. code-block:: python >>> o = obj(a=5,b=6) >>> @@ -1437,7 +1437,7 @@ Here ``p`` is just another name for ``o``, while ``q`` is a fully independent co Conditional Statements: ``if/elif/else`` ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -:: +.. code-block:: python a = 5 if a is None: @@ -1459,7 +1459,7 @@ The "``\#end if``" is not part of Python syntax, but you will see text like this Iteration: ``for`` ^^^^^^^^^^^^^^^^^^ -:: +.. code-block:: python from developer import obj @@ -1497,7 +1497,7 @@ Iteration: ``for`` Functions: ``def``, argument syntax ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -:: +.. code-block:: python def f(a,b,c=5): # basic function, c has a default value print(a,b,c) diff --git a/docs/lab_qmc_statistics.rst b/docs/lab_qmc_statistics.rst index 5462831142..e0b23d438c 100644 --- a/docs/lab_qmc_statistics.rst +++ b/docs/lab_qmc_statistics.rst @@ -480,7 +480,7 @@ can lead to autocorrelation since the new samples will be in the neighborhood of previous samples. Type ``grep timestep H.xml`` to see the varying time step values in this QMCPACK input file (``H.xml``): -:: +.. code-block:: xml 10 5 diff --git a/docs/methods.rst b/docs/methods.rst index 6f66db7868..225b102de7 100644 --- a/docs/methods.rst +++ b/docs/methods.rst @@ -85,7 +85,7 @@ Additional information: The particle configurations are written to a ``.config.h5`` file. -.. code-block:: +.. code-block:: xml :caption: The following is an example of running a simulation that can be restarted. :name: Listing 42 @@ -101,7 +101,7 @@ Check that this file exists before attempting a restart. To continue a run, specify the ``mcwalkerset`` element before your VMC/DMC block: -.. code-block:: +.. code-block:: xml :caption: Restart (read walkers from previous run). :name: Listing 43 @@ -119,7 +119,7 @@ In the project id section, make sure that the series number is different from an ``qmc`` element may contain ``qmcsystem`` elements for selecting specific wavefunction and hamiltonian pairs by name. In most QMC methods, only one pair of wavefunction and hamiltonian is needed, ``qmcsystem`` is only necessary -when more than one pair of ``wavefunction`` and ``hamiltonian`` elements where specified in the simultion system specificiation. +when more than one pair of ``wavefunction`` and ``hamiltonian`` elements where specified in the simulation system specification. CSVMC driver requires at least two entries of ``qmcsystem`` elements. +-----------------+---------------+ @@ -156,7 +156,7 @@ Note that changing the number of crowds does not change the statistics of a run crowds only affects how the work is distributed, not the amount of work. Due to differences in scheduling and random number utilization, otherwise identical runs with different numbers of crowds will not give numerically identical results at each step. The overall statistical properties and results are unchanged. -Crowds are owned by MPI processes and the number of crowds is specifed on a per MPI process basis. If a user requests 4 crowds +Crowds are owned by MPI processes and the number of crowds is specified on a per MPI process basis. If a user requests 4 crowds and there are 16 walkers per MPI rank, then each crowd will have 4 walkers. For the purposes of pure CPU runs, it is generally sufficient to have the number of crowds match the number of threads spawned by each MPI process and one walker per crowd. For large GPU runs, either for large electron @@ -185,7 +185,7 @@ There are notable changes in the driver input section when moving from classic d - When running on GPUs, tuning ``walkers_per_rank`` or ``total_walkers`` is needed to maximize GPU throughput, just like tuning ``walkers`` in the classic drivers. - - ``crowds`` can be optionally added in batched drivers to specify the number of crowds and optimize peformance on GPUs. + - ``crowds`` can be optionally added in batched drivers to specify the number of crowds and optimize performance on GPUs. - Only particle-by-particle moves are supported. All-particle moves are not yet supported. Provide feedback if you have a use for these. @@ -310,7 +310,7 @@ Additional information: An example VMC section for a simple batched ``vmc`` run: -:: +.. code-block:: xml @@ -443,7 +443,7 @@ Additional information: An example VMC section for a simple VMC run: -:: +.. code-block:: xml @@ -460,7 +460,7 @@ Here we set 256 ``walkers`` per MPI, have a brief initial equilibration of 100 ` The following is an example of VMC section storing configurations (walker samples) for optimization. -:: +.. code-block:: xml @@ -496,7 +496,7 @@ can therefore make use of crowds, batching, and supports running a large number A typical optimization block looks like the following. It starts with method="linear" and contains three blocks of parameters. -:: +.. code-block:: xml @@ -589,7 +589,7 @@ Additional information: The cost function consists of three components: energy, unreweighted variance, and reweighted variance. -:: +.. code-block:: xml 0.95 0.00 @@ -606,7 +606,7 @@ If variational parameters are set as not optimizable in the predominant way, the The following example shows optimizing subsets of parameters in stages in a single QMCPACK run. -:: +.. code-block:: xml ... @@ -652,7 +652,7 @@ optimizers can be switched among “OneShiftOnly” (default), “adaptive,” “descent,” “hybrid,” "sr_cg," and “quartic” (old) using the following line in the optimization block: -:: +.. code-block:: xml THE METHOD YOU LIKE @@ -716,7 +716,7 @@ also use large ``minwalkers``, for example adding three-body Jastrow factor to c developing a reliable optimization recipe for a new system, one should check convergence of the process with significantly increased samples, e.g. 4x, and repeat the check each time the flexibility in the wavefunction and number of parameters is increased. -:: +.. code-block:: xml @@ -901,7 +901,7 @@ Recommendations: filtration is on so that accelerated descent can be used to optimize parameters that the LM leaves untouched. :cite:`Otis2021` -:: +.. code-block:: xml @@ -1081,8 +1081,7 @@ Additional information and recommendations: it may be useful to try the hybrid optimization approach described in the next subsection. -:: - +.. code-block:: xml @@ -1148,8 +1147,7 @@ There are two additional parameters used in the hybrid optimization and it requi | ``Stored_Vectors`` | integer | :math:`> 0` | 5 | Number of vectors to transfer to BLM | +---------------------+--------------+-------------+-------------+--------------------------------------+ -:: - +.. code-block:: xml @@ -1245,7 +1243,7 @@ By default, the parameter update is accepted as is, and the size of the proposed We are currently investigating various improvements to make this a more reliable optimizer. -``sr_cg` method: +``sr_cg`` method: parameters: @@ -1304,7 +1302,7 @@ Recommendations: 3-Body J), set ``exp0`` to 0 and do a single inner iteration (max its=1) per sample of configurations. -:: +.. code-block:: xml quartic @@ -1347,15 +1345,15 @@ stored in HDF5 format. The optimization header block will have to specify that the new CI coefficients will be saved to HDF5 format. If the tag is not added coefficients will not be saved. -:: +.. code-block:: xml - The rest of the optimization block remains the same. +The rest of the optimization block remains the same. When running the optimization, the new coefficients will be stored in a ``*.sXXX.opt.h5`` file, where XXX corresponds to the series number. The H5 file contains only the optimized coefficients. The corresponding ``*.sXXX.opt.xml`` will be updated for each optimization block as follows: -:: +.. code-block:: xml @@ -1376,7 +1374,7 @@ The gradients of the energy with respect to the variational parameters can be ch The check compares the analytic derivatives with a finite difference approximation. These are activated by giving a ``gradient_test`` method in an ``optimize`` block, as follows: -:: +.. code-block:: xml @@ -1399,7 +1397,7 @@ It contains one line per loop iteration, to allow using existing tools to comput The input would look like the following: -:: +.. code-block:: xml @@ -1563,7 +1561,7 @@ where :math:`E_\text{ref}` is the :math:`E_\text{pop\_avg}` average over all the 'limited_history' uses weighted average of :math:`E_\text{pop\_avg}` of the latest at maximum min(1, int(1.0 / (feedback * tau))) steps collected post warm-up. Default 'unlimited_history'. -.. code-block:: +.. code-block:: xml :caption: The following is an example of a minimal DMC section using the batched ``dmc`` driver :name: Listing 48b @@ -1836,7 +1834,7 @@ where :math:`E_\text{ref}` is the :math:`E_\text{pop\_avg}` average over all the wavefunction quality via the term :math:`\sigma`. :math:`\mathrm{sigmaBound}` is default to 10. -.. code-block:: +.. code-block:: xml :caption: The following is an example of a very simple DMC section. :name: Listing 44 @@ -1850,7 +1848,7 @@ where :math:`E_\text{ref}` is the :math:`E_\text{pop\_avg}` average over all the The time step should be individually adjusted for each problem. Please refer to the theory section on diffusion Monte Carlo. -.. code-block:: +.. code-block:: xml :caption: The following is an example of running a simulation that can be restarted. :name: Listing 45 @@ -1866,7 +1864,7 @@ This also works in VMC. This will output an h5 file with the name attempting a restart. To read in this file for a continuation run, specify the following: -.. code-block:: +.. code-block:: xml :caption: Restart (read walkers from previous run). :name: Listing 46 @@ -1876,7 +1874,7 @@ BH is the project id, and s002 is the calculation number to read in the walkers Combining VMC and DMC in a single run (wavefunction optimization can be combined in this way too) is the standard way in which QMCPACK is typically run. There is no need to run two separate jobs since method sections can be stacked and walkers are transferred between them. -.. code-block:: +.. code-block:: xml :caption: Combined VMC and DMC run. :name: Listing 47 @@ -1906,7 +1904,7 @@ Combining VMC and DMC in a single run (wavefunction optimization can be combined Reptation Monte Carlo --------------------- -Note: repatation Monte Carlo is not currently supported as a batched driver. +Note: reptation Monte Carlo is not currently supported as a batched driver. It can only be run by selecting use of legacy drivers via the driver_version project level setting, see :ref:`driver-version-parameter`. To aid prioritization, potential users are welcome to request porting and describe their science case. @@ -2010,7 +2008,7 @@ declaration to ensure correct sampling: -.. _walker_logging +.. _walker_logging: Walker Data Logging =================== @@ -2029,7 +2027,7 @@ The default walker data logging functionality is enabled by including the XML element (once) just before the QMC driver sections, for example: -:: +.. code-block:: xml diff --git a/docs/performance_portable.rst b/docs/performance_portable.rst index f652f81916..0b911ff6b2 100644 --- a/docs/performance_portable.rst +++ b/docs/performance_portable.rst @@ -61,7 +61,7 @@ Use the following changes to update input files to use the batched drivers. 1. Update the project block to include the ``driver_version`` parameter. While not required (their use is the default), specifying the ``driver_version`` helps indicate that the input is for the modern code. For example: -:: +.. code-block:: xml batch diff --git a/docs/requirements.txt b/docs/requirements.txt index 976e4e1bdb..d2f2f065a7 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -18,7 +18,7 @@ docutils==0.22.4 # sphinx # sphinx-rtd-theme # sphinxcontrib-bibtex -idna==3.11 +idna==3.15 # via requests imagesize==1.4.1 # via sphinx @@ -36,7 +36,7 @@ pybtex==0.25.1 # sphinxcontrib-bibtex pybtex-docutils==1.0.3 # via sphinxcontrib-bibtex -pygments==2.19.2 +pygments==2.20.0 # via sphinx pyyaml==6.0.3 # via pybtex @@ -70,5 +70,5 @@ sphinxcontrib-qthelp==2.0.0 # via sphinx sphinxcontrib-serializinghtml==2.0.0 # via sphinx -urllib3==2.6.3 +urllib3==2.7.0 # via requests diff --git a/docs/simulationcell.rst b/docs/simulationcell.rst index 7d9ca71822..afd842ca15 100644 --- a/docs/simulationcell.rst +++ b/docs/simulationcell.rst @@ -41,7 +41,7 @@ Attribute: An example of a block is given below: -:: +.. code-block:: xml @@ -107,7 +107,7 @@ specified axes. An example of a ``simulationcell`` block using is given below. The size of the box along the z-axis increases from 12 to 18 by the vacuum scale of 1.5. -:: +.. code-block:: xml @@ -320,7 +320,7 @@ Example use cases .. centered:: Particleset elements for ions and electrons randomizing electron start positions. -:: +.. code-block:: xml @@ -352,7 +352,7 @@ Example use cases .. centered:: Particleset elements for ions and electrons specifying electron start positions. -:: +.. code-block:: xml @@ -397,7 +397,7 @@ Example use cases .. centered:: Particleset elements for ions specifying positions by ion type. -:: +.. code-block:: xml diff --git a/docs/spin_orbit.rst b/docs/spin_orbit.rst index 78a7669705..0e24d98726 100644 --- a/docs/spin_orbit.rst +++ b/docs/spin_orbit.rst @@ -51,7 +51,7 @@ Using the generated single particle spinors, we build the many-body wavefunction where we now utilize determinants of spinors, as opposed to the usual product of up and down determinants. An example xml input block for the trial wave function is show below: -.. code-block:: +.. code-block:: xml :caption: wavefunction specification for a single determinant trial wave function :name: slisting1 @@ -92,7 +92,7 @@ The electon-electron cusp in this case should be -1/2, as discussed in :cite:`Me We also make a small modification in the particleset specification -.. code-block:: +.. code-block:: xml :caption: specification for the electron particle when performing spin-orbit calculations :name: slisting2 @@ -138,7 +138,7 @@ Note that this includes a contribution from the *spin drift* :math:`\mathbf{v}_{ In both the VMC and DMC methods, there are no required changes to a typical input -.. code-block:: +.. code-block:: xml 50 @@ -152,7 +152,7 @@ Whether or not spin moves are used is determined internally by the ``spinor=yes` By default, the spin mass :math:`\mu_s` (which controls the rate of spin sampling relative to the spatial sampling) is set to 1.0. This can be changed by adding an additional parameter to the QMC input -.. code-block:: +.. code-block:: xml 0.25 @@ -194,7 +194,7 @@ We note the following relations between the two representations of the relativis The structure of the spin-orbit ``.xml`` is -.. code-block:: +.. code-block:: xml @@ -217,7 +217,7 @@ In order to accumulate the spin-orbit energy, but exclude it from the local ener the ``physicalSO`` flag should be set to no in the Hamiltonian input. A typical application will include the SOC terms in the local energy, and an example input block is given as -.. code-block:: +.. code-block:: xml diff --git a/docs/unit_testing.rst b/docs/unit_testing.rst index 6181a94164..ad961cbb59 100644 --- a/docs/unit_testing.rst +++ b/docs/unit_testing.rst @@ -48,7 +48,7 @@ Example The first example is one test from ``src/Numerics/tests/test_grid_functor.cpp``. -.. code-block:: +.. code-block:: cpp :caption: Unit test example using Catch. :name: Listing 75 @@ -169,7 +169,7 @@ The ``Libxml2Document`` class has a ``parseFromString`` function to parse XML in The following code fragment to read the xml is common -.. code-block:: +.. code-block:: cpp const char* xml_str = R"()"; Libxml2Document doc; diff --git a/examples/molecules/H2O/simple-H2O.xml b/examples/molecules/H2O/simple-H2O.xml index 43a7d0bd30..bad07ff913 100644 --- a/examples/molecules/H2O/simple-H2O.xml +++ b/examples/molecules/H2O/simple-H2O.xml @@ -4,7 +4,7 @@ Simple Example of moleculear H2O - legacy + batched @@ -64,9 +64,7 @@ - 1 - 64 - 1 + 128 5 100 1 @@ -75,8 +73,7 @@ - 128 - no + 128 100 0.005 10 diff --git a/examples/molecules/He/he_bspline_jastrow.xml b/examples/molecules/He/he_bspline_jastrow.xml index 66da2def5f..7a2c38a2d4 100644 --- a/examples/molecules/He/he_bspline_jastrow.xml +++ b/examples/molecules/He/he_bspline_jastrow.xml @@ -1,7 +1,7 @@ - legacy + batched @@ -99,7 +99,7 @@ 2000 - 100 + 200000 100 0.1 diff --git a/examples/molecules/He/he_example_wf.xml b/examples/molecules/He/he_example_wf.xml index 9647671221..2510e5139b 100644 --- a/examples/molecules/He/he_example_wf.xml +++ b/examples/molecules/He/he_example_wf.xml @@ -1,7 +1,7 @@ - legacy + batched @@ -53,9 +53,8 @@ - 100 + 100 25 - 1 20 0.5 51200 @@ -77,7 +76,7 @@ 500 - 100 + 50000 100 0.1 diff --git a/examples/molecules/He/he_from_gamess.xml b/examples/molecules/He/he_from_gamess.xml index 6606d873c1..f35b0fd906 100644 --- a/examples/molecules/He/he_from_gamess.xml +++ b/examples/molecules/He/he_from_gamess.xml @@ -1,7 +1,7 @@ - legacy + batched @@ -2068,7 +2068,6 @@ 100 25 - 1 20 0.5 51200 @@ -2090,7 +2089,7 @@ 2000 - 100 + 200000 100 0.1 diff --git a/examples/molecules/He/he_simple.xml b/examples/molecules/He/he_simple.xml index 21fe02a0ec..6a5f59f99f 100644 --- a/examples/molecules/He/he_simple.xml +++ b/examples/molecules/He/he_simple.xml @@ -1,7 +1,7 @@ - legacy + batched @@ -71,7 +71,7 @@ 500 - 100 + 50000 100 0.1 diff --git a/examples/molecules/He/he_simple_dmc.xml b/examples/molecules/He/he_simple_dmc.xml index 8d3c9c4aa0..e3d9cc381b 100644 --- a/examples/molecules/He/he_simple_dmc.xml +++ b/examples/molecules/He/he_simple_dmc.xml @@ -1,7 +1,7 @@ - legacy + batched diff --git a/examples/molecules/He/he_simple_opt.xml b/examples/molecules/He/he_simple_opt.xml index 14c97e74af..cfbd37648c 100644 --- a/examples/molecules/He/he_simple_opt.xml +++ b/examples/molecules/He/he_simple_opt.xml @@ -1,7 +1,7 @@ - legacy + batched @@ -73,9 +73,8 @@ - 100 + 100 25 - 1 20 0.5 51200 @@ -97,7 +96,7 @@ 500 - 100 + 50000 100 0.1 diff --git a/examples/solids/simple-LiH.xml b/examples/solids/simple-LiH.xml index ab27c56f4f..26f0c19092 100644 --- a/examples/solids/simple-LiH.xml +++ b/examples/solids/simple-LiH.xml @@ -4,7 +4,7 @@ Simple Example of solid LiH - legacy + batched @@ -87,9 +87,7 @@ - 1 - 64 - 1 + 128 5 100 1 @@ -98,8 +96,7 @@ - 128 - no + 128 100 0.005 10 diff --git a/labs/lab1_qmc_statistics/average/average.py b/labs/lab1_qmc_statistics/average/average.py index d2559ae824..0b243fadf7 100755 --- a/labs/lab1_qmc_statistics/average/average.py +++ b/labs/lab1_qmc_statistics/average/average.py @@ -8,4 +8,4 @@ (-0.46204733302) )/5. -print average +print(average) diff --git a/labs/lab1_qmc_statistics/average/stddev.py b/labs/lab1_qmc_statistics/average/stddev.py index a30b8c39a0..ee04825af7 100755 --- a/labs/lab1_qmc_statistics/average/stddev.py +++ b/labs/lab1_qmc_statistics/average/stddev.py @@ -9,4 +9,4 @@ ) )**0.5 -print stddev +print(stddev) diff --git a/labs/lab1_qmc_statistics/average/stddev2.py b/labs/lab1_qmc_statistics/average/stddev2.py index 6f267b9d9e..7088c11bf9 100755 --- a/labs/lab1_qmc_statistics/average/stddev2.py +++ b/labs/lab1_qmc_statistics/average/stddev2.py @@ -9,4 +9,4 @@ ) )**0.5 -print stddev +print(stddev) diff --git a/nexus/README.md b/nexus/README.md index 27d7a10475..a3dc1a7907 100644 --- a/nexus/README.md +++ b/nexus/README.md @@ -79,7 +79,7 @@ If you would like to install these packages manually, this can be done via `pip` Please see the [Nexus User Guide](https://nexus-workflows.readthedocs.io/en/latest/index.html) for more information about installing dependencies and how they are used by Nexus. -### c. Legacy Installation Instructions +### c. Manual Installation Instructions (via PYTHONPATH) All that should be needed to get Nexus working on your system is to add the path to its library files to the PYTHONPATH environment variable. @@ -97,16 +97,14 @@ The executables packaged with Nexus can be used once they are added to the PATH ```bash export PATH=/your/path/to/nexus/bin/:$PATH ``` -Both of these steps can alternately be performed by the installer packaged with Nexus. To use it, simply type the following at the command line: +Both of these steps can alternately be performed by the installer packaged with Nexus. To use it, simply type the following at the command line (shown for bash): ```bash -> /your/path/to/nexus/install +> /your/path/to/nexus/manual_install ~/.bashrc ``` Check the end of your `.bashrc` (or equivalent) to make sure the `$PATH` and `$PYTHONPATH` variables have been set properly. -If you want the binaries to be copied to a location outside the downloaded Nexus distribution, then just provide that as a path to the installer: -```bash -> /your/path/to/nexus/install /some/other/location -``` +Note that this installation route will take precedence over existing pip, uv, or other manual installations. This can be useful when downloading a recently updated version of Nexus for a bugfix, etc. + ## 3) Summary of important library files diff --git a/nexus/docs/code-style.rst b/nexus/docs/code-style.rst index ddc3c4740d..968c5e48df 100644 --- a/nexus/docs/code-style.rst +++ b/nexus/docs/code-style.rst @@ -407,3 +407,36 @@ For example, all ``generate_*`` functions should have user documentation, but sa If functionality includes operations commonly used by materials/chemical scientists, e.g. structure manipulation, adding documentation to the manual is also encouraged. +.. _uv_lock: + +The ``uv.lock`` file +-------------------- + +A recent addition to Nexus is a lockfile generated by ``uv``. This is an automatically generated file that provides a set of exact versions for anyone looking to use a reproducible Python environment, most commonly for testing and development. + +To sync your ``uv`` virtual environment to this file, you can simply run + +.. code-block:: + + uv sync + +To get all of the dependencies, you can run + +.. code-block:: + + uv sync --all-groups --all-extras + +which will install all of the optional dependencies for Nexus. + +Updating the lockfile +^^^^^^^^^^^^^^^^^^^^^ + +Updating the ``uv.lock`` file should only be done when there has been a bump in the Nexus version or if a dependency has been added/removed from Nexus. + +To update the ``uv.lock`` file, run + +.. code-block:: + + uv lock --upgrade + +which will automatically determine the correct versions of each package for each version of Python that is supported. \ No newline at end of file diff --git a/nexus/docs/examples.rst b/nexus/docs/examples.rst index b3fc3dd98e..908a2f2fdd 100644 --- a/nexus/docs/examples.rst +++ b/nexus/docs/examples.rst @@ -2012,4 +2012,29 @@ tool into Nexus workflows, as long as the tool can read input files and produce output files that can be tracked for completion status. For templating input files, ``input_template`` function is based on the standard Python ``string.Template`` class, hence uses ``$`` as the default delimiter. If users want to use a different delimiter, -that is more suitable for their code syntax, they can develop their own template class. \ No newline at end of file +that is more suitable for their code syntax, they can develop their own template class. + + + + +.. _dynamic-workflows: + + +Examples for Features Under Active Development: Dynamic Workflows +----------------------------------------------------------------- + +The files for these examples are found in: + +.. code:: rest + + /your_download_path/nexus/nexus/examples/dynamic_workflows + +This feature allows the development of algorithms composed of many simulation runs, a simple example being convergence of key parameters such as a planewave energy cutoff for DFT. Dynamic workflows are composed and run directly in full native Python, replacing the static graph-type execution typical of Nexus prior to this feature. + +Two early examples are provided: + +1. A basic demonstration of how dependencies are processed. +2. A sequence of planewave energy cutoff and k-poing grid size based on a total energy tolerance. + +See the ``README.rst`` file in the directory noted above and the descriptions at the top of the example `.py` files. + diff --git a/nexus/docs/installation.rst b/nexus/docs/installation.rst index b299667ee8..7c01eb8bc6 100644 --- a/nexus/docs/installation.rst +++ b/nexus/docs/installation.rst @@ -186,7 +186,7 @@ Installing Python dependencies When manually installing Nexus, you must also install the Python dependencies. The ``numpy`` module must be installed for Nexus to function at a basic level. To realize the full range of functionality available, it is recommended that the ``scipy``, -``matplotlib``, ``h5py``, ``pydot``, ``spglib``, ``pycifrw``, ``cif2cell`` and ``seekpath`` modules be installed as well. In +``matplotlib``, ``h5py``, ``pydot``, ``spglib``, ``pycifrw``, ``cif2cell``, ``seekpath``, and ``pytest`` modules be installed as well. In supercomputing environments, most of these packages will *not* be available via system modules due to their specialized nature; you will need to install them via ``pip``, ``uv``, or individual manual installation. @@ -203,21 +203,20 @@ You can perform a user level installation via ``pip``. If using ``uv``, prepend pip3 install --user PyCifRW pip3 install --user cif2cell pip3 install --user seekpath + pip3 install --user pytest .. note:: ``PyCifRW`` is a dependency of ``cif2cell``, thus if you install ``cif2cell`` you will already have ``PyCifRW`` installed as well. While Nexus does not have strict version requirements, most recent dependency versions that have been tested and are known to work -can be found at ``qmcpack/nexus/requirements.txt``. These specific library versions can be installed using the following command: +can be found at ``qmcpack/nexus/pyproject.toml``. These specific library versions can be installed using the following command: .. code-block:: bash - pip3 install --user -r requirements.txt - -``qmcpack/nexus/requirements_minimal.txt`` can be used similarly but only contains a recently tested version of ``numpy``. + pip3 install --user -r pyproject.toml .. note:: - Additionally, for users of ``uv``, the project's ``pyproject.toml`` can be used to install dependencies in a similar fashion: ``uv pip install -r pyproject.toml``. + Additionally, for users of ``uv``, the project's ``uv.lock`` file can be used to install the exact versions of dependencies that Nexus is tested with using the command ``uv sync --all-extras --locked``. If you are making a system-wide installation, on a Linux-based system, such as Ubuntu or Fedora, installation of these Python modules can be accomplished using the distribution's package manager (e.g. ``apt`` for Debian-based systems like Ubuntu). For @@ -229,6 +228,7 @@ example, here is how one may install some of the packages with ``apt``: sudo apt install python3-scipy python3-matplotlib python3-h5py sudo apt install python3-pydot sudo apt install python3-pip + sudo apt install python3-pytest Simple substitutions will be needed on distributions with different package managers (e.g. ``dnf``). Note that the most specialist packages may not be available via this route. @@ -259,6 +259,9 @@ The purpose of each library is described below: ``seekpath`` Used to find high symmetry lines in reciprocal space for excited state calculations with QMCPACK. +``pytest`` + Used to test your Nexus installation. + Of course, to run full calculations, the simulation codes and converters involved must be installed as well. These include a patched version of Quantum ESPRESSO (``pw.x``, ``pw2qmcpack.x``, optionally ``pw2casino.x``), QMCPACK (``qmcpack``, ``qmcpack_complex``, ``convert4qmc``, ``wfconvert``, ``ppconvert``), VASP, and/or GAMESS. Complete coverage of this task is beyond the scope of the @@ -267,163 +270,90 @@ current document, but please see :ref:`install-code`. Testing your Nexus installation ------------------------------- -Nexus is packaged with an extensive suite of tests that can be run with -either the ``nxs-test`` executable packaged with Nexus or with -``pytest``. If you have installed Nexus, the ``nxs-test`` tool should be -in your ``PATH``. Installation is successful if all tests pass: - -:: - - > nxs-test - - 1/67 versions................................ Passed 0.01 sec - 2/67 required_dependencies................... Passed 0.00 sec - 3/67 nexus_base.............................. Passed 0.00 sec - 4/67 nexus_imports........................... Passed 0.02 sec - 5/67 testing................................. Passed 0.03 sec - 6/67 execute................................. Passed 0.00 sec - 7/67 memory.................................. Passed 0.00 sec - 8/67 generic................................. Passed 0.01 sec - 9/67 developer............................... Passed 0.00 sec - 10/67 unit_converter.......................... Passed 0.00 sec - 11/67 periodic_table.......................... Passed 0.00 sec - 12/67 numerics................................ Passed 0.02 sec - 13/67 grid_functions.......................... Passed 0.70 sec - 14/67 fileio.................................. Passed 0.02 sec - 15/67 hdfreader............................... Passed 0.00 sec - 16/67 xmlreader............................... Passed 0.00 sec - 17/67 structure............................... Passed 0.50 sec - 18/67 physical_system......................... Passed 0.03 sec - 19/67 basisset................................ Passed 0.02 sec - 20/67 pseudopotential......................... Passed 0.29 sec - 21/67 machines................................ Passed 0.98 sec - 22/67 simulation_module....................... Passed 0.34 sec - 23/67 bundle.................................. Passed 0.00 sec - 24/67 project_manager......................... Passed 2.90 sec - 25/67 settings................................ Passed 0.00 sec - 26/67 vasp_input.............................. Passed 0.01 sec - 27/67 pwscf_input............................. Passed 0.01 sec - 28/67 pwscf_postprocessor_input............... Passed 0.00 sec - 29/67 gamess_input............................ Passed 0.00 sec - 30/67 pyscf_input............................. Passed 0.01 sec - 31/67 quantum_package_input................... Passed 0.06 sec - 32/67 rmg_input............................... Passed 0.06 sec - 33/67 qmcpack_converter_input................. Passed 0.00 sec - 34/67 qmcpack_input........................... Passed 0.06 sec - 35/67 vasp_analyzer........................... Passed 0.02 sec - 36/67 pwscf_analyzer.......................... Passed 0.16 sec - 37/67 pwscf_postprocessor_analyzers........... Passed 0.00 sec - 38/67 gamess_analyzer......................... Passed 0.00 sec - 39/67 pyscf_analyzer.......................... Passed 0.00 sec - 40/67 quantum_package_analyzer................ Passed 0.00 sec - 41/67 rmg_analyzer............................ Passed 0.00 sec - 42/67 qmcpack_converter_analyzers............. Passed 0.00 sec - 43/67 qmcpack_analyzer........................ Passed 0.23 sec - 44/67 vasp_simulation......................... Passed 0.02 sec - 45/67 pwscf_simulation........................ Passed 0.01 sec - 46/67 gamess_simulation....................... Passed 0.00 sec - 47/67 pyscf_simulation........................ Passed 0.00 sec - 48/67 quantum_package_simulation.............. Passed 0.00 sec - 49/67 rmg_simulation.......................... Passed 0.00 sec - 50/67 pwscf_postprocessor_simulations......... Passed 0.00 sec - 51/67 qmcpack_converter_simulations........... Passed 0.01 sec - 52/67 qmcpack_simulation...................... Passed 0.20 sec - 53/67 observables............................. Passed 0.00 sec - 54/67 nxs_redo................................ Passed 0.92 sec - 55/67 nxs_sim................................. Passed 2.03 sec - 56/67 qmca.................................... Passed 2.90 sec - 57/67 qmc_fit................................. Passed 0.00 sec - 58/67 qdens................................... Passed 0.00 sec - 59/67 qdens_radial............................ Passed 0.00 sec - 60/67 example_gamess_H2O...................... Passed 1.01 sec - 61/67 example_pwscf_relax_Ge_T................ Passed 0.47 sec - 62/67 example_qmcpack_H2O..................... Passed 0.54 sec - 63/67 example_qmcpack_LiH..................... Passed 0.54 sec - 64/67 example_qmcpack_c20..................... Passed 0.52 sec - 65/67 example_qmcpack_diamond................. Passed 0.73 sec - 66/67 example_qmcpack_graphene................ Passed 0.59 sec - 67/67 example_qmcpack_oxygen_dimer............ Passed 0.50 sec - - 100% tests passed, 0 tests failed out of 67 - - Total test time = 17.54 sec - -Only portions of Nexus consistent with your Python installed Python libraries will be tested. - -To run the tests with ``pytest`` (``pip install --user pytest``), enter the unit test directory and simply invoke the ``pytest`` command: +Nexus's testing suite is designed to run with ``pytest >= 6.2.4``. +We make optional use of the ``pytest-cov`` and ``pytest-order`` plugins. They will not cause test failure if they are not installed. + +If you have installed Nexus through ``pip`` or ``uv``, you can run the Nexus testing suite through the ``nxs-test`` command line script, which will automatically run the tests for the version of Nexus installed in your Python environment. + +If you have cloned ``qmcpack`` and are using the version of Nexus that comes with it, or if you are working on developing Nexus, you can enter the ``nexus`` directory and simply invoke the ``pytest`` command: .. code-block:: bash - > cd nexus/tests/unit/ + > cd nexus/ > pytest =========================== test session starts ============================ - platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 - rootdir: qmcpack/nexus + platform linux -- Python 3.14.4, pytest-9.0.3, pluggy-1.6.0 + rootdir: /home/brock/Documents/github/qmcpack/nexus configfile: pyproject.toml - plugins: cov-7.0.0 - collected 393 items + plugins: order-1.3.0, cov-7.1.0 + collected 397 items - test_basisset.py ..... [ 1%] - test_bundle.py .. [ 1%] - test_developer.py ... [ 2%] + test_versions.py ..... [ 1%] + test_required_dependencies.py . [ 1%] + test_nexus_imports.py . [ 1%] + test_testing.py .... [ 2%] test_execute.py .. [ 3%] - test_fileio.py ....... [ 4%] - test_gamess_analyzer.py ... [ 5%] - test_gamess_input.py ....... [ 7%] - test_gamess_simulation.py ...... [ 8%] - test_generic.py ... [ 9%] - test_grid_functions.py ...................... [ 15%] - test_hdfreader.py .. [ 15%] - test_machines.py ...................... [ 21%] - test_memory.py .... [ 22%] - test_nexus_base.py ..... [ 23%] - test_nexus_imports.py . [ 23%] - test_numerics.py ............... [ 27%] - test_nxs_redo.py . [ 27%] - test_nxs_sim.py . [ 28%] - test_observables.py .. [ 28%] - test_optional_dependencies.py ....... [ 30%] - test_periodic_table.py ... [ 31%] - test_physical_system.py ....... [ 33%] - test_project_manager.py ........... [ 35%] - test_pseudopotential.py ...... [ 37%] - test_pwscf_analyzer.py ... [ 38%] - test_pwscf_input.py ... [ 38%] - test_pwscf_postprocessor_analyzers.py ... [ 39%] - test_pwscf_postprocessor_input.py ..... [ 40%] - test_pwscf_postprocessor_simulations.py ...... [ 42%] - test_pwscf_simulation.py ...... [ 44%] - test_pyscf_analyzer.py .. [ 44%] - test_pyscf_input.py .... [ 45%] - test_pyscf_simulation.py ..... [ 46%] - test_qdens.py . [ 47%] - test_qdens_radial.py . [ 47%] - test_qmc_fit.py . [ 47%] - test_qmca.py ........... [ 50%] - test_qmcpack_analyzer.py ...... [ 51%] - test_qmcpack_converter_analyzers.py .... [ 52%] - test_qmcpack_converter_input.py .......... [ 55%] - test_qmcpack_converter_simulations.py .................. [ 60%] - test_qmcpack_input.py ............. [ 63%] - test_qmcpack_simulation.py ...... [ 64%] - test_quantum_package_analyzer.py .. [ 65%] - test_quantum_package_input.py .... [ 66%] - test_quantum_package_simulation.py ...... [ 67%] - test_required_dependencies.py . [ 68%] - test_rmg_analyzer.py .. [ 68%] - test_rmg_input.py ...... [ 70%] - test_rmg_simulation.py .. [ 70%] - test_settings.py .. [ 71%] - test_simulation_module.py ......................................... [ 81%] - test_structure.py ................................... [ 90%] - test_testing.py .... [ 91%] - test_unit_converter.py ... [ 92%] - test_vasp_analyzer.py .... [ 93%] - test_vasp_input.py ....... [ 95%] - test_vasp_simulation.py ....... [ 96%] - test_versions.py ..... [ 98%] - test_xmlreader.py ....... [100%] - + test_memory.py .... [ 4%] + test_generic.py ... [ 5%] + test_developer.py ... [ 5%] + test_unit_converter.py ... [ 6%] + test_periodic_table.py ...... [ 8%] + test_numerics.py ............... [ 11%] + test_grid_functions.py ...................... [ 17%] + test_fileio.py ....... [ 19%] + test_hdfreader.py .. [ 19%] + test_xmlreader.py ....... [ 21%] + test_structure.py ................................... [ 30%] + test_physical_system.py ....... [ 31%] + test_basisset.py ..... [ 33%] + test_pseudopotential.py ...... [ 34%] + test_nexus_base.py ..... [ 36%] + test_machines.py ...................... [ 41%] + test_simulation_module.py ......................................... [ 51%] + test_bundle.py .. [ 52%] + test_project_manager.py ........... [ 55%] + test_settings.py .. [ 55%] + test_pwscf_input.py ... [ 56%] + test_pwscf_postprocessor_input.py ..... [ 57%] + test_gamess_input.py ....... [ 59%] + test_pyscf_input.py .... [ 60%] + test_quantum_package_input.py .... [ 61%] + test_rmg_input.py ...... [ 62%] + test_qmcpack_converter_input.py .......... [ 65%] + test_qmcpack_input.py ............. [ 68%] + test_vasp_analyzer.py .... [ 69%] + test_vasp_input.py ....... [ 71%] + test_pwscf_analyzer.py ... [ 72%] + test_pwscf_postprocessor_analyzers.py ... [ 73%] + test_gamess_analyzer.py ... [ 73%] + test_pyscf_analyzer.py .. [ 74%] + test_quantum_package_analyzer.py .. [ 74%] + test_rmg_analyzer.py .. [ 75%] + test_qmcpack_converter_analyzers.py .... [ 76%] + test_qmcpack_analyzer.py ...... [ 77%] + test_vasp_simulation.py ....... [ 79%] + test_pwscf_simulation.py ...... [ 81%] + test_gamess_simulation.py ...... [ 82%] + test_pyscf_simulation.py ..... [ 83%] + test_quantum_package_simulation.py ...... [ 85%] + test_rmg_simulation.py .. [ 85%] + test_pwscf_postprocessor_simulations.py ...... [ 87%] + test_qmcpack_converter_simulations.py .................. [ 91%] + test_qmcpack_simulation.py ...... [ 93%] + test_observables.py .. [ 93%] + test_nxs_redo.py . [ 94%] + test_nxs_sim.py . [ 94%] + test_qmc_fit.py . [ 94%] + test_qdens.py . [ 94%] + test_qdens_radial.py . [ 95%] + test_qmca.py ........... [ 97%] + test_user_examples_alt.py ........ [100%] + + ==================== 397 passed, 43 warnings in 58.38s ===================== + +Some tests may be skipped depending on what dependencies you have available, or if they are marked to be skipped. +Additionally, you may see a number of warnings appear; some of these may be warnings about Nexus, but it is likely that the majority arise from a Nexus dependency. +In general it is safe to ignore these warnings as they likely do not affect the functionality of Nexus. Developer Topics ---------------- @@ -435,74 +365,95 @@ Code coverage can be assessed by using the ``pytest-cov`` plugin (``pip install .. code-block:: bash - >cd nexus - >pytest-cov --cov=nexus + > cd nexus + > pytest --cov=nexus ... - >coverage report - - nexus/basisset.py 631 375 41% - nexus/bundle.py 191 68 64% - nexus/debug.py 12 6 50% - nexus/developer.py 261 97 63% - nexus/execute.py 13 2 85% - nexus/fileio.py 957 373 61% - nexus/gamess.py 102 20 80% - nexus/gamess_analyzer.py 305 149 51% - nexus/gamess_input.py 597 167 72% - nexus/generic.py 817 173 79% - nexus/grid_functions.py 1192 435 64% - nexus/hdfreader.py 215 61 72% - nexus/machines.py 1887 463 75% - nexus/memory.py 60 7 88% - nexus/nexus.py 297 140 53% - nexus/nexus_base.py 74 11 85% - nexus/numerics.py 756 372 51% - nexus/periodic_table.py 1505 24 98% - nexus/physical_system.py 427 73 83% - nexus/plotting.py 22 7 68% - nexus/project_manager.py 234 37 84% - nexus/pseudopotential.py 1225 559 54% - nexus/pwscf.py 198 73 63% - nexus/pwscf_analyzer.py 634 316 50% - nexus/pwscf_data_reader.py 132 120 9% - nexus/pwscf_input.py 1261 563 55% - nexus/pwscf_postprocessors.py 434 56 87% - nexus/pyscf_analyzer.py 3 0 100% - nexus/pyscf_input.py 181 26 86% - nexus/pyscf_sim.py 57 8 86% - nexus/qmcpack.py 344 146 58% - nexus/qmcpack_analyzer.py 457 104 77% - nexus/qmcpack_analyzer_base.py 327 137 58% - nexus/qmcpack_converters.py 507 83 84% - nexus/qmcpack_input.py 3605 1439 60% - nexus/qmcpack_method_analyzers.py 198 64 68% - nexus/qmcpack_property_analyzers.py 205 97 53% - nexus/qmcpack_quantity_analyzers.py 2070 1789 14% - nexus/qmcpack_result_analyzers.py 285 142 50% - nexus/quantum_package.py 253 141 44% - nexus/quantum_package_analyzer.py 3 0 100% - nexus/quantum_package_input.py 338 164 51% - nexus/simulation.py 1019 169 83% - nexus/structure.py 3830 2055 46% - nexus/superstring.py 311 199 36% - nexus/testing.py 409 67 84% - nexus/unit_converter.py 121 4 97% - nexus/vasp.py 94 15 84% - nexus/vasp_analyzer.py 548 73 87% - nexus/vasp_input.py 906 412 55% - nexus/versions.py 335 50 85% - nexus/xmlreader.py 260 54 79% - -The first column is the total number of statements, the second is the number not yet covered by the tests and the third is the percent covered. By averaging the third column, you can tell roughly what percent of Nexus is covered by testing. From the testing shown above, code coverage is at ~67.5%. + > coverage report + + Name Stmts Miss Cover + --------------------------------------------------------- + nexus/__init__.py 305 99 68% + nexus/_bin.py 25 25 0% + nexus/basisset.py 645 387 40% + nexus/bin/nxs-redo 90 31 66% + nexus/bin/nxs-sim 148 62 58% + nexus/bin/qdens 846 438 48% + nexus/bin/qdens-radial 282 84 70% + nexus/bin/qmc-fit 380 186 51% + nexus/bin/qmca 887 326 63% + nexus/bundle.py 191 68 64% + nexus/debug.py 12 6 50% + nexus/developer.py 265 88 67% + nexus/execute.py 14 2 86% + nexus/fileio.py 1019 407 60% + nexus/gamess.py 151 62 59% + nexus/gamess_analyzer.py 306 131 57% + nexus/gamess_input.py 593 167 72% + nexus/gaussian_process.py 943 943 0% + nexus/generic.py 842 184 78% + nexus/grid_functions.py 1641 689 58% + nexus/hdfreader.py 205 59 71% + nexus/machines.py 2593 705 73% + nexus/memory.py 60 7 88% + nexus/nexus_base.py 76 10 87% + nexus/nexus_version.py 2 0 100% + nexus/numerics.py 904 461 49% + nexus/numpy_extensions.py 7 1 86% + nexus/observables.py 891 492 45% + nexus/periodic_table.py 301 4 99% + nexus/physical_system.py 429 67 84% + nexus/project_manager.py 233 37 84% + nexus/pseudopotential.py 1675 1003 40% + nexus/pwscf.py 216 86 60% + nexus/pwscf_analyzer.py 653 283 57% + nexus/pwscf_data_reader.py 130 120 8% + nexus/pwscf_input.py 1387 494 64% + nexus/pwscf_postprocessors.py 517 113 78% + nexus/pyscf_analyzer.py 3 0 100% + nexus/pyscf_input.py 285 44 85% + nexus/pyscf_sim.py 64 14 78% + nexus/qmcpack.py 1044 789 24% + nexus/qmcpack_analyzer.py 456 106 77% + nexus/qmcpack_analyzer_base.py 326 136 58% + nexus/qmcpack_converters.py 673 215 68% + nexus/qmcpack_input.py 4440 1906 57% + nexus/qmcpack_method_analyzers.py 196 64 67% + nexus/qmcpack_property_analyzers.py 204 100 51% + nexus/qmcpack_quantity_analyzers.py 2095 1818 13% + nexus/qmcpack_result_analyzers.py 289 144 50% + nexus/quantum_package.py 253 141 44% + nexus/quantum_package_analyzer.py 3 0 100% + nexus/quantum_package_input.py 337 164 51% + nexus/rmg.py 33 10 70% + nexus/rmg_analyzer.py 293 265 10% + nexus/rmg_input.py 682 148 78% + nexus/simulation.py 1055 185 82% + nexus/structure.py 4121 2099 49% + nexus/template_simulation.py 64 64 0% + nexus/testing.py 451 87 81% + nexus/unit_converter.py 120 2 98% + nexus/utilities.py 56 16 71% + nexus/vasp.py 93 15 84% + nexus/vasp_analyzer.py 547 73 87% + nexus/vasp_input.py 958 454 53% + nexus/versions.py 348 52 85% + nexus/xmlreader.py 298 53 82% + --------------------------------------------------------- + TOTAL 39651 17491 56% + +The first column is the total number of statements, the second is the number not yet covered by the tests and the third is the percent covered. At the bottom is the sum total of all covered lines, all missed lines, and the average coverage percent. To obtain an annotated view of the statements in the source that are not yet covered, run: .. code-block:: bash - > pytest --cov=nexus --cov-report html + > pytest --cov=nexus --cov-report=html -Open ``htmlcov/index.html`` in a browser to view the report. More information regarding the ``coverage`` tool can be found at https://coverage.readthedocs.io/en/v4.5.x/. +Open ``htmlcov/index.html`` in a browser to view the report. More information regarding the ``coverage`` tool can be found at https://coverage.readthedocs.io/en/latest/. +.. note:: + If you are planning on adding a new feature to Nexus, please add a test for the new feature. + Additionally, if you are planning on changing an existing Nexus feature, you must ensure that you either write a test for it, update the existing test, or ensure that your changes do not fail the existing test; your changes will not get merged otherwise! Creating Portable Nexus Builds ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -512,7 +463,7 @@ With recent changes to Nexus's structure, it has become possible to build binary Wheel files are compressed ZIP-format archives that are officially recommended by the `Python Packaging Authority (PyPA) `__ and can be built by anyone with the right tools. To get started, you must have a tool capable of building a project; here we will be describing how to use ``uv`` for building distributions. First, start by cloning the QMCPACK GitHub repository and navigating to the ``nexus`` directory. -Next, though this step is not always necessary, it is recommended to run ``nxs-test`` to ensure you have a clean Nexus installation. +Next, though this step is not always necessary, it is recommended to run ``pytest`` to ensure you have a clean Nexus installation. Finally, you can run the command ``uv build``, which will create a ``qmcpack/nexus/dist`` directory, and build two files to go in it. The first is a tar archive of the source code, and the second is a ``.whl`` file. This wheel file is then usable as an installation source, which you can access via the following command (if you are in a virtual environment): diff --git a/nexus/docs/overview.rst b/nexus/docs/overview.rst index 885f126fb8..0d8a717210 100644 --- a/nexus/docs/overview.rst +++ b/nexus/docs/overview.rst @@ -31,7 +31,7 @@ optimization, Variational Monte Carlo (VMC), and Diffusion Monte Carlo (DMC) in periodic or open boundary conditions), automated job management on workstations (by acting as a virtual queue) and clusters/supercomputers including handling of dependencies -between calculations and job bundling, and extraction of results from +between calculations and job bundling, and extraction of results from completed calculations for analysis. The integration of these capabilities permits the user to focus on the high-level tasks of problem formulation and interpretation of the results without (in principle) becoming too involved @@ -50,3 +50,8 @@ with if/else logic and for loops. Knowledge of the Python programming language is helpful to perform complex calculations, but not essential for use of Nexus. Starting from working "input files" such as those covered on the :ref:`examples` page is a good way to proceed. + +Citing Nexus +------------ + +The citation paper for Nexus is J. T. Krogel, Computer Physics Communications **198** 154 (2016), https://doi.org/10.1016/j.cpc.2015.08.012 . diff --git a/nexus/docs/requirements.txt b/nexus/docs/requirements.txt index 976e4e1bdb..50ce02358a 100644 --- a/nexus/docs/requirements.txt +++ b/nexus/docs/requirements.txt @@ -12,13 +12,13 @@ certifi==2026.1.4 # via requests charset-normalizer==3.4.4 # via requests -docutils==0.22.4 +docutils==0.21.2 # via # pybtex-docutils # sphinx # sphinx-rtd-theme # sphinxcontrib-bibtex -idna==3.11 +idna==3.15 # via requests imagesize==1.4.1 # via sphinx @@ -36,28 +36,26 @@ pybtex==0.25.1 # sphinxcontrib-bibtex pybtex-docutils==1.0.3 # via sphinxcontrib-bibtex -pygments==2.19.2 +pygments==2.20.0 # via sphinx pyyaml==6.0.3 # via pybtex requests==2.33.0 # via sphinx -roman-numerals==4.1.0 - # via sphinx snowballstemmer==3.0.1 # via sphinx -sphinx==9.1.0 +sphinx==8.1.3 # via - # -r requirements.in + # -r docs/requirements.in # sphinx-rtd-theme # sphinxcontrib-bibtex # sphinxcontrib-jquery sphinx-rtd-theme==3.1.0 - # via -r requirements.in + # via -r docs/requirements.in sphinxcontrib-applehelp==2.0.0 # via sphinx sphinxcontrib-bibtex==2.6.5 - # via -r requirements.in + # via -r docs/requirements.in sphinxcontrib-devhelp==2.0.0 # via sphinx sphinxcontrib-htmlhelp==2.1.0 @@ -70,5 +68,7 @@ sphinxcontrib-qthelp==2.0.0 # via sphinx sphinxcontrib-serializinghtml==2.0.0 # via sphinx -urllib3==2.6.3 +tomli==2.4.1 + # via sphinx +urllib3==2.7.0 # via requests diff --git a/nexus/manual_install b/nexus/manual_install new file mode 100755 index 0000000000..41307fa1da --- /dev/null +++ b/nexus/manual_install @@ -0,0 +1,151 @@ +#! /usr/bin/env python3 + +""" +Users can execute this script to install Nexus in a simple way. + +This script performs a path-based installation of Nexus by +updating the PATH and PYTHONPATH environment variables in a +user's .bashrc file (or similar for other shells): + + export PATH=/your/path/to/nexus/nexus/bin:$PATH + export PYTHONPATH=/your/path/to/nexus:$PYTHONPATH + +Text similar to this is added directly to the end of the rc file. + +In this example, this script (manual_install) resides at: + + /your/path/to/nexus/manual_install + +Since these path environment variables are added to a user's +shell configuration file, they will have persistent access to +Nexus' binaries and be able to create operational Nexus workflow +scripts each time they login to their machine. + +See README.md section 2 for details on the pip, uv, and manual +installation routes. +""" + + +import os +import sys +import shutil + +#=======# +# setup # +#=======# + +# find paths to install script and source directory +installer = os.path.realpath(__file__) +source_dir = os.path.dirname(installer) +lib_dir = source_dir +bin_dir = os.path.join(source_dir,'nexus/bin') + +# function to report errors +def error(msg): + print('\nmanual_install error: '+msg+'\n') + sys.exit(1) + + +#================# +# main execution # +#================# + +# extract force flag +args = sys.argv[1:] +force = False +if '-f' in args: + args.pop(args.index('-f')) + force = True + +# determine config file and shell from user-provided rc file path +if len(args)==0 or len(args) > 2: + error('\ninstall takes the path to an rc file and an optional shell name.' + f'\n\nFor example: {sys.argv[0]} ~/.bashrc' + f'\nOr : {sys.argv[0]} ~/.profile bash' + '\n\nSupported shells are: bash, zsh, tcsh, csh, and ksh.') + +rc_file = os.path.expanduser(args[0]) +if not os.path.exists(rc_file): + error('specified config (rc) file "{0}" does not exist'.format(rc_file)) + +rc_name = os.path.basename(rc_file) + +def infer_shell_from_rc(rc_name): + if 'bash' in rc_name: + return 'bash' + if 'zsh' in rc_name: + return 'zsh' + if 'tcsh' in rc_name: + return 'tcsh' + if 'csh' in rc_name: + return 'csh' + if 'ksh' in rc_name: + return 'ksh' + error('could not infer shell type from rc file name "{0}"'.format(rc_name)) + +if len(args) == 2: + # shell explicitly provided by user + shell = args[1] +else: + # infer shell from rc file name + shell = infer_shell_from_rc(rc_name) + +# get format for setting env variables in shell +set_env_formats = dict( + ksh = 'export {0}={1}\n', + csh = 'setenv {0} {1}\n', + tcsh = 'setenv {0} {1}\n', + bash = 'export {0}={1}\n', + zsh = 'export {0}={1}\n', + ) +if shell not in set_env_formats: + error('shell "{0}" is not supported; must be one of: {1}'.format(shell,', '.join(sorted(set_env_formats.keys())))) +set_env_fmt = set_env_formats[shell] + +header_start = '### added by Nexus ' +header = '### added by Nexus installer ###' +footer = '### end Nexus additions ###' +paths = set_env_fmt.format('PATH',bin_dir+':$PATH') +paths += set_env_fmt.format('PYTHONPATH',lib_dir+':$PYTHONPATH') + +path_install = header+'\n' +path_install += paths +path_install += footer+'\n' + +if not force: + print('\nThe following will be appended to file "{}"'.format(rc_file)) + print() + print(path_install) + print('Note: this installation will override any prior ones (e.g. via pip/uv).') + try: + import nexus + print('\n A prior Nexus installation exists at:\n {}\n'.format(os.path.split(nexus.__file__)[0])) + except: + print() + pass + response = input('Do you want to proceed? [y/n]') + if response.lower() not in ('y','yes'): + print('\nNexus installation aborted.') + print('\nNo changes have been made to file "{}"\n'.format(rc_file)) + sys.exit(0) + +# add lib path to PYTHONPATH in config file +shutil.copy2(rc_file,rc_file+'-nexus.bak') +with open(rc_file,'r') as f: + rc_contents = f.read() +if header_start in rc_contents and footer in rc_contents: + header_loc = rc_contents.find(header_start) + footer_loc = rc_contents.find(footer) + before_header = rc_contents[:header_loc] + after_footer = rc_contents[footer_loc+len(footer):] + rc_contents = before_header + after_footer +rc_contents = rc_contents.rstrip()+'\n\n\n' +rc_contents += path_install +f = open(rc_file,'w') +f.write(rc_contents) +f.close() + +print('\nNexus installation complete.') +print(f'\nExecute "source {rc_file}" to make Nexus available in the current session.') +print(f'\nIf you later wish to remove this installation, remove the text headed by "added by Nexus" from {rc_file}.\n') + diff --git a/nexus/nexus/__init__.py b/nexus/nexus/__init__.py index 3d5ea94c47..163c7a5a22 100644 --- a/nexus/nexus/__init__.py +++ b/nexus/nexus/__init__.py @@ -22,17 +22,20 @@ #====================================================================# import os +import sys +import importlib +from importlib.metadata import PackageNotFoundError from .nexus_version import nexus_version -from .versions import current_versions, policy_versions, check_versions from .generic import generic_settings from .developer import obj, error, log from .debug import ci +from .utilities import path_string from .nexus_base import NexusCore, nexus_core, nexus_noncore, nexus_core_noncore, restore_nexus_core_defaults, nexus_core_defaults from .machines import Job, job, Machine, Supercomputer, get_machine -from .simulation import generate_simulation, input_template, multi_input_template, generate_template_input, generate_multi_template_input, graph_sims -from .project_manager import ProjectManager +from .simulation import generate_simulation, input_template, multi_input_template, generate_template_input, generate_multi_template_input, graph_sims, DynamicProcess +from .project_manager import ProjectManager, DynamicWorkflowManager, workflow_manager from .structure import Structure, generate_structure, generate_cell, read_structure from .physical_system import PhysicalSystem, generate_physical_system @@ -85,6 +88,7 @@ def run_project(*args,**kwargs): return pm #end def run_project + # test needed # read input function # place here for now as it depends on all other input functions @@ -127,7 +131,7 @@ class Settings(NexusCore): pseudo_dir sleep local_directory remote_directory monitor skip_submit load_images stages verbose debug trace progress_tty - graph_sims command_line + graph_sims command_line dynamic '''.split()) core_process_vars = set(''' @@ -191,6 +195,17 @@ def error(self,message,header='settings',exit=True,trace=True): # sets up Nexus core class behavior and passes information to broader class structure def __call__(self,**kwargs): kwargs = obj(**kwargs) + # Ensure no pathlib.Path objects are stored + core_path_vars = ( + "runs", + "results", + "pseudo_dir", + "local_directory", + "remote_directory", + ) + for var in core_path_vars: + if var in kwargs: + kwargs[var] = path_string(kwargs[var]) # guard against invalid settings not_allowed = set(kwargs.keys()) - Settings.allowed_vars @@ -212,15 +227,82 @@ def __call__(self,**kwargs): NexusCore.write_splash() # print version information + self.log("Checking current machine for Nexus dependencies...\n") + pkg_sort = { + "numpy": 0, + "scipy": 1, + "h5py": 2, + "matplotlib": 3, + "spglib": 4, + "cif2cell": 5, + "pydot": 6, + "seekpath": 7, + } + try: - from .versions import versions - if versions is not None: - err,s,serr = versions.check(write=False,full=True) - self.log(s) - #end if - except Exception: - pass - #end try + nxs_requirements = importlib.metadata.requires("nexus") + nxs_deps = {} + for req in nxs_requirements: + pkg_name = req.split("=")[0][:-1] + pkg_ver_min = req.split(">=")[-1] + if ";" in pkg_ver_min: + pkg_ver_min = pkg_ver_min.split(";")[0] + status = "optional" + else: + status = "required" + + nxs_deps[pkg_name] = {"min_ver": pkg_ver_min, "status": status} + except PackageNotFoundError: + nxs_deps = { + "numpy": {"min_ver": "x.x.x", "status": "required"}, + "scipy": {"min_ver": "x.x.x", "status": "optional"}, + "h5py": {"min_ver": "x.x.x", "status": "optional"}, + "matplotlib": {"min_ver": "x.x.x", "status": "optional"}, + "spglib": {"min_ver": "x.x.x", "status": "optional"}, + "cif2cell": {"min_ver": "x.x.x", "status": "optional"}, + "pydot": {"min_ver": "x.x.x", "status": "optional"}, + "seekpath": {"min_ver": "x.x.x", "status": "optional"}, + } + + nxs_deps = {k:v for k, v in sorted(nxs_deps.items(), key=lambda x: pkg_sort.get(x[0], 1000))} + + available_pkgs = {} + for module in nxs_deps.keys(): + if importlib.util.find_spec(module) is not None: + available_pkgs[module] = importlib.metadata.version(module) + else: + available_pkgs[module] = "Unavailable" + + version_text = "" + + name_align = max([len(i) for i in nxs_deps.keys()]) + version_text += " Currently Available Nexus Dependencies:\n" + version_text += f" {'Python':<{name_align}} = {sys.version.split()[0]}\n" + for pkg_name, pkg_ver in available_pkgs.items(): + version_text += f" {pkg_name:<{name_align}} = {pkg_ver:<11} ({nxs_deps[pkg_name]['status']})\n" + + version_text += "\n" + version_text += " Recommended Nexus Dependencies:\n" + version_text += f" {'Python':<{name_align}} >= 3.10.0\n" + for pkg_name, pkg_info in nxs_deps.items(): + version_text += f" {pkg_name:<{name_align}} >= {pkg_info['min_ver']:<10} ({pkg_info['status']})\n" + + version_text += "\n" + missing_deps = set(nxs_deps) - set([i for i, a in available_pkgs.items() if a != "Unavailable"]) + if len(missing_deps) > 0: + version_text += " Required dependencies are met,\n" + version_text += " however some optional dependencies are missing.\n" + version_text += " Some features of Nexus may be unavailable.\n\n" + + version_text += " Missing dependencies:\n" + for missing in missing_deps: + version_text += f" - {missing} ({nxs_deps[pkg_name]['status']})\n" + else: + version_text += " All dependencies are present.\n" + + version_text += "\n" + + self.log(version_text) self.log('Applying user settings') @@ -530,9 +612,9 @@ def process_core_settings(self,kw): if 'file_locations' in kw: fl = kw.file_locations if isinstance(fl,str): - nexus_core.file_locations.extend([fl]) + nexus_core.file_locations.extend([path_string(fl)]) else: - nexus_core.file_locations.extend(list(fl)) + nexus_core.file_locations.extend([path_string(f) for f in fl]) #end if #end if if 'pseudo_dir' not in kw: diff --git a/nexus/nexus/basisset.py b/nexus/nexus/basisset.py index fda39dec83..29a22f987e 100644 --- a/nexus/nexus/basisset.py +++ b/nexus/nexus/basisset.py @@ -4,10 +4,12 @@ import os +from pathlib import Path import numpy as np -from .periodic_table import is_element +from .periodic_table import Elements from .developer import DevBase, obj, error, to_str, unavailable from .fileio import TextFile +from .utilities import path_string try: import matplotlib.pyplot as plt @@ -32,7 +34,7 @@ def __init__(self,*basissets): for bs in basissets: if isinstance(bs,BasisFile): bss.append(bs) - elif isinstance(bs,str): + elif isinstance(bs,(str, Path)): bsfiles.append(bs) else: self.error('expected BasisFile type or filepath, got '+str(type(bs)),exit=False) @@ -70,12 +72,13 @@ def readbs(self,*bsfiles): self.log('') self.log(' Basissets') for filepath in bsfiles: - self.log(' reading basis: '+filepath) - ext = filepath.split('.')[-1].lower() + filepath_str = str(filepath) + self.log(' reading basis: '+filepath_str) + ext = filepath_str.split('.')[-1].lower() if ext=='gms_bas' or ext=='bas': - bs = gamessBasisFile(filepath) + bs = gamessBasisFile(filepath_str) else: - bs = BasisFile(filepath) + bs = BasisFile(filepath_str) #end if bss.append(bs) #end for @@ -107,14 +110,15 @@ def __init__(self,filepath=None): self.filename = None self.location = None if filepath is not None: + filepath = path_string(filepath) self.filename = os.path.basename(filepath) - self.location = os.path.abspath(filepath) + self.location = os.path.realpath(filepath) elem_label = self.filename.split('.')[0] - is_elem,symbol = is_element(elem_label,symbol=True) + is_elem, elem = Elements.is_element(elem_label, return_element=True) if not is_elem: self.error('cannot determine element for basis file: {0}\nbasis file names must be prefixed by an atomic symbol or label\n(e.g. Si, Si1, etc)'.format(filepath)) #end if - self.element = symbol + self.element = elem.symbol self.element_label = elem_label #end if #end def __init__ @@ -125,8 +129,6 @@ def cleaned_text(self): #end class BasisFile - - class gaussBasisFile(BasisFile): angular_terms = 'spdfghiklmn' @@ -154,6 +156,7 @@ def read(self,filepath=None): #end if file = TextFile(filepath) self.read_file(file) + file.close() #end def read def read_file(self,file): @@ -162,7 +165,6 @@ def read_file(self,file): #end class gaussBasisFile - class gamessBasisFile(gaussBasisFile): def read_file(self,file): dstart = file.find('$DATA') @@ -204,11 +206,6 @@ def read_file(self,file): #end class gamessBasisFile - - - - - def process_gaussian_text(text,format,pp=True,basis=True,preserve_spacing=False): if format=='gamess' or format=='gaussian' or format=='atomscf': rawlines = text.splitlines() @@ -291,8 +288,6 @@ def process_gaussian_text(text,format,pp=True,basis=True,preserve_spacing=False) #end def process_gaussian_text - - class GaussianBasisSet(DevBase): lset_full = tuple('spdfghijk') lstyles = obj(s='g-',p='r-',d='b-',f='m-',g='c-',h='k-',i='g-.',j='r-.',k='b-.') @@ -327,7 +322,8 @@ def read(self,filepath,format=None): #end if #self.name = split_delims(os.path.split(filepath)[1])[0] self.name = os.path.split(filepath)[1].split('.')[0] - text = open(filepath,'r').read() + with open(filepath, "r") as f: + text = f.read() self.read_text(text,format) #end def read @@ -340,7 +336,8 @@ def write(self,filepath=None,format=None): #end if text = self.write_text(format) if filepath is not None: - open(filepath,'w').write(text) + with open(filepath,'w') as fobj: + fobj.write(text) #end if return text #end def write @@ -433,7 +430,6 @@ def read_lines(self,basis_lines,format=None): #end def read_lines - def write_text(self,format=None,occ=None): text = '' format = format.lower() diff --git a/nexus/nexus/bin/eshdf b/nexus/nexus/bin/eshdf index c08bf48377..1965d6bd2d 100755 --- a/nexus/nexus/bin/eshdf +++ b/nexus/nexus/bin/eshdf @@ -6,6 +6,16 @@ import sys from pathlib import Path from optparse import OptionParser +if sys.version_info[0:3] < (3, 10, 0): + v = sys.version_info[0:3] + print( + f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n" + "To use Nexus, please install at least Python 3.10.0 or higher!\n\n" + "If you already have a higher version installed, ensure that your Python\n" + "environment is properly activated and your $PATH is set correctly." + ) + sys.exit(1) + # Non-standard Python library imports import numpy as np diff --git a/nexus/nexus/bin/nxs-redo b/nexus/nexus/bin/nxs-redo index bf4b352ed1..3082fef45f 100755 --- a/nexus/nexus/bin/nxs-redo +++ b/nexus/nexus/bin/nxs-redo @@ -1,9 +1,20 @@ #! /usr/bin/env python3 import os +import sys from pathlib import Path from optparse import OptionParser +if sys.version_info[0:3] < (3, 10, 0): + v = sys.version_info[0:3] + print( + f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n" + "To use Nexus, please install at least Python 3.10.0 or higher!\n\n" + "If you already have a higher version installed, ensure that your Python\n" + "environment is properly activated and your $PATH is set correctly." + ) + sys.exit(1) + # Copied from qmca. Modification must done on qmca first # Locate and import the closely coupled Nexus module search_basepath = Path(__file__).resolve().parent.parent diff --git a/nexus/nexus/bin/nxs-sim b/nexus/nexus/bin/nxs-sim index ff944a474a..66af5db4ae 100755 --- a/nexus/nexus/bin/nxs-sim +++ b/nexus/nexus/bin/nxs-sim @@ -1,9 +1,20 @@ #! /usr/bin/env python3 import os +import sys from pathlib import Path from optparse import OptionParser +if sys.version_info[0:3] < (3, 10, 0): + v = sys.version_info[0:3] + print( + f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n" + "To use Nexus, please install at least Python 3.10.0 or higher!\n\n" + "If you already have a higher version installed, ensure that your Python\n" + "environment is properly activated and your $PATH is set correctly." + ) + sys.exit(1) + # Copied from qmca. Modification must done on qmca first # Locate and import the closely coupled Nexus module search_basepath = Path(__file__).resolve().parent.parent diff --git a/nexus/nexus/bin/nxs-test b/nexus/nexus/bin/nxs-test index d1df7803b3..827c68818b 100755 --- a/nexus/nexus/bin/nxs-test +++ b/nexus/nexus/bin/nxs-test @@ -1,2565 +1,77 @@ #! /usr/bin/env python3 -import os -import sys -import shutil -import traceback -from optparse import OptionParser - -# find the path to the nxs-test executable and its parent directory -scriptpath=os.path.realpath(__file__) -parent_dir=os.path.dirname(os.path.dirname(scriptpath)) - -# allow override during install -host_dir = None -if host_dir is not None: - parent_dir = host_dir -#end if - -# save nexus directories -library_dir = os.path.dirname(parent_dir) -test_dir = os.path.join(parent_dir,'tests') -reference_dir = os.path.join(parent_dir,'tests/reference') -example_dir = os.path.join(parent_dir,'examples') - -# ensure that nxs-test executable is resident in a nexus directory tree -dirs_check = [ - "tests/", - "bin/", - "basisset.py", - "bundle.py", - "debug.py", - "developer.py", - "execute.py", - "fileio.py", - "gamess_analyzer.py", - "gamess_input.py", - "gamess.py", - "gaussian_process.py", - "generic.py", - "grid_functions.py", - "hdfreader.py", - "__init__.py", - "machines.py", - "memory.py", - "nexus_base.py", - "nexus_version.py", - "numerics.py", - "observables.py", - "periodic_table.py", - "physical_system.py", - "project_manager.py", - "pseudopotential.py", - "pwscf_analyzer.py", - "pwscf_data_reader.py", - "pwscf_input.py", - "pwscf_postprocessors.py", - "pwscf.py", - "pyscf_analyzer.py", - "pyscf_input.py", - "pyscf_sim.py", - "qmcpack_analyzer_base.py", - "qmcpack_analyzer.py", - "qmcpack_converters.py", - "qmcpack_input.py", - "qmcpack_method_analyzers.py", - "qmcpack_property_analyzers.py", - "qmcpack.py", - "qmcpack_quantity_analyzers.py", - "qmcpack_result_analyzers.py", - "quantum_package_analyzer.py", - "quantum_package_input.py", - "quantum_package.py", - "rmg_analyzer.py", - "rmg_input.py", - "rmg.py", - "_bin.py", - "simulation.py", - "structure.py", - "template_simulation.py", - "testing.py", - "unit_converter.py", - "utilities.py", - "vasp_analyzer.py", - "vasp_input.py", - "vasp.py", - "versions.py", - "xmlreader.py", -] -for d in dirs_check: - pd = os.path.join(parent_dir,d) - if not os.path.exists(pd): - print('nxs-test executable is not run within a Nexus directory tree\nthe following directories must be present: {0}\nthe following directories are present: {1}\nexecutable launched from path: {2}'.format(dirs_check,os.listdir(parent_dir),parent_dir)) - exit(1) - #end if -#end for - -# enforce association between nxs-test executable and Nexus library -sys.path.insert(0,library_dir) - -# add unit test modules -#sys.path.append(os.path.realpath(os.path.join(__file__,'..','..','nexus','tests'))) - -unit_test_module_lists = dict() -unit_test_modules = dict() - -import inspect -import importlib - -def import_unit_test_module_list(module_name): - if module_name not in unit_test_module_lists: - module = importlib.import_module(module_name) - unit_test_list = [] - for name,member in inspect.getmembers(module): - if name.startswith('test_') and inspect.isfunction(member): - unit_test = member - unit_test_list.append((name,unit_test)) - #end if - #end for - unit_test_module_lists[module_name] = unit_test_list - #end if - return unit_test_module_lists[module_name] -#end def import unit_test_module_list - - -def import_unit_test_module(module_name): - if module_name not in unit_test_modules: - unit_test_list = import_unit_test_module_list(module_name) - unit_test_modules[module_name] = dict(unit_test_list) - #end if - return unit_test_modules[module_name] -#end def import unit_test_module - - -def import_from_unit_test_module(module_name,test_name): - module = import_unit_test_module(module_name) - if test_name not in module: - print('function "{}" is not in module "{}"\nfunctions present: {}'.format(test_name,module_name,sorted(module.keys()))) - exit(1) - #end if - return module[test_name] -#end def import_from_unit_test_module - - -# exception indicating test failure -class NexusTestFail(Exception): - None -#end class NexusTestFail - -# exception indicating that developer constructed test incorrectly -class NexusTestMisconstructed(Exception): - None -#end class NexusTestMisconstructed - -# exception used during detailed developer checks of the testing system -class NexusTestTripped(Exception): - None -#end class NexusTestTripped - - - - -class NexusTestBase(object): - nexus_test_dir = '.nexus_test' # nxs-test directory - - launch_path = None # path from which nxs-test exe was launched - current_test = None # current NexusTest - current_label = '' # current nlabel() - test_count = 0 # current test count - label_count = 0 # current label count in NexusTest.operation() - current_assert = 0 # current assert count - - assert_trip = -1 # developer tool to trip assert's one by one - # if set to n, an exception will be raised for the - # n-th assert call - - # keep a running count of assert calls - @staticmethod - def assert_called(): - NexusTestBase.current_assert+=1 - ca = NexusTestBase.current_assert - if ca==NexusTestBase.assert_trip: - raise NexusTestTripped - #end if - #end def assert_called - - # provide a directory path to place test output data in - @staticmethod - def test_path(): - test = NexusTestBase.current_test - label = NexusTestBase.current_label - label = label.replace(' ','_').replace('-','_') - tcount = str(NexusTestBase.test_count).zfill(2) - lcount = str(NexusTestBase.label_count).zfill(2) - if test.test_dir is None: - test_dir = '{0}_{1}'.format(tcount,test.name) - else: - test_dir = test.test_dir - #end if - label_dir = '{0}_{1}'.format(lcount,label) - ntdir = NexusTestBase.nexus_test_dir - nlpath = NexusTestBase.launch_path - if len(label)==0: - testpath = os.path.join(nlpath,ntdir,test_dir) - else: - testpath = os.path.join(nlpath,ntdir,test_dir,label_dir) - #end if - return testpath - #end def test_path - - @staticmethod - def test_path_from_dir(test_dir): - ntdir = NexusTestBase.nexus_test_dir - nlpath = NexusTestBase.launch_path - return os.path.join(nlpath,ntdir,test_dir) - #end def test_path_from_dir -#end class NexusTestBase - - - -# class used to divert log output when desired -class FakeLog: - def __init__(self): - self.reset() - #end def __init__ - - def reset(self): - self.s = '' - #end def reset - - def write(self,s): - self.s+=s - #end def write - - def close(self): - None - #end def close -#end class FakeLog - - -# dict to temporarily store logger when log output is diverted -logging_storage = dict() - - -# developer function interface for test creation below - -# label a section of tests -def nlabel(label): - os.chdir(NexusTestBase.launch_path) - NexusTestBase.current_label = label - NexusTestBase.label_count += 1 - NexusTestBase.current_test.subtests.append(label) -#end def nlabel - - -# divert nexus log output -def nlog_divert(): - from nexus.generic import generic_settings,object_interface - logging_storage['devlog'] = generic_settings.devlog - logging_storage['objlog'] = object_interface._logfile - logfile = FakeLog() - generic_settings.devlog = logfile - object_interface._logfile = logfile -#end def nlog_divert - - -# restore nexus log output -def nlog_restore(): - from nexus.generic import generic_settings,object_interface - generic_settings.devlog = logging_storage['devlog'] - object_interface._logfile = logging_storage['devlog'] -#end def nlog_restore - - -# logging functions for tests -def nlog(msg,n=0,indent=' '): - if len(msg)>0: - indent = n*indent - msg=indent+msg.replace('\n','\n'+indent)+'\n' - #end if - sys.stdout.write(msg) -#end def nlog - -def nmessage(msg,header=None,n=0): - if header is None: - nlog(msg,n=n) - else: - nlog(header,n=n) - nlog(msg,n=n+1) - #end if -#end def nmessage - -def nerror(msg,header='nexus test',n=0): - nmessage(msg,header+' error:',n=n) - sys.exit(1) -#end def nerror - - -# enter the current testing directory -def nenter(path=None,preserve=False,relative=False): - if not relative: - testpath = NexusTestBase.test_path() - if path is None: - path = testpath - else: - path = os.path.join(testpath,path) - #end if - #end if - if not preserve and os.path.exists(path): - try: - shutil.rmtree(path) - except Exception as e: - if os.path.exists(path): - raise e - #end if - #end try - #end if - if not os.path.exists(path): - os.makedirs(path) - #end if - os.chdir(path) - NexusTestBase.entered = True - return path -#end def nenter - - -# leave the current testing directory -def nleave(): - os.chdir(NexusTestBase.launch_path) - NexusTestBase.entered = False -#end def nleave - - -# create multiple directories in the local test directory -def ncreate_dirs(*dirs): - if not NexusTestBase.entered: - raise NexusTestMisconstructed - #end if - for dir in dirs: - if not os.path.exists(dir): - os.makedirs(dir) - #end if - #end for -#end def ncreate_dirs - - -# create a single directory, optionally filled with files -def ncreate_dir(dir,files): - ncreate_dirs(dir) - filepaths = [os.path.join(dir,file) for file in files] - ncreate_files(*filepaths) -#end def ncreate_dir - - -# create a set of empty files in the local test directory -def ncreate_files(*files): - if not NexusTestBase.entered: - raise NexusTestMisconstructed - #end if - for file in files: - if not os.path.exists(file): - open(file,'w').close() - #end if - #end for -#end def ncreate_files - - -# declare that a test has passed -def npass(): - None -#end def npass - - -# declare that a test has failed -def nfail(msg=''): - exception = NexusTestFail(msg) - raise exception -#end def nfail - - -# check an assertion -def nassert(result): - if not isinstance(result,bool): - raise NexusTestMisconstructed - elif not result: - nfail() - else: - npass() - #end if - NexusTestBase.assert_called() -#end def nassert - - -# run a unit test from an external file -def nunit(test_name): - module_name = 'nexus.tests.test_'+NexusTestBase.current_test.name - if not test_name.startswith('test_'): - test_name = 'test_'+test_name - #end if - unit_test = import_from_unit_test_module(module_name,test_name) - load_external_unit_tests() - run_external_unit_test(test_name,unit_test) -#end def nunit - - -# run all uncalled unit tests from an external file -def nunit_all(): - nexus_test = NexusTestBase.current_test - module_name = 'nexus.tests.test_'+NexusTestBase.current_test.name - module = import_unit_test_module(module_name) - load_external_unit_tests() - uncalled_tests = sorted(nexus_test.unit_tests-nexus_test.unit_tests_called) - for test_name in uncalled_tests: - unit_test = module[test_name] - run_external_unit_test(test_name,unit_test) - #end for -#end def nunit_all - - -# ensure all external unit tests are loaded -def load_external_unit_tests(): - nexus_test = NexusTestBase.current_test - if len(nexus_test.unit_tests)==0: - module_name = 'nexus.tests.test_'+nexus_test.name - module = import_unit_test_module(module_name) - nexus_test.unit_tests = set(module.keys()) - #end if -#end def load_external_unit_tests - - -# actually execute the unit test (not to be called directly within a Nexus test) -def run_external_unit_test(test_name,unit_test): - nexus_test = NexusTestBase.current_test - if test_name not in nexus_test.unit_tests: - raise NexusTestMisconstructed('unit test "{}" does not exist for function "{}"'.format(test_name,nexus_test.name)) - elif test_name in nexus_test.unit_tests_called: - raise NexusTestMisconstructed('unit test "{}" has already been called in function "{}"'.format(test_name,nexus_test.name)) - #end if - nlabel(test_name) - nexus_test.unit_tests_called.add(test_name) - unit_test() -#end def run_external_unit_test - - -# class to represent a test -# a test is created by writing a single function -# each test function contains subtests labeled with nlabel -# each subtest has a collection of assert statements, etc -class NexusTest(NexusTestBase): - - status_options = dict( - unused = 0, - passed = 1, - failed = 2, - ) - - status_map = dict() - for k,v in status_options.items(): - status_map[v] = k - #end for - - test_list = [] - test_dict = {} - - # capture launch path and clear out any old test data - # to be called once at user launch - @staticmethod - def setup(): - NexusTestBase.launch_path = os.getcwd() - nexus_test_dir = './'+NexusTestBase.nexus_test_dir - #end def setup - - - # register the current test object in the global test list - def __init__(self,operation,name=None,op_inputs=None,test_dir=None,optional=False): - if not callable(operation): - raise NexusTestMisconstructed - #end if - if name is None: - name = operation.__name__ - elif not isinstance(name,str): - raise NexusTestMisconstructed - #end if - if op_inputs is not None and not isinstance(op_inputs,(tuple,dict)): - raise NexusTestMisconstructed - #end if - if test_dir is not None and not isinstance(test_dir,str): - raise NexusTestMisconstructed - #end if - self.name = name - self.operation = operation - self.op_inputs = op_inputs - self.test_dir = test_dir - self.optional = optional - self.exception = None - self.status = NexusTest.status_options['unused'] - self.unit_tests = set() # complete set of unit tests - self.unit_tests_called = set() # set of unit tests called so far - self.subtests = [] # list of subtests called - NexusTest.test_list.append(self) - NexusTest.test_dict[self.name] = self - #end def __init__ - - - @property - def unused(self): - return self.status==NexusTest.status_options['unused'] - #end def unused - - @property - def passed(self): - return self.status==NexusTest.status_options['passed'] - #end def passed - - @property - def failed(self): - return self.status==NexusTest.status_options['failed'] - #end def failed - - - # run the current test - def run(self): - from nexus.testing import check_final_state - - nleave() - NexusTestBase.current_test = self - NexusTestBase.current_label = '' - NexusTestBase.test_count += 1 - NexusTestBase.label_count = 0 - failed = False - try: - if self.op_inputs is None: - self.operation() - elif isinstance(self.op_inputs,tuple): - self.operation(*self.op_inputs) - elif isinstance(self.op_inputs,dict): - self.operation(**self.op_inputs) - else: - raise NexusTestMisconstructed - #end if - check_final_state() - self.status=NexusTest.status_options['passed'] - except Exception as e: - t,v,tb = sys.exc_info() - self.exception = e - self.traceback = tb - self.status=NexusTest.status_options['failed'] - failed = True - #end try - uncalled_unit_tests = self.unit_tests-self.unit_tests_called - if not failed and len(uncalled_unit_tests)>0: - raise NexusTestMisconstructed('not all unit tests were called\n uncalled unit tests: {}\n please add these either by calling "nunit" for each of them\n or by calling "nunit_all" at the end of function "{}"'.format(sorted(uncalled_unit_tests),self.name)) - #end if - #end def run - - - # generate a message describing the outcome of the test - def message(self): - s = '' - s+='Test name : {0}\n'.format(self.name) - status = NexusTest.status_map[self.status] - if self.failed and self.exception is not None:# and not isinstance(self.exception,NexusTestFail): - if len(NexusTestBase.current_label)>0: - s+='Test sublabel : {0}\n'.format(NexusTestBase.current_label) - #end if - e = self.exception - btrace = traceback.format_tb(self.traceback) - if isinstance(e,NexusTestFail): - btrace = btrace[:-1] - msg = str(e) - if len(msg)>0: - s+='Test exception: {0}\n'.format('\n '+msg.replace('\n','\n ')) - #end if - elif isinstance(e,NexusTestMisconstructed): - btrace = btrace[:-1] - s+='Test exception: Nexus test is misconstructed. Please contact developers.\n' - else: - s+='Test exception: "{0}"\n'.format(e.__class__.__name__+': '+str(e).replace('\n','\n ')) - #end if - s+='Test backtrace:\n' - for s2 in btrace: - s+=s2 - #end for - #end if - return s - #end def message -#end class NexusTest - - - - -#===============================================# -# testing infrastructure above, tests below # -#===============================================# - - - -def versions(): - nunit('import') - - nunit('constants') - - nunit('time') - - nunit('version_processing') - - nunit('versions_object') - - nunit_all() -#end def versions - - - -def required_dependencies(): - nunit('numpy_available') - - nunit_all() -#end def required_dependencies - - - -def optional_dependencies(): - nunit('scipy_available') - - nunit('h5py_available') - - nunit('matplotlib_available') - - nunit('pydot_available') - - nunit('spglib_available') - - nunit('pycifrw_available') - - nunit('seekpath_available') - - nunit_all() -#end def optional_dependencies - - - -def nexus_imports(): - nunit('imports') - - nunit_all() -#end def nexus_imports - - - -def testing(): - nunit('import') - - nunit('value_checks') - - nunit('object_checks') - - nunit('text_checks') - - nunit_all() -#end def testing - - - -def execute(): - nunit('import') - - nunit('execute') - - nunit_all() -#end def execute - - - -def memory(): - nunit('import') - - nunit('memory') - - nunit('resident') - - nunit('stacksize') - - nunit_all() -#end def memory - - - -def generic_operation(): - nunit('logging') - - nunit('intrinsics') - - nunit('extensions') - - nunit_all() -#end def generic_operation - - - -def developer(): - nunit('import') - - nunit('unavailable') - - nunit('valid_variable_name') - - nunit_all() -#end def developer - - - -def unit_converter(): - nunit('import') - - nunit('convert') - - nunit('convert_scalar_to_all') - - nunit_all() -#end def unit_converter - - - -def periodic_table(): - nunit('import') - - nunit('periodic_table') - - nunit('is_element') - - nunit_all() -#end def periodic_table - - - -def numerics(): - nunit('import') - - nunit('ndgrid') - - nunit('distance_table') - - nunit('nearest_neighbors') - - nunit('simplestats') - - nunit('simstats') - - nunit('equilibration_length') - - nunit('morse') - - nunit('eos') - - nunit_all() -#end def numerics - - - -def grid_functions(): - nunit('imports') - - # supporting functions - nunit('coord_conversion') - - nunit('unit_grid_points') - - nunit('parallelotope_grid_points') - - nunit('spheroid_grid_points') - - # Grid tests - nunit('grid_initialization') - - nunit('parallelotope_grid_initialization') - - nunit('grid_reset') - - nunit('grid_set_operations') - - nunit('grid_copy') - - nunit('grid_translate') - - nunit('grid_reshape') - - nunit('grid_unit_points') - - nunit('grid_cell_indices') - - nunit('grid_inside') - - nunit('grid_project') - - nunit('grid_radius') - - nunit('grid_axes_volume') - - nunit('grid_volume') - - nunit('grid_cell_volumes') - - nunit('grid_unit_metric') - - # GridFunction tests - - # any remaining tests - nunit_all() -#end def grid_functions - - - -def fileio(): - nunit('files') - - nunit('import') - - nunit('textfile') - - nunit('xsffile') - - nunit('xsffile_density') - - nunit('poscar_file') - - nunit('chgcar_file') - - nunit_all() -#end def fileio - - - -def hdfreader(): - nunit('import') - - nunit_all() -#end def hdfreader - - - -def xmlreader(): - nunit('files') - - nunit('import') - - nunit('read') - - nunit('parse_string') - - nunit('find_pair') - - nunit('remove_pair_sections') - - nunit('remove_empty_lines') - - nunit_all() -#end def xmlreader - - - -def structure(): - - nunit('files') - - nunit('import') - - nunit('empty_init') - - nunit('reference_inputs') - - nunit('direct_init') - - nunit('generate_init') - - nunit('crystal_init') - - nunit('diagonal_tiling') - - nunit('matrix_tiling') - - nunit('gen_molecule') - - nunit('gen_diamond_direct') - - nunit('gen_diamond_lattice') - - nunit('gen_graphene') - - nunit('read_write') - - nunit('bounding_box') - - nunit('opt_tiling') - - nunit('unit_coords') - - nunit('monkhorst_pack_kpoints') - - nunit('count_kshells') - - nunit('rinscribe') - - nunit('rwigner') - - nunit('volume') - - nunit('min_image_distances') - - nunit('freeze') - - nunit('interpolate') - - nunit_all() -#end def structure - - - -def physical_system(): - nunit('import') - - nunit('particle_initialization') - - nunit('physical_system_initialization') - - nunit('change_units') - - nunit('rename') - - nunit('tile') - - nunit('kf_rpa') - - nunit_all() -#end def physical_system - - - -def basisset(): - nunit('files') - - nunit('import') - - nunit('basissets') - - nunit('process_gaussian_text') - - nunit('gaussianbasisset') - - nunit_all() -#end def basisset - - - -def pseudopotential(): - nunit('files') - - nunit('import') - - nunit('pp_elem_label') - - nunit('pseudopotentials') - - nunit('ppset') - - nunit('pseudopotential_classes') - - nunit_all() -#end def pseudopotential - - - -def nexus_base(): - nunit('import') - - nunit('namespaces') - - nunit('empty_init') - - nunit('write_splash') - - nunit('enter_leave') - - nunit_all() -#end def nexus_base - - - -def machines(): - - nunit('import') - - nunit('cpu_count') - - nunit('options') - - nunit('job_init') - - nunit('job_time') - - nunit('job_set_id') - - nunit('job_get_machine') - - nunit('job_set_environment') - - nunit('job_clone') - - nunit('job_serial_clone') - - nunit('machine_virtuals') - - nunit('machine_list') - - nunit('machine_add') - - nunit('machine_get') - - nunit('machine_instantiation') - - nunit('workstation_init') - - nunit('workstation_scheduling') - - nunit('supercomputer_init') - - nunit('supercomputer_scheduling') - - nunit('process_job') - - nunit('job_run_command') - - nunit('write_job') - - nunit_all() -#end def machines - - - -def simulation(): - - nunit('import') - - nunit('simulation_input') - - nunit('simulation_analyzer') - - nunit('simulation_input_template') - - nunit('simulation_input_multi_template') - - nunit('code_name') - - nunit('init') - - nunit('virtuals') - - nunit('reset_indicators') - - nunit('indicator_checks') - - nunit('create_directories') - - nunit('file_text') - - nunit('depends') - - nunit('undo_depends') - - nunit('has_generic_input') - - nunit('check_dependencies') - - nunit('get_dependencies') - - nunit('downstream_simids') - - nunit('copy_file') - - nunit('save_load_image') - - nunit('load_analyzer_image') - - nunit('save_attempt') - - nunit('write_inputs') - - nunit('send_files') - - nunit('submit') - - nunit('update_process_id') - - nunit('check_status') - - nunit('get_output') - - nunit('analyze') - - nunit('progress') - - nunit('execute') - - nunit('reset_wait_ids') - - nunit('check_subcascade') - - nunit('block_dependents') - - nunit('reconstruct_cascade') - - nunit('traverse_cascade') - - nunit('traverse_full_cascade') - - nunit('test_write_dependents') - - nunit('generate_simulation') - - nunit_all() -#end def simulation - - - -def bundle(): - nunit('import') - - nunit('bundle') - - nunit_all() -#end def bundle - - - -def project_manager(): - nunit('import') - - nunit('init') - - nunit('add_simulations') - - nunit('traverse_cascades') - - nunit('screen_fake_sims') - - nunit('resolve_file_collisions') - - nunit('propagate_blockages') - - nunit('load_cascades') - - nunit('check_dependencies') - - nunit('write_simulation_status') - - nunit('run_project') - - nunit_all() -#end def project_manager - - - -def settings_operation(): - nunit('import') - - nunit('settings') - - nunit_all() -#end def settings_operation - - - -def vasp_input(): - nunit('files') - - nunit('import') - - nunit('keyword_consistency') - - nunit('empty_init') - - nunit('read') - - nunit('write') - - nunit('generate') - - nunit_all() -#end def vasp_input - - - -def pwscf_input(): - nunit('files') - - nunit('import') - - nunit('input') - - nunit_all() -#end def pwscf_input - - - -def pwscf_postprocessor_input(): - nunit('import') - - nunit('empty_init') - - nunit('read') - - nunit('write') - - nunit('generate') - - nunit_all() -#end def pwscf_postprocessor_input - - - -def gamess_input(): - nunit('files') - - nunit('import') - - nunit('keyspec_groups') - - nunit('empty_init') - - nunit('read') - - nunit('write') - - nunit('generate') - - nunit_all() -#end def gamess_input - - - -def pyscf_input(): - nunit('import') - - nunit('empty_init') - - nunit('generate') - - nunit('write') - - nunit_all() -#end def pyscf_input - - - -def quantum_package_input(): - nunit('import') - - nunit('empty_init') - - nunit('read') - - nunit('generate') - - nunit_all() -#end def quantum_package_input - - - -def rmg_input(): - nunit('files') - - nunit('import') - - nunit('empty_init') - - nunit('read') - - nunit('write') - - nunit('generate') - - nunit_all() -#end def rmg_input - - - -def qmcpack_converter_input(): - nunit('import') - - nunit('pw2qmcpack_input_empty_init') - - nunit('pw2qmcpack_input_read') - - nunit('pw2qmcpack_input_write') - - nunit('pw2qmcpack_input_generate') - - nunit('convert4qmc_input_empty_init') - - nunit('convert4qmc_input_generate') - - nunit('convert4qmc_input_write') - - nunit('pyscf_to_afqmc_input_init') - - nunit('pyscf_to_afqmc_input_write') - - nunit_all() -#end def qmcpack_converter_input - - - -def qmcpack_input(): - nunit('files') - - nunit('import') - - nunit('qixml_class_init') - - nunit('compose') - - nunit('generate') - - nunit('read') - - nunit('write') - - nunit('get') - - nunit('incorporate_system') - - nunit('generate_kspace_jastrow') - - nunit('excited_state') - - nunit_all() -#end def qmcpack_input - - - -def vasp_analyzer(): - nunit('files') - - nunit('import') - - nunit('empty_init') - - nunit('analyze') - - nunit_all() -#end def vasp_analyzer - - - -def pwscf_analyzer(): - nunit('import') - - nunit('empty_init') - - nunit('analyze') - - nunit_all() -#end def pwscf_analyzer - - - -def pwscf_postprocessor_analyzers(): - nunit('import') - - nunit('empty_init') - - nunit('projwfc_analyzer') - - nunit_all() -#end def pwscf_postprocessor_analyzers - - - -def gamess_analyzer(): - nunit('import') - - nunit('empty_init') - - nunit('analyze') - - nunit_all() -#end def gamess_analyzer - - - -def pyscf_analyzer(): - nunit('import') - - nunit('empty_init') - - nunit_all() -#end def pyscf_analyzer - - - -def quantum_package_analyzer(): - nunit('import') - - nunit('empty_init') - - nunit_all() -#end def quantum_package_analyzer - - - -def rmg_analyzer(): - nunit('import') - - nunit('empty_init') - - nunit_all() -#end def rmg_analyzer - - - -def qmcpack_converter_analyzers(): - nunit('import') - - nunit('pw2qmcpack_analyzer_init') - - nunit('convert4qmc_analyzer_init') - - nunit('pyscf_to_afqmc_analyzer_init') - - nunit_all() -#end def qmcpack_converter_analyzers - - - -def qmcpack_analyzer(): - nunit('import') - - nunit('empty_init') - - nunit('vmc_dmc_analysis') - - nunit('optimization_analysis') - - nunit('twist_average_analysis') - - nunit_all() -#end def qmcpack_analyzer - - - -def vasp_simulation(): - nunit('import') - - nunit('minimal_init') - - nunit('check_result') - - nunit('get_result') - - nunit('incorporate_result') - - nunit('check_sim_status') - - nunit('get_output_files') - - nunit_all() -#end def vasp_simulation - - - -def pwscf_simulation(): - nunit('import') - - nunit('minimal_init') - - nunit('check_result') - - nunit('get_result') - - nunit('incorporate_result') - - nunit('check_sim_status') - - nunit_all() -#end def pwscf_simulation - - - -def gamess_simulation(): - nunit('import') - - nunit('minimal_init') - - nunit('check_result') - - nunit('get_result') - - nunit('incorporate_result') - - nunit('check_sim_status') - - nunit_all() -#end def gamess_simulation - - - -def pyscf_simulation(): - nunit('import') - - nunit('minimal_init') - - nunit('check_result') - - nunit('get_result') - - nunit('check_sim_status') - - nunit_all() -#end def pyscf_simulation - - - -def quantum_package_simulation(): - nunit('import') - - nunit('minimal_init') - - nunit('check_result') - - nunit('get_result') - - nunit('incorporate_result') - - nunit('check_sim_status') - - nunit_all() -#end def quantum_package_simulation - - - -def rmg_simulation(): - nunit('import') - - #nunit('minimal_init') - - nunit_all() -#end def rmg_simulation - - - -def pwscf_postprocessor_simulations(): - nunit('import') - - nunit('minimal_init') - - nunit('check_result') - - nunit('get_result') - - nunit('incorporate_result') - - nunit('check_sim_status') - - nunit_all() -#end def pwscf_postprocessor_simulations - - - -def qmcpack_converter_simulations(): - nunit('pw2qmcpack_import') - - nunit('pw2qmcpack_minimal_init') - - nunit('pw2qmcpack_check_result') - - nunit('pw2qmcpack_get_result') - - nunit('pw2qmcpack_incorporate_result') - - nunit('pw2qmcpack_check_sim_status') - - - nunit('convert4qmc_import') - - nunit('convert4qmc_minimal_init') - - nunit('convert4qmc_check_result') - - nunit('convert4qmc_get_result') - - nunit('convert4qmc_incorporate_result') - - nunit('convert4qmc_check_sim_status') - - - nunit('pyscf_to_afqmc_import') - - nunit('pyscf_to_afqmc_minimal_init') - - nunit('pyscf_to_afqmc_check_result') - - nunit('pyscf_to_afqmc_get_result') - - nunit('pyscf_to_afqmc_incorporate_result') - - nunit('pyscf_to_afqmc_check_sim_status') - - nunit_all() -#end def qmcpack_converter_simulations - - - -def qmcpack_simulation(): - nunit('import') - - nunit('minimal_init') - - nunit('check_result') - - nunit('get_result') - - nunit('incorporate_result') - - nunit('check_sim_status') - - nunit_all() -#end def qmcpack_simulation - - - -def observables(): - nunit('import') - - nunit('defined_attribute_base') - - nunit_all() -#end def observables - - - -def nxs_redo(): - nunit('test_redo') - - nunit_all() -#end def nxs_redo - - - -def nxs_sim(): - nunit('sim') - - nunit_all() -#end def nxs_sim - - - -def qmc_fit(): - nunit_all() -#end def qmc_fit - - - -def qdens(): - nunit_all() -#end def qdens - - -def qdens_radial(): - nunit_all() -#end def qdens - - -def qmca(): - nunit('help') - - nunit('examples') - - nunit('unit_conversion') - - nunit('selected_quantities') - - nunit('all_quantities') - - nunit('energy_variance') - - nunit('multiple_equilibration') - - nunit('join') - - nunit('multiple_directories') - - nunit('twist_average') - - nunit('weighted_twist_average') - - nunit_all() -#end def qmca +"""This script is designed to run Nexus's test suite using Pytest. +In general, it should only be run by users who have installed Nexus and +are looking to ensure their installation works in their environment. +Developers should NOT use this script to run the test suite as it will +suppress all warnings and fail fast, which is generally not desirable +for development. +""" +import sys -example_information = dict( - pwscf_relax_Ge_T = dict( - path = 'quantum_espresso/relax_Ge_T_vs_kpoints', - scripts = [ - 'relax_vs_kpoints_example.py', - ], - files = [ - ('pwscf' ,'input','runs/relax/kgrid_111/relax.in'), - ('pwscf' ,'input','runs/relax/kgrid_222/relax.in'), - ('pwscf' ,'input','runs/relax/kgrid_444/relax.in'), - ('pwscf' ,'input','runs/relax/kgrid_666/relax.in'), - ], - ), - gamess_H2O = dict( - path = 'gamess/H2O', - scripts = [ - 'h2o_pp_hf.py', - 'h2o_pp_cisd.py', - 'h2o_pp_casscf.py', - ], - files = [ - ('gamess' ,'input','runs/pp_hf/rhf.inp'), - ('gamess' ,'input','runs/pp_cisd/rhf.inp'), - ('gamess' ,'input','runs/pp_cisd/cisd.inp'), - ('gamess' ,'input','runs/pp_casscf/rhf.inp'), - ('gamess' ,'input','runs/pp_casscf/cas.inp'), - ], - ), - qmcpack_H2O = dict( - path = 'qmcpack/rsqmc_misc/H2O', - scripts = [ - 'H2O.py', - ], - files = [ - ('pwscf' ,'input','runs/scf.in'), - ('pw2qmcpack','input','runs/p2q.in'), - ('qmcpack' ,'input','runs/opt.in.xml'), - ('qmcpack' ,'input','runs/dmc.in.xml'), - ], - ), - qmcpack_LiH = dict( - path = 'qmcpack/rsqmc_misc/LiH', - scripts = [ - 'LiH.py', - ], - files = [ - ('pwscf' ,'input','runs/scf.in'), - ('pwscf' ,'input','runs/nscf.in'), - ('pw2qmcpack','input','runs/p2q.in'), - ('qmcpack' ,'input','runs/opt.in.xml'), - ('qmcpack' ,'input','runs/dmc.in.xml'), - ], - ), - qmcpack_c20 = dict( - path = 'qmcpack/rsqmc_misc/c20', - scripts = [ - 'c20.py', - ], - files = [ - ('pwscf' ,'input','runs/c20/scf/scf.in'), - ('pw2qmcpack','input','runs/c20/nscf/p2q.in'), - ('qmcpack' ,'input','runs/c20/opt/opt.in.xml'), - ('qmcpack' ,'input','runs/c20/qmc/qmc.in.xml'), - ], - ), - qmcpack_diamond = dict( - path = 'qmcpack/rsqmc_misc/diamond', - scripts = [ - 'diamond.py', - 'diamond_vacancy.py', - ], - files = [ - ('pwscf' ,'input','runs/diamond/scf/scf.in'), - ('pw2qmcpack','input','runs/diamond/scf/conv.in'), - ('qmcpack' ,'input','runs/diamond/vmc/vmc.in.xml'), - ('pwscf' ,'input','runs/diamond_vacancy/relax/relax.in'), - ('pwscf' ,'input','runs/diamond_vacancy/scf/scf.in'), - ], - ), - qmcpack_graphene = dict( - path = 'qmcpack/rsqmc_misc/graphene', - scripts = [ - 'graphene.py', - ], - files = [ - ('pwscf' ,'input','runs/graphene/scf/scf.in'), - ('pwscf' ,'input','runs/graphene/nscf/nscf.in'), - ('pw2qmcpack','input','runs/graphene/nscf/p2q.in'), - ('pwscf' ,'input','runs/graphene/nscf_opt/nscf.in'), - ('pw2qmcpack','input','runs/graphene/nscf_opt/p2q.in'), - ('qmcpack' ,'input','runs/graphene/opt/opt.in.xml'), - ('qmcpack' ,'input','runs/graphene/qmc/qmc.in.xml'), - ], - ), - qmcpack_oxygen_dimer = dict( - path = 'qmcpack/rsqmc_misc/oxygen_dimer', - scripts = [ - 'oxygen_dimer.py', - ], - files = [ - ('pwscf' ,'input','scale_1.0/scf.in'), - ('pw2qmcpack','input','scale_1.0/p2q.in'), - ('qmcpack' ,'input','scale_1.0/opt.in.xml'), - ('qmcpack' ,'input','scale_1.0/qmc.in.xml'), - ], - ), +if sys.version_info[0:3] < (3, 10, 0): + v = sys.version_info[0:3] + print( + f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n" + "To use Nexus, please install at least Python 3.10.0 or higher!\n\n" + "If you already have a higher version installed, ensure that your Python\n" + "environment is properly activated and your $PATH is set correctly." ) + sys.exit(1) -user_examples_data = dict() - -def user_examples(label): - - from nexus.pwscf_input import PwscfInput - from nexus.qmcpack_converters import Pw2qmcpackInput - from nexus.gamess_input import GamessInput - from nexus.qmcpack_input import QmcpackInput - import nexus.testing as nexus_testing - - # load information for a single user example - if label not in example_information: - raise NexusTestMisconstructed - #end if - einfo = example_information[label] - - # create local directory for these tests - test_dir = nenter(preserve=True) - - # create a local file to track any test failures - # this is optionally used when updating reference files automatically - example_failures_filename = 'test_failures.txt' - test_failures_file = user_examples_data['failures_file'] - if test_failures_file is None: - test_failures_file = open(user_examples_data['failures_filepath'],'w') - user_examples_data['failures_file'] = test_failures_file - #end if - - # copy over nexus user examples into reference generation directory - # only do this the first time as all user example tests share a test directory - if not os.path.exists(os.path.join(test_dir,'qmcpack')): - command = 'rsync -av --ignore-existing {0}/* {1}/'.format(example_dir,test_dir) - out,err,rc = execute(command) - if rc>0: - nfail('copying example directory failed\nattempted command:\n'+command) - #end if - #end if - - # execute all example scripts in generate_only mode - path = einfo['path'] - cwd = os.getcwd() - tpath = os.path.join(test_dir,path) - # remove prexisting example files - nenter(tpath,relative=True) - # copy over nexus examples files just for this example - epath = os.path.realpath(os.path.join(example_dir,path)) - command = 'rsync -av {0}/* ./'.format(epath) - out,err,rc = execute(command) - if rc>0: - nfail('copying example directory failed\nattempted command:\n'+command) - #end if - for script in einfo['scripts']: - # run the example script - command = sys.executable+' ./'+script+' --generate_only --sleep=0.01' - out,err,rc = nexus_testing.execute(command) - #end for - os.chdir(cwd) - - # check that generated files match reference files - ref_example_dir = os.path.join(reference_dir,'user_examples') - input_classes = dict( - pwscf = PwscfInput, - pw2qmcpack = Pw2qmcpackInput, - gamess = GamessInput, - qmcpack = QmcpackInput, - ) - example_path = einfo['path'] - for code,filetype,filepath in einfo['files']: - ref_filepath = os.path.join(ref_example_dir,example_path,filepath) - gen_filepath = os.path.join(test_dir,example_path,filepath) - # check that the reference file exists - if not os.path.exists(ref_filepath): - nfail('reference file is missing\nfile should be located at: {0}'.format(ref_filepath)) - #end if - # check that the generated file exists - if not os.path.exists(gen_filepath): - nfail('input file was not generated: {0}'.format(gen_filepath)) - #end if - # check that the generated file matches the reference file - # read the files into Nexus' object representation - # use object_diff to compare object represenations - # this is needed to compare floats within a tolerance - if filetype=='input': - input_class = input_classes[code] - ref_input = input_class(ref_filepath) - gen_input = input_class(gen_filepath) - diff,dgen,dref = nexus_testing.object_diff(gen_input,ref_input,full=True) - if diff: - # assume failure - failed = True - # if difference due to periodically equivalent points - # then it is not a failure - check_pbc = False - if len(dgen)==1 and len(dref)==1: - kgen = list(dgen.keys())[0].rsplit('/',1)[1] - kref = list(dref.keys())[0].rsplit('/',1)[1] - check_pbc |= code=='qmcpack' and kgen==kref=='position' - check_pbc |= code=='pwscf' and kgen==kref=='positions' - #end if - if check_pbc: - try: - # extract Structure objects from SimulationInput objects - rs = ref_input.return_structure() - gs = gen_input.return_structure() - # compare minimum image distances of all atomic coordinates - d = rs.min_image_distances(gs.pos,pairs=False) - # allow for small deviation due to precision of ascii floats in the text input files - if d.min()<1e-6: - failed = False - #end if - except: - None - #end try - #end if - if failed: - # store failing reference files - test_failures_file.write(ref_filepath+'\n') - # report on failures - from nexus.generic import obj - dgen = obj(dgen) - dref = obj(dref) - msg = 'reference and generated input files differ\n' - msg += 'reference file: '+filepath+'\n' - msg += 'reference file difference\n' - msg += 40*'='+'\n' - msg += str(dref) - msg += 'generated file difference\n' - msg += 40*'='+'\n' - msg += str(dgen) - nfail(msg) - #end if - #end if - else: - raise NexusTestMisconstructed - #end if - #end for -#end def user_examples - - - -# create labeled tests from simple functions above - -# ordered according to logical dependencies -NexusTest( versions ) -NexusTest( required_dependencies ) -NexusTest( optional_dependencies , optional=True) -NexusTest( nexus_base ) -NexusTest( nexus_imports ) -NexusTest( testing ) -NexusTest( execute ) -NexusTest( memory ) -NexusTest( generic_operation , 'generic' ) -NexusTest( developer ) -NexusTest( unit_converter ) -NexusTest( periodic_table ) -NexusTest( numerics ) -NexusTest( grid_functions ) -NexusTest( fileio ) -NexusTest( hdfreader ) -NexusTest( xmlreader ) -NexusTest( structure ) -NexusTest( physical_system ) -NexusTest( basisset ) -NexusTest( pseudopotential ) -NexusTest( machines ) -NexusTest( simulation , 'simulation_module' ) -NexusTest( bundle ) -NexusTest( project_manager ) -NexusTest( settings_operation , 'settings' ) -NexusTest( vasp_input ) -NexusTest( pwscf_input ) -NexusTest( pwscf_postprocessor_input ) -NexusTest( gamess_input ) -NexusTest( pyscf_input ) -NexusTest( quantum_package_input ) -NexusTest( rmg_input ) -NexusTest( qmcpack_converter_input ) -NexusTest( qmcpack_input ) -NexusTest( vasp_analyzer ) -NexusTest( pwscf_analyzer ) -NexusTest( pwscf_postprocessor_analyzers ) -NexusTest( gamess_analyzer ) -NexusTest( pyscf_analyzer ) -NexusTest( quantum_package_analyzer ) -NexusTest( rmg_analyzer ) -NexusTest( qmcpack_converter_analyzers ) -NexusTest( qmcpack_analyzer ) -NexusTest( vasp_simulation ) -NexusTest( pwscf_simulation ) -NexusTest( gamess_simulation ) -NexusTest( pyscf_simulation ) -NexusTest( quantum_package_simulation ) -NexusTest( rmg_simulation ) -NexusTest( pwscf_postprocessor_simulations ) -NexusTest( qmcpack_converter_simulations ) -NexusTest( qmcpack_simulation ) -NexusTest( observables ) -NexusTest( nxs_redo ) -NexusTest( nxs_sim ) -NexusTest( qmca ) -NexusTest( qmc_fit ) -NexusTest( qdens ) -NexusTest( qdens_radial ) - -# ordered alphabetically (pytest order) -#NexusTest( basisset ) -#NexusTest( bundle ) -#NexusTest( developer ) -#NexusTest( execute ) -#NexusTest( fileio ) -#NexusTest( gamess_analyzer ) -#NexusTest( gamess_input ) -#NexusTest( gamess_simulation ) -#NexusTest( generic_operation , 'generic' ) -#NexusTest( grid_functions ) -#NexusTest( hdfreader ) -#NexusTest( machines ) -#NexusTest( memory ) -#NexusTest( nexus_base ) -#NexusTest( nexus_imports ) -#NexusTest( numerics ) -#NexusTest( nxs_redo ) -#NexusTest( nxs_sim ) -#NexusTest( observables ) -#NexusTest( optional_dependencies , optional=True) -#NexusTest( periodic_table ) -#NexusTest( physical_system ) -#NexusTest( project_manager ) -#NexusTest( pseudopotential ) -#NexusTest( pwscf_analyzer ) -#NexusTest( pwscf_input ) -#NexusTest( pwscf_postprocessor_analyzers ) -#NexusTest( pwscf_postprocessor_input ) -#NexusTest( pwscf_postprocessor_simulations ) -#NexusTest( pwscf_simulation ) -#NexusTest( pyscf_analyzer ) -#NexusTest( pyscf_input ) -#NexusTest( pyscf_simulation ) -#NexusTest( qdens ) -#NexusTest( qdens_radial ) -#NexusTest( qmc_fit ) -#NexusTest( qmca ) -#NexusTest( qmcpack_analyzer ) -#NexusTest( qmcpack_converter_analyzers ) -#NexusTest( qmcpack_converter_input ) -#NexusTest( qmcpack_converter_simulations ) -#NexusTest( qmcpack_input ) -#NexusTest( qmcpack_simulation ) -#NexusTest( quantum_package_analyzer ) -#NexusTest( quantum_package_input ) -#NexusTest( quantum_package_simulation ) -#NexusTest( required_dependencies ) -#NexusTest( settings_operation , 'settings' ) -#NexusTest( simulation , 'simulation_module' ) -#NexusTest( structure ) -#NexusTest( testing ) -#NexusTest( unit_converter ) -#NexusTest( vasp_analyzer ) -#NexusTest( vasp_simulation ) -#NexusTest( vasp_input ) -#NexusTest( versions ) -#NexusTest( xmlreader ) - -for label in sorted(example_information.keys()): - NexusTest( - name = 'example_'+label, # individually label tests - operation = user_examples, # all tests call the same test function - op_inputs = dict(label=label), # but with different inputs - test_dir = 'user_examples', # all tests are run in the same base directory - ) -#end for - - - -# launch the actual testing framework - -# Returns failure error code to OS. -# Explicitly prints 'fail' after an optional message. -def exit_fail(msg=None): - if msg!=None: - print(msg) - #end if - print('Test status: fail') - exit(1) -#end def exit_fail - -# Returns success error code to OS. -# Explicitly prints 'pass' after an optional message. -def exit_pass(msg=None): - if msg!=None: - print(msg) - #end if - print('Test status: pass') - exit(0) -#end def exit_pass - -# execute function -from subprocess import Popen,PIPE -def execute(command,verbose=False,skip=False): - out,err = '','' - if skip: - if verbose: - print('Would have executed:\n '+command) - #end if - else: - if verbose: - print('Executing:\n '+command) - #end if - process = Popen(command,shell=True,stdout=PIPE,stderr=PIPE,close_fds=True) - out,err = process.communicate() - #end if - return out,err,process.returncode -#end def execute - - - -def regenerate_reference(update=False): - # create directory for reference file generation - refgen_dir = './reference_regen' - if os.path.exists(refgen_dir): - shutil.rmtree(refgen_dir) - #end if - os.makedirs(refgen_dir) - - nlog('generating reference data in {0}'.format(refgen_dir)) - - # create directory for example reference generation - exdir = user_examples_data['dir'] - refgen_example_dir = os.path.join(refgen_dir,exdir) - if not os.path.exists(refgen_example_dir): - os.makedirs(refgen_example_dir) - #end if - - # copy over nexus user examples into reference generation directory - out,err,rc = execute('rsync -av {0}/* {1}/'.format(example_dir,refgen_example_dir)) - if rc>0: - nerror('rsync of example directory failed, exiting',n=1) - #end if - - # execute all example scripts in generate_only mode - for label,einfo in example_information.items(): - example_path = einfo['path'] - for script in einfo['scripts']: - nlog('generating reference data for '+script,n=1) - path = os.path.join(refgen_example_dir,example_path) - cwd = os.getcwd() - nlog('current directory: '+cwd,n=2) - nlog('entering directory: '+path,n=2) - os.chdir(path) - if not os.path.exists('./'+script): - nerror('script file {} does not exist'.format(script),n=2) - #end if - command = sys.executable+' ./'+script+' --generate_only --sleep=0.1' - nlog('executing command: '+command,n=2) - out,err,rc = execute(command) - if rc>0: - nerror('example script failed to run',n=2) - #end if - os.chdir(cwd) - #end for - #end for - - # update the reference set of example files - if update: - nlog('\nupdating reference data') - if options.update_dryrun: - nlog('performing a dryrun, no files will be updated',n=1) - #end if - failures_filepath = user_examples_data['failures_filepath'] - nlog('attempting to load example failures file',n=1) - nlog('file location: {}'.format(failures_filepath),n=2) - failures_list = [] - if os.path.exists(failures_filepath): - f = open(failures_filepath,'r') - failures_list.extend(f.read().splitlines()) - f.close() - nlog('file read successfully',n=2) - nlog('files for previously failed examples:',n=2) - for filepath in failures_list: - nlog(filepath,n=3) - #end for - else: - nlog('file does not exist, skipping',n=2) - #end if - nlog('collecting file transfer information',n=1) - new_examples = [] - failed_examples = [] - all_examples = [] - ref_example_dir = os.path.join(reference_dir,exdir) - for label,einfo in example_information.items(): - example_path = einfo['path'] - for code,filetype,filepath in einfo['files']: - ref_filepath = os.path.join(ref_example_dir,example_path,filepath) - gen_filepath = os.path.join(refgen_example_dir,example_path,filepath) - ref_path,ref_file = os.path.split(ref_filepath) - transfer = label,gen_filepath,ref_filepath - if not os.path.exists(ref_filepath): - new_examples.append(transfer) - elif ref_filepath in failures_list: - failed_examples.append(transfer) - #end if - all_examples.append(transfer) - #end for - #end for - if options.update_mode=='new': - nlog('only new examples will be updated',n=1) - update_examples = new_examples - elif options.update_mode=='failed': - nlog('both failed and new examples will be updated',n=1) - update_examples = failed_examples + new_examples - elif options.update_mode=='all': - nlog('all examples will be updated',n=1) - update_examples = all_examples - #end if - if len(update_examples)==0: - nlog('no examples selected for update!',n=1) - for label,gen_filepath,ref_filepath in update_examples: - ref_path,ref_file = os.path.split(ref_filepath) - nlog('update for '+label,n=2) - nlog('ref file: '+ref_filepath,n=3) - nlog('gen file: '+gen_filepath,n=3) - if options.update_dryrun: - nlog('reference file not updated',n=3) - else: - if not os.path.exists(ref_path): - os.makedirs(ref_path) - #end if - shutil.copy2(gen_filepath,ref_path) - nlog('reference file updated',n=3) - #end if - #end for - #end if - -#end def regenerate_reference - - - - - -def find_nexus_modules(): - import sys - nexus_lib = os.path.realpath(os.path.join(__file__,'..','..')) - assert(os.path.exists(nexus_lib)) - sys.path.append(nexus_lib) -#end def find_nexus_modules - - -def import_nexus_module(module_name): - import importlib - return importlib.import_module(module_name) -#end def import_nexus_module - - -# Get Nexus version try: - # Attempt specialized path-based imports. - # (The executable should still work even if Nexus is not installed) - find_nexus_modules() - - nxs_ver_mod = import_nexus_module('nexus.nexus_version') - nexus_version = nxs_ver_mod.nexus_version - del nxs_ver_mod -except: - try: - from nexus.nexus_version import nexus_version - except: - nexus_version = 0,0,0 - #end try -#end try + import pytest +except ImportError: + print( + "You must have pytest installed to run Nexus's testing suite!\n" + "You can install it using one of the following commands:\n" + "$ pip3 install pytest\n" + "$ uv pip install pytest\n\n" + "It is also recommended to install pytest-order to aid in potential debugging:\n" + "$ pip3 install pytest-order\n" + "$ uv pip install pytest-order\n" + ) + sys.exit(1) +if __name__ == "__main__": + import os + from pathlib import Path -if __name__=='__main__': - import re - from time import time # used to get user wall clock rather than cpu time - tstart_all = time() + test_dir = Path(__file__).resolve().parent.parent / "tests" - testing_wrong_nexus_install = False try: - import nexus - nexus_file = os.path.realpath(os.path.join(nexus.__file__,'../')) - test_file = os.path.realpath(os.path.join(__file__,'../..')) - testing_wrong_nexus_install = nexus_file!=test_file - except: + # This makes the output from pytest cleaner in that it doesn't print + # the full path from the user's CWD to the Nexus libraries. + os.chdir(test_dir) + except PermissionError: pass - if testing_wrong_nexus_install: - print('\n\n\nInstalled Nexus package does not reside with this nxs-test executable.\n Currently installed nexus package: {}\n Correct Nexus package : {}\n Please install the correct Nexus package above.\n\n'.format(nexus_file,test_file)) - sys.exit(1) - - # read command line input - regex = None - ctest = False - - parser = OptionParser( - usage='usage: %prog [options]', - add_help_option=False, - version='%prog {}.{}.{}'.format(*nexus_version) - ) - - parser.add_option('-h','--help',dest='help', - action='store_true',default=False, - help='Print help information and exit (default=%default).' - ) - parser.add_option('-v','--verbose',dest='verbose', - action='store_true',default=False, - help='Print detailed information (default=%default).' - ) - parser.add_option('-R','--regex',dest='regex', - default='none', - help='Tests with names matching the regular expression (regex) will be run. The default behavior is to run all tests (default=%default).' - ) - parser.add_option('--list',dest='list', - action='store_true',default=False, - help='List tests in human readable format. (default=%default).' - ) - parser.add_option('--full',dest='full', - action='store_true',default=False, - help='Test optional features (default=%default).' - ) - parser.add_option('--ctestlist',dest='ctestlist', - action='store_true',default=False, - help='List tests in CMake format. Intended for use within CTest (default=%default).' - ) - parser.add_option('--ctest',dest='ctest', - action='store_true',default=False, - help='Compatibility mode for calls from the CTest framework (default=%default).' - ) - parser.add_option('--pythonpath',dest='pythonpath', - default='none', - help='Sets PYTHONPATH environment variable for any scripts executed by nxs-test. The default behavior is to use PYTHONPATH as already defined in the host environment.' - ) - parser.add_option('--trip',dest='trip', - default='none', - help='Cause the "trip"-th assertion statement to fail. Useful when to ensure that the CMake script is working properly when interfacing with CTest (default=%default).' - ) - parser.add_option('--generate_reference',dest='generate_reference', - action='store_true',default=False, - help='Regenerate reference data, but do not overwrite existing reference files. Intended for developer use (default=%default).' - ) - parser.add_option('--update_reference',dest='update_reference', - action='store_true',default=False, - help='Regenerate reference data and update existing reference files. Intended for developer use (default=%default).' - ) - parser.add_option('--update_mode',dest='update_mode', - default='new', - help='Modes of operation when updating reference files. Intended for developer use. Options are "new", "failed", "all" (default=%default).' - ) - parser.add_option('--update_dryrun',dest='update_dryrun', - action='store_true',default=False, - help='Perform a dryrun of updating reference files, reporting on files that will be update in a non-dryrun. Intended for developer use (default=%default).' - ) - parser.add_option('--job_ref_table',dest='job_ref_table', - action='store_true',default=False, - help='Print reference data for job run commands on various machines. Intended for developer use (default=%default).' - ) - - options,files_in = parser.parse_args() - - if options.help: - print('\n'+parser.format_help().strip()) - exit() - #end if - - if options.regex!='none': - regex = options.regex - #end if - ctest = options.ctest - if options.trip!='none': - try: - NexusTestBase.assert_trip = int(options.trip) - except: - msg='command line option "--trip" must be an integer, received {0}'.format(options.trip) - exit_fail(msg) - #end try - #end if - - # clear out old test data - NexusTest.setup() - - # initialize user example data - ued = user_examples_data - ued['dir'] = 'user_examples' - ued['test_path'] = NexusTestBase.test_path_from_dir(ued['dir']) - ued['failures_filename'] = 'test_failures.txt' - ued['failures_filepath'] = os.path.join(ued['test_path'],ued['failures_filename']) - ued['failures_file'] = None - - # If requested, regenerate reference data and exit - update_modes = ('new','failed','all') - if options.update_mode not in update_modes: - msg = 'command line option "--update_mode" must be {}, received {}'.format(update_modes,options.update_mode) - exit_fail(msg) - #end if - if options.generate_reference: - regenerate_reference(update=False) - exit() - #end if - if options.update_reference: - #exit_fail('Automatic update of reference data is not yet supported.') - regenerate_reference(update=True) - exit() - #end if - - # remove failures file prior to testing - if os.path.exists(ued['failures_filepath']): - os.remove(ued['failures_filepath']) - #end if - del ued - - # identify test list to run - tests = [] - for test in NexusTest.test_list: - if regex is None: - tests.append(test) - elif re.search(regex,test.name): - tests.append(test) - #end if - #end for - if options.list: - print('Test list:') - for test in tests: - print(' ',test.name) - #end for - exit() - #end if - if len(tests)!=1 and ctest: - exit_fail('Exactly one test should be selected when using ctest\n tests requested: {0}'.format([test.name for test in tests])) - #end if - if options.ctestlist: - c = '' - for test in tests: - c+=test.name+';' - #end for - sys.stdout.write(c[:-1]) - exit() - #end if - if options.pythonpath!='none': - os.environ['PYTHONPATH']=options.pythonpath - #end if - try: - from nexus.generic import generic_settings - except Exception as exception: - print("\n\n") - print(40*"!") - print(exception) - print(40*"!","\n\n") - print("Can not load nexus.generic, please check the offending modules!\n") - sys.exit(1) - - generic_settings.raise_error = True - - # import core testing functions (shared between nxs-test and unit tests) - try: - from nexus.testing import global_data, numpy_available - except Exception as exception: - print("\n\n") - print(40*"!") - print(exception) - print(40*"!","\n\n") - print("Can not load nexus.testing, please check the offending modules!\n") - sys.exit(1) - - global_data['verbose'] = options.verbose - global_data['job_ref_table'] = options.job_ref_table - - # guard against missing numpy (required) - if len(tests)>0 and not numpy_available: - print('\nNumPy is required to run the tests.\nPlease install NumPy and try again.\n') - exit(1) - #end if - - # run each test and print the test outcome - if not ctest: - print('') - #end if - nrunnable = 0 - for test in tests: - if test.optional and not options.full: - continue - #end if - nrunnable += 1 - #end for - n=0 - npassed = 0 - nfailed = 0 - nrun = 0 - for test in tests: - t1 = time() - - # skip optional tests, unless requested - if test.optional and not options.full: - continue - #end if - n+=1 - - # run the test - test.run() - nrun += 1 - - # print the pass/fail line - if len(test.name)<40: - title = test.name+(40-len(test.name))*'.' - else: - title = test.name - #end if - if test.passed: - status = 'Passed' - npassed+=1 - elif test.failed: - status = 'Failed' - nfailed+=1 - else: - status = 'Unknown' - #end if - t2 = time() - if not ctest: - slt = str(nrunnable) - sn = str(n) - if len(sn) 1: + if "-h" in sys.argv or "--help" in sys.argv: + print( + "Usage:\n" + '$ nxs-test \n\n' + "See https://docs.pytest.org/en/stable/how-to/usage.html\n" + "for specification of arguments.\n\n" + "To select only specific tests, use `-k ''` from\n" + "Pytest's section on specifying which tests to run.\n" + "The other methods listed there are not supported by nxs-test." + ) + sys.exit(1) + + for arg in sys.argv[1:]: + pytest_args.append(arg) + + retcode = pytest.main([ + "--exitfirst", + "--disable-warnings", + *pytest_args, + f"{test_dir}", + ]) + + sys.exit(retcode) diff --git a/nexus/nexus/bin/qdens b/nexus/nexus/bin/qdens index 07b9ae5795..844603aa18 100755 --- a/nexus/nexus/bin/qdens +++ b/nexus/nexus/bin/qdens @@ -2,9 +2,20 @@ import gc import os +import sys from pathlib import Path from optparse import OptionParser +if sys.version_info[0:3] < (3, 10, 0): + v = sys.version_info[0:3] + print( + f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n" + "To use Nexus, please install at least Python 3.10.0 or higher!\n\n" + "If you already have a higher version installed, ensure that your Python\n" + "environment is properly activated and your $PATH is set correctly." + ) + sys.exit(1) + # Copied from qmca. Modification must done on qmca first # Locate and import the closely coupled Nexus module search_basepath = Path(__file__).resolve().parent.parent diff --git a/nexus/nexus/bin/qdens-radial b/nexus/nexus/bin/qdens-radial index 1315116817..748821c6c4 100755 --- a/nexus/nexus/bin/qdens-radial +++ b/nexus/nexus/bin/qdens-radial @@ -2,6 +2,17 @@ from pathlib import Path from optparse import OptionParser +import sys + +if sys.version_info[0:3] < (3, 10, 0): + v = sys.version_info[0:3] + print( + f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n" + "To use Nexus, please install at least Python 3.10.0 or higher!\n\n" + "If you already have a higher version installed, ensure that your Python\n" + "environment is properly activated and your $PATH is set correctly." + ) + sys.exit(1) # Copied from qmca. Modification must done on qmca first # Locate and import the closely coupled Nexus module diff --git a/nexus/nexus/bin/qmc-fit b/nexus/nexus/bin/qmc-fit index 732378dedc..64bb847d9e 100755 --- a/nexus/nexus/bin/qmc-fit +++ b/nexus/nexus/bin/qmc-fit @@ -5,6 +5,16 @@ import sys import argparse from pathlib import Path +if sys.version_info[0:3] < (3, 10, 0): + v = sys.version_info[0:3] + print( + f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n" + "To use Nexus, please install at least Python 3.10.0 or higher!\n\n" + "If you already have a higher version installed, ensure that your Python\n" + "environment is properly activated and your $PATH is set correctly." + ) + sys.exit(1) + try: import numpy as np except: diff --git a/nexus/nexus/bin/qmca b/nexus/nexus/bin/qmca index 26de06b7e0..7a5bcfb45b 100755 --- a/nexus/nexus/bin/qmca +++ b/nexus/nexus/bin/qmca @@ -5,6 +5,15 @@ from pathlib import Path import sys from optparse import OptionParser +if sys.version_info[0:3] < (3, 10, 0): + v = sys.version_info[0:3] + print( + f"Your version of Python ({v[0]}.{v[1]}.{v[2]}) is less than the minimum required for Nexus!\n" + "To use Nexus, please install at least Python 3.10.0 or higher!\n\n" + "If you already have a higher version installed, ensure that your Python\n" + "environment is properly activated and your $PATH is set correctly." + ) + sys.exit(1) # Gold implementation. All the Nexus scripts need to be updated once modified. # Locate and import the closely coupled Nexus module diff --git a/nexus/nexus/developer.py b/nexus/nexus/developer.py index 92c4fd70a0..ee20449688 100644 --- a/nexus/nexus/developer.py +++ b/nexus/nexus/developer.py @@ -37,8 +37,12 @@ class DevBase(obj): - def not_implemented(self): - self.error('a base class function has not been implemented',trace=True) + def not_implemented(self,name=None): + if name is None: + msg = 'a member function has not been implemented for class "{}"'.format(self.__class__.__name__) + else: + msg = 'member function "{}" has not been implemented for class "{}"'.format(name,self.__class__.__name__) + self.error(msg,trace=True) #end def not_implemented #end class DevBase diff --git a/nexus/nexus/examples/dynamic_workflows/01_basic_dependencies/dyn_basic_dep.py b/nexus/nexus/examples/dynamic_workflows/01_basic_dependencies/dyn_basic_dep.py new file mode 100755 index 0000000000..073d6b937f --- /dev/null +++ b/nexus/nexus/examples/dynamic_workflows/01_basic_dependencies/dyn_basic_dep.py @@ -0,0 +1,133 @@ +#! /usr/bin/env python3 + +''' +This example shows how a familiar DAG-like Nexus workflow +is translated to the dynamic setting. + +Here, a relaxation calculation passes a relaxed structure +to subsequent SCF and NSCF runs, now at the moment of completion. + +Similarly, SCF produces and provides a charge density for +the final NSCF run. +''' + +import numpy as np +from nexus import settings,job +from nexus import generate_physical_system +from nexus import generate_pwscf +from nexus import workflow_manager + + +settings( + results = '', + pseudo_dir = '../../qmcpack/pseudopotentials', + machine = 'ws8', + dynamic = True, + ) + + +system = generate_physical_system( + structure = 'diamond', + cell = 'prim', + kgrid = (2,1,1), + C = 4, + ) + + +# small random displacement +s = system.structure +disp = 0.003*np.random.randn(*s.pos.shape) +disp = np.abs(disp) +disp = np.dot(disp,s.axes) +s.pos += disp + + +relax = generate_pwscf( + identifier = 'relax', + path = 'relax', + job = job(cores=8), + system = system, + pseudos = ['C.BFD.upf'], + input_type = 'relax', + input_dft = 'pbe', + ecut = 200, + conv_thr = 1e-6, + kgrid = (2,1,1), + kshift = (1,1,1), + # combined [path,identifier,dynamic_id] must be unique + dynamic_id = 'relax1', + # requires nothing (runs immediately) + requires = 'none', + ) + + +scf = generate_pwscf( + identifier = 'scf', + path = 'scf', + job = job(cores=4), + system = system, + pseudos = ['C.BFD.upf'], + input_type = 'generic', + ecutwfc = 200, + kgrid = (2,2,1), + nosym = True, + dynamic_id = 'scf1', + # needs structure prior to run + requires = 'structure', + ) + + +nscf = generate_pwscf( + identifier = 'nscf', + path = 'nscf', + job = job(cores=4), + system = system, + pseudos = ['C.BFD.upf'], + input_type = 'generic', + calculation = 'nscf', + ecutwfc = 200, + dynamic_id = 'nscf1', + # needs structure and charge density prior to run + requires = ('charge_density','structure'), + ) + + +# Workflow manager oversees dynamic workflow +wm = workflow_manager() + + +# Poll to submit/check runs +max_polls = 500 +for i in range(max_polls): + print('\npoll ' + str(i)) + + if relax.succ: + print('\nRelaxation completed successfully,\npassing on structure.') + scf.structure = relax.structure + nscf.structure = relax.structure + + if scf.succ: + print('\nSCF completed successfully,\npassing on charge density.') + nscf.charge_density = scf.charge_density + + if relax.fail or scf.fail or nscf.done: + if nscf.succ: + print('\nNSCF completed successfully.') + break + + # Runs execute immediately at poll if ready. + # Poll should go at loops end. + wm.poll(1) # Sleep for 1 second between polls. + + +# Check end status +if i==max_polls-1: + print('\nMax polls exceeded without runs finishing.') +elif relax.fail: + print('\nRelaxation failed.') +elif scf.fail: + print('\nSCF failed.') +elif nscf.fail: + print('\nSCF failed.') +else: + print('\nAll runs completed successfully!') diff --git a/nexus/nexus/examples/dynamic_workflows/02_energy_convergence/dyn_energy_conv.py b/nexus/nexus/examples/dynamic_workflows/02_energy_convergence/dyn_energy_conv.py new file mode 100755 index 0000000000..456dbd2da5 --- /dev/null +++ b/nexus/nexus/examples/dynamic_workflows/02_energy_convergence/dyn_energy_conv.py @@ -0,0 +1,225 @@ +#! /usr/bin/env python3 + +''' +A simple type of dynamic workflow is to automatically determine +converged parameter values. In DFT, two such cases are convergence +of the total energy with respect to increasing planewave energy +cutoff and to increasingly large k-poing grids. + +This example first iteratively finds a converged planewave energy +cutoff for a diamond primitive cell using a BFD potential for carbon +and terminating when successive iterations produce total energies +within 1e-4 Ry of each other. The resulting energy cutoff is then +fed into another iterative convergence procedure for the k-point grid, +which stops when a tolerance of 1e-3 Ry has been met. The converged +values for the energy cutoff and k-point grid are 330 Ry and 7x7x7, +respectively. + +From this example, it is clear how the workflow can be extended to +include subsequent supercell expansion, Jastrow factor optimization, +and VMC/DMC runs with total energies converged below a specified +minimum statistical errorbar. +''' + +from nexus import settings,job,workflow_manager +from nexus import generate_physical_system +from nexus import generate_pwscf + + +settings( + results = '', + pseudo_dir = '../../qmcpack/pseudopotentials', + machine = 'ws8', + dynamic = True, + ) + + +def gen_system(tiling=None,kgrid=(1,1,1)): + system = generate_physical_system( + structure = 'diamond', + cell = 'prim', + tiling = tiling, + kgrid = kgrid, + C = 4, + ) + return system + + +# convenience function to make QE sims +def gen_qe(run_type = 'scf', + dynamic_id = 'qe', + path = None, + system = None, + ecutwfc = None, + nkgrid = None, + ): + if nkgrid is None: + nkgrid = 1 + path = '01_ecut_conv/ecut_'+str(ecutwfc) + else: + path = '02_kgrid_conv/kgrid_{0}{0}{0}'.format(nkgrid) + assert run_type in ('scf','nscf') + if run_type=='scf': + kgrid = 3*[nkgrid] + extra = dict(kgrid=kgrid,requires='none') + elif run_type=='nscf': + extra = dict(nosym=True,requires='charge_density') + if system is None: + system = gen_system() + qe = generate_pwscf( + identifier = run_type, + path = path, + job = job(cores=4), + system = system, + pseudos = ['C.BFD.upf'], + input_type = 'generic', + ecutwfc = ecutwfc, + dynamic_id = dynamic_id, + **extra + ) + return qe + + +# create the dynamic workflow manager +wm = workflow_manager() + + + +#==============================================# +# Planewave energy cutoff convergence workflow # +# # +# Iteratively increase the cutoff until the # +# energy difference between iterations falls # +# below a tolerance threshold. # +#==============================================# + +# convenience function for log printing +def print_progress(ecut,energies): + print() + print(50*'=') + print(' ecuts :',ecuts) + print(' energies:',energies) + if len(energies)>=2: + dE = abs(energies[-1]-energies[-2]) + print(' dE = {:7.5f} , tol = {:7.5f}'.format(dE,tol)) + print(50*'=') + print() + + +print(3*'\n'+70*'*') +print('Determining converged PW energy cutoff') +print(70*'*'+'\n') +max_runs = 10 # maximum number of scf runs allowed +energies = [] # total energy history +ecut = 50 # initial energy cutoff +tol = 1e-4 # tolerance for convergence (Ry) +converged = False +ecuts = [] + +# Start with a single QE simulation, ecut = 50 Ry +nruns = 1 +qe = gen_qe(ecutwfc=ecut) + +# Convergence iterations +while not converged: + print('poll') + + if qe.succ: + # Current QE run succeeded + # Capture the total energy and the energy cutoff + energies.append(qe.products.energy) + ecuts.append(ecut) + # Check if the tolerance has been met + if len(energies)<2 or abs(energies[-1]-energies[-2])>tol: + print_progress(ecut,energies) + # If not, increase the energy cutoff by 50% + ecut = int(((1.5*ecut)//10)*10) + # Run subsequent QE with higher cutoff + nruns += 1 + if nruns>max_runs: + dE = abs(energies[-1]-energies[-2]) + print('\n'+50*'*') + print('Maximum number of runs exceeded ({})'.format(max_runs)) + print('Convergence level requested: {:6.4e}'.format(tol)) + print('Convergence level reached : {:6.4e}'.format(abs(dE))) + print(50*'*'+'\n') + exit(1) + qe = gen_qe(ecutwfc=ecut) + else: + # When converged, report the final energy cutoff + print_progress(ecut,energies) + print('\n'+50*'*') + print('Converged!!! Final energy cutoff: '+str(ecut)) + print(50*'*') + converged = True # to exit polling loop + elif qe.fail: + print('\nQE run failed!!!') + exit(1) + + # Run simulations actively upon poll + wm.poll(1) + + + +#==============================================# +# k-point grid convergence workflow # +# # +# Iteratively increase the k-point grid until # +# the energy difference between iterations # +# falls below a tolerance threshold. # +#==============================================# + +# convenience function for log printing +def print_progress(nkgrid,energies): + print() + print(50*'=') + print(' nkgrids :',nkgrids) + print(' energies:',energies) + if len(energies)>=2: + dE = abs(energies[-1]-energies[-2]) + print(' dE = {:6.4f} , tol = {:6.4f}'.format(dE,tol)) + print(50*'=') + print() + +print(3*'\n'+70*'*') +print('Determining converged k-point grid') +print(70*'*'+'\n') +max_runs = 10 +energies = [] +nkgrid = 1 +tol = 1e-3 +converged = False +nkgrids = [] +nruns = 1 +qe = gen_qe(ecutwfc=ecut,nkgrid=nkgrid) +while not converged: + print('poll') + if qe.succ: + energies.append(qe.products.energy) + nkgrids.append(nkgrid) + if len(energies)<2 or abs(energies[-1]-energies[-2])>tol: + print_progress(nkgrid,energies) + nkgrid += 1 + nruns += 1 + if nruns>max_runs: + dE = abs(energies[-1]-energies[-2]) + print('\n'+50*'*') + print('Maximum number of runs exceeded ({})'.format(max_runs)) + print('Convergence level requested: {:6.4e}'.format(tol)) + print('Convergence level reached : {:6.4e}'.format(abs(dE))) + print(50*'*'+'\n') + exit(1) + qe = gen_qe(ecutwfc=ecut,nkgrid=nkgrid) + else: + print_progress(nkgrid,energies) + print('\n'+50*'*') + print('Converged!!! Final kgrid: {0}x{0}x{0}'.format(nkgrid)) + print(50*'*') + converged = True # to exit polling loop + elif qe.fail: + print('\nQE run failed!!!') + exit(1) + wm.poll(1) + + + diff --git a/nexus/nexus/examples/dynamic_workflows/02_energy_convergence/dyn_energy_conv_brief.py b/nexus/nexus/examples/dynamic_workflows/02_energy_convergence/dyn_energy_conv_brief.py new file mode 100755 index 0000000000..a7e3df17ec --- /dev/null +++ b/nexus/nexus/examples/dynamic_workflows/02_energy_convergence/dyn_energy_conv_brief.py @@ -0,0 +1,146 @@ +#! /usr/bin/env python3 + +from nexus import settings,job,workflow_manager +from nexus import generate_physical_system +from nexus import generate_pwscf + +''' +A simple type of dynamic workflow is to automatically determine +converged parameter values. In DFT, two such cases are convergence +of the total energy with respect to increasing planewave energy +cutoff and to increasingly large k-poing grids. + +This example first iteratively finds a converged planewave energy +cutoff for a diamond primitive cell using a BFD potential for carbon +and terminating when successive iterations produce total energies +within 1e-4 Ry of each other. The resulting energy cutoff is then +fed into another iterative convergence procedure for the k-point grid, +which stops when a tolerance of 1e-3 Ry has been met. The converged +values for the energy cutoff and k-point grid are 330 Ry and 7x7x7, +respectively. + +From this example, it is clear how the workflow can be extended to +include subsequent supercell expansion, Jastrow factor optimization, +and VMC/DMC runs with total energies converged below a specified +minimum statistical errorbar. +''' + +settings( + results = '', + pseudo_dir = '../../qmcpack/pseudopotentials', + machine = 'ws8', + dynamic = True, + ) + + +def gen_system(tiling=None,kgrid=(1,1,1)): + system = generate_physical_system( + structure = 'diamond', + cell = 'prim', + tiling = tiling, + kgrid = kgrid, + C = 4, + ) + return system + + +def gen_qe(run_type = 'scf', + dynamic_id = 'qe', + path = None, + system = None, + ecutwfc = None, + nkgrid = None, + ): + if nkgrid is None: + nkgrid = 1 + path = '01_ecut_conv/ecut_'+str(ecutwfc) + else: + path = '02_kgrid_conv/kgrid_{0}{0}{0}'.format(nkgrid) + assert run_type in ('scf','nscf') + if run_type=='scf': + kgrid = 3*[nkgrid] + extra = dict(kgrid=kgrid,requires='none') + elif run_type=='nscf': + extra = dict(nosym=True,requires='charge_density') + if system is None: + system = gen_system() + qe = generate_pwscf( + identifier = run_type, + path = path, + job = job(cores=4), + system = system, + pseudos = ['C.BFD.upf'], + input_type = 'generic', + ecutwfc = ecutwfc, + dynamic_id = dynamic_id, + **extra + ) + return qe + + +# start the workflow manager +wm = workflow_manager() + + +# determine planewave energy cutoff +max_runs = 10 +energies = [] +ecut = 50 +tol = 1e-4 +converged = False +ecuts = [] +nruns = 1 +qe = gen_qe(ecutwfc=ecut) +while not converged: + if qe.succ: + energies.append(qe.products.energy) + ecuts.append(ecut) + if len(energies)<2 or abs(energies[-1]-energies[-2])>tol: + nruns +=1 + if nruns>max_runs: + dE = abs(energies[-1]-energies[-2]) + print('\nMaximum number of runs exceeded!!!') + exit(1) + # dynamic portion + ecut = int(((1.5*ecut)//10)*10) + qe = gen_qe(ecutwfc=ecut) + else: + print('Converged!!! Final energy cutoff: '+str(ecut)) + converged = True + elif qe.fail: + print('\nQE run failed!!!') + exit(1) + wm.poll(1) + +# determine k-point grid, using the converged energy cutoff +max_runs = 10 +energies = [] +nkgrid = 1 +tol = 1e-3 +converged = False +nkgrids = [] +nruns = 1 +qe = gen_qe(ecutwfc=ecut,nkgrid=nkgrid) +while not converged: + if qe.succ: + energies.append(qe.products.energy) + nkgrids.append(nkgrid) + if len(energies)<2 or abs(energies[-1]-energies[-2])>tol: + nruns +=1 + if nruns>max_runs: + dE = abs(energies[-1]-energies[-2]) + print('\nMaximum number of runs exceeded!!!') + exit(1) + # dynamic portion + nkgrid += 1 + qe = gen_qe(ecutwfc=ecut,nkgrid=nkgrid) + else: + print('Converged!!! Final kgrid: {0}x{0}x{0}'.format(nkgrid)) + converged = True + elif qe.fail: + print('\nQE run failed!!!') + exit(1) + wm.poll(1) + + + diff --git a/nexus/nexus/examples/dynamic_workflows/README.rst b/nexus/nexus/examples/dynamic_workflows/README.rst new file mode 100644 index 0000000000..d04eefd281 --- /dev/null +++ b/nexus/nexus/examples/dynamic_workflows/README.rst @@ -0,0 +1,36 @@ +Dynamic Workflow Examples +========================= + +These examples illustrate the basic features of dynamic workflows in Nexus. +Dynamic workflows release the requirement that simulations be networked +together in a directed acyclic graph (DAG). This new feature allows workflows +to be programmed directly in native Python, which lays the foundation to +design and implement QMC algorithms constructed from multiple simulation +runs (e.g. SHDMC). + +Please note that this feature is under active development, so the interface +to dynamic workflows and the code in these examples may change at any time. + +Two examples are provided: + +1. A basic demonstration of how dependencies are processed. +2. A sequence of planewave energy cutoff and k-poing grid size based on a total energy tolerance. + +See the descriptions at the top of the example `.py` files. + + +Basic dependencies +------------------ + +This example shows how a familiar DAG-like Nexus workflow is translated to the dynamic setting. Here, a relaxation calculation passes a relaxed structure to subsequent SCF and NSCF runs, now at the moment of completion. Similarly, SCF produces and provides a charge density for the final NSCF run. + +Energy convergence +------------------ + +A simple type of dynamic workflow is to automatically determine converged parameter values. In DFT, two such cases are convergence of the total energy with respect to increasing planewave energy cutoff and to increasingly large k-poing grids. + +This example first iteratively finds a converged planewave energy cutoff for a diamond primitive cell using a BFD potential for carbon and terminating when successive iterations produce total energies within 1e-4 Ry of each other. The resulting energy cutoff is then fed into another iterative convergence procedure for the k-point grid, which stops when a tolerance of 1e-3 Ry has been met. The converged values for the energy cutoff and k-point grid are 330 Ry and 7x7x7, respectively. + +From this example, it is clear how the workflow can be extended to include subsequent supercell expansion, Jastrow factor optimization, and VMC/DMC runs with total energies converged below a specified minimum statistical errorbar. + + diff --git a/nexus/nexus/fileio.py b/nexus/nexus/fileio.py index 5f271f3296..d2ee7cbf39 100644 --- a/nexus/nexus/fileio.py +++ b/nexus/nexus/fileio.py @@ -27,9 +27,10 @@ import numpy as np from numpy.linalg import det, norm from .developer import DevBase, obj, error, to_str -from .periodic_table import is_element, pt as ptable +from .periodic_table import Elements from .unit_converter import convert from . import numpy_extensions as npe +from .utilities import path_string class TextFile(DevBase): # interface to mmap files @@ -39,11 +40,13 @@ def __init__(self,filepath=None): self.mm = None self.f = None if filepath is not None: + filepath = path_string(filepath) self.open(filepath) #end if #end def __init__ def open(self,filepath): + filepath = path_string(filepath) if not os.path.exists(filepath): self.error('cannot open non-existent file: {0}'.format(filepath)) #end if @@ -243,7 +246,8 @@ class StandardFile(DevBase): def __init__(self,filepath=None): if filepath is None: None - elif isinstance(filepath, (str, Path)): + elif isinstance(filepath, str | bytes | Path): + filepath = path_string(filepath) self.read(filepath) else: self.error('unsupported input: {0}'.format(filepath)) @@ -255,7 +259,9 @@ def read(self,filepath): if not os.path.exists(filepath): self.error('read failed\nfile does not exist: {0}'.format(filepath)) #end if - self.read_text(open(filepath,'r').read()) + with open(filepath, "r") as f: + self.read_text(f.read()) + self.check_valid('read failed') #end def read @@ -264,7 +270,8 @@ def write(self,filepath=None): self.check_valid('write failed') text = self.write_text() if filepath is not None: - open(filepath,'w').write(text) + with open(filepath, "w") as f: + f.write(text) #end if return text #end def write @@ -826,9 +833,9 @@ def incorporate_structure(self,structure): s.recenter() elem = [] for e in s.elem: - is_elem,e = is_element(e,symbol=True) + is_elem, e = Elements.is_element(e, return_element=True) if is_elem: - elem.append(ptable.elements[e].atomic_number) + elem.append(e.atomic_number) else: elem.append(0) #end if @@ -1127,7 +1134,7 @@ def validity_checks(self): msgs.append('elem must be an array of text') else: for e in self.elem: - iselem,symbol = is_element(e,symbol=True) + iselem, e = Elements.is_element(e, return_element=True) if not iselem: msgs.append('elem entry "{0}" is not an element'.format(e)) #end if @@ -1193,11 +1200,11 @@ def write_text(self): #end for if self.elem is not None: for e in self.elem: - iselem,symbol = is_element(e,symbol=True) + iselem, e = Elements.is_element(e, return_element=True) if not iselem: self.error('{0} is not an element'.format(e)) #end if - text += e+' ' + text += e.symbol+' ' #end for text += '\n' #end if @@ -1269,7 +1276,7 @@ def incorporate_xsf(self,xsf): species_ind = species species = [] for i in species_ind: - species.append(ptable.simple_elements[i].symbol) + species.append(Elements(i).symbol) #end for self.scale = 1.0 diff --git a/nexus/nexus/gamess.py b/nexus/nexus/gamess.py index 1267997beb..1fcc81f8f6 100644 --- a/nexus/nexus/gamess.py +++ b/nexus/nexus/gamess.py @@ -225,7 +225,8 @@ def app_command(self): def check_sim_status(self): - output = open(os.path.join(self.locdir,self.outfile),'r').read() + with open(os.path.join(self.locdir,self.outfile), "r") as out: + output = out.read() #errors = open(os.path.join(self.locdir,self.errfile),'r').read() self.failed = 'EXECUTION OF GAMESS TERMINATED -ABNORMALLY-' in output diff --git a/nexus/nexus/gamess_analyzer.py b/nexus/nexus/gamess_analyzer.py index ca5783d0a5..7e003f7180 100644 --- a/nexus/nexus/gamess_analyzer.py +++ b/nexus/nexus/gamess_analyzer.py @@ -21,6 +21,7 @@ from .fileio import TextFile from .simulation import SimulationAnalyzer,Simulation from .gamess_input import GamessInput +from .utilities import path_string def assign_value(host,dest,file,string): @@ -68,6 +69,7 @@ def __init__(self,arg0=None,prefix=None,analyze=False,exit=False,**outfilenames) infile = arg0 #end if if infile is not None: + infile = path_string(infile) info = self.info info.path = os.path.dirname(infile) info.input = GamessInput(infile) @@ -194,6 +196,8 @@ def analyze_log(self): self.ao_populations = ao_populations #end if #end if + if log is not None: + log.close() #end def analyze_log @@ -484,6 +488,7 @@ def analyze_punch(self): #end if punch.norbitals = norbs #end if + text.close() #end if except: if self.info.exit: diff --git a/nexus/nexus/gamess_input.py b/nexus/nexus/gamess_input.py index 64559c8af7..f6dac9184f 100644 --- a/nexus/nexus/gamess_input.py +++ b/nexus/nexus/gamess_input.py @@ -32,10 +32,11 @@ import numpy as np -from .periodic_table import pt +from .periodic_table import Elements from .developer import DevBase, obj, error, warn from .nexus_base import nexus_noncore from .simulation import SimulationInput +from .utilities import path_string class GIbase(DevBase): @@ -801,6 +802,7 @@ class GamessInput(SimulationInput,GIbase): def __init__(self,filepath=None): if filepath is not None: + filepath = path_string(filepath) self.read(filepath) #end if #end def __init__ @@ -1116,7 +1118,7 @@ def generate_any_gamess_input(**kwargs): #end if for i in range(len(elem)): a = elem[i] - Z = pt[a].atomic_number + Z = Elements(a).atomic_number data+='{0} {1:3.2f} {2:16.8f} {3:16.8f} {4:16.8f}\n'.format(a,Z,*pos[i]) if a in bss: data+=bss[a].text+'\n\n' @@ -1129,7 +1131,7 @@ def generate_any_gamess_input(**kwargs): ) pps = nexus_noncore.pseudopotentials.pseudos_by_atom(*pskw.pseudos) for i,a in enumerate(elem): - Z = pt[a].atomic_number + Z = Elements(a).atomic_number data+='{0} {1} {2:16.8f} {3:16.8f} {4:16.8f}\n'.format(a,Z,*pos[i]) if a in pps: data += pps[a].basis_text+'\n\n' diff --git a/nexus/nexus/gaussian_process.py b/nexus/nexus/gaussian_process.py deleted file mode 100644 index 722dde934d..0000000000 --- a/nexus/nexus/gaussian_process.py +++ /dev/null @@ -1,2253 +0,0 @@ -################################################################## -## (c) Copyright 2018- by Richard K. Archibald ## -## and Jaron T. Krogel ## -################################################################## - - -#====================================================================# -# gaussian_process.py # -# Uses Gaussian Processes to estimate optimization surfaces of # -# noisy data. # -# # -# Content summary: # -# lhs # -# Function to generate a latin-hypercube design. # -# # -# _lhsmaximin # -# Function to maximize the minimum distance between points. # -# Subroutine of lhs. # -# # -# _lhsclassic # -# Subroutine of _lhsmaximin # -# # -# _pdist # -# Function to calculate the pair-wise point distances of a # -# matrix. Subroutine of lhsmaximin. # -# # -# _fdist # -# Function to calculate distances between all points. # -# Subroutine of find_hyperparameters, find_min, and # -# find_new_points. # -# # -# cfgp # -# Function to calculate correlation function for Gaussian # -# Process. Subroutine of cmgp. # -# # -# cmgp # -# Function to calculate correlation matrix for Gaussian # -# Process. Subroutine of find_min. # -# # -# find_hyperparameters # -# Function to find best Gaussian Process hyperparameters. # -# Subroutine of gp_opt. # -# # -# find_min # -# Function to find local minimum of Gaussian Process surface. # -# Subroutine of gp_opt. # -# # -# find_new_points # -# Function to estimate optimal new points for Gaussian Process. # -# Subroutine of gp_opt. # -# # -# multiscale_E # -# Function to perform multiscale normalization of E. # -# Subroutine of gp_opt. # -# # -# inv_multiscale_E # -# Function to reverse multiscale normalization of E. # -# Subroutine of gp_opt. # -# # -# norm_pos # -# Function to normalize molecular positions to unit hyper cube. # -# Subroutine of gp_opt. # -# # -# inv_norm_pos # -# Function to reverse normalization of molecular positions. # -# Subroutine of gp_opt. # -# # -# gp_opt_setup # -# Function that sets up parameters and variables for GP. # -# # -# gp_opt # -# Function that performs one iteration of Gaussian Process # -# optimization. This is the main interface to Gaussian Process # -# iterations. # -# # -# opt_surface_f # -# Example function to optimize. # -# # -# gp_opt_example # -# Example using Gaussian Process optimization on opt_surface_f. # -# # -#====================================================================# - -import os -import numpy as np -from .developer import DevBase, obj, unavailable, error -from . import numpy_extensions as npe - -try: - import matplotlib.pyplot as plt -except: - plt = unavailable('matplotlib.pyplot') -#end try -try: - from scipy.spatial import Delaunay -except: - Delaunay = unavailable('scipy.spatial','Delaunay') -#end try -try: - from scipy.linalg import logm -except: - logm = unavailable('scipy.linalg','logm') -#end try - - -class GParmFlags: - """ - Define an empty class to store GP parameters and information - """ - pass - -def lhs(n, samples=None, iterations=None): - """ - Generate a latin-hypercube design - - Parameters - ---------- - n : int - The number of factors to generate samples for - - Optional - -------- - samples : int - The number of samples to generate for each factor (Default: n) - - iterations : int - The number of iterations in the maximin and correlations algorithms - (Default: 5). - - Returns - ------- - H : 2d-array - An n-by-samples design matrix that has been normalized so factor - values are uniformly spaced between zero and one. - - - Example - ------- - - A 4-factor design with 5 samples and 10 iterations:: - - >>> lhs(4, samples=5, iterations=10) - - """ - H = None - - if samples is None: - samples = n - - if iterations is None: - iterations = 5 - - H = _lhsmaximin(n, samples, iterations) - - - return H - -############################################################################### - -def _lhsclassic(n, samples): - # Generate the intervals - cut = np.linspace(0, 1, samples + 1) - - # Fill points uniformly in each interval - u = np.random.rand(samples, n) - a = cut[:samples] - b = cut[1:samples + 1] - rdpoints = np.zeros_like(u) - for j in range(n): - rdpoints[:, j] = u[:, j]*(b-a) + a - - # Make the random pairings - H = np.zeros_like(rdpoints) - for j in range(n): - order = np.random.permutation(range(samples)) - H[:, j] = rdpoints[order, j] - - return H - - -############################################################################### - -def _lhsmaximin(n, samples, iterations): - maxdist = 0 - - # Maximize the minimum distance between points - for i in range(iterations): - Hcandidate = _lhsclassic(n, samples) - - d = _pdist(Hcandidate) - if maxdist>> x = np.array([[0.1629447, 0.8616334], - ... [0.5811584, 0.3826752], - ... [0.2270954, 0.4442068], - ... [0.7670017, 0.7264718], - ... [0.8253975, 0.1937736]]) - >>> _pdist(x) - array([ 0.6358488, 0.4223272, 0.6189940, 0.9406808, 0.3593699, - 0.3908118, 0.3087661, 0.6092392, 0.6486001, 0.5358894]) - - """ - - x = np.atleast_2d(x) - assert len(x.shape)==2, 'Input array must be 2d-dimensional' - - m, n = x.shape - if m<2: - return [] - - d = np.zeros((m**2-m)/2) - c_v = 0 - for i in range(m - 1): - d[0+c_v:m-i-1+c_v]=np.sqrt(np.sum((np.repeat(np.reshape(x[i, :],\ - [1,n]),m-i-1,axis=0)-x[i+1:m+1, :])**2,axis=1)) - c_v = c_v+m-i-1 - - return d - -############################################################################### - -def _fdist(x): - - """ - Calculate Distance between all points - - - Parameters - ---------- - x: n x d array of points - - Returns - ------- - Dm : n x m correlation matrix - - """ - - [n,d] = x.shape - Dm = np.zeros([n,n]) - - for jn in range(n): - Dm[jn,:] = np.sqrt(np.sum((np.repeat(np.reshape(x[jn,:],[1,d]),\ - n,axis=0)-x)**2,axis=1)) - - - return Dm -############################################################################### - -def opt_surface_f(x,opt_fun): - - """ - Optimization Surface Function - - Parameters - ---------- - x: n x d-array, x \in Hyper cube - opt_fun: Optimization Function case - - Returns - ------- - y : value of optimization surface function - - """ - [n,d] = x.shape - - if opt_fun == 1: - y = np.zeros([n,1]) - for jp in range(n): - y[jp,0] = lennard_jones(x[jp,:]) - elif opt_fun == 2: - y = np.zeros([n,1]) - for jp in range(n): - y[jp,0] = beale(x[jp,:]) - elif opt_fun == 3: - y = np.zeros([n,1]) - for jp in range(n): - y[jp,0] = rosenbrock(x[jp,:]) - elif opt_fun == 4: - y = np.zeros([n,1]) - for jp in range(n): - y[jp,0] = goldstein_price(x[jp,:]) - else: - y = np.reshape(2.0*np.sin(np.pi*np.sum(x**2,1)/2)-1,[n,1]) - - - return y - - -############################################################################### -def lennard_jones(x): - # parameters, 1+2+3*nx - x = x.ravel() - nparams = len(x) - if nparams!=1 and nparams%3!=0 or nparams==0: - print('invalid number of parameters for lennard jones') - exit() - #end if - r = [[ 0,0,0], - [x[0],0,0]] - if nparams>1: - r.append([x[1],x[2],0]) - #end if - if nparams>3: - i=3 - while i+2=0 - ep: val ep>0 - - Returns - ------- - y : value of correlation function - - """ - - y = np.exp(-ep*r**2) - - return y - -############################################################################### - -def cmgp(S1,S2,ep): - - """ - Calculate correlation matrix for Gaussian Process - - - Parameters - ---------- - S1: n x d array of points - S2: m x d array of points - ep: GP kernel parameter ep>0 - - Returns - ------- - K : n x m correlation matrix - - """ - - n = S1.shape[0] - d = S1.shape[1] - m = S2.shape[0] - K = np.zeros([n,m]) - - for jn in range(n): - K[jn,:] = np.sqrt(np.sum((np.repeat(np.reshape(S1[jn,:],[1,d]),\ - m,axis=0)-S2)**2,axis=1)) - - K = cfgp(K,ep) - - return K - -############################################################################### - -def find_hyperparameters(mol_pos,E,dE): - - """ - Finds best Gaussian Process hyperparameters - - - Parameters - ---------- - mol_pos: GP centers - E: Energy for GP centers - dE: Uncertainty in energy - - Returns - ------- - hyp_parm: GP hyperparameters - Co_GP: GP coefficents - """ - [Nc,d] = mol_pos.shape - - W = np.diag(dE[:,0]) - - D =_fdist(mol_pos) - - hyp_parm = np.zeros(2) - - hyp_parm[0] = np.log(np.max(np.min(D+np.max(D)*np.eye(Nc),axis=1)))/2.0 - dhyp_parm = np.zeros(2) - dhyp_parm[:] = 1e-1*np.abs(hyp_parm[0]) - tol = 1e-2*np.abs(hyp_parm[0]) - - K = np.exp(2.0*hyp_parm[1])*cfgp(D,np.exp(-2.0*hyp_parm[0])) - Kw_inv = np.linalg.pinv(K+W) - Co_GP = np.matmul(Kw_inv,E) - - b_loocv_err = np.matmul(np.transpose(E),Co_GP)+np.trace(logm(K+W)) - - while max(dhyp_parm)>tol: - for jp in range(hyp_parm.shape[0]): - did_move = 0 - chyp_parm = np.copy(hyp_parm) - chyp_parm[jp] = chyp_parm[jp]+dhyp_parm[jp] - K = np.exp(2.0*chyp_parm[1])*cfgp(D,np.exp(-2.0*chyp_parm[0])) - Kw_inv = np.linalg.pinv(K+W) - Co_GP = np.matmul(Kw_inv,E) - - c_loocv_err = np.matmul(np.transpose(E),Co_GP)+np.trace(logm(K+W)) - - if c_loocv_err1: - T = Delaunay(mol_pos) - us_ind = np.setdiff1d(np.arange(Nc),np.unique(T.convex_hull)) - if us_ind.shape[0] == 0: - us_ind = np.zeros(1, dtype=int) - us_ind[0] = np.argmin(E) - else: - us_ind = np.arange(Nc) - - D =_fdist(mol_pos) - best_pos = mol_pos - ref_dis = np.min(np.min(D+np.max(D)*np.eye(Nc),axis=1))/10 - K = np.exp(2.0*hyp_parm[1])*cfgp(D,np.exp(-2.0*hyp_parm[0])) - W = np.diag(dE[:,0]) - Kw_inv = np.linalg.pinv(K+W) - - cnum = np.linalg.cond(K+W) - if cnum>1e16: - print('Warning high condition number results may suffer') - - delta_pos = ref_dis+np.zeros([Nc,d]) - tol_pos = ref_dis/10 - best_E = np.matmul(K,Co_GP) - Nc_search = us_ind.shape[0] - - - delta_pos = delta_pos[us_ind,:] - best_E = best_E[us_ind,:] - best_pos = best_pos[us_ind,:] - - - while np.max(delta_pos)>tol_pos: - for jp in range(Nc_search): - for jd in range(d): - did_move = 0 - c_pos = np.copy(best_pos) - c_pos[jp,jd]= min(best_pos[jp,jd]+delta_pos[jp,jd],1.0) - - Kc = np.exp(2.0*hyp_parm[1])*cmgp(np.reshape(c_pos[jp,:],[1,d]),mol_pos,np.exp(-2.0*hyp_parm[0])) - c_E = np.matmul(Kc,Co_GP) - if c_E1: - us_ind = np.argwhere(T.find_simplex(best_pos)>-1) - if us_ind.shape[0] == 0: - us_ind = np.argwhere(T.simplices==np.argmin(E)) - c_E = np.zeros([us_ind.shape[0],1]) - for jp in range(us_ind.shape[0]): - c_E[jp] = np.mean(E[T.simplices[us_ind[jp,0],:],:]) - - best_ind = np.argmin(c_E[:,0]) - best_E = np.reshape(c_E[best_ind,:],[1,1]) - best_pos = np.mean(mol_pos[T.simplices[us_ind[best_ind,0],:],:],axis=0) - else: - best_E = best_E[us_ind[:,0],:] - best_pos = best_pos[us_ind[:,0],:] - else: - us_ind = np.union1d(np.argwhere(best_pos[:,0]>min(mol_pos)),np.argwhere(best_pos[:,0]1: - jp = 0 - ind_T = T.find_simplex(best_pos) - ind_T = np.reshape(ind_T,[ind_T.shape[0],1]) - while jp1: - min_ind = np.argmin(best_E[us_ind[:,0],0]) - best_E[us_ind[0,0],0] = best_E[us_ind[min_ind,0],0] - best_pos[us_ind[0,0],:] = best_pos[us_ind[min_ind,0],:] - best_E = np.delete(best_E,us_ind[1:us_ind.shape[0],0],0) - best_pos = np.delete(best_pos,us_ind[1:us_ind.shape[0],0],0) - ind_T = np.delete(ind_T,us_ind[1:us_ind.shape[0],0],0) - - jp += 1 - - jp = 0 - while jp1: - min_ind = np.argmin(best_E[us_ind[:,0],0]) - best_E[us_ind[0,0],0] = best_E[us_ind[min_ind,0],0] - best_pos[us_ind[0,0],:] = best_pos[us_ind[min_ind,0],:] - best_E = np.delete(best_E,us_ind[1:us_ind.shape[0],0],0) - best_pos = np.delete(best_pos,us_ind[1:us_ind.shape[0],0],0) - - jp += 1 - - ind_T = T.find_simplex(best_pos) - ind_T = np.reshape(ind_T,[ind_T.shape[0],1]) - - if best_E.shape[0] > 1: - ind_sort = np.argsort(best_E[:,0]) - ind_rm = np.argwhere(best_E[ind_sort,0]>np.mean(E)-np.std(E)) - if ind_rm.shape[0]>0: - if ind_rm[0,0] == 0: - ind_rm = 1 - else: - ind_rm = min(ind_rm[0,0],d+1) - - ind_sort = ind_sort[0:ind_rm] - - best_E = best_E[ind_sort,:] - best_pos = best_pos[ind_sort,:] - ind_T = ind_T[ind_sort,:] - - neig_data_ind = T.simplices[ind_T[:,0],:] - else: - - jp = 0 - while jp1: - min_ind = np.argmin(best_E[us_ind[:,0],0]) - best_E[us_ind[0,0],0] = best_E[us_ind[min_ind,0],0] - best_pos[us_ind[0,0],:] = best_pos[us_ind[min_ind,0],:] - best_E = np.delete(best_E,us_ind[1:us_ind.shape[0],0],0) - best_pos = np.delete(best_pos,us_ind[1:us_ind.shape[0],0],0) - - jp += 1 - - if best_E.shape[0] > 1: - ind_sort = np.argsort(best_E[:,0]) - ind_rm = np.argwhere(best_E[ind_sort,0]>np.mean(E)-np.std(E)) - if ind_rm.shape[0]>0: - if ind_rm[0,0] == 0: - ind_rm = 1 - else: - ind_rm = ind_rm[0,0] - - ind_sort = ind_sort[0:ind_rm] - - best_E = best_E[ind_sort,:] - best_pos = best_pos[ind_sort,:] - - neig_data_ind = np.zeros([best_pos.shape[0],2], dtype=int) - for jp in range(best_pos.shape[0]): - c_dis = np.sqrt(np.sum((np.repeat(np.reshape(best_pos[jp,:],[1,d]),\ - mol_pos.shape[0],axis=0)-mol_pos)**2,axis=1)) - sort_ind = np.argsort(c_dis) - neig_data_ind[jp,0]=sort_ind[0] - neig_data_ind[jp,1]=sort_ind[1] - - ## Estimate Error - K_res = np.exp(2.0*hyp_parm[1])*cmgp(best_pos,mol_pos,np.exp(-2.0*hyp_parm[0])) - best_dE = np.reshape(2*np.abs(np.exp(2.0*hyp_parm[1])-\ - np.diag(np.matmul(K_res,np.matmul(Kw_inv,np.transpose(K_res))))),[best_pos.shape[0],1]) - - return best_pos,best_E,best_dE,neig_data_ind - - -############################################################################### -def find_new_points(mol_pos,best_pos,delta_r,Nc0): - - """ - Estimate optimal new points for Gaussian Process - - - Parameters - ---------- - best_pos: Estimated local minimum - best_E: Estimated local energies - delta_r: Maximum distance of new search space - Nc0: Number of points to add - - Returns - ------- - new_points: New sample points for GP - """ - - [Nc,d] = mol_pos.shape - - if best_pos.shape[0]>Nc0: - best_pos = best_pos[0:Nc0,:] - - new_points = np.zeros([Nc0,d]) - n_clusters = best_pos.shape[0] - ind_clusters = np.round(np.linspace(0,n_clusters,n_clusters+1)*Nc0/(n_clusters)) - ind_clusters = ind_clusters.astype(int) - shyper_cube = np.zeros([d,2]) - n_min_d = 5 - - for jc in range(n_clusters): - n_pnts = ind_clusters[jc+1]-ind_clusters[jc] - shyper_cube[:,0] = np.maximum(best_pos[jc,:]-delta_r,0) - shyper_cube[:,1] = np.minimum(best_pos[jc,:]+delta_r,1) - c_dis = min(np.sqrt(np.sum((np.repeat(np.reshape(best_pos[jc,:],[1,d]),\ - mol_pos.shape[0],axis=0)-mol_pos)**2,axis=1))) - - test_points = np.repeat(np.reshape(shyper_cube[:,1]-shyper_cube[:,0],[1,d]) \ - ,n_pnts,axis=0)*lhs(d,n_pnts)+np.repeat(np.reshape(shyper_cube[:,0],[1,d]),n_pnts,axis=0) - - D =_fdist(np.append(mol_pos,new_points[0:ind_clusters[jc]+n_pnts,:],axis=0)) - b_mes_v = np.min(D+np.max(D)*np.eye(Nc+ind_clusters[jc]+n_pnts),axis=1) - - ## Only includes best_pos if it is significantly different from mol_pos ## - if c_dis>min(b_mes_v): - test_points[0,:] = best_pos[jc,:] - b_mes_v[0] = c_dis - - b_mes = np.sum(b_mes_v) - new_points[ind_clusters[jc]:ind_clusters[jc]+n_pnts,:] = test_points - - for jit in range(n_min_d): - cnew_points = np.copy(new_points) - test_points = np.repeat(np.reshape(shyper_cube[:,1]-shyper_cube[:,0],[1,d]) \ - ,n_pnts,axis=0)*lhs(d,n_pnts)+ \ - np.repeat(np.reshape(shyper_cube[:,0],[1,d]),n_pnts,axis=0) - - D =_fdist(np.append(mol_pos,cnew_points[0:ind_clusters[jc]+n_pnts,:],axis=0)) - c_mes_v = np.min(D+np.max(D)*np.eye(Nc+ind_clusters[jc]+n_pnts),axis=1) - ## Only includes best_pos if it is significantly different from mol_pos ## - if c_dis>min(c_mes_v): - test_points[0,:] = best_pos[jc,:] - c_mes_v[0] = c_dis - - cnew_points[ind_clusters[jc]:ind_clusters[jc]+n_pnts,:] = test_points - c_mes = np.sum(c_mes_v) - - if c_mes>b_mes: - new_points = np.copy(cnew_points) - b_mes = c_mes - - - return new_points - -############################################################################### - -def multiscale_E(E,dE): - - """ - Multiscale normalization of E - - - Parameters - ---------- - E: Energy - dE: Uncertainty in Energy - - Returns - ------- - E_parm: Scale parameters - E_scaled: Scaled energies - dE_scaled: Scaled uncertainties in energies - """ - - E_parm = np.zeros(3) - E_parm[0] = min(E) - us_ind = np.argsort(E, axis=0) - E_parm[1] = E[us_ind[np.int(np.round(E.shape[0]/4.0)),0],0] - E_parm[1] = min(max(E_parm[1],E_parm[0]+100*np.mean(dE[np.argwhere(E<=E_parm[1])])),max(E)) - if E_parm[1] == E_parm[0]: - E_parm[1] = min(E_parm[0]+1,max(E)) - - E_scaled = (np.copy(E)-E_parm[0])/(E_parm[1]-E_parm[0]) - dE_scaled = np.copy(dE)/(E_parm[1]-E_parm[0]) - us_ind = np.argwhere(E_scaled[:,0]>1.0) - - if us_ind.shape[0]>0: - dE_scaled[us_ind[:,0],:] = np.log(1+dE_scaled[us_ind[:,0],:]/E_scaled[us_ind[:,0],:]) - E_scaled[us_ind[:,0],:] = np.log(E_scaled[us_ind[:,0],:])+1 - E_parm[2] = max(E_scaled) - E_scaled[us_ind[:,0],:] = 9.0*(E_scaled[us_ind[:,0],:]-1)/(E_parm[2]-1) +1 - dE_scaled[us_ind[:,0],:] = 9.0*dE_scaled[us_ind[:,0],:]/(E_parm[2]-1) - dE_scaled[us_ind[:,0],:] = np.maximum(dE_scaled[us_ind[:,0],:],np.mean(dE_scaled[np.argwhere(E<=E_parm[1])])) - - - - return E_parm,E_scaled,dE_scaled - -############################################################################### - -def inv_multiscale_E(E_parm,E_scaled,dE_scaled): - - """ - Reverses Multiscale normalization of E - - - Parameters - ---------- - E_parm: Scale parameters - E_scaled: Scaled energies - - Returns - ------- - E: Energy - """ - E = np.copy(E_scaled) - dE = np.copy(dE_scaled) - if E_parm[2]>0: - us_ind = np.argwhere(E[:,0]>1.0) - if us_ind.shape[0]>0: - E[us_ind[:,0],:] = np.exp((E[us_ind[:,0],:]-1)*(E_parm[2]-1)/9.0) - - E = E*(E_parm[1]-E_parm[0])+E_parm[0] - dE = dE*(E_parm[1]-E_parm[0]) - - return E,dE - -############################################################################### - -def inv_norm_pos(mol_pos_norm,hyper_cube): - - """ - Reverses normalization of molecular positions to unit hyper cube - - - Parameters - ---------- - hyper_cube: Hyper cube - mol_pos_norm: Normalized GP centers - - - Returns - ------- - mol_pos: GP centers - """ - - [n,d] = mol_pos_norm.shape - mol_pos = np.repeat(np.reshape(hyper_cube[:,1]-hyper_cube[:,0],[1,d]) \ - ,n,axis=0)*mol_pos_norm+ \ - np.repeat(np.reshape(hyper_cube[:,0],[1,d]),n,axis=0) - - - return mol_pos - - -############################################################################### - -def norm_pos(mol_pos,hyper_cube): - - """ - Reverses normalization of molecular positions to unit hyper cube - - - Parameters - ---------- - hyper_cube: Hyper cube - mol_pos_norm: Normalized GP centers - - - Returns - ------- - mol_pos: GP centers - """ - - [n,d] = mol_pos.shape - mol_pos_norm = (mol_pos-np.repeat(np.reshape(hyper_cube[:,0],[1,d]),n,axis=0))/ \ - np.repeat(np.reshape(hyper_cube[:,1]-hyper_cube[:,0],[1,d]),n,axis=0) - - - return mol_pos_norm - -############################################################################### - - -def gp_opt_setup(GP_info): - """ - Setup parameters and variables for GP - - - Parameters - ---------- - GP_info: GP information - E_b: Scale parameters - E_scaled: Scaled energies - - - Returns - ------- - E: - """ - - ## Define Empty arrays for energies, positions, and uncertainties - E = [] - dE = [] - mol_pos = [] - - best_pos =[] - best_E = [] - - d = GP_info.hyper_cube.shape[0] - try: - GP_info.n_its - except: - GP_info.n_its = 5 # Number of maximum iterations - - try: - GP_info.do_vis - except: - GP_info.do_vis = 0 # Visualize Error - - - try: - GP_info.Nc0 - except: - GP_info.Nc0 = (d+2)*(d+1) # Number of points to add per iteration - - try: - GP_info.delta_r - except: - GP_info.delta_r = 0.5 # Initial Radius of Convergence - - try: - GP_info.delta_r_s - except: - GP_info.delta_r_s = 1.25 # Radius shrink factor - - - try: - GP_info.n_min_d - except: - GP_info.n_min_d = 10 # Number of times to resample LHC - - return E,dE,mol_pos,best_pos,best_E,GP_info - -############################################################################### - -def gp_opt(E,dE,mol_pos,GP_info): - """ - Setup parameters and variables for GP - - - Parameters - ---------- - best_pos: Estimated local minimum - best_E: Estimated local energies - mol_pos: GP centers - GP_info: GP information - - E: Energy for GP centers - dE: Uncertainty in energy for GP centers - mol_pos: GP coefficents - GP_info: GP information - - Returns - ------- - new_points: New points to sample - best_pos: Estimated local minimum - best_E: Estimated local energies - GP_info: GP information - """ - - ## Define Empty arrays for energies, positions, and uncertainties - d = GP_info.hyper_cube.shape[0] - - if GP_info.jits == 0: - mol_pos_norm = lhs(d,GP_info.Nc0,GP_info.n_min_d) - new_points = inv_norm_pos(mol_pos_norm,GP_info.hyper_cube) - best_pos = [] - best_E =[] - best_dE = [] - neig_data = [] - else: - GP_info.delta_r = GP_info.delta_r/GP_info.delta_r_s - mol_pos_norm = norm_pos(mol_pos,GP_info.hyper_cube) - - - E_parm,E_scaled,dE_scaled = multiscale_E(E,dE) - ## Best Approximation of Optimization Surface ## - hyp_parm,Co_GP = find_hyperparameters(mol_pos_norm,E_scaled,dE_scaled) - ## Find Global Min ## - best_pos_norm,best_E_scaled,best_dE_scaled,neig_data_ind = find_min(Co_GP,mol_pos_norm,E_scaled,dE_scaled,hyp_parm) - best_E,best_dE = inv_multiscale_E(E_parm,best_E_scaled,best_dE_scaled) - best_pos = inv_norm_pos(best_pos_norm,GP_info.hyper_cube) - - new_points = find_new_points(mol_pos_norm,best_pos_norm,GP_info.delta_r,GP_info.Nc0) - new_points = inv_norm_pos(new_points,GP_info.hyper_cube) - - neig_data = E[neig_data_ind,0] - neig_data = np.append(neig_data,dE[neig_data_ind,0],axis=0) - - if GP_info.do_vis == 1: - - - neig_bool = neig_data[0:best_E.shape[0],:]- \ - 2*neig_data[best_E.shape[0]:2*best_E.shape[0],:] - neig_bool = neig_bool1: - GP_info.hyper_cube[1:d,0] = 0 - GP_info.n_its = 5 - - if d == 3: - print('True min: f(x) = -3, x = [1 .5 sqrt(3)/2]') - else: - print('True min: f(x) = -1, x = 1') - - elif opt_fun == 2: - d = 2 - GP_info.hyper_cube = np.ones([d,2]) # Upper and lower bound for each dimension - GP_info.hyper_cube[0,0] = 2 - GP_info.hyper_cube[1,0] = -.5 - GP_info.hyper_cube[0,1] = 4 - GP_info.hyper_cube[1,1] = 1 - - print('Only defined for d=2') - print('2D function, global minimum at (3,.5)' ) - - elif opt_fun == 3: - - if d>7: - d = 2 - elif d<3: - d = 3 - - - GP_info.Nc0 = 2*(d+2)*(d+1) - GP_info.hyper_cube = 1.5*np.ones([d,2]) # Upper and lower bound for each dimension - GP_info.hyper_cube[:,0] = 0.5 - - print('Only defined for d=3-7') - print('Global minimum at (1,1,...,1)') - - elif opt_fun == 4: - d = 2 - GP_info.hyper_cube = np.ones([d,2]) # Upper and lower bound for each dimension - GP_info.hyper_cube[0,0] = -1 - GP_info.hyper_cube[1,0] = -2 - GP_info.hyper_cube[0,1] = 1 - GP_info.hyper_cube[1,1] = 0 - - print('Only defined for d=2') - print('2D function, global minimum at (0,-1)' ) - - else: - GP_info.hyper_cube = np.ones([d,2])/2 # Upper and lower bound for each dimension - GP_info.hyper_cube[:,0] = -GP_info.hyper_cube[:,0] - - GP_info.n_its = 4 - - print('True min: f(x) = -1, x = 0') - - ## Setup Gausian Process Structure ## - try: - GP_info.hyper_cube - E,dE,mol_pos,best_pos,best_E,GP_info = gp_opt_setup(GP_info) - except: - print('Please Define GP_info.hyper_cube') - exit - - ## Do Gausian Process Iteration ## - - for jits in range(GP_info.n_its): - GP_info.jits = jits - new_points,best_pos,best_E,best_dE,GP_info,neig_data = gp_opt(E,dE,mol_pos,GP_info) - if jits < GP_info.n_its-1: - ## Simulate random uncertainty in optimization function - new_dE = (sigma_b-sigma_a)*np.random.rand(GP_info.Nc0,1)+sigma_a - new_E = opt_surface_f(new_points,opt_fun)+new_dE*np.random.randn(GP_info.Nc0, 1) - if jits == 0: - mol_pos = np.copy(new_points) - E = np.copy(new_E) - dE = np.copy(new_dE) - else: - mol_pos = np.append(mol_pos,new_points,axis=0) - E = np.append(E,new_E,axis=0) - dE = np.append(dE,new_dE,axis=0) - - - print('Best Guess in position: ') - print(best_pos) - print('Best Guess in energy: ') - print(best_E) -#end def gp_opt_example - - -############################################################################### - - - - -class GPState(DevBase): - """ - Represents internal state of a Gaussian Process iteration. - - The GPState class is the primary interface to the procedural GP optimization - approach represented by the gp_opt function and sub-functions. This class - represents the state of the GP at each iteration and allows for the state - to be stored and loaded from disk. This allows for interruptible GP - optimizations, which is useful when interfacing to target functions that - are expensive to evaluate, such as a QMC energy surface that is evaluated - on an HPC machine with Nexus driven workflows. - - GPState is not intended for public instantiation. GaussianProcessOptimizer - class is the sole intended owner. Read only access (intended) is granted - by GaussianProcessOptimizer to the user when a GPState instance is passed in - to the user-provided energy_function. See GaussianProcessOptimizer.optimize. - """ - - def __init__(self, - param_lower = None, - param_upper = None, - niterations = None, - save_path = './', - ): - """ - Setup initial GP data. - - Parameters - ---------- - param_lower : Lower bounds of the parameter search domain (list-like). - param_upper : Upper bounds of the parameter search domain (list-like). - niterations : Number of GP iterations to perform. - save_path : (Optional) directory where state snapshots will be saved. - """ - if isinstance(param_lower,GPState): - o = param_lower.copy() - self.__dict__ = o.__dict__ - return - #end if - dim = -1 - Pdomain = None - E = None - dE = None - P = None - Popt = None - Eopt = None - GP_info = None - if param_lower is not None: - dim = len(param_lower) - param_lower = np.array(param_lower) - param_upper = np.array(param_upper) - hyper_cube = np.zeros([dim,2],dtype=float) - hyper_cube[:,0] = param_lower - hyper_cube[:,1] = param_upper - Pdomain = hyper_cube.copy() - # Setup Gaussian Process data structure - GP_info = GParmFlags() - GP_info.n_its = niterations - GP_info.Nc0 = 2*(dim+2)*(dim+1) - GP_info.hyper_cube = hyper_cube - E,dE,P,Popt,Eopt,GP_info = gp_opt_setup(GP_info) - #end if - self.save_path = save_path - self.dim = dim - self.Pdomain = Pdomain - self.E = E - self.dE = dE - self.P = P - self.Popt = Popt - self.Eopt = Eopt - self.GP_info = GP_info - self.iteration = -1 - self.Pnew = None - self.neig_data = None - self.Popt_hist = [] - self.Eopt_hist = [] - #end def __init__ - - - def gp_inputs(self): - """ - Returns inputs required by the gp_opt function. - """ - return self.list('E dE P GP_info'.split()) - #end def gp_inputs - - - def update_gp(self,gp_opt_outputs): - """ - Stores outputs from the gp_opt_function. - """ - self.Pnew = gp_opt_outputs[0] - self.Popt = gp_opt_outputs[1] - self.Eopt = gp_opt_outputs[2] - self.dEopt = gp_opt_outputs[3] - self.GP_info = gp_opt_outputs[4] - self.neig_data = gp_opt_outputs[5] - #end def update_gp - - - def parameters(self): - """ - Returns parameters generated/sampled in the current iteration. - """ - return self.Pnew.copy() - #end def parameters - - - def sample_parameters(self): - """ - Calls the gp_opt function to obtain LHC parameter samples and predicted - optimal parameters and energies. - """ - self.GP_info.jits = self.iteration - self.update_gp(gp_opt(*self.gp_inputs())) - return self.parameters() - #end def sample_parameters - - - def update_energies(self,energies,errors): - """ - Appends parameter and energy+error data to internal state arrays. - """ - - if self.iteration==0: - self.P = self.Pnew.copy() - self.E = energies.copy() - self.dE = errors.copy() - else: - self.P = np.append(self.P ,self.Pnew,axis=0) - self.E = np.append(self.E ,energies ,axis=0) - self.dE = np.append(self.dE,errors ,axis=0) - #end if - #end def update_energies - - - def optimal_parameters(self): - """ - Returns predicted optimal parameters for the current iteration. - """ - return self.Popt.copy() - #end def optimal_parameters - - - def optimal_energies(self): - """ - Returns predicted optimal energies for the current iteration. - """ - return self.Eopt.copy() - #end def optimal_energies - - - def update_optimal_trajectory(self): - """ - Stores a history of predicted optimal parameters/energies across all - iterations. - """ - Popt = self.optimal_parameters() - Eopt = self.optimal_energies() - self.Popt_hist.append(Popt) - self.Eopt_hist.append(Eopt) - return Popt,Eopt - #end def update_optimal_trajectory - - - def optimal_trajectory(self): - """ - Returns the predicted optimal parameters/energies across all iterations. - """ - return self.Popt_hist,self.Eopt_hist - #end def optimal_trajectory - - - def state_filepath(self,label=None,path=None,prefix='gp_state',filepath=None): - """ - Returns the filepath used to store the state of the current iteration. - """ - if filepath is not None: - return filepath - #end if - if path is None: - path = self.save_path - #end if - filename = prefix+'_iteration_{0}'.format(self.iteration) - if label is not None: - filename += '_'+label - #end if - filename += '.p' - filepath = os.path.join(path,filename) - return filepath - #end def state_filepath - - - def save(self,*args,**kwargs): - """ - Saves the state of the current iteration to disk. - """ - filepath = self.state_filepath(*args,**kwargs) - path,file = os.path.split(filepath) - if not os.path.exists(path): - os.makedirs(path) - #end if - s = obj(self) - s.save(filepath) - #end def save - - - def load(self,*args,**kwargs): - """ - Loads the state of the current iteration from disk. - """ - filepath = self.state_filepath(*args,**kwargs) - s = obj() - s.load(filepath) - self.transfer_from(s) - #end def load - - - def attempt_load(self,*args,**kwargs): - """ - Attempts to load current iteration state from disk. - """ - loaded = False - filepath = self.state_filepath(*args,**kwargs) - if os.path.exists(filepath): - self.load(filepath=filepath) - loaded = True - #end if - return loaded - #end def attempt_load -#end class GPState - - - -class GaussianProcessOptimizer(DevBase): - """ - Offers the main user interface to Gaussian Process optimization. - - Apart from instantiation, the user should only need to call the "optimize" - member function. - - Examples - -------- - :: - - # minimize a 2D parabola over the domain -1 < x,y < 1 - def x2(x,s): - E = (x**2).sum(axis=1,keepdims=1) - dE = 0*E - return E,dE - #end def x2 - gpo = GaussianProcessOptimizer(5,[-1,-1],[1,1],x2) - P0,E0 = gpo.optimize() - print 'optimal parameters:',P0[-1] - print 'optimal energy :',E0[-1] - """ - - allowed_modes = 'stateless stateful'.split() - - def __init__(self, - niterations = None, - param_lower = None, - param_upper = None, - energy_function = None, - state_path = './opt_gp_states', - output_path = './opt_gp_output', - mode = 'stateful', - verbose = True, - exit_on_save = False, - ): - """ - Parameters - ---------- - niterations : Number of GP iterations to perform. - param_lower : Lower bounds of the parameter search domain (list-like). - param_upper : Upper bounds of the parameter search domain (list-like). - energy_function : Target function for optimization. Must accept parameters - and a GPState instance as arguments and return energies - and errorbars for the energies (function-like). - state_path : (Optional) directory where state snapshots will be saved. - output_path : (Optional) directory where parameter/energy data will be - saved for each iteration. - mode : (Optional) selects whether or not to save state during - the GP optimization. Can be "stateless" or "stateful", - default is "stateful". - verbose : (Optional) selects whether detailed information is - printed (bool). - exit_on_save : (Optional) testing parameter that selects whether to - exit each time state is saved to disk. This enables - the user to check that the optimizer can suspend and - resume properly. - """ - if niterations is None: - self.error('niterations is required') - #end if - if param_lower is None: - self.error('param_lower is required') - #end if - if param_upper is None: - self.error('param_upper is required') - #end if - if energy_function is None: - self.error('energy_function is required') - #end if - self.niterations = niterations - self.state_path = state_path - self.output_path = output_path - self.state = GPState(param_lower,param_upper,niterations,state_path) - self.energy_function = energy_function - self.mode = mode - self.verbose = verbose - self.exit_on_save = exit_on_save - if self.mode not in self.allowed_modes: - self.error('mode {0} is not allowed\nallowed modes are: {1}'.format(self.mode,self.allowed_modes)) - #end if - self.state_hist = obj() - #end def __init__ - - - def optimize(self): - """ - Runs the main optimization cycle. - """ - self.vlog('Beginning Gaussian Process optimization') - res = None - if self.mode=='stateless': - res = self.optimize_stateless() - elif self.mode=='stateful': - res = self.optimize_stateful() - else: - self.error('cannot optimize, mode "{0}" has not been implemented'.format(self.mode)) - #end if - self.vlog('Gaussian Process optimization finished') - return res - #end def optimize - - - def optimize_stateless(self): - """ - Optimizes energy_function without saving state. - """ - state = self.state - for i in range(self.niterations+1): - state.iteration+=1 - self.vlog('iteration {0}'.format(state.iteration),n=1) - self.vlog('sampling parameters',n=2) - params = state.sample_parameters() - if i>0: - self.vlog('updating predicted optimal params/energies',n=2) - state.update_optimal_trajectory() - #end if - if i0: - Popt,Eopt = state.update_optimal_trajectory() - self.save_optimal(Popt,Eopt) - #end if - self.save_parameters(params) - else: - params = state.parameters() - #end if - if i1: - r.append([x[1],x[2],0]) - #end if - if nparams>3: - i=3 - while i+21: - E = np.log(E)+1 - #end if - return E - #end def trunc_log_lennard_jones - - - sphere2 = GPTestFunction( - name = 'sphere2', - niterations = 6, - param_lower = [-1,-1], - param_upper = [ 1, 1], - function = sphere, - Pmin = [0,0], - deterministic = True, - sigma = 1e-6, - ) - - ackley2 = GPTestFunction( - name = 'ackley2', - niterations = 5, - param_lower = [-1,-1], - param_upper = [ 1, 1], - function = ackleyf, - Pmin = [0,0], - deterministic = True, - sigma = 1e-6, - ) - - ackley4 = GPTestFunction( - name = 'ackley4', - niterations = 10, - param_lower = [-1,-1,-1,-1], - param_upper = [ 1, 1, 1, 1], - function = ackleyf, - Pmin = [0,0,0,0], - deterministic = True, - sigma = 1e-6, - ) - - rosenbrock2 = GPTestFunction( - name = 'rosenbrock2', - niterations = 8, - param_lower = [-2,-2], - param_upper = [ 2, 2], - function = rosenbrock, - Pmin = [1,1], - deterministic = True, - sigma = 1e-6, - ) - - beale2 = GPTestFunction( - name = 'beale2', - niterations = 8, - param_lower = [-4.5,-4.5], - param_upper = [ 4.5, 4.5], - function = beale, - Pmin = [3,0.5], - deterministic = True, - sigma = 1e-6, - ) - - goldstein_price2 = GPTestFunction( - name = 'goldstein_price2', - niterations = 8, - param_lower = [-2,-2], - param_upper = [ 2, 2], - function = goldstein_price, - Pmin = [0,-1], - deterministic = True, - sigma = 1e-6, - ) - - himmelblau2 = GPTestFunction( - name = 'himmelblau2', - niterations = 10, - param_lower = [-5,-5], - param_upper = [ 5, 5], - function = himmelblau, - Pmin = [-3.779310,-3.283186], - deterministic = True, - sigma = 1e-6, - ) - - holdertable2 = GPTestFunction( - name = 'holdertable2', - niterations = 10, - param_lower = [-10,-10], - param_upper = [ 10, 10], - function = holder_table, - Pmin = [8.05502,-9.66459], - deterministic = True, - sigma = 1e-6, - ) - - lennardjones1 = GPTestFunction( - name = 'lennardjones1', - niterations = 10, - #param_lower = [ 0 ], - param_lower = [ 0.4 ], - param_upper = [ 2 ], - function = lennard_jones, - Pmin = [1.0], - deterministic = True, - sigma = 1e-6, - #plot = True, - ) - - lennardjones3 = GPTestFunction( - name = 'lennardjones3', - niterations = 5, - #param_lower = [ 0, 0, 0], - param_lower = [ 0.4, 0.4, 0.4], - param_upper = [ 2, 2, 2], - function = lennard_jones, - #function = trunc_log_lennard_jones, - Pmin = [1.0,0.5,np.sqrt(3.)/2], - deterministic = True, - sigma = 1e-6, - #plot = True, - ) - - lennardjones6 = GPTestFunction( - name = 'lennardjones6', - niterations = 10, - param_lower = [ 0, 0, 0, 0, 0, 0], - param_upper = [ 2, 2, 2, 2, 2, 2], - function = lennard_jones, - Pmin = [1.0,0.5,np.sqrt(3.)/2,0.5,1./(2*np.sqrt(3.)),np.sqrt(2./3)], - deterministic = True, - sigma = 1e-6, - ) - - - sphere2_save_state = GPTestFunction( - name = 'sphere2', - niterations = 6, - param_lower = [-1,-1], - param_upper = [ 1, 1], - function = sphere, - Pmin = [0,0], - deterministic = True, - sigma = 1e-6, - mode = 'stateful', - verbose = True, - exit_on_save = False, - ) - - #sphere2.test() - #ackley2.test() - #ackley4.test() - #rosenbrock2.test() - #beale2.test() - #goldstein_price2.test() - #himmelblau2.test() - #holdertable2.test() - lennardjones1.test() - #lennardjones3.test() - #lennardjones6.test() - - #sphere2_save_state.test() - -#end if diff --git a/nexus/nexus/generic.py b/nexus/nexus/generic.py index 84b4ff3fcf..9103d85178 100644 --- a/nexus/nexus/generic.py +++ b/nexus/nexus/generic.py @@ -32,12 +32,14 @@ import sys import traceback +from typing import TextIO from copy import deepcopy import pickle from pickle import UnpicklingError from random import randint +from pathlib import Path -from .utilities import sorted_py2 +from .utilities import sorted_py2, path_string class generic_settings: @@ -62,67 +64,7 @@ def nocopy(value): sorted_generic = sorted_py2 -# There must be a better way to do this than store these, but this was faster for testing -nexus_modules = [ - "xmlreader", - "fileio", - "quantum_package_analyzer", - "pwscf", - "pwscf_analyzer", - "quantum_package_input", - "testing", - "rmg_input", - "machines", - "qmcpack_converters", - "simulation", - "pwscf_postprocessors", - "pyscf_sim", - "unit_converter", - "execute", - "qmcpack_result_analyzers", - "basisset", - "project_manager", - "gamess_input", - "quantum_package", - "pwscf_input", - "pyscf_input", - "physical_system", - "pseudopotential", - "nexus_version", - "periodic_table", - "rmg_analyzer", - "memory", - "vasp_input", - "qmcpack", - "numerics", - "qmcpack_analyzer", - "structure", - "gamess_analyzer", - "developer", - "template_simulation", - "bundle", - "qmcpack_property_analyzers", - "qmcpack_quantity_analyzers", - "rmg", - "grid_functions", - "hdfreader", - "utilities", - "qmcpack_analyzer_base", - "vasp", - "generic", - "nexus_base", - "debug", - "qmcpack_method_analyzers", - "observables", - "gamess", - "versions", - "vasp_analyzer", - "gaussian_process", - "pwscf_data_reader", - "qmcpack_input", - "pyscf_analyzer", -] - +nexus_modules = [mod.stem for mod in Path(__file__).parent.iterdir() if mod.suffix == ".py"] class NexusUnpickler(pickle.Unpickler): """This class is designed for backwards compatibility with pickles generated @@ -195,7 +137,55 @@ def warn(msg,header=None,indent=' ',logfile=None): #end def warn -def error(msg,header=None,exit=True,trace=True,indent=' ',logfile=None): +def error( + msg : str, + header : str | None = None, + exit : bool = True, + trace : int | None = -1, + indent : str = ' ', + logfile : TextIO | None = None, + ): + """Report an error. + + Parameters + ---------- + msg : str + The message to write + header : str, optional + Header to print before the message. Will have ``" error:"`` appended to + it. + exit : bool, default=True + Whether or not to force an exit through ``sys.exit()``. See Notes. + trace : int or None, default=-1 + How much of the traceback to print. + + ``None`` prints the full traceback, positive integers limit to a number + of frames relative to this function, and negative integers limit to a + number of frames up to this function. Setting this to ``0`` will disable + the traceback completely. + + The default value is ``-1``, which will print only the traceback up to + the location that this function was called, but will not show the + location of this function. + indent : str, default=" " + A string that will be used to indent the error message. + logfile : TextIO, default=generic_settings.devlog + The already-opened file to write to. Typically this is ``sys.stdout``. + + Raises + ------ + NexusError + If ``generic_settings.raise_error = True``. + + Notes + ----- + If you set ``exit=True``, then this will call ``sys.exit(1)``, which will + force an exit that can not be caught or handled. + + See Also + -------- + generic_settings + """ if generic_settings.raise_error: raise NexusError(msg) #end if @@ -206,8 +196,9 @@ def error(msg,header=None,exit=True,trace=True,indent=' ',logfile=None): message(msg,header,post_header,indent,logfile) if exit: log(' exiting.\n') - if trace: - traceback.print_stack() + if trace is True: # Preserve old behavior + trace = None + traceback.print_stack(limit=trace) #end if exit_call() #end if @@ -577,7 +568,13 @@ def warn(self,message,header=None): warn(message,header,logfile=self._logfile) #end def warn - def error(self,message,header=None,exit=True,trace=True): + def error(self,message,header=None,exit=True,trace=-2): + """Report an error inside a class. + + This is the same as ``generic.error()``, but with ``trace=-2`` as the + default. This has the benefit of only printing a traceback up to the + call location, and not inadvertently pointing someone to ``generic.py``. + """ if header is None: header = self.__class__.__name__ #end if @@ -598,7 +595,14 @@ def class_warn(cls,message,header=None,post_header=' Warning:'): #end def class_warn @classmethod - def class_error(cls,message,header=None,exit=True,trace=True,post_header=' Error:'): + def class_error(cls,message,header=None,exit=True,trace=-2,post_header=' Error:'): + """Report an error relating to a class. + + See Also + -------- + object_interface.error : Used inside subclasses of ``object_interface``. + generic.error : Called when you are not reporting an error specific to a class. + """ if header is None: header = cls.__name__ #end if @@ -1106,7 +1110,8 @@ def inverse(self): def path_exists(self,path): o = self - if isinstance(path,str): + if isinstance(path, str | bytes | Path): + path = path_string(path) path = path.split('/') #end if for p in path: @@ -1121,7 +1126,8 @@ def path_exists(self,path): def set_path(self,path,value=None): o = self cls = self.__class__ - if isinstance(path,str): + if isinstance(path, str | bytes | Path): + path = path_string(path) path = path.split('/') #end if for p in path[0:-1]: @@ -1135,7 +1141,8 @@ def set_path(self,path,value=None): def get_path(self,path,value=None): o = self - if isinstance(path,str): + if isinstance(path, str | bytes | Path): + path = path_string(path) path = path.split('/') #end if for p in path[0:-1]: diff --git a/nexus/nexus/hdfreader.py b/nexus/nexus/hdfreader.py index 1050593255..0779ac0fc4 100644 --- a/nexus/nexus/hdfreader.py +++ b/nexus/nexus/hdfreader.py @@ -22,6 +22,7 @@ import keyword from inspect import getmembers from .developer import DevBase, obj, unavailable, valid_variable_name +from .utilities import path_string try: import h5py @@ -263,7 +264,7 @@ def sum(self,*names): class HDFreader(DevBase): def __init__(self,fpath,verbose=False,view=False): - + fpath = path_string(fpath) HDFglobals.view = view if verbose: diff --git a/nexus/nexus/machines.py b/nexus/nexus/machines.py index e87c02f6a5..716138881b 100644 --- a/nexus/nexus/machines.py +++ b/nexus/nexus/machines.py @@ -44,6 +44,7 @@ import os +from pathlib import Path #from multiprocessing import cpu_count from socket import gethostname from subprocess import Popen @@ -51,6 +52,7 @@ from .developer import DevBase, obj from .nexus_base import NexusCore, nexus_core from .execute import execute +from .utilities import path_string import importlib.util import importlib.machinery @@ -239,6 +241,25 @@ def zero_time(cls): def __init__(self,**kwargs): # rewrap keyword arguments kw = obj(**kwargs) + # Ensure no pathlib.Path objects are stored + path_arguments = ( + "directory", + "subdir", + "outfile", + "errfile", + "subfile", + ) + for arg in path_arguments: + if arg in kw: + kw[arg] = path_string(kw[arg]) + + # Theoretically a bash alias can have invalid filename characters, + # so we treat app_name with some more special logic. + if "app_name" in kw: + if isinstance(kw.app_name, Path): + kw.app_name = path_string(kw.app_name) + elif not isinstance(kw.app_name, str): + self.error("app_name must be a str or Path object!") # save information used to initialize job object self.init_info = kw.copy() @@ -1421,10 +1442,17 @@ def requeue_job(self,job): #end if self.process_job(job) self.jobs[jid] = job - job.status = job.states.running - self.running.add(jid) - process = obj(job=job) - self.processes[pid] = process + if not nexus_core.dynamic: + self.running.add(jid) + process = obj(job=job) + self.processes[pid] = process + else: + # If a workstation job is requeued + # then it is waking from interruption + # and should be resubmitted from the top + job.status = job.states.running + job.status = job.states.waiting + self.waiting.add(jid) else: self.error('requeue_job received non-Job instance '+job.__class__.__name__) #end if diff --git a/nexus/nexus/nexus_base.py b/nexus/nexus/nexus_base.py index 31bfae9ecc..4b4657fd98 100644 --- a/nexus/nexus/nexus_base.py +++ b/nexus/nexus/nexus_base.py @@ -27,6 +27,8 @@ import os import gc as garbage_collector +from os import PathLike +from .utilities import path_string from .nexus_version import nexus_version from .memory import resident from .developer import DevBase, obj, log @@ -100,6 +102,8 @@ progress_tty = False, # used by: ProjectManager graph_sims = False, # used by: ProjectManager command_line = True, # used by: Settings + dynamic = False, # used by: DynamicWorkflowManager + # Simulation **nexus_core_noncore_defaults ) @@ -213,9 +217,24 @@ def tlog(self,*texts,**kwargs): #end if #end def tlog - def enter(self,directory,changedir=True,msg=''): + def enter(self, directory: PathLike, changedir: bool = True, msg: str = ''): + """Have Nexus enter a directory and change its current working directory. + + Parameters + ---------- + directory : PathLike + Directory to enter. Can be a ``str`` or ``pathlib.Path`` + object. + changedir : bool, default=True + Default of ``True`` will change the CWD, setting to ``False`` + will not change the CWD. + msg : str, optional + Optional message to pass to the output log. + """ NexusCore.working_directory = os.getcwd() - self.log(' Entering '+directory,msg) + directory = path_string(directory) + + self.log(' Entering ' + directory, msg) if changedir: os.chdir(directory) #end if @@ -227,3 +246,12 @@ def leave(self): os.chdir(NexusCore.working_directory) #end def leave #end class NexusCore + + +# support dynamic workflows +dynamic_storage = obj( + simulations = obj(), # all sims, in dyn proc or not + simulation_ids = set(), + dynamic_processes = obj(), + dynamic_process_ids = set(), + ) diff --git a/nexus/nexus/nexus_version.py b/nexus/nexus/nexus_version.py index 14f7751a39..6a9a0914fb 100644 --- a/nexus/nexus/nexus_version.py +++ b/nexus/nexus/nexus_version.py @@ -9,7 +9,7 @@ #====================================================================# -nexus_version = 2,2,9 +nexus_version = 2,3,9 """ Current Nexus version. """ diff --git a/nexus/nexus/numerics.py b/nexus/nexus/numerics.py index 2a88eb0111..d66a147e62 100644 --- a/nexus/nexus/numerics.py +++ b/nexus/nexus/numerics.py @@ -88,7 +88,7 @@ from numpy.linalg import norm from .developer import obj, unavailable, error from .unit_converter import convert -from .periodic_table import pt as ptable +from .periodic_table import Elements try: from scipy.special import betainc @@ -146,13 +146,14 @@ def morse_params(re, a, De, E_inf): return re, 1./a, De, E_inf # morse_reduced_mass gives the reduced mass in Hartree units # m1 and m2 are masses or atomic symbols def morse_reduced_mass(m1,m2=None): + amu_me = convert(1., "amu", "me") if isinstance(m1,str): - m1 = ptable[m1].atomic_weight.me + m1 = Elements(m1).atomic_weight * amu_me #end if if m2 is None: m2 = m1 elif isinstance(m2,str): - m2 = ptable[m2].atomic_weight.me + m2 = Elements(m2).atomic_weight * amu_me #end if m = 1./(1./m1+1./m2) # reduced mass return m diff --git a/nexus/nexus/periodic_table.py b/nexus/nexus/periodic_table.py index cdfce24d0c..ffa0b7320a 100644 --- a/nexus/nexus/periodic_table.py +++ b/nexus/nexus/periodic_table.py @@ -20,1885 +20,519 @@ # # #====================================================================# - -from .developer import DevBase, obj -from .unit_converter import UnitConverter - - -def phys_value_dict(value=None,units=None): - vdict = UnitConverter.convert_scalar_to_all(units,value) - return obj(**vdict) -#end def phys_value_dict - - - - -class SimpleElement(DevBase): - def __init__(self): - - self.atomic_number = None - self.name = None - self.symbol = None - self.group = None - self.atomic_weight = None - self.atomic_radius = None - self.nuclear_charge = None - self.abundance = None - self.electron_affinity = None - self.electronegativity = None - self.ionization_energy = None - self.ionic_radius = None - self.melting_point = None - self.boiling_point = None - - self.string_rep = None - self.var_dict = None - #end def __init__ - - def create_var_dict(self): - self.var_dict = dict() - self.var_dict['atomic_number' ] = self.atomic_number - self.var_dict['name' ] = self.name - self.var_dict['symbol' ] = self.symbol - self.var_dict['group' ] = self.group - self.var_dict['atomic_weight' ] = self.atomic_weight - self.var_dict['atomic_radius' ] = self.atomic_radius - self.var_dict['nuclear_charge' ] = self.nuclear_charge - self.var_dict['abundance' ] = self.abundance - self.var_dict['electron_affinity'] = self.electron_affinity - self.var_dict['electronegativity'] = self.electronegativity - self.var_dict['ionization_energy'] = self.ionization_energy - self.var_dict['ionic_radius' ] = self.ionic_radius - self.var_dict['melting_point' ] = self.melting_point - self.var_dict['boiling_point' ] = self.boiling_point - - self.replace_None() - #end def create_var_dict - - def replace_None(self): - none_rep = -1.0 - for k,v in self.var_dict.items(): - if v is None: - self.var_dict[k] = none_rep - #end if - #end for - self.atomic_number = self.var_dict['atomic_number' ] - self.name = self.var_dict['name' ] - self.symbol = self.var_dict['symbol' ] - self.group = self.var_dict['group' ] - self.atomic_weight = self.var_dict['atomic_weight' ] - self.atomic_radius = self.var_dict['atomic_radius' ] - self.nuclear_charge = self.var_dict['nuclear_charge' ] - self.abundance = self.var_dict['abundance' ] - self.electron_affinity = self.var_dict['electron_affinity'] - self.electronegativity = self.var_dict['electronegativity'] - self.ionization_energy = self.var_dict['ionization_energy'] - self.ionic_radius = self.var_dict['ionic_radius' ] - self.melting_point = self.var_dict['melting_point' ] - self.boiling_point = self.var_dict['boiling_point' ] - #end def replace_None - - def create_string_representation(self): - ind = 4*' ' - - iformat = '%6i' - rformat = '%7.5f' - - s = '' - s += self.symbol+'{\n' - s += ind + 'atomic_number = ' + str(self.atomic_number)+'\n' - s += ind + 'name = ' + str(self.name)+'\n' - s += ind + 'symbol = ' + str(self.symbol)+'\n' - s += ind + 'group = ' + str(self.group)+'\n' - s += ind + 'atomic_weight = ' + str(self.atomic_weight)+'\n' - s += ind + 'atomic_radius = ' + str(self.atomic_radius)+'\n' - s += ind + 'nuclear_charge = ' + str(self.nuclear_charge)+'\n' - s += ind + 'abundance = ' + str(self.abundance)+'\n' - s += ind + 'electron_affinity = ' + str(self.electron_affinity)+'\n' - s += ind + 'electronegativity = ' + str(self.electronegativity)+'\n' - s += ind + 'ionization_energy = ' + str(self.ionization_energy)+'\n' - s += ind + 'ionic_radius = ' + str(self.ionic_radius)+'\n' - s += ind + 'melting_point = ' + str(self.melting_point)+'\n' - s += ind + 'boiling_point = ' + str(self.boiling_point)+'\n' - s += '}\n' - - self.string_rep = s - - #end def create_string_representation -#end class SimpleElement - - -class Element(SimpleElement): - def __init__(self,se): - SimpleElement.__init__(self) - - awu = PeriodicTable.atomic_weight_unit - aru = PeriodicTable.atomic_radius_unit - ncu = PeriodicTable.nuclear_charge_unit - eau = PeriodicTable.electron_affinity_unit - ieu = PeriodicTable.ionization_energy_units - iru = PeriodicTable.ionic_radius_units - tcu = PeriodicTable.thermal_cond_units - mpu = PeriodicTable.melting_point_units - bpu = PeriodicTable.boiling_point_units - - self.atomic_number = se.atomic_number - self.name = se.name - self.symbol = se.symbol - self.group = PeriodicTable.group_dict[se.group] - self.abundance = se.abundance - - self.atomic_weight = phys_value_dict(se.atomic_weight , awu) - self.atomic_radius = phys_value_dict(se.atomic_radius , aru) - self.nuclear_charge = phys_value_dict(se.nuclear_charge , ncu) - self.electron_affinity = phys_value_dict(se.electron_affinity, eau) - self.ionization_energy = phys_value_dict(se.ionization_energy, ieu) - self.ionic_radius = phys_value_dict(se.ionic_radius , iru) - self.thermal_cond = phys_value_dict(se.thermal_cond , tcu) - self.melting_point = phys_value_dict(se.melting_point , mpu) - self.boiling_point = phys_value_dict(se.boiling_point , bpu) - - #end def __init__ +from __future__ import annotations +from dataclasses import dataclass +from enum import Enum + + +@dataclass(frozen=True) +class ElementData: + """Dataclass for storing element data.""" + symbol: str + atomic_number: int + atomic_weight: float + group: int + isotopes: dict[int, float] + + def __hash__(self): + return hash(( + self.symbol, + self.atomic_number, + self.atomic_weight, + self.group, + tuple(self.isotopes.keys()), + tuple(self.isotopes.values()), + )) +#end class ElementData + + +class Elements(ElementData, Enum): + """Enumeration of all elements in the periodic table. + + Attributes + ---------- + symbol : str + In titlecase (H, He, ...) + atomic_number : int + Use 0 for a dummy element + (symbol "Xx", name "Unknown", all properties zero) + atomic_weight : float + Average atomic weight in amu [1]_. + group : int + Group of the element on the periodic table. + Lanthanides and Actinides are 0. + isotopes : dict[int, float] + A dictionary of the isotopes for the element [2]_. + This can be accessed as ``Element.Name.isotopes[mass_number]``, + which yields the relative atomic mass. + + References + ---------- + .. [1] https://iupac.qmul.ac.uk/AtWt/ + .. [2] https://www.nist.gov/pml/atomic-weights-and-isotopic-compositions-relative-atomic-masses + + Examples + -------- + The fastest way to grab element data is with the following signatures: + + >>> Elements("Hydrogen") is Elements.Hydrogen + True + >>> Elements("H") is Elements.Hydrogen + True + >>> Elements(1) is Elements.Hydrogen + True + + If you're unsure of the case of the input you can reliably get + case-insensitive parsing with the default interface. + + >>> Elements("h") is Elements.Hydrogen + True + >>> Elements("hydrogen") is Elements.Hydrogen + True + + It can also handle leading and trailing whitespace + + >>> Elements("Hydrogen ") is Elements.Hydrogen + True + >>> Elements(" H") is Elements.Hydrogen + True + + If you think the input is up to **one** step from the correct + signature, (e.g. ``Elements(int(val))``) you can still expect the + default call to work. + + >>> Elements("1") is Elements.Hydrogen + True + >>> Elements(1.0) is Elements.Hydrogen + True + + Printing an element calls its ``__str__`` method which will return + just the atomic symbol. + + >>> print(Elements.Hydrogen) + H + + This also works with f-strings and ``str.format`` calls. + + >>> print(f"{Elements.Hydrogen}") + H + + If you want to see the data attached to the enum member + (minus the isotopes), use ``repr``. + + >>> print(repr(Elements.Hydrogen)) + + + You can also get this view by just directly typing the element. + + >>> Elements.Hydrogen + + """ + + def __new__( + cls, + symbol: str, + atomic_number: int, + atomic_weight: float, + group: int, + isotopes: dict[int, float] + ): + element = ElementData.__new__(cls) + element._value_ = atomic_number + return element + + + # Override to not print isotopes + def __repr__(self): + # This prints on one line, but since it's nearly impossible to + # grep for this regardless of if it's on one line in the code + # it is split here for readability. + return ( + f"<{self.__class__.__name__}.{self.name}: " + f"symbol='{self.symbol}', " + f"atomic_number={self.atomic_number}, " + f"atomic_weight={self.atomic_weight}, " + f"group={self.group}>" + ) + + + def __str__(self) -> str: + return self.symbol + + + @classmethod + def _missing_(cls, value): + """Workaround to not having access to ``_add_alias_`` or + ``_add_value_alias_`` from Python 3.13. This function + automatically gets called when the traditional lookup fails. + """ + if isinstance(value, str): + value = value.strip() + if value.isalpha(): # `Elements("h")` or `Elements("hydrogen")` + val_title = value.title() + if val_title in cls.__members__: + return cls.__members__[val_title] + + elif value.isdecimal(): # `Elements("1")` + try: + value = int(value) + except ValueError: # We don't support `Elements("1.0")` + pass + + if isinstance(value, int) and value <= cls.num_elements(): + return cls._value2member_map_[value] + + raise ValueError(f"Can not determine element for input value: {value}!") + + + @staticmethod + def is_element( + value: str, + return_element: bool = False, + ) -> bool | tuple[bool, Elements]: + """Robust method that will try to match a wide array of element + identifier formats, including all that are handled by the parent + call signature ``Elements(value)``. + + Parameters + ---------- + value : str + The string to be checked. + return_element : bool, default=False + Return the element that was identified. + This will return ``value`` if it could not be identified as + an element. + + Examples + -------- + Regular elements + + >>> Elements.is_element("H") + True + >>> Elements.is_element("He") + True + + Elements with integer identifiers + + >>> Elements.is_element("H1") + True + >>> Elements.is_element("H10") + True + >>> Elements.is_element("He1") + True + >>> Elements.is_element("He10") + True + + Elements with integer identifiers and underscores + + >>> Elements.is_element("H_1") + True + >>> Elements.is_element("H_10") + True + >>> Elements.is_element("He_1") + True + >>> Elements.is_element("He_10") + True + + Elements with integer identifiers and hyphens + + >>> Elements.is_element("H-1") + True + >>> Elements.is_element("H-10") + True + >>> Elements.is_element("He-1") + True + >>> Elements.is_element("He-10") + True + + You can optionally return the element as well + + >>> Elements.is_element("H_10", return_element=True) + (True, ) + >>> Elements.is_element("He-1", return_element=True) + (True, ) + + If it can't determine the element and you asked it to return the + element then it will return ``False`` and the supplied value. + + >>> Elements.is_element("Bean", return_element=True) + (False, 'Bean') + """ + + if isinstance(value, Elements): + if return_element: + return True, value + else: + return True + + val_len = len(value) + if "_" in value: # H_1 + value = value.split("_", maxsplit=1)[0] + elif "-" in value: # H-1 + value = value.split("-", maxsplit=1)[0] + elif val_len >= 2 and value[1:].isdigit(): # H1 / H10 + value = value[0:1] + elif val_len >= 3 and value[2:].isdigit(): # He1 / He10 + value = value[0:2] + + value = value.title() + if value in Elements.__members__: + if return_element: + return True, Elements(value) + else: + return True + else: + if return_element: + return False, value + else: + return False + + @staticmethod + def num_elements() -> int: + return len(Elements) - 1 # Dummy atom + + # Name Symbol Number Mass Group Isotopes + Unknown = "Xx", 0, 0.0, 0, {0:0.0} + Hydrogen = "H", 1, 1.0080, 1, {1:1.00782503223, 2:2.01410177812, 3:3.0160492779} + Helium = "He", 2, 4.002602, 18, {3:3.0160293201, 4:4.00260325413} + Lithium = "Li", 3, 6.94, 1, {6:6.0151228874, 7:7.0160034366} + Beryllium = "Be", 4, 9.0121831, 2, {9:9.012183065} + Boron = "B", 5, 10.81, 13, {10:10.01293695, 11:11.00930536} + Carbon = "C", 6, 12.011, 14, {12:12.0000000, 13:13.00335483507, 14:14.0032419884} + Nitrogen = "N", 7, 14.007, 15, {14:14.00307400443, 15:15.00010889888} + Oxygen = "O", 8, 15.999, 16, {16:15.99491461957, 17:16.9991317565, 18:17.99915961286} + Fluorine = "F", 9, 18.998403162, 17, {19:18.99840316273} + Neon = "Ne", 10, 20.1797, 18, {20:19.9924401762, 21:20.993846685, 22:21.991385114} + Sodium = "Na", 11, 22.98976928, 1, {23:22.989769282} + Magnesium = "Mg", 12, 24.305, 2, {24:23.985041697, 25:24.985836976, 26:25.982592968} + Aluminum = "Al", 13, 26.9815384, 13, {27:26.98153853} + Silicon = "Si", 14, 28.085, 14, {28:27.97692653465, 29:28.9764946649, 30:29.973770136} + Phosphorus = "P", 15, 30.973761998, 15, {31:30.97376199842} + Sulfur = "S", 16, 32.06, 16, {32:31.9720711744, 33:32.9714589098, 34:33.967867004, 36:35.96708071} + Chlorine = "Cl", 17, 35.45, 17, {35:34.968852682, 37:36.965902602} + Argon = "Ar", 18, 39.95, 18, {36:35.967545105, 38:37.96273211, 40:39.9623831237} + Potassium = "K", 19, 39.0983, 1, {39:38.9637064864, 40:39.963998166, 41:40.9618252579} + Calcium = "Ca", 20, 40.078, 2, {40:39.962590863, 42:41.95861783, 43:42.95876644, 44:43.95548156, 46:45.953689, 48:47.95252276} + Scandium = "Sc", 21, 44.955907, 3, {45:44.95590828} + Titanium = "Ti", 22, 47.867, 4, {46:45.95262772, 47:46.95175879, 48:47.94794198, 49:48.94786568, 50:49.94478689} + Vanadium = "V", 23, 50.9415, 5, {50:49.94715601, 51:50.94395704} + Chromium = "Cr", 24, 51.9961, 6, {50:49.94604183, 52:51.94050623, 53:52.94064815, 54:53.93887916} + Manganese = "Mn", 25, 54.938043, 7, {55:54.93804391} + Iron = "Fe", 26, 55.845, 8, {54:53.93960899, 56:55.93493633, 57:56.93539284, 58:57.93327443} + Cobalt = "Co", 27, 58.933194, 9, {59:58.93319429} + Nickel = "Ni", 28, 58.6934, 10, {58:57.93534241, 60:59.93078588, 61:60.93105557, 62:61.92834537, 64:63.92796682} + Copper = "Cu", 29, 63.546, 11, {63:62.92959772, 65:64.9277897} + Zinc = "Zn", 30, 65.38, 12, {64:63.92914201, 66:65.92603381, 67:66.92712775, 68:67.92484455, 70:69.9253192} + Gallium = "Ga", 31, 69.723, 13, {69:68.9255735, 71:70.92470258} + Germanium = "Ge", 32, 72.630, 14, {70:69.92424875, 72:71.922075826, 73:72.923458956, 74:73.921177761, 76:75.921402726} + Arsenic = "As", 33, 74.921595, 15, {75:74.92159457} + Selenium = "Se", 34, 78.971, 16, {74:73.922475934, 76:75.919213704, 77:76.919914154, 78:77.91730928, 80:79.9165218, 82:81.9166995} + Bromine = "Br", 35, 79.904, 17, {79:78.9183376, 81:80.9162897} + Krypton = "Kr", 36, 83.798, 18, {78:77.92036494, 80:79.91637808, 82:81.91348273, 83:82.91412716, 84:83.9114977282, 86:85.9106106269} + Rubidium = "Rb", 37, 85.4678, 1, {85:84.9117897379, 87:86.909180531} + Strontium = "Sr", 38, 87.62, 2, {84:83.9134191, 86:85.9092606, 87:86.9088775, 88:87.9056125} + Yttrium = "Y", 39, 88.905838, 3, {89:88.9058403} + Zirconium = "Zr", 40, 91.222, 4, {90:89.9046977, 91:90.9056396, 92:91.9050347, 94:93.9063108, 96:95.9082714} + Niobium = "Nb", 41, 92.90637, 5, {93:92.906373} + Molybdenum = "Mo", 42, 95.95, 6, {92:91.90680796, 94:93.9050849, 95:94.90583877, 96:95.90467612, 97:96.90601812, 98:97.90540482, 100:99.9074718} + Technetium = "Tc", 43, 97.0, 7, {97:96.9063667, 98:97.9072124, 99:98.9062508} + Ruthenium = "Ru", 44, 101.07, 8, {96:95.90759025, 98:97.9052868, 99:98.9059341, 100:99.9042143, 101:100.9055769, 102:101.9043441, 104:103.9054275} + Rhodium = "Rh", 45, 102.90549, 9, {103:102.905498} + Palladium = "Pd", 46, 106.42, 10, {102:101.9056022, 104:103.9040305, 105:104.9050796, 106:105.9034804, 108:107.9038916, 110:109.9051722} + Silver = "Ag", 47, 107.8682, 11, {107:106.9050916, 109:108.9047553} + Cadmium = "Cd", 48, 112.414, 12, {106:105.9064599, 108:107.9041834, 110:109.90300661, 111:110.90418287, 112:111.90276287, 113:112.90440813, 114:113.90336509, 116:115.90476315} + Indium = "In", 49, 114.818, 13, {113:112.90406184, 115:114.903878776} + Tin = "Sn", 50, 118.710, 14, {112:111.90482387, 114:113.9027827, 115:114.903344699, 116:115.9017428, 117:116.90295398, 118:117.90160657, 119:118.90331117, 120:119.90220163, 122:121.9034438, 124:123.9052766} + Antimony = "Sb", 51, 121.760, 15, {121:120.903812, 123:122.9042132} + Tellurium = "Te", 52, 127.60, 16, {120:119.9040593, 122:121.9030435, 123:122.9042698, 124:123.9028171, 125:124.9044299, 126:125.9033109, 128:127.90446128, 130:129.906222748} + Iodine = "I", 53, 126.90447, 17, {127:126.9044719} + Xenon = "Xe", 54, 131.293, 18, {124:123.905892, 126:125.9042983, 128:127.903531, 129:128.9047808611, 130:129.903509349, 131:130.90508406, 132:131.9041550856, 134:133.90539466, 136:135.907214484} + Cesium = "Cs", 55, 132.90545196, 1, {133:132.905451961} + Barium = "Ba", 56, 137.327, 2, {130:129.9063207, 132:131.9050611, 134:133.90450818, 135:134.90568838, 136:135.90457573, 137:136.90582714, 138:137.905247} + Lanthanum = "La", 57, 138.90547, 3, {138:137.9071149, 139:138.9063563} + Cerium = "Ce", 58, 140.116, 0, {136:135.90712921, 138:137.905991, 140:139.9054431, 142:141.9092504} + Praseodymium = "Pr", 59, 140.90766, 0, {141:140.9076576} + Neodymium = "Nd", 60, 144.242, 0, {142:141.907729, 143:142.90982, 144:143.910093, 145:144.9125793, 146:145.9131226, 148:147.9168993, 150:149.9209022} + Promethium = "Pm", 61, 145.0, 0, {145:144.9127559, 147:146.915145} + Samarium = "Sm", 62, 150.36, 0, {144:143.9120065, 147:146.9149044, 148:147.9148292, 149:148.9171921, 150:149.9172829, 152:151.9197397, 154:153.9222169} + Europium = "Eu", 63, 151.964, 0, {151:150.9198578, 153:152.921238} + Gadolinium = "Gd", 64, 157.249, 0, {152:151.9197995, 154:153.9208741, 155:154.9226305, 156:155.9221312, 157:156.9239686, 158:157.9241123, 160:159.9270624} + Terbium = "Tb", 65, 158.925354, 0, {159:158.9253547} + Dysprosium = "Dy", 66, 162.500, 0, {156:155.9242847, 158:157.9244159, 160:159.9252046, 161:160.9269405, 162:161.9268056, 163:162.9287383, 164:163.9291819} + Holmium = "Ho", 67, 164.930329, 0, {165:164.9303288} + Erbium = "Er", 68, 167.259, 0, {162:161.9287884, 164:163.9292088, 166:165.9302995, 167:166.9320546, 168:167.9323767, 170:169.9354702} + Thulium = "Tm", 69, 168.934219, 0, {169:168.9342179} + Ytterbium = "Yb", 70, 173.045, 0, {168:167.9338896, 170:169.9347664, 171:170.9363302, 172:171.9363859, 173:172.9382151, 174:173.9388664, 176:175.9425764} + Lutetium = "Lu", 71, 174.96669, 0, {175:174.9407752, 176:175.9426897} + Hafnium = "Hf", 72, 178.486, 4, {174:173.9400461, 176:175.9414076, 177:176.9432277, 178:177.9437058, 179:178.9458232, 180:179.946557} + Tantalum = "Ta", 73, 180.94788, 5, {180:179.9474648, 181:180.9479958} + Tungsten = "W", 74, 183.84, 6, {180:179.9467108, 182:181.94820394, 183:182.95022275, 184:183.95093092, 186:185.9543628} + Rhenium = "Re", 75, 186.207, 7, {185:184.9529545, 187:186.9557501} + Osmium = "Os", 76, 190.23, 8, {184:183.9524885, 186:185.953835, 187:186.9557474, 188:187.9558352, 189:188.9581442, 190:189.9584437, 192:191.961477} + Iridium = "Ir", 77, 192.217, 9, {191:190.9605893, 193:192.9629216} + Platinum = "Pt", 78, 195.084, 10, {190:189.9599297, 192:191.9610387, 194:193.9626809, 195:194.9647917, 196:195.96495209, 198:197.9678949} + Gold = "Au", 79, 196.966570, 11, {197:196.96656879} + Mercury = "Hg", 80, 200.592, 12, {196:195.9658326, 198:197.9667686, 199:198.96828064, 200:199.96832659, 201:200.97030284, 202:201.9706434, 204:203.97349398} + Thallium = "Tl", 81, 204.38, 13, {203:202.9723446, 205:204.9744278} + Lead = "Pb", 82, 207.2, 14, {204:203.973044, 206:205.9744657, 207:206.9758973, 208:207.9766525} + Bismuth = "Bi", 83, 208.98040, 15, {209:208.9803991} + Polonium = "Po", 84, 209.0, 16, {209:208.9824308, 210:209.9828741} + Astatine = "At", 85, 210.0, 17, {210:209.9871479, 211:210.9874966} + Radon = "Rn", 86, 222.0, 18, {211:210.9906011, 220:220.0113941, 222:222.0175782} + Francium = "Fr", 87, 223.0, 1, {223:223.019736} + Radium = "Ra", 88, 226.0, 2, {223:223.0185023, 224:224.020212, 226:226.0254103, 228:228.0310707} + Actinium = "Ac", 89, 227.0, 3, {227:227.0277523} + Thorium = "Th", 90, 232.0377, 0, {230:230.0331341, 232:232.0380558} + Protactinium = "Pa", 91, 231.03588, 0, {231:231.0358842} + Uranium = "U", 92, 238.02891, 0, {233:233.0396355, 234:234.0409523, 235:235.0439301, 236:236.0455682, 238:238.0507884} + Neptunium = "Np", 93, 237.0, 0, {236:236.04657, 237:237.0481736} + Plutonium = "Pu", 94, 244.0, 0, {238:238.0495601, 239:239.0521636, 240:240.0538138, 241:241.0568517, 242:242.0587428, 244:244.0642053} + Americium = "Am", 95, 243.0, 0, {241:241.0568293, 243:243.0613813} + Curium = "Cm", 96, 247.0, 0, {243:243.0613893, 244:244.0627528, 245:245.0654915, 246:246.0672238, 247:247.0703541, 248:248.0723499} + Berkelium = "Bk", 97, 247.0, 0, {247:247.0703073, 249:249.0749877} + Californium = "Cf", 98, 251.0, 0, {249:249.0748539, 250:250.0764062, 251:251.0795886, 252:252.0816272} + Einsteinium = "Es", 99, 252.0, 0, {252:252.08298} + Fermium = "Fm", 100, 257.0, 0, {257:257.0951061} + Mendelevium = "Md", 101, 258.0, 0, {258:258.0984315, 260:260.10365} + Nobelium = "No", 102, 259.0, 0, {259:259.10103} + Lawrencium = "Lr", 103, 262.0, 0, {262:262.10961} + Rutherfordium = "Rf", 104, 267.0, 4, {267:267.12179} + Dubnium = "Db", 105, 270.0, 5, {268:268.12567} + Seaborgium = "Sg", 106, 269.0, 6, {271:271.13393} + Bohrium = "Bh", 107, 270.0, 7, {272:272.13826} + Hassium = "Hs", 108, 270.0, 8, {270:270.13429} + Meitnerium = "Mt", 109, 278.0, 9, {276:276.15159} + Darmstadtium = "Ds", 110, 281.0, 10, {281:281.16451} + Roentgenium = "Rg", 111, 281.0, 11, {280:280.16514} + Copernicium = "Cn", 112, 285.0, 12, {285:285.17712} + Nihonium = "Nh", 113, 286.0, 13, {284:284.17873} + Flerovium = "Fl", 114, 289.0, 14, {289:289.19042} + Moscovium = "Mc", 115, 289.0, 15, {288:288.19274} + Livermorium = "Lv", 116, 293.0, 16, {293:293.20449} + Tennessine = "Ts", 117, 293.0, 17, {292:292.20746} + Oganesson = "Og", 118, 294.0, 18, {294:294.21392} + # Name Symbol Number Mass Group Isotopes + + # Add aliases for each element. + # Once we can use features from Python 3.13, this will be replaced by + # the Enum sunder `_add_alias_` + Xx = Unknown + H = Hydrogen + He = Helium + Li = Lithium + Be = Beryllium + B = Boron + C = Carbon + N = Nitrogen + O = Oxygen + F = Fluorine + Ne = Neon + Na = Sodium + Mg = Magnesium + Al = Aluminum + Si = Silicon + P = Phosphorus + S = Sulfur + Cl = Chlorine + Ar = Argon + K = Potassium + Ca = Calcium + Sc = Scandium + Ti = Titanium + V = Vanadium + Cr = Chromium + Mn = Manganese + Fe = Iron + Co = Cobalt + Ni = Nickel + Cu = Copper + Zn = Zinc + Ga = Gallium + Ge = Germanium + As = Arsenic + Se = Selenium + Br = Bromine + Kr = Krypton + Rb = Rubidium + Sr = Strontium + Y = Yttrium + Zr = Zirconium + Nb = Niobium + Mo = Molybdenum + Tc = Technetium + Ru = Ruthenium + Rh = Rhodium + Pd = Palladium + Ag = Silver + Cd = Cadmium + In = Indium + Sn = Tin + Sb = Antimony + Te = Tellurium + I = Iodine + Xe = Xenon + Cs = Cesium + Ba = Barium + La = Lanthanum + Ce = Cerium + Pr = Praseodymium + Nd = Neodymium + Pm = Promethium + Sm = Samarium + Eu = Europium + Gd = Gadolinium + Tb = Terbium + Dy = Dysprosium + Ho = Holmium + Er = Erbium + Tm = Thulium + Yb = Ytterbium + Lu = Lutetium + Hf = Hafnium + Ta = Tantalum + W = Tungsten + Re = Rhenium + Os = Osmium + Ir = Iridium + Pt = Platinum + Au = Gold + Hg = Mercury + Tl = Thallium + Pb = Lead + Bi = Bismuth + Po = Polonium + At = Astatine + Rn = Radon + Fr = Francium + Ra = Radium + Ac = Actinium + Th = Thorium + Pa = Protactinium + U = Uranium + Np = Neptunium + Pu = Plutonium + Am = Americium + Cm = Curium + Bk = Berkelium + Cf = Californium + Es = Einsteinium + Fm = Fermium + Md = Mendelevium + No = Nobelium + Lr = Lawrencium + Rf = Rutherfordium + Db = Dubnium + Sg = Seaborgium + Bh = Bohrium + Hs = Hassium + Mt = Meitnerium + Ds = Darmstadtium + Rg = Roentgenium + Cn = Copernicium + Nh = Nihonium + Fl = Flerovium + Mc = Moscovium + Lv = Livermorium + Ts = Tennessine + Og = Oganesson #end class Element - - - -class PeriodicTable(DevBase): - - element_set=set([ - 'Ac','Al','Am','Sb','Ar','As','At','Ba','Bk','Be','Bi','B' ,'Br', - 'Cd','Ca','Cf','C' ,'Ce','Cs','Cl','Cr','Co','Cu','Cm','Dy','Es', - 'Er','Eu','Fm','F' ,'Fr','Gd','Ga','Ge','Au','Hf','Ha','Hs','He', - 'Ho','H' ,'In','I' ,'Ir','Fe','Kr','La','Lr','Pb','Li','Lu','Mg', - 'Mn','Mt','Md','Hg','Mo','Ns','Nd','Ne','Np','Ni','Nb','N' ,'No', - 'Os','O' ,'Pd','P' ,'Pt','Pu','Po','K' ,'Pr','Pm','Pa','Ra','Rn', - 'Re','Rh','Rb','Ru','Rf','Sm','Sc','Sg','Se','Si','Ag','Na','Sr', - 'S' ,'Ta','Tc','Te','Tb','Tl','Th','Tm','Sn','Ti','W' ,'U' ,'V' , - 'Xe','Yb','Y' ,'Zn','Zr']) - - - element_dict=dict({ - 'Ac':'Actinium', - 'Al':'Aluminum', - 'Am':'Americium', - 'Sb':'Antimony', - 'Ar':'Argon', - 'As':'Arsenic', - 'At':'Astatine', - 'Ba':'Barium', - 'Bk':'Berkelium', - 'Be':'Beryllium', - 'Bi':'Bismuth', - 'B':'Boron', - 'Br':'Bromine', - 'Cd':'Cadmium', - 'Ca':'Calcium', - 'Cf':'Californium', - 'C' :'Carbon', - 'Ce':'Cerium', - 'Cs':'Cesium', - 'Cl':'Chlorine', - 'Cr':'Chromium', - 'Co':'Cobalt', - 'Cu':'Copper', - 'Cm':'Curium', - 'Dy':'Dysprosium', - 'Es':'Einsteinium', - 'Er':'Erbium', - 'Eu':'Europium', - 'Fm':'Fermium', - 'F' :'Flourine', - 'Fr':'Francium', - 'Gd':'Gadolinium', - 'Ga':'Gallium', - 'Ge':'Germanium', - 'Au':'Gold', - 'Hf':'Hafnium', - 'Ha':'Hahnium', - 'Hs':'Hassium', - 'He':'Helium', - 'Ho':'Holmium', - 'H' :'Hydrogen', - 'In':'Indium', - 'I' :'Iodine', - 'Ir':'Iridium', - 'Fe':'Iron', - 'Kr':'Krypton', - 'La':'Lanthanum', - 'Lr':'Lawrencium', - 'Pb':'Lead', - 'Li':'Lithium', - 'Lu':'Lutetium', - 'Mg':'Magnesium', - 'Mn':'Manganese', - 'Mt':'Meitnerium', - 'Md':'Mendelevium', - 'Hg':'Mercury', - 'Mo':'Molybdenum', - 'Ns':'Neilsborium', - 'Nd':'Neodymium', - 'Ne':'Neon', - 'Np':'Neptunium', - 'Ni':'Nickel', - 'Nb':'Niobium', - 'N' :'Nitrogen', - 'No':'Nobelium', - 'Os':'Osmium', - 'O' :'Oxygen', - 'Pd':'Palladium', - 'P' :'Phosphorus', - 'Pt':'Platinum', - 'Pu':'Plutonium', - 'Po':'Polonium', - 'K' :'Potassium', - 'Pr':'Praseodymium', - 'Pm':'Promethium', - 'Pa':'Protactinium', - 'Ra':'Radium', - 'Rn':'Radon', - 'Re':'Rhenium', - 'Rh':'Rhodium', - 'Rb':'Rubidium', - 'Ru':'Ruthenium', - 'Rf':'Rutherfordium', - 'Sm':'Samarium', - 'Sc':'Scandium', - 'Sg':'Seaborgium', - 'Se':'Selenium', - 'Si':'Silicon', - 'Ag':'Silver', - 'Na':'Sodium', - 'Sr':'Strontium', - 'S' :'Sulfur', - 'Ta':'Tantalum', - 'Tc':'Technetium', - 'Te':'Tellurium', - 'Tb':'Terbium', - 'Tl':'Thalium', - 'Th':'Thorium', - 'Tm':'Thulium', - 'Sn':'Tin', - 'Ti':'Titanium', - 'W' :'Tungsten', - 'U' :'Uranium', - 'V' :'Vanadium', - 'Xe':'Xenon', - 'Yb':'Ytterbium', - 'Y' :'Yttrium', - 'Zn':'Zinc', - 'Zr':'Zirconium', - }) - - group_dict = dict([ - (0 ,'LanAct'), - (1 ,'IA'), - (2 ,'IIA'), - (3 ,'IIIB'), - (4 ,'IVB'), - (5 ,'VB'), - (6 ,'VIB'), - (7 ,'VIIB'), - (8 ,'VII'), - (9 ,'VII'), - (10,'VII'), - (11,'IB'), - (12,'IIB'), - (13,'IIIA'), - (14,'IVA'), - (15,'VA'), - (16,'VIA'), - (17,'VIIA'), - (18,'0') - ]) - - - atomic_weight_unit = 'amu' - atomic_radius_unit = 'pm' - nuclear_charge_unit = 'e' - electron_affinity_unit = 'kJ_mol' - ionization_energy_units = 'eV' - ionic_radius_units = 'pm' - thermal_cond_units = 'W_mK' - melting_point_units = 'degC' - boiling_point_units = 'degC' - - def __init__(self): - self.nelements = None - self.elements = None - - nelements = 103 - e = obj() - for i in range(1,nelements+1): - e[i] = SimpleElement() - #end for - - for i in range(1,nelements+1): - e[i].atomic_number = i - #end for - - - e[1].symbol='H' - e[2].symbol='He' - e[3].symbol='Li' - e[4].symbol='Be' - e[5].symbol='B' - e[6].symbol='C' - e[7].symbol='N' - e[8].symbol='O' - e[9].symbol='F' - e[10].symbol='Ne' - e[11].symbol='Na' - e[12].symbol='Mg' - e[13].symbol='Al' - e[14].symbol='Si' - e[15].symbol='P' - e[16].symbol='S' - e[17].symbol='Cl' - e[18].symbol='Ar' - e[19].symbol='K' - e[20].symbol='Ca' - e[21].symbol='Sc' - e[22].symbol='Ti' - e[23].symbol='V' - e[24].symbol='Cr' - e[25].symbol='Mn' - e[26].symbol='Fe' - e[27].symbol='Co' - e[28].symbol='Ni' - e[29].symbol='Cu' - e[30].symbol='Zn' - e[31].symbol='Ga' - e[32].symbol='Ge' - e[33].symbol='As' - e[34].symbol='Se' - e[35].symbol='Br' - e[36].symbol='Kr' - e[37].symbol='Rb' - e[38].symbol='Sr' - e[39].symbol='Y' - e[40].symbol='Zr' - e[41].symbol='Nb' - e[42].symbol='Mo' - e[43].symbol='Tc' - e[44].symbol='Ru' - e[45].symbol='Rh' - e[46].symbol='Pd' - e[47].symbol='Ag' - e[48].symbol='Cd' - e[49].symbol='In' - e[50].symbol='Sn' - e[51].symbol='Sb' - e[52].symbol='Te' - e[53].symbol='I' - e[54].symbol='Xe' - e[55].symbol='Cs' - e[56].symbol='Ba' - e[57].symbol='La' - e[58].symbol='Ce' - e[59].symbol='Pr' - e[60].symbol='Nd' - e[61].symbol='Pm' - e[62].symbol='Sm' - e[63].symbol='Eu' - e[64].symbol='Gd' - e[65].symbol='Tb' - e[66].symbol='Dy' - e[67].symbol='Ho' - e[68].symbol='Er' - e[69].symbol='Tm' - e[70].symbol='Yb' - e[71].symbol='Lu' - e[72].symbol='Hf' - e[73].symbol='Ta' - e[74].symbol='W' - e[75].symbol='Re' - e[76].symbol='Os' - e[77].symbol='Ir' - e[78].symbol='Pt' - e[79].symbol='Au' - e[80].symbol='Hg' - e[81].symbol='Tl' - e[82].symbol='Pb' - e[83].symbol='Bi' - e[84].symbol='Po' - e[85].symbol='At' - e[86].symbol='Rn' - e[87].symbol='Fr' - e[88].symbol='Ra' - e[89].symbol='Ac' - e[90].symbol='Th' - e[91].symbol='Pa' - e[92].symbol='U' - e[93].symbol='Np' - e[94].symbol='Pu' - e[95].symbol='Am' - e[96].symbol='Cm' - e[97].symbol='Bk' - e[98].symbol='Cf' - e[99].symbol='Es' - e[100].symbol='Fm' - e[101].symbol='Md' - e[102].symbol='No' - e[103].symbol='Lr' - - for i in range(1,len(e)): - e[i].name = PeriodicTable.element_dict[e[i].symbol] - #end for - - e[1].group = 1 - e[2].group = 18 - e[3].group = 1 - e[4].group = 2 - e[5].group = 13 - e[6].group = 14 - e[7].group = 15 - e[8].group = 16 - e[9].group = 17 - e[10].group = 18 - e[11].group = 1 - e[12].group = 2 - e[13].group = 13 - e[14].group = 14 - e[15].group = 15 - e[16].group = 16 - e[17].group = 17 - e[18].group = 18 - e[19].group = 1 - e[20].group = 2 - e[21].group = 3 - e[22].group = 4 - e[23].group = 5 - e[24].group = 6 - e[25].group = 7 - e[26].group = 8 - e[27].group = 9 - e[28].group = 10 - e[29].group = 11 - e[30].group = 12 - e[31].group = 13 - e[32].group = 14 - e[33].group = 15 - e[34].group = 16 - e[35].group = 17 - e[36].group = 18 - e[37].group = 1 - e[38].group = 2 - e[39].group = 3 - e[40].group = 4 - e[41].group = 5 - e[42].group = 6 - e[43].group = 7 - e[44].group = 8 - e[45].group = 9 - e[46].group = 10 - e[47].group = 11 - e[48].group = 12 - e[49].group = 13 - e[50].group = 14 - e[51].group = 15 - e[52].group = 16 - e[53].group = 17 - e[54].group = 18 - e[55].group = 1 - e[56].group = 2 - e[57].group = 3 - e[58].group = 0 - e[59].group = 0 - e[60].group = 0 - e[61].group = 0 - e[62].group = 0 - e[63].group = 0 - e[64].group = 0 - e[65].group = 0 - e[66].group = 0 - e[67].group = 0 - e[68].group = 0 - e[69].group = 0 - e[70].group = 0 - e[71].group = 0 - e[72].group = 4 - e[73].group = 5 - e[74].group = 6 - e[75].group = 7 - e[76].group = 8 - e[77].group = 9 - e[78].group = 10 - e[79].group = 11 - e[80].group = 12 - e[81].group = 13 - e[82].group = 14 - e[83].group = 15 - e[84].group = 16 - e[85].group = 17 - e[86].group = 18 - e[87].group = 1 - e[88].group = 2 - e[89].group = 3 - e[90].group = 0 - e[91].group = 0 - e[92].group = 0 - e[93].group = 0 - e[94].group = 0 - e[95].group = 0 - e[96].group = 0 - e[97].group = 0 - e[98].group = 0 - e[99].group = 0 - e[100].group = 0 - e[101].group = 0 - e[102].group = 0 - e[103].group = 0 - - e[1].atomic_weight = 1.00794 - e[2].atomic_weight = 4.002602 - e[3].atomic_weight = 6.941 - e[4].atomic_weight = 9.0122 - e[5].atomic_weight = 10.811 - e[6].atomic_weight = 12.011000 - e[7].atomic_weight = 14.007 - e[8].atomic_weight = 15.999 - e[9].atomic_weight = 18.998 - e[10].atomic_weight = 20.180 - e[11].atomic_weight = 22.990 - e[12].atomic_weight = 24.305 - e[13].atomic_weight = 26.982 - e[14].atomic_weight = 28.086 - e[15].atomic_weight = 30.974 - e[16].atomic_weight = 32.064 - e[17].atomic_weight = 35.453 - e[18].atomic_weight = 39.948 - e[19].atomic_weight = 39.098 - e[20].atomic_weight = 40.08 - e[21].atomic_weight = 44.956 - e[22].atomic_weight = 47.90 - e[23].atomic_weight = 50.942 - e[24].atomic_weight = 51.996 - e[25].atomic_weight = 54.938 - e[26].atomic_weight = 55.845 - e[27].atomic_weight = 58.933 - e[28].atomic_weight = 58.69 - e[29].atomic_weight = 63.546 - e[30].atomic_weight = 65.38 - e[31].atomic_weight = 65.38 - e[32].atomic_weight = 72.61 - e[33].atomic_weight = 74.992 - e[34].atomic_weight = 78.96 - e[35].atomic_weight = 79.904 - e[36].atomic_weight = 83.80 - e[37].atomic_weight = 85.47 - e[38].atomic_weight = 87.956 - e[39].atomic_weight = 88.905 - e[40].atomic_weight = 91.22 - e[41].atomic_weight = 92.906 - e[42].atomic_weight = 95.94 - e[43].atomic_weight = 98.00 - e[44].atomic_weight = 101.07 - e[45].atomic_weight = 102.91 - e[46].atomic_weight = 106.42 - e[47].atomic_weight = 107.87 - e[48].atomic_weight = 112.41 - e[49].atomic_weight = 114.82 - e[50].atomic_weight = 118.69 - e[51].atomic_weight = 121.175 - e[52].atomic_weight = 127.60 - e[53].atomic_weight = 126.90 - e[54].atomic_weight = 131.29 - e[55].atomic_weight = 132.91 - e[56].atomic_weight = 137.33 - e[57].atomic_weight = 138.92 - e[58].atomic_weight = 140.12 - e[59].atomic_weight = 140.91 - e[60].atomic_weight = 144.24 - e[61].atomic_weight = 145.00 - e[62].atomic_weight = 150.36 - e[63].atomic_weight = 151.97 - e[64].atomic_weight = 157.25 - e[65].atomic_weight = 158.924 - e[66].atomic_weight = 162.5 - e[67].atomic_weight = 164.930 - e[68].atomic_weight = 167.26 - e[69].atomic_weight = 169.934 - e[70].atomic_weight = 173.04 - e[71].atomic_weight = 174.97 - e[72].atomic_weight = 178.49 - e[73].atomic_weight = 180.948 - e[74].atomic_weight = 183.85 - e[75].atomic_weight = 186.2 - e[76].atomic_weight = 190.2 - e[77].atomic_weight = 192.2 - e[78].atomic_weight = 195.09 - e[79].atomic_weight = 196.197 - e[80].atomic_weight = 200.59 - e[81].atomic_weight = 204.37 - e[82].atomic_weight = 207.19 - e[83].atomic_weight = 208.980 - e[84].atomic_weight = 209.0 - e[85].atomic_weight = 210.0 - e[86].atomic_weight = 222.0 - e[87].atomic_weight = 223.0 - e[88].atomic_weight = 226.0 - e[89].atomic_weight = 227.028 - e[90].atomic_weight = 204.37 - e[91].atomic_weight = 231.0 - e[92].atomic_weight = 238.03 - e[93].atomic_weight = 237.05 - e[94].atomic_weight = 244.0 - e[95].atomic_weight = 243.0 - e[96].atomic_weight = 245.0 - e[97].atomic_weight = 247.0 - e[98].atomic_weight = 249.0 - e[99].atomic_weight = 254.0 - e[100].atomic_weight = 252.0 - e[101].atomic_weight = 256.0 - e[102].atomic_weight = 254.0 - e[103].atomic_weight = 257 - - #atomic radius (in picometers) - e[1].atomic_radius = 78.000000 - e[2].atomic_radius = 128.000000 - e[3].atomic_radius = 152.000000 - e[4].atomic_radius = 111.300000 - e[5].atomic_radius = 79.500000 - e[6].atomic_radius = 77.200000 - e[7].atomic_radius = 54.900000 - e[8].atomic_radius = 60.400000 - e[9].atomic_radius = 70.900000 - e[10].atomic_radius = 0.000000 - e[11].atomic_radius = 185.800000 - e[12].atomic_radius = 159.900000 - e[13].atomic_radius = 143.200000 - e[14].atomic_radius = 117.600000 - e[15].atomic_radius = 110.500000 - e[16].atomic_radius = 103.500000 - e[17].atomic_radius = 99.400000 - e[18].atomic_radius = 180.000000 - e[19].atomic_radius = 227.200000 - e[20].atomic_radius = 197.400000 - e[21].atomic_radius = 160.600000 - e[22].atomic_radius = 144.800000 - e[23].atomic_radius = 131.100000 - e[24].atomic_radius = 124.900000 - e[25].atomic_radius = 136.700000 - e[26].atomic_radius = 124.100000 - e[27].atomic_radius = 125.300000 - e[28].atomic_radius = 124.600000 - e[29].atomic_radius = 127.800000 - e[30].atomic_radius = 133.500000 - e[31].atomic_radius = 122.100000 - e[32].atomic_radius = 122.500000 - e[33].atomic_radius = 124.500000 - e[34].atomic_radius = 116.000000 - e[35].atomic_radius = 114.500000 - e[36].atomic_radius = 0.000000 - e[37].atomic_radius = 247.500000 - e[38].atomic_radius = 215.100000 - e[39].atomic_radius = 177.600000 - e[40].atomic_radius = 159.000000 - e[41].atomic_radius = 142.900000 - e[42].atomic_radius = 136.300000 - e[43].atomic_radius = 135.200000 - e[44].atomic_radius = 132.500000 - e[45].atomic_radius = 134.500000 - e[46].atomic_radius = 137.600000 - e[47].atomic_radius = 144.500000 - e[48].atomic_radius = 148.900000 - e[49].atomic_radius = 162.600000 - e[50].atomic_radius = 140.500000 - e[51].atomic_radius = 145.000000 - e[52].atomic_radius = 143.200000 - e[53].atomic_radius = 133.100000 - e[54].atomic_radius = 210.000000 - e[55].atomic_radius = 265.500000 - e[56].atomic_radius = 217.400000 - e[57].atomic_radius = 187.000000 - e[58].atomic_radius = 182.500000 - e[59].atomic_radius = 182.000000 - e[60].atomic_radius = 181.400000 - e[61].atomic_radius = 181.000000 - e[62].atomic_radius = 180.200000 - e[63].atomic_radius = 199.500000 - e[64].atomic_radius = 178.700000 - e[65].atomic_radius = 176.300000 - e[66].atomic_radius = 175.200000 - e[67].atomic_radius = 174.300000 - e[68].atomic_radius = 173.400000 - e[69].atomic_radius = 172.400000 - e[70].atomic_radius = 194.000000 - e[71].atomic_radius = 171.800000 - e[72].atomic_radius = 156.400000 - e[73].atomic_radius = 143.000000 - e[74].atomic_radius = 137.000000 - e[75].atomic_radius = 137.100000 - e[76].atomic_radius = 133.800000 - e[77].atomic_radius = 135.700000 - e[78].atomic_radius = 137.300000 - e[79].atomic_radius = 144.200000 - e[80].atomic_radius = 150.300000 - e[81].atomic_radius = 170.000000 - e[82].atomic_radius = 175.000000 - e[83].atomic_radius = 154.500000 - e[84].atomic_radius = 167.300000 - e[85].atomic_radius = 0.000000 - e[86].atomic_radius = 0.000000 - e[87].atomic_radius = 270.000000 - e[88].atomic_radius = 223.000000 - e[89].atomic_radius = 187.800000 - e[90].atomic_radius = 179.800000 - e[91].atomic_radius = 156.100000 - e[92].atomic_radius = 138.500000 - e[93].atomic_radius = 130.000000 - e[94].atomic_radius = 151.300000 - e[95].atomic_radius = 0.000000 - e[96].atomic_radius = 0.000000 - e[97].atomic_radius = 0.000000 - e[98].atomic_radius = 0.000000 - e[99].atomic_radius = 0.000000 - e[100].atomic_radius = 0.000000 - e[101].atomic_radius = 0.000000 - e[102].atomic_radius = 0.000000 - e[103].atomic_radius = 0.000000 - - # Nuclear charge (Slater) - # 0 for those not available - e[1].nuclear_charge = 1.00 - e[2].nuclear_charge = 1.70 - e[3].nuclear_charge = 1.30 - e[4].nuclear_charge = 1.95 - e[5].nuclear_charge = 2.60 - e[6].nuclear_charge = 3.25 - e[7].nuclear_charge = 3.90 - e[8].nuclear_charge = 4.55 - e[9].nuclear_charge = 5.20 - e[10].nuclear_charge = 5.85 - e[11].nuclear_charge = 2.20 - e[12].nuclear_charge = 2.85 - e[13].nuclear_charge = 3.50 - e[14].nuclear_charge = 4.15 - e[15].nuclear_charge = 4.80 - e[16].nuclear_charge = 5.45 - e[17].nuclear_charge = 6.10 - e[18].nuclear_charge = 6.75 - e[19].nuclear_charge = 2.20 - e[20].nuclear_charge = 2.85 - e[21].nuclear_charge = 3.00 - e[22].nuclear_charge = 3.15 - e[23].nuclear_charge = 3.30 - e[24].nuclear_charge = 3.45 - e[25].nuclear_charge = 3.60 - e[26].nuclear_charge = 3.75 - e[27].nuclear_charge = 3.90 - e[28].nuclear_charge = 4.05 - e[29].nuclear_charge = 4.20 - e[30].nuclear_charge = 4.35 - e[31].nuclear_charge = 5.00 - e[32].nuclear_charge = 5.65 - e[33].nuclear_charge = 6.30 - e[34].nuclear_charge = 6.95 - e[35].nuclear_charge = 7.60 - e[36].nuclear_charge = 8.25 - e[37].nuclear_charge = 2.20 - e[38].nuclear_charge = 2.85 - e[39].nuclear_charge = 3.00 - e[40].nuclear_charge = 3.15 - e[41].nuclear_charge = 3.30 - e[42].nuclear_charge = 3.45 - e[43].nuclear_charge = 3.60 - e[44].nuclear_charge = 3.75 - e[45].nuclear_charge = 3.90 - e[46].nuclear_charge = 4.05 - e[47].nuclear_charge = 4.20 - e[48].nuclear_charge = 4.35 - e[49].nuclear_charge = 5.00 - e[50].nuclear_charge = 5.65 - e[51].nuclear_charge = 6.30 - e[52].nuclear_charge = 6.95 - e[53].nuclear_charge = 7.60 - e[54].nuclear_charge = 8.25 - e[55].nuclear_charge = 2.20 - e[56].nuclear_charge = 2.85 - e[57].nuclear_charge = 2.85 - e[58].nuclear_charge = 2.85 - e[59].nuclear_charge = 2.85 - e[60].nuclear_charge = 2.85 - e[61].nuclear_charge = 2.85 - e[62].nuclear_charge = 2.85 - e[63].nuclear_charge = 2.85 - e[64].nuclear_charge = 2.85 - e[65].nuclear_charge = 2.85 - e[66].nuclear_charge = 2.85 - e[67].nuclear_charge = 2.85 - e[68].nuclear_charge = 2.85 - e[69].nuclear_charge = 2.85 - e[70].nuclear_charge = 2.854 - e[71].nuclear_charge = 3.00 - e[72].nuclear_charge = 3.15 - e[73].nuclear_charge = 3.30 - e[74].nuclear_charge = 4.35 - e[75].nuclear_charge = 3.60 - e[76].nuclear_charge = 3.75 - e[77].nuclear_charge = 3.90 - e[78].nuclear_charge = 4.05 - e[79].nuclear_charge = 4.20 - e[80].nuclear_charge = 4.35 - e[81].nuclear_charge = 5.00 - e[82].nuclear_charge = 5.65 - e[83].nuclear_charge = 6.30 - e[84].nuclear_charge = 6.95 - e[85].nuclear_charge = 7.60 - e[86].nuclear_charge = 8.25 - e[87].nuclear_charge = 2.20 - e[88].nuclear_charge = 1.65 - e[89].nuclear_charge = 1.8 - e[90].nuclear_charge = 1.95 - e[91].nuclear_charge = 1.80 - e[92].nuclear_charge = 1.80 - e[93].nuclear_charge = 1.80 - e[94].nuclear_charge = 1.65 - e[95].nuclear_charge = 4.65 - e[96].nuclear_charge = 1.80 - e[97].nuclear_charge = 1.65 - e[98].nuclear_charge = 1.65 - e[99].nuclear_charge = 1.65 - e[100].nuclear_charge = 1.65 - e[101].nuclear_charge = 1.65 - e[102].nuclear_charge = 1.65 - e[103].nuclear_charge = 1.8 - - e[1].abundance = 0.880000 - e[2].abundance = 0.000000 - e[3].abundance = 0.006000 - e[4].abundance = 0.000500 - e[5].abundance = 0.001000 - e[6].abundance = 0.090000 - e[7].abundance = 0.030000 - e[8].abundance = 49.400000 - e[9].abundance = 0.030000 - e[10].abundance = 0.000000 - e[11].abundance = 2.640000 - e[12].abundance = 1.940000 - e[13].abundance = 7.570000 - e[14].abundance = 25.800000 - e[15].abundance = 0.090000 - e[16].abundance = 0.050000 - e[17].abundance = 0.190000 - e[18].abundance = 0.000400 - e[19].abundance = 2.400000 - e[20].abundance = 3.390000 - e[21].abundance = 0.000500 - e[22].abundance = 0.410000 - e[23].abundance = 0.010000 - e[24].abundance = 0.020000 - e[25].abundance = 0.090000 - e[26].abundance = 4.700000 - e[27].abundance = 0.004000 - e[28].abundance = 0.010000 - e[29].abundance = 0.010000 - e[30].abundance = 0.010000 - e[31].abundance = 0.001000 - e[32].abundance = 0.000600 - e[33].abundance = 0.000600 - e[34].abundance = 0.000100 - e[35].abundance = 0.000600 - e[36].abundance = 0.000000 - e[37].abundance = 0.030000 - e[38].abundance = 0.010000 - e[39].abundance = 0.003000 - e[40].abundance = 0.020000 - e[41].abundance = 0.002000 - e[42].abundance = 0.001000 - e[43].abundance = 0.000000 - e[44].abundance = 0.000002 - e[45].abundance = 0.000000 - e[46].abundance = 0.000001 - e[47].abundance = 0.000010 - e[48].abundance = 0.000030 - e[49].abundance = 0.000010 - e[50].abundance = 0.001000 - e[51].abundance = 0.000100 - e[52].abundance = 0.000001 - e[53].abundance = 0.000006 - e[54].abundance = 0.000000 - e[55].abundance = 0.000600 - e[56].abundance = 0.030000 - e[57].abundance = 0.002000 - e[58].abundance = 0.004000 - e[59].abundance = 0.000500 - e[60].abundance = 0.002000 - e[61].abundance = 0.000000 - e[62].abundance = 0.000600 - e[63].abundance = 0.000010 - e[64].abundance = 0.000600 - e[65].abundance = 0.000090 - e[66].abundance = 0.000400 - e[67].abundance = 0.000100 - e[68].abundance = 0.000200 - e[69].abundance = 0.000020 - e[70].abundance = 0.000020 - e[71].abundance = 0.000070 - e[72].abundance = 0.000400 - e[73].abundance = 0.000800 - e[74].abundance = 0.006000 - e[75].abundance = 0.000000 - e[76].abundance = 0.000001 - e[77].abundance = 0.000000 - e[78].abundance = 0.000000 - e[79].abundance = 0.000000 - e[80].abundance = 0.000040 - e[81].abundance = 0.000030 - e[82].abundance = 0.002000 - e[83].abundance = 0.000020 - e[84].abundance = 0.000000 - e[85].abundance = 0.000000 - e[86].abundance = 0.000000 - e[87].abundance = 0.000000 - e[88].abundance = 0.000000 - e[89].abundance = 0.000000 - e[90].abundance = 0.001000 - e[91].abundance = 9.0 - e[92].abundance = 0.000300 - e[93].abundance = 0.000000 - e[94].abundance = 0.000000 - e[95].abundance = 0.000000 - e[96].abundance = 0.000000 - e[97].abundance = 0.000000 - e[98].abundance = 0.000000 - e[99].abundance = 0.000000 - e[100].abundance = 0.000000 - e[101].abundance = 0.000000 - e[102].abundance = 0.000000 - e[103].abundance = 0.000000 - - # Electron Aff. - # 0 for those not available - # Defined as 0 for Elements 2, 25,66 and 72 - e[1].electron_affinity = 72.8 - e[2].electron_affinity = 0.0 - e[3].electron_affinity = 59.6 - e[4].electron_affinity = -18 - e[5].electron_affinity = 26.7 - e[6].electron_affinity = 121.9 - e[7].electron_affinity = -7 - e[8].electron_affinity = 141 - e[9].electron_affinity = 328 - e[10].electron_affinity = -29 - e[11].electron_affinity = 52.9 - e[12].electron_affinity = -21 - e[13].electron_affinity = 44 - e[14].electron_affinity = 133.6 - e[15].electron_affinity = 72 - e[16].electron_affinity = 200.4 - e[17].electron_affinity = 349.0 - e[18].electron_affinity = -35 - e[19].electron_affinity = 48.4 - e[20].electron_affinity = -186 - e[21].electron_affinity = 18.1 - e[22].electron_affinity = 7.6 - e[23].electron_affinity = 50.7 - e[24].electron_affinity = 64.3 - e[25].electron_affinity = 0 - e[26].electron_affinity = 15.7 - e[27].electron_affinity = 63.8 - e[28].electron_affinity = 156 - e[29].electron_affinity = 188.5 - e[30].electron_affinity = 9 - e[31].electron_affinity = 30 - e[32].electron_affinity = 116 - e[33].electron_affinity = 78 - e[34].electron_affinity = 195 - e[35].electron_affinity = 324.7 - e[36].electron_affinity = -39 - e[37].electron_affinity = 46.9 - e[38].electron_affinity = -164 - e[39].electron_affinity = 29.6 - e[40].electron_affinity = 41.1 - e[41].electron_affinity = 86.2 - e[42].electron_affinity = 72.0 - e[43].electron_affinity = 96 - e[44].electron_affinity = 101 - e[45].electron_affinity = 109.7 - e[46].electron_affinity = 53.7 - e[47].electron_affinity = 125.7 - e[48].electron_affinity = -26 - e[49].electron_affinity = 30 - e[50].electron_affinity = 116 - e[51].electron_affinity = 101 - e[52].electron_affinity = 190.2 - e[53].electron_affinity = 295.2 - e[54].electron_affinity = -41 - e[55].electron_affinity = 45.5 - e[56].electron_affinity = -46 - e[57].electron_affinity = 50 - e[58].electron_affinity = 50 - e[59].electron_affinity = 50 - e[60].electron_affinity = 50 - e[61].electron_affinity = 50 - e[62].electron_affinity = 50 - e[63].electron_affinity = 50 - e[64].electron_affinity = 50 - e[65].electron_affinity = 50 - e[66].electron_affinity = 0 - e[67].electron_affinity = 50 - e[68].electron_affinity = 50 - e[69].electron_affinity = 50 - e[70].electron_affinity = 50 - e[71].electron_affinity = 50 - e[72].electron_affinity = 0 - e[73].electron_affinity = 14 - e[74].electron_affinity = 78.6 - e[75].electron_affinity = 14 - e[76].electron_affinity = 106 - e[77].electron_affinity = 151 - e[78].electron_affinity = 205.3 - e[79].electron_affinity = 222.8 - e[80].electron_affinity = -18 - e[81].electron_affinity = 20 - e[82].electron_affinity = 35.1 - e[83].electron_affinity = 91.3 - e[84].electron_affinity = 183 - e[85].electron_affinity = 270 - e[86].electron_affinity = -41 - e[87].electron_affinity = 44 - e[88].electron_affinity = 159 - e[89].electron_affinity = 406 - e[90].electron_affinity = 598.3 - e[91].electron_affinity = 607 - e[92].electron_affinity = 535.6 - e[93].electron_affinity = 0 - e[94].electron_affinity = 0 - e[95].electron_affinity = 0 - e[96].electron_affinity = 0 - e[97].electron_affinity = 0 - e[98].electron_affinity = 0 - e[99].electron_affinity = 50 - e[100].electron_affinity = 0 - e[101].electron_affinity = 0 - e[102].electron_affinity = 0 - e[103].electron_affinity = 0 - - # Electronegativity (Pauling) - # 0 for those not available - # Some noble gases defined as zero - e[1].electronegativity = 2.20 - e[2].electronegativity = 0 - e[3].electronegativity = 0.98 - e[4].electronegativity = 1.57 - e[5].electronegativity = 2.04 - e[6].electronegativity = 2.55 - e[7].electronegativity = 3.04 - e[8].electronegativity = 3.44 - e[9].electronegativity = 3.98 - e[10].electronegativity = 0 - e[11].electronegativity = 0.93 - e[12].electronegativity = 1.31 - e[13].electronegativity = 1.61 - e[14].electronegativity = 1.90 - e[15].electronegativity = 2.19 - e[16].electronegativity = 2.58 - e[17].electronegativity = 3.16 - e[18].electronegativity = 0 - e[19].electronegativity = 0.82 - e[20].electronegativity = 1.00 - e[21].electronegativity = 1.36 - e[22].electronegativity = 1.54 - e[23].electronegativity = 1.63 - e[24].electronegativity = 1.66 - e[25].electronegativity = 1.55 - e[26].electronegativity = 1.83 - e[27].electronegativity = 1.88 - e[28].electronegativity = 1.91 - e[29].electronegativity = 1.90 - e[30].electronegativity = 1.65 - e[31].electronegativity = 1.81 - e[32].electronegativity = 2.01 - e[33].electronegativity = 2.18 - e[34].electronegativity = 2.55 - e[35].electronegativity = 2.96 - e[36].electronegativity = 0 - e[37].electronegativity = 0.82 - e[38].electronegativity = 0.95 - e[39].electronegativity = 1.22 - e[40].electronegativity = 1.33 - e[41].electronegativity = 1.6 - e[42].electronegativity = 2.16 - e[43].electronegativity = 1.9 - e[44].electronegativity = 2.2 - e[45].electronegativity = 2.28 - e[46].electronegativity = 2.20 - e[47].electronegativity = 1.93 - e[48].electronegativity = 1.96 - e[49].electronegativity = 1.78 - e[50].electronegativity = 1.96 - e[51].electronegativity = 2.05 - e[52].electronegativity = 2.1 - e[53].electronegativity = 2.66 - e[54].electronegativity = 2.6 - e[55].electronegativity = 0.79 - e[56].electronegativity = 0.89 - e[57].electronegativity = 1.10 - e[58].electronegativity = 1.12 - e[59].electronegativity = 1.13 - e[60].electronegativity = 1.14 - e[61].electronegativity = 0 - e[62].electronegativity = 1.17 - e[63].electronegativity = 0 - e[64].electronegativity = 1.20 - e[65].electronegativity = 0 - e[66].electronegativity = 1.22 - e[67].electronegativity = 1.23 - e[68].electronegativity = 1.24 - e[69].electronegativity = 1.25 - e[70].electronegativity = 0 - e[71].electronegativity = 1.27 - e[72].electronegativity = 1.3 - e[73].electronegativity = 1.5 - e[74].electronegativity = 2.36 - e[75].electronegativity = 1.9 - e[76].electronegativity = 2.2 - e[77].electronegativity = 2.20 - e[78].electronegativity = 2.28 - e[79].electronegativity = 2.54 - e[80].electronegativity = 2.00 - e[81].electronegativity = 2.04 - e[82].electronegativity = 2.33 - e[83].electronegativity = 2.02 - e[84].electronegativity = 2.0 - e[85].electronegativity = 2.2 - e[86].electronegativity = 0 - e[87].electronegativity = 0.7 - e[88].electronegativity = 0.89 - e[89].electronegativity = 1.1 - e[90].electronegativity = 1.3 - e[91].electronegativity = 1.5 - e[92].electronegativity = 1.38 - e[93].electronegativity = 1.36 - e[94].electronegativity = 1.28 - e[95].electronegativity = 1.3 - e[96].electronegativity = 1.3 - e[97].electronegativity = 1.3 - e[98].electronegativity = 1.3 - e[99].electronegativity = 1.3 - e[100].electronegativity = 1.3 - e[101].electronegativity = 1.3 - e[102].electronegativity = 1.3 - e[103].electronegativity = 1.3 - - # ionization energy (in electronvolts].ionization_energy - e[1].ionization_energy = 13.598 - e[2].ionization_energy = 24.587000 - e[3].ionization_energy = 5.392000 - e[4].ionization_energy = 9.322000 - e[5].ionization_energy = 8.298000 - e[6].ionization_energy = 11.260000 - e[7].ionization_energy = 14.534000 - e[8].ionization_energy = 13.618000 - e[9].ionization_energy = 17.422000 - e[10].ionization_energy = 21.564000 - e[11].ionization_energy = 5.139000 - e[12].ionization_energy = 7.646000 - e[13].ionization_energy = 5.986000 - e[14].ionization_energy = 8.151000 - e[15].ionization_energy = 10.486000 - e[16].ionization_energy = 10.360000 - e[17].ionization_energy = 12.967000 - e[18].ionization_energy = 15.759000 - e[19].ionization_energy = 4.341000 - e[20].ionization_energy = 6.113000 - e[21].ionization_energy = 6.540000 - e[22].ionization_energy = 6.820000 - e[23].ionization_energy = 6.740000 - e[24].ionization_energy = 6.766000 - e[25].ionization_energy = 7.435000 - e[26].ionization_energy = 7.870000 - e[27].ionization_energy = 7.860000 - e[28].ionization_energy = 7.635000 - e[29].ionization_energy = 7.726000 - e[30].ionization_energy = 9.394000 - e[31].ionization_energy = 5.999000 - e[32].ionization_energy = 7.899000 - e[33].ionization_energy = 9.810000 - e[34].ionization_energy = 9.752000 - e[35].ionization_energy = 11.814000 - e[36].ionization_energy = 13.999000 - e[37].ionization_energy = 4.177000 - e[38].ionization_energy = 5.695000 - e[39].ionization_energy = 6.380000 - e[40].ionization_energy = 6.840000 - e[41].ionization_energy = 6.880000 - e[42].ionization_energy = 7.099000 - e[43].ionization_energy = 7.280000 - e[44].ionization_energy = 7.370000 - e[45].ionization_energy = 7.460000 - e[46].ionization_energy = 8.340000 - e[47].ionization_energy = 7.576000 - e[48].ionization_energy = 8.993000 - e[49].ionization_energy = 5.786000 - e[50].ionization_energy = 7.344000 - e[51].ionization_energy = 8.641000 - e[52].ionization_energy = 9.009000 - e[53].ionization_energy = 10.451000 - e[54].ionization_energy = 12.130000 - e[55].ionization_energy = 3.894000 - e[56].ionization_energy = 5.212000 - e[57].ionization_energy = 5.577000 - e[58].ionization_energy = 5.470000 - e[59].ionization_energy = 5.420000 - e[60].ionization_energy = 5.490000 - e[61].ionization_energy = 5.550000 - e[62].ionization_energy = 5.630000 - e[63].ionization_energy = 5.670000 - e[64].ionization_energy = 6.140000 - e[65].ionization_energy = 5.850000 - e[66].ionization_energy = 5.930000 - e[67].ionization_energy = 6.020000 - e[68].ionization_energy = 6.100000 - e[69].ionization_energy = 6.180000 - e[70].ionization_energy = 6.254000 - e[71].ionization_energy = 5.426000 - e[72].ionization_energy = 7.000000 - e[73].ionization_energy = 7.890000 - e[74].ionization_energy = 7.980000 - e[75].ionization_energy = 7.880000 - e[76].ionization_energy = 8.700000 - e[77].ionization_energy = 9.100000 - e[78].ionization_energy = 9.000000 - e[79].ionization_energy = 9.255000 - e[80].ionization_energy = 10.437000 - e[81].ionization_energy = 6.108000 - e[82].ionization_energy = 6.108000 - e[83].ionization_energy = 7.289000 - e[84].ionization_energy = 8.420000 - e[85].ionization_energy = 9.500000 - e[86].ionization_energy = 10.748000 - e[87].ionization_energy = 4.000000 - e[88].ionization_energy = 5.279000 - e[89].ionization_energy = 6.900000 - e[90].ionization_energy = 6.950000 - e[91].ionization_energy = 0.000000 - e[92].ionization_energy = 6.080000 - e[93].ionization_energy = 0.000000 - e[94].ionization_energy = 5.800000 - e[95].ionization_energy = 6.000000 - e[96].ionization_energy = 0.000000 - e[97].ionization_energy = 0.000000 - e[98].ionization_energy = 0.000000 - e[99].ionization_energy = 0.000000 - e[100].ionization_energy = 0.000000 - e[101].ionization_energy = 0.000000 - e[102].ionization_energy = 0.000000 - e[103].ionization_energy = 0.000000 - - - # Ionic Radius (picometers) - # Radius for smallest charge where more than one possible - # Radius for H is for hydride - # 0 for those not available or those that don't form ions - e[1].ionic_radius = 154 - e[2].ionic_radius = 0 - e[3].ionic_radius = 78 - e[4].ionic_radius = 34 - e[5].ionic_radius = 23 - e[6].ionic_radius = 260 - e[7].ionic_radius = 171 - e[8].ionic_radius = 132 - e[9].ionic_radius = 133 - e[10].ionic_radius = 112 - e[11].ionic_radius = 98 - e[12].ionic_radius = 78 - e[13].ionic_radius = 57 - e[14].ionic_radius = 271 - e[15].ionic_radius = 212 - e[16].ionic_radius = 184 - e[17].ionic_radius = 181 - e[18].ionic_radius = 154 - e[19].ionic_radius = 133 - e[20].ionic_radius = 106 - e[21].ionic_radius = 83 - e[22].ionic_radius = 80 - e[23].ionic_radius = 72 - e[24].ionic_radius = 84 - e[25].ionic_radius = 91 - e[26].ionic_radius = 82 - e[27].ionic_radius = 82 - e[28].ionic_radius = 78 - e[29].ionic_radius = 96 - e[30].ionic_radius = 83 - e[31].ionic_radius = 113 - e[32].ionic_radius = 90 - e[33].ionic_radius = 69 - e[34].ionic_radius = 69 - e[35].ionic_radius = 196 - e[36].ionic_radius = 169 - e[37].ionic_radius = 149 - e[38].ionic_radius = 127 - e[39].ionic_radius = 106 - e[40].ionic_radius = 109 - e[41].ionic_radius = 74 - e[42].ionic_radius = 92 - e[43].ionic_radius = 95 - e[44].ionic_radius = 77 - e[45].ionic_radius = 86 - e[46].ionic_radius = 86 - e[47].ionic_radius = 113 - e[48].ionic_radius = 114 - e[49].ionic_radius = 132 - e[50].ionic_radius = 93 - e[51].ionic_radius = 89 - e[52].ionic_radius = 211 - e[53].ionic_radius = 220 - e[54].ionic_radius = 190 - e[55].ionic_radius = 165 - e[56].ionic_radius = 143 - e[57].ionic_radius = 122 - e[58].ionic_radius = 107 - e[59].ionic_radius = 106 - e[60].ionic_radius = 104 - e[61].ionic_radius = 106 - e[62].ionic_radius = 111 - e[63].ionic_radius = 112 - e[64].ionic_radius = 97 - e[65].ionic_radius = 93 - e[66].ionic_radius = 91 - e[67].ionic_radius = 89 - e[68].ionic_radius = 89 - e[69].ionic_radius = 87 - e[70].ionic_radius = 113 - e[71].ionic_radius = 85 - e[72].ionic_radius = 84 - e[73].ionic_radius = 72 - e[74].ionic_radius = 68 - e[75].ionic_radius = 72 - e[76].ionic_radius = 89 - e[77].ionic_radius = 89 - e[78].ionic_radius = 85 - e[79].ionic_radius = 137 - e[80].ionic_radius = 127 - e[81].ionic_radius = 149 - e[82].ionic_radius = 132 - e[83].ionic_radius = 96 - e[84].ionic_radius = 65 - e[85].ionic_radius = 227 - e[86].ionic_radius = 0 - e[87].ionic_radius = 180 - e[88].ionic_radius = 152 - e[89].ionic_radius = 118 - e[90].ionic_radius = 101 - e[91].ionic_radius = 113 - e[92].ionic_radius = 103 - e[93].ionic_radius = 110 - e[94].ionic_radius = 108 - e[95].ionic_radius = 107 - e[96].ionic_radius = 119 - e[97].ionic_radius =118 - e[98].ionic_radius = 117 - e[99].ionic_radius = 116 - e[100].ionic_radius = 115 - e[101].ionic_radius = 114 - e[102].ionic_radius = 113 - e[103].ionic_radius = 112 - - # Thermal Conditions (W/mK at 300K) - # 0 for those not available - e[1].thermal_cond = 0.1815 - e[2].thermal_cond = 0.152 - e[3].thermal_cond = 84.7 - e[4].thermal_cond = 200 - e[5].thermal_cond = 27 - e[6].thermal_cond = 1960 - e[7].thermal_cond = 0.02598 - e[8].thermal_cond = 0.2674 - e[9].thermal_cond = 0.0279 - e[10].thermal_cond = 0.0493 - e[11].thermal_cond = 141 - e[12].thermal_cond = 156 - e[13].thermal_cond = 273 - e[14].thermal_cond = 148 - e[15].thermal_cond = 0.235 - e[16].thermal_cond = 0.269 - e[17].thermal_cond = 0.0089 - e[18].thermal_cond = 0.0177 - e[19].thermal_cond = 102.4 - e[20].thermal_cond = 200 - e[21].thermal_cond = 15.8 - e[22].thermal_cond = 21.9 - e[23].thermal_cond = 30.7 - e[24].thermal_cond = 93.7 - e[25].thermal_cond = 7.82 - e[26].thermal_cond = 80.2 - e[27].thermal_cond = 100 - e[28].thermal_cond = 90.7 - e[29].thermal_cond = 401 - e[30].thermal_cond = 116 - e[31].thermal_cond = 40.6 - e[32].thermal_cond = 59.9 - e[33].thermal_cond = 50.0 - e[34].thermal_cond = 2.04 - e[35].thermal_cond = 0.122 - e[36].thermal_cond = 0.00949 - e[37].thermal_cond = 58.2 - e[38].thermal_cond = 35.3 - e[39].thermal_cond = 17.2 - e[40].thermal_cond = 22.7 - e[41].thermal_cond = 53.7 - e[42].thermal_cond = 138 - e[43].thermal_cond = 50.6 - e[44].thermal_cond = 117 - e[45].thermal_cond = 150 - e[46].thermal_cond = 71.8 - e[47].thermal_cond = 429 - e[48].thermal_cond = 96.8 - e[49].thermal_cond = 81.6 - e[50].thermal_cond = 66.6 - e[51].thermal_cond = 24.3 - e[52].thermal_cond = 2.35 - e[53].thermal_cond = 0.449 - e[54].thermal_cond = 0.00569 - e[55].thermal_cond = 35.9 - e[56].thermal_cond = 18.4 - e[57].thermal_cond = 13.5 - e[58].thermal_cond = 11.4 - e[59].thermal_cond = 12.5 - e[60].thermal_cond = 16.5 - e[61].thermal_cond = 17.9 - e[62].thermal_cond = 13.3 - e[63].thermal_cond = 13.9 - e[64].thermal_cond = 10.6 - e[65].thermal_cond = 11.1 - e[66].thermal_cond = 10.7 - e[67].thermal_cond = 16.2 - e[68].thermal_cond = 14.3 - e[69].thermal_cond = 16.8 - e[70].thermal_cond = 34.9 - e[71].thermal_cond = 16.4 - e[72].thermal_cond = 23 - e[73].thermal_cond = 57.5 - e[74].thermal_cond = 174 - e[75].thermal_cond = 47.9 - e[76].thermal_cond = 87.6 - e[77].thermal_cond = 147 - e[78].thermal_cond = 71.6 - e[79].thermal_cond = 317 - e[80].thermal_cond = 8.34 - e[81].thermal_cond = 46.1 - e[82].thermal_cond = 35.3 - e[83].thermal_cond = 7.87 - e[84].thermal_cond = 20 - e[85].thermal_cond = 1.7 - e[86].thermal_cond = 0.00364 - e[87].thermal_cond = 15 - e[88].thermal_cond = 18.6 - e[89].thermal_cond = 12 - e[90].thermal_cond = 54.0 - e[91].thermal_cond = 47 - e[92].thermal_cond = 27.6 - e[93].thermal_cond = 6.3 - e[94].thermal_cond = 6.74 - e[95].thermal_cond = 10 - e[96].thermal_cond = 10 - e[97].thermal_cond = 10 - e[98].thermal_cond = 10 - e[99].thermal_cond = 10 - e[100].thermal_cond = 10 - e[101].thermal_cond = 10 - e[102].thermal_cond = 10 - e[103].thermal_cond = 10 - - # mpt.m creates e[deg C].melting_point - e[1].melting_point=-259.14 - e[2].melting_point=-272.2 - e[3].melting_point=180.54 - e[4].melting_point=1278.000000 - e[5].melting_point=2300. - e[6].melting_point=3550.000000 - e[7].melting_point=-209.86 - e[8].melting_point=-218.4 - e[9].melting_point=-219.62 - e[10].melting_point=-248.67 - e[11].melting_point=97.81 - e[12].melting_point=648.8 - e[13].melting_point=660.37 - e[14].melting_point=1410. - e[15].melting_point=44.100000 - e[16].melting_point=112.8 - e[17].melting_point=-100.98 - e[18].melting_point=-189.2 - e[19].melting_point=63.65 - e[20].melting_point=839.000 - e[21].melting_point=1541. - e[22].melting_point=1660. - e[23].melting_point=1890. - e[24].melting_point=1857. - e[25].melting_point=1244. - e[26].melting_point=1553. - e[27].melting_point=1495. - e[28].melting_point=1453. - e[29].melting_point=1083.4 - e[30].melting_point=419.58 - e[31].melting_point=29.78 - e[32].melting_point=937.4 - e[33].melting_point=817.00 - e[34].melting_point=217. - e[35].melting_point=-7.2 - e[36].melting_point=-156.6 - e[37].melting_point=38.89 - e[38].melting_point=769. - e[39].melting_point=1522 - e[40].melting_point=1852.00 - e[41].melting_point=2468. - e[42].melting_point=2617. - e[43].melting_point=2172. - e[44].melting_point=2310. - e[45].melting_point=1966 - e[46].melting_point=1552. - e[47].melting_point=961.93 - e[48].melting_point=320.9 - e[49].melting_point=156.61 - e[50].melting_point=231.9681 - e[51].melting_point=630.74 - e[52].melting_point=449.5 - e[53].melting_point=113.5 - e[54].melting_point=-111.9 - e[55].melting_point=28.40 - e[56].melting_point=725. - e[57].melting_point=921 - e[58].melting_point=799 - e[59].melting_point=931 - e[60].melting_point=1021 - e[61].melting_point=1168 - e[62].melting_point=1077 - e[63].melting_point=822 - e[64].melting_point=1313 - e[65].melting_point=1356 - e[66].melting_point=1356 - e[67].melting_point=1474 - e[68].melting_point=1529 - e[69].melting_point=1545 - e[70].melting_point=819 - e[71].melting_point=1663 - e[72].melting_point=2227.0 - e[73].melting_point=2996 - e[74].melting_point=3410. - e[75].melting_point=3180. - e[76].melting_point=3045. - e[77].melting_point=2410. - e[78].melting_point=1772. - e[79].melting_point=1064.43 - e[80].melting_point=-38.87 - e[81].melting_point=303.5 - e[82].melting_point=327.502 - e[83].melting_point=271.3 - e[84].melting_point=254. - e[85].melting_point=302. - e[86].melting_point=-71. - e[87].melting_point=27. - e[88].melting_point=700. - e[89].melting_point=1050. - e[90].melting_point=1750. - e[91].melting_point=1554.000000 - e[92].melting_point=1132.3 - e[93].melting_point=640. - e[94].melting_point=641. - e[95].melting_point=994. - e[96].melting_point=1340. - e[97].melting_point=986. - e[98].melting_point=900.0000 - - # bpt.m creates e[deg C].boiling_point - e[1].boiling_point=-252.87 - e[2].boiling_point=-268.934 - e[3].boiling_point=1347 - e[4].boiling_point=2870.0 - e[5].boiling_point=2550 - e[6].boiling_point=4827.0 - e[7].boiling_point=-195.8 - e[8].boiling_point=-183.962 - e[9].boiling_point=-188.14 - e[10].boiling_point=-246.048 - e[11].boiling_point=882.9 - e[12].boiling_point=1090 - e[13].boiling_point=2467 - e[14].boiling_point=2355 - e[15].boiling_point=280 - e[16].boiling_point=444.674 - e[17].boiling_point=-34.6 - e[18].boiling_point=-185.7 - e[19].boiling_point=774 - e[20].boiling_point=1484 - e[21].boiling_point=2831 - e[22].boiling_point=3287 - e[23].boiling_point=3380 - e[24].boiling_point=2672 - e[25].boiling_point=1962 - e[26].boiling_point=2750 - e[27].boiling_point=2870 - e[28].boiling_point=2732 - e[29].boiling_point=2567 - e[30].boiling_point=907 - e[31].boiling_point=2403 - e[32].boiling_point=2830 - e[33].boiling_point=613.0 - e[34].boiling_point=684.9 - e[35].boiling_point=58.78 - e[36].boiling_point=-152.30 - e[37].boiling_point=688 - e[38].boiling_point=1384 - e[39].boiling_point=3338 - e[40].boiling_point=4377 - e[41].boiling_point=4742 - e[42].boiling_point=4612 - e[43].boiling_point=4877 - e[44].boiling_point=3900 - e[45].boiling_point=3727 - e[46].boiling_point=3140 - e[47].boiling_point=2212 - e[48].boiling_point=765 - e[49].boiling_point=2080 - e[50].boiling_point=2270 - e[51].boiling_point=1750 - e[52].boiling_point=989.8 - e[53].boiling_point=184.35 - e[54].boiling_point=-107.100000 - e[55].boiling_point=678.4 - e[56].boiling_point=1640 - e[57].boiling_point=3457 - e[58].boiling_point=3426 - e[59].boiling_point=3512 - e[60].boiling_point=3068 - e[61].boiling_point=2700 - e[62].boiling_point=1791 - e[63].boiling_point=1597 - e[64].boiling_point=3266 - e[65].boiling_point=3123 - e[66].boiling_point=2562 - e[67].boiling_point=2695 - e[68].boiling_point=2863 - e[69].boiling_point=1947 - e[70].boiling_point=1194 - e[71].boiling_point=3395 - e[72].boiling_point=4602 - e[73].boiling_point=5425 - e[74].boiling_point=5660 - e[75].boiling_point=5627 - e[76].boiling_point=5027 - e[77].boiling_point=4130 - e[78].boiling_point=3827 - e[79].boiling_point=2807 - e[80].boiling_point=356.58 - e[81].boiling_point=1457 - e[82].boiling_point=1740 - e[83].boiling_point=560 - e[84].boiling_point=962 - e[85].boiling_point=337 - e[86].boiling_point=-61.8 - e[87].boiling_point=677 - e[88].boiling_point=1140 - e[86].boiling_point=3200 - e[90].boiling_point=4790 - e[92].boiling_point=3818 - e[93].boiling_point=3902 - e[94].boiling_point=3232 - e[95].boiling_point=2607 - - for i in range(1,nelements+1): - e[i].create_var_dict() - #end for - - #for i in range(len(e)): - # e[i].create_string_representation() - ##end for - - - isotope_masses = obj( - H = {1:1.00782503207, 2:2.0141017778, 3:3.0160492777}, - He = {3:3.0160293191, 4:4.00260325415}, - Li = {6:6.015122795, 7:7.01600455}, - Be = {9:9.0121822}, - B = {10:10.0129370, 11:11.0093054}, - C = {12:12.0000000, 13:13.0033548378, 14:14.003241989}, - N = {14:14.0030740048, 15:15.0001088982}, - O = {16:15.99491461956, 17:16.99913170, 18:17.9991610}, - F = {19:18.99840322}, - Ne = {20:19.9924401754, 21:20.99384668, 22:21.991385114}, - Na = {23:22.9897692809}, - Mg = {24:23.985041700, 25:24.98583692, 26:25.982592929}, - Al = {27:26.98153863}, - Si = {28:27.9769265325, 29:28.976494700, 30:29.97377017}, - P = {31:30.97376163}, - S = {32:31.97207100, 33:32.97145876, 34:33.96786690, 36:35.96708076}, - Cl = {35:34.96885268, 37:36.96590259}, - Ar = {36:35.967545106, 38:37.9627324, 40:39.9623831225}, - K = {39:38.96370668, 40:39.96399848, 41:40.96182576}, - Ca = {40:39.96259098, 42:41.95861801, 43:42.9587666, 44:43.9554818, 46:45.9536926, 48:47.952534}, - Sc = {45:44.9559119}, - Ti = {46:45.9526316, 47:46.9517631, 48:47.9479463, 49:48.9478700, 50:49.9447912}, - V = {50:49.9471585, 51:50.9439595}, - Cr = {50:49.9460442, 52:51.9405075, 53:52.9406494, 54:53.9388804}, - Mn = {55:54.9380451}, - Fe = {54:53.9396105, 56:55.9349375, 57:56.9353940, 58:57.9332756}, - Co = {59:58.9331950}, - Ni = {58:57.9353429, 60:59.9307864, 61:60.9310560, 62:61.9283451, 64:63.9279660}, - Cu = {63:62.9295975, 65:64.9277895}, - Zn = {64:63.9291422, 66:65.9260334, 67:66.9271273, 68:67.9248442, 70:69.9253193}, - Ga = {69:68.9255736, 71:70.9247013}, - Ge = {70:69.9242474, 72:71.9220758, 73:72.9234589, 74:73.9211778, 76:75.9214026}, - As = {75:74.9215965}, - Se = {74:73.9224764, 76:75.9192136, 77:76.9199140, 78:77.9173091, 80:79.9165213, 82:81.9166994}, - Br = {79:78.9183371, 81:80.9162906}, - Kr = {78:77.9203648, 80:79.9163790, 82:81.9134836, 83:82.914136, 84:83.911507, 86:85.91061073}, - Rb = {85:84.911789738, 87:86.909180527}, - Sr = {84:83.913425, 86:85.9092602, 87:86.9088771, 88:87.9056121}, - Y = {89:88.9058483}, - Zr = {90:89.9047044, 91:90.9056458, 92:91.9050408, 94:93.9063152, 96:95.9082734}, - Nb = {93:92.9063781}, - Mo = {92:91.906811, 94:93.9050883, 95:94.9058421, 96:95.9046795, 97:96.9060215, 98:97.9054082, 100:99.907477}, - Tc = {97:96.906365, 98:97.907216, 99:98.9062547}, - Ru = {96:95.907598, 98:97.905287, 99:98.9059393, 100:99.9042195, 101:100.9055821, 102:101.9043493, 104:103.905433}, - Rh = {103:102.905504}, - Pd = {102:101.905609, 104:103.904036, 105:104.905085, 106:105.903486, 108:107.903892, 110:109.905153}, - Ag = {107:106.905097, 109:108.904752}, - Cd = {106:105.906459, 108:107.904184, 110:109.9030021, 111:110.9041781, 112:111.9027578, 113:112.9044017, 114:113.9033585, 116:115.904756}, - In = {113:112.904058, 115:114.903878}, - Sn = {112:111.904818, 114:113.902779, 115:114.903342, 116:115.901741, 117:116.902952, 118:117.901603, 119:118.903308, 120:119.9021947, 122:121.9034390, 124:123.9052739}, - Sb = {121:120.9038157, 123:122.9042140}, - Te = {120:119.904020, 122:121.9030439, 123:122.9042700, 124:123.9028179, 125:124.9044307, 126:125.9033117, 128:127.9044631, 130:129.9062244}, - I = {127:126.904473}, - Xe = {124:123.9058930, 126:125.904274, 128:127.9035313, 129:128.9047794, 130:129.9035080, 131:130.9050824, 132:131.9041535, 134:133.9053945, 136:135.907219}, - Cs = {133:132.905451933}, - Ba = {130:129.9063208, 132:131.9050613, 134:133.9045084, 135:134.9056886, 136:135.9045759, 137:136.9058274, 138:137.9052472}, - La = {138:137.907112, 139:138.9063533}, - Ce = {136:135.907172, 138:137.905991, 140:139.9054387, 142:141.909244}, - Pr = {141:140.9076528}, - Nd = {142:141.9077233, 143:142.9098143, 144:143.9100873, 145:144.9125736, 146:145.9131169, 148:147.916893, 150:149.920891}, - Pm = {145:144.912749, 147:146.9151385}, - Sm = {144:143.911999, 147:146.9148979, 148:147.9148227, 149:148.9171847, 150:149.9172755, 152:151.9197324, 154:153.9222093}, - Eu = {151:150.9198502, 153:152.9212303}, - Gd = {152:151.9197910, 154:153.9208656, 155:154.9226220, 156:155.9221227, 157:156.9239601, 158:157.9241039, 160:159.9270541}, - Tb = {159:158.9253468}, - Dy = {156:155.924283, 158:157.924409, 160:159.9251975, 161:160.9269334, 162:161.9267984, 163:162.9287312, 164:163.9291748}, - Ho = {165:164.9303221}, - Er = {162:161.928778, 164:163.929200, 166:165.9302931, 167:166.9320482, 168:167.9323702, 170:169.9354643}, - Tm = {169:168.9342133}, - Yb = {168:167.933897, 170:169.9347618, 171:170.9363258, 172:171.9363815, 173:172.9382108, 174:173.9388621, 176:175.9425717}, - Lu = {175:174.9407718, 176:175.9426863}, - Hf = {174:173.940046, 176:175.9414086, 177:176.9432207, 178:177.9436988, 179:178.9458161, 180:179.9465500}, - Ta = {180:179.9474648, 181:180.9479958}, - W = {180:179.946704, 182:181.9482042, 183:182.9502230, 184:183.9509312, 186:185.9543641}, - Re = {185:184.9529550, 187:186.9557531}, - Os = {184:183.9524891, 186:185.9538382, 187:186.9557505, 188:187.9558382, 189:188.9581475, 190:189.9584470, 192:191.9614807}, - Ir = {191:190.9605940, 193:192.9629264}, - Pt = {190:189.959932, 192:191.9610380, 194:193.9626803, 195:194.9647911, 196:195.9649515, 198:197.967893}, - Au = {197:196.9665687}, - Hg = {196:195.965833, 198:197.9667690, 199:198.9682799, 200:199.9683260, 201:200.9703023, 202:201.9706430, 204:203.9734939}, - Tl = {203:202.9723442, 205:204.9744275}, - Pb = {204:203.9730436, 206:205.9744653, 207:206.9758969, 208:207.9766521}, - Bi = {209:208.9803987}, - Po = {209:208.9824304, 210:209.9828737}, - At = {210:209.987148, 211:210.9874963}, - Rn = {211:210.990601, 220:220.0113940, 222:222.0175777}, - Fr = {223:223.0197359}, - Ra = {223:223.0185022, 224:224.0202118, 226:226.0254098, 228:228.0310703}, - Ac = {227:227.0277521}, - Th = {230:230.0331338, 232:232.0380553}, - Pa = {231:231.0358840}, - U = {233:233.0396352, 234:234.0409521, 235:235.0439299, 236:236.0455680, 238:238.0507882}, - Np = {236:236.046570, 237:237.0481734}, - Pu = {238:238.0495599, 239:239.0521634, 240:240.0538135, 241:241.0568515, 242:242.0587426, 244:244.064204}, - Am = {241:241.0568291, 243:243.0613811}, - Cm = {243:243.0613891, 244:244.0627526, 245:245.0654912, 246:246.0672237, 247:247.070354, 248:248.072349}, - Bk = {247:247.070307, 249:249.0749867}, - Cf = {249:249.0748535, 250:250.0764061, 251:251.079587, 252:252.081626}, - Es = {252:252.082980}, - Fm = {257:257.095105}, - Md = {258:258.098431, 260:260.10365}, - No = {259:259.10103}, - Lr = {262:262.10963}, - Rf = {265:265.11670}, - Db = {268:268.12545}, - Sg = {271:271.13347}, - Bh = {272:272.13803}, - Hs = {270:270.13465}, - Mt = {276:276.15116}, - Ds = {281:281.16206}, - Rg = {280:280.16447}, - Cn = {285:285.17411} - ) - - - self.nelements = nelements - self.simple_elements = e - - self.elements = obj() - for i in range(1,self.nelements+1): - elem = self.simple_elements[i] - element = Element(elem) - self.elements[elem.symbol] = element - self[elem.symbol] = element - #end for - - isotopes = obj() - for symbol,element in self.elements.items(): - elem_isotopes = obj() - for mass_number,mass in isotope_masses[symbol].items(): - isotope = element.copy() - isotope.atomic_weight = phys_value_dict(mass,'amu') - elem_isotopes[mass_number] = isotope - #end for - isotopes[symbol] = elem_isotopes - #end for - self.isotopes = isotopes - - #end def __init__ - - def show(self): - for i in range(self.nelements): - print() - print(self.elements[i].string_rep) - #end for - #end def show -#end class PeriodicTable - - -pt = PeriodicTable() -periodic_table = pt -ptable = pt - - - - -def is_element(name,symbol=False): - s = name - iselem = False - if isinstance(name,str): - iselem = name in periodic_table.elements - if not iselem: - nlen = len(name) - if name.find('_')!=-1: - s,n = name.split('_',1) - elif nlen>1 and name[1:].isdigit(): - s = name[0:1] - elif nlen>2 and name[2:].isdigit(): - s = name[0:2] - #end if - if len(s)==1: - s = s.upper() - elif len(s)==2: - s = s[0].upper()+s[1].lower() - #end if - iselem = s in periodic_table.elements - #end if - #end if - if symbol: - return iselem,s - else: - return iselem - #end if -#end def is_element - - - - - - - - - - diff --git a/nexus/nexus/physical_system.py b/nexus/nexus/physical_system.py index 79a55bcd36..4d4af3ea59 100644 --- a/nexus/nexus/physical_system.py +++ b/nexus/nexus/physical_system.py @@ -33,11 +33,12 @@ #====================================================================# import os +from pathlib import Path from copy import deepcopy import numpy as np from .developer import DevBase, obj from .unit_converter import convert -from .periodic_table import is_element, ptable +from .periodic_table import Elements from .structure import Structure, generate_structure, read_structure @@ -60,7 +61,12 @@ def new_particles(cls,*particles,**named_particles): #end def new_particles def is_element(self,name,symbol=False): - return is_element(name,symbol=symbol) + if symbol: + is_elem, element = Elements.is_element(name, return_element=symbol) + return is_elem, element.symbol + else: + is_elem = Elements.is_element(name) + return is_elem #end def is_element #end class Matter @@ -221,31 +227,41 @@ def electron_counts(self): #end def electron_counts #end class Particles -me_amu = convert(1.,'me','amu') +amu_me = convert(1.,'amu','me') plist = [ Particle('up_electron' ,1.0,-1, 1), Particle('down_electron',1.0,-1,-1), ] -for name,a in ptable.elements.items(): - spin = 0 # don't have this data - protons = a.atomic_number - neutrons = int(round(a.atomic_weight['amu']-a.atomic_number)) - p = Ion(a.symbol,a.atomic_weight['me'],a.atomic_number,spin,protons,neutrons) - plist.append(p) +for elem in Elements: + plist.append( + Ion( + name = elem.symbol, + mass = elem.atomic_weight * amu_me, + charge = elem.atomic_number, + spin = 0, # Don't have this data + protons = elem.atomic_number, + neutrons = round(elem.atomic_weight-elem.atomic_number), + ) + ) #end for -for name,iso in ptable.isotopes.items(): - for mass_number,a in iso.items(): - spin = 0 # don't have this data - protons = a.atomic_number - neutrons = int(round(a.atomic_weight['amu']-a.atomic_number)) - p = Ion(a.symbol+'_'+str(mass_number),a.atomic_weight['me'],a.atomic_number,spin,protons,neutrons) - plist.append(p) +for elem in Elements: + for mass_number, rel_atomic_mass in elem.isotopes.items(): + plist.append( + Ion( + name = f"{elem.symbol}_{mass_number}", + mass = rel_atomic_mass * amu_me, + charge = elem.atomic_number, + spin = 0, # Don't have this data + protons = elem.atomic_number, + neutrons = round(rel_atomic_mass - elem.atomic_number), + ) + ) #end for #end for -Matter.set_elements(ptable.elements.keys()) +Matter.set_elements([e.symbol for e in Elements]) Matter.set_particle_collection(Particles(plist)) del plist @@ -256,7 +272,6 @@ class PhysicalSystem(Matter): def __init__(self,structure=None,net_charge=0,net_spin=0,particles=None,**valency): self.pseudized = False - if structure is None: self.structure = Structure() else: @@ -653,7 +668,7 @@ def generate_physical_system(**kwargs): if 'structure' in kwargs: s = kwargs['structure'] is_str = isinstance(s,str) - if is_str: + if is_str or isinstance(s, Path): if os.path.exists(s): if 'elem' in kwargs: s = read_structure(s,elem=kwargs['elem']) @@ -704,7 +719,7 @@ def generate_physical_system(**kwargs): remove = [] for var in kwargs: #if var in Matter.elements: - if is_element(var): + if Elements.is_element(var): valency[var] = kwargs[var] remove.append(var) #end if diff --git a/nexus/nexus/project_manager.py b/nexus/nexus/project_manager.py index df561fdab0..f86d9972a8 100644 --- a/nexus/nexus/project_manager.py +++ b/nexus/nexus/project_manager.py @@ -18,9 +18,10 @@ import time from . import memory -from .developer import obj -from .nexus_base import NexusCore, nexus_core +from .developer import obj, error +from .nexus_base import NexusCore, nexus_core, dynamic_storage from .simulation import Simulation +from .machines import Machine,Job def trivial(sim,*args,**kwargs): @@ -381,3 +382,132 @@ def write_cascade_dependents(self): #end class ProjectManager + + +class DynamicWorkflowManager(NexusCore): + '''Replacement for ProjectManager for dynamic workflows''' + + # all dynamic processes encountered + all_dp = set() # all dp found via add_new_dyn_procs + all_sims = set() # all sims associated w/ dp + + def __init__(self): + # dynamic processes by status + self.untouched_dp = obj() # newly minted, perform initial setup + self.blocked_dp = obj() # blocked by the user, do nothing + self.active_dp = obj() # actively progressing through run stages + self.finished_dp = obj() # system or batch process no longer running + self.succeeded_dp = obj() # may have failed if detection is faulty + self.failed_dp = obj() # known to have failed + self.machine = Machine.get(Job.machine) + self.add_new_dyn_procs() + #end def __init__ + + + def add_new_dyn_procs(self): + new_dps = dynamic_storage.dynamic_process_ids-self.all_dp + if len(new_dps)>0: + for dpid in new_dps: + dp = dynamic_storage.dynamic_processes[dpid] + self.all_dp.add(dpid) + self.untouched_dp[dpid] = dp + sim = dp.sim + self.all_sims.add(sim.simid) + if len(sim.dependencies)>0 or len(sim.dependents)>0: + self.error('encountered simulation with explicit dependencies, but these are not allowed in dynamic workflows.\nSimulation id: {}\nSimulation directory: {}'.format(sim.simid,sim.locdir)) + # screen for simulations not associated with dyn process + all_sims = dynamic_storage.simulation_ids + rogue_sims = all_sims-self.all_sims + if len(rogue_sims)>0: + msg = 'encountered simulations not associated with any dynamic process.\nSimulation ids: {}\nSimulation directories:' + paths = [all_sims[simid].locdir for simid in rogue_sims] + for p in sorted(paths): + msg += '\n'+p + msg += '\nThis is likely a developer error.\nPlease contact the developers.' + self.error(msg) + #end def add_new_dyn_procs + + + def poll(self,sleep=None): + if sleep is None: + sleep = nexus_core.sleep + + # find and add newly created dynamic process objects + self.add_new_dyn_procs() + + # update the machine queue for currently running jobs + self.machine.query_queue() + + # setup new sims + rem = [] + for dp in self.untouched_dp.values(): + sim = dp.sim + assert len(sim.dependencies)==0 + assert len(sim.dependents)==0 + if sim.block: + self.blocked_dp[dp.dpid] = dp + del self.untouched_dp[dp.dpid] + continue + if not sim.created_directories: + sim.create_directories() + if not sim.setup: + sim.write_inputs() + if not sim.sent_files: + sim.send_files() + self.active_dp[dp.dpid] = dp + rem.append(dp.dpid) + for dpid in rem: + del self.untouched_dp[dpid] + + # manage active sims + rem = [] + for dp in self.active_dp.values(): + #if not dp.requirements_met(): + # self.error('Requirements not met for simulation execution.\nSimulation type: {}\nSimulation id: {}\nSimulation directory: {}\nDynamic process id: {}\nUnmet requirements: {}'.format(sim.__class__.__name__,sim.simid,sim.locdir,dp.dpid,dp.unmet_reqs)) + sim = dp.sim + assert len(sim.dependencies)==0 + assert len(sim.dependents)==0 + if len(dp.unmet_reqs)>0: + continue + if not sim.finished: + sim.submit() + if sim.finished: + if not sim.got_output: + sim.get_output() + if not sim.analyzed: + sim.analyze() + self.finished_dp[dp.dpid] = dp + if sim.failed: + self.failed_dp[dp.dpid] = dp + else: + self.succeeded_dp[dp.dpid] = dp + rem.append(dp.dpid) + for dpid in rem: + del self.active_dp[dpid] + + # submit jobs on the machine and store machine pid in sim + self.machine.submit_jobs() + for dp in self.active_dp.values(): + dp.sim.update_process_id() + + # wait until next poll + time.sleep(sleep) + #end def poll + +#end class DynamicWorkflowManager + + + + +def workflow_manager(**kw): + if not hasattr(workflow_manager,'first'): + workflow_manager.first = True + else: + workflow_manager.first = False + if not nexus_core.dynamic: + error('workflow_manager is only compatible with dynamic workflows.\nIf you intend to use dynamic workflows, please set dynamic=True in settings.') + elif not workflow_manager.first: + error('function "workflow_manager" should only be called once') + wm = DynamicWorkflowManager(**kw) + return wm +#end def workflow_manager diff --git a/nexus/nexus/pseudopotential.py b/nexus/nexus/pseudopotential.py index 1c4a94acc2..258a774865 100644 --- a/nexus/nexus/pseudopotential.py +++ b/nexus/nexus/pseudopotential.py @@ -37,16 +37,18 @@ #====================================================================# import os +from pathlib import Path import numpy as np from .execute import execute from .fileio import TextFile from .xmlreader import readxml -from .periodic_table import pt, is_element +from .periodic_table import Elements from .unit_converter import convert from .developer import DevBase, obj, unavailable, error from .basisset import process_gaussian_text, GaussianBasisSet from .physical_system import PhysicalSystem from .testing import object_eq +from .utilities import path_string, is_valid_filename try: import matplotlib.pyplot as plt @@ -56,6 +58,9 @@ def pp_elem_label(filename,guard=False): + if guard and not is_valid_filename(filename): + error(f"Pseudopotential file name {filename} is invalid!") + el = '' for c in filename: if c=='.' or c=='_' or c=='-': @@ -64,14 +69,21 @@ def pp_elem_label(filename,guard=False): el+=c #end for elem_label = el - is_elem,symbol = is_element(el,symbol=True) + is_elem, element = Elements.is_element(el, return_element=True) if guard: if not is_elem: - error('cannot determine element for pseudopotential file: {0}\npseudopotential file names must be prefixed by an atomic symbol or label\n(e.g. Si, Si1, etc)'.format(filename)) + error( + 'cannot determine element for pseudopotential file: {0}\n' + 'pseudopotential file names must be prefixed by an atomic symbol or label\n' + '(e.g. Si, Si1, etc)'.format(filename) + ) #end if - return elem_label,symbol + return elem_label, element.symbol else: - return elem_label,symbol,is_elem + if isinstance(element, Elements): + return elem_label, element.symbol, is_elem + else: + return elem_label, element, is_elem #end if #end def pp_elem_label @@ -112,7 +124,8 @@ def __init__(self,filepath=None): #end def __init__ def read(self,filepath): - lines = open(filepath,'r').read().splitlines() + with open(filepath, "r") as f: + lines = f.read().splitlines() new_block = True tokens = [] block = '' @@ -168,8 +181,8 @@ def __init__(self,*pseudopotentials): for pp in pseudopotentials: if isinstance(pp,PseudoFile): pps.append(pp) - elif isinstance(pp,str): - ppfiles.append(pp) + elif isinstance(pp, str | Path): + ppfiles.append(path_string(pp)) else: self.error('expected PseudoFile type or filepath, got '+str(type(pp)),exit=False) errors = True @@ -289,16 +302,18 @@ def __call__(self,label,**code_pps): #end if ppcoll = obj() for pp in pps: - if not isinstance(pp,str): + if not isinstance(pp, (str, Path)): self.error('incorrect use of ppset\nnon-filename provided with set labeled "{0}" for simulation code "{1}"\neach pseudopential file name must be a string\nreceived type: {2}\nwith value: {3}'.format(label,code,pp.__class__.__name__,pp)) - #end if - elem_label,symbol,is_elem = pp_elem_label(pp) + else: + pp = path_string(pp) + elem_label, symbol, is_elem = pp_elem_label(pp) + if not is_elem: self.error('invalid filename provided to ppset\ncannot determine element for pseudopotential file: {0}\npseudopotential file names must be prefixed by an atomic symbol or label\n(e.g. Si, Si1, etc)'.format(pp)) elif symbol in ppcoll: self.error('incorrect use of ppset\nmore than one pseudopotential file provided for element "{0}" for code "{1}" in set labeled "{2}"\nfirst file: {3}\nsecond file: {4}'.format(symbol,code,label,ppcoll[symbol],pp)) #end if - ppcoll[symbol] = pp + ppcoll[symbol] = path_string(pp) #end for pseudos[clow] = ppcoll #end for @@ -372,6 +387,7 @@ def transfer_core_from(self,other): def read(self,filepath,format=None): + filepath = path_string(filepath) if self.requires_format: if format is None: self.error('format keyword must be specified to read file {0}\nvalid options are: {1}'.format(filepath,self.formats)) @@ -383,7 +399,8 @@ def read(self,filepath,format=None): self.error('cannot read {0}, file does not exist'.format(filepath)) #end if self.element = pp_elem_label(os.path.split(filepath)[1])[0] - text = open(filepath,'r').read() + with open(filepath, "r") as f: + text = f.read() self.read_text(text,format,filepath=filepath) #end def read @@ -398,7 +415,8 @@ def write(self,filepath=None,format=None): #end if text = self.write_text(format) if filepath is not None: - open(filepath,'w').write(text) + with open(filepath, "w") as f: + f.write(text) #end if return text #end def write @@ -1482,7 +1500,8 @@ def write_qmcpack(self,filepath=None): text = header+grid+L2+semilocal+footer if filepath is not None: - open(filepath,'w').write(text) + with open (filepath, "w") as f: + f.write(text) #end if return text #end def write_qmcpack @@ -1621,7 +1640,7 @@ def read_text(self,text,format=None,filepath=None): else: atomic_number = int(conv_atomic_number[-2:]) #end if - element = pt.simple_elements[atomic_number].symbol + element = Elements(atomic_number).symbol if 'input' not in lines[i].lower(): self.error('INPUT must be present for crystal pseudpotential read') #end if @@ -1679,7 +1698,7 @@ def read_text(self,text,format=None,filepath=None): Zval = int(Zval) lmax = int(lmax)-1 element = self.element - Zcore = int(pt[element].atomic_number)-Zval + Zcore = int(Elements(element).atomic_number)-Zval ns = [int(n) for n in lines[i].split()]; i+=1 while ilen(pt.simple_elements): + if Zatom > Elements.num_elements(): self.error('element {0} is not in the periodic table') #end if - element = pt.simple_elements[Zatom].symbol + element = Elements(Zatom).symbol units = file.readtokensf('Energy units',str) if units not in self.unitmap: self.error('units {0} unrecognized from casino PP file {1}'.format(units,filepath)) @@ -2649,7 +2669,7 @@ def read(self,filepath,format=None): #end for lpots.append(convert(v,self.unitmap[units],'Ha')) #end while - + file.close() # fill in SemilocalPP class data obtained from read self.element = element self.Zval = int(Z) @@ -2657,7 +2677,7 @@ def read(self,filepath,format=None): if self.Zcore==0: self.core = '0' else: - self.core = pt.simple_elements[self.Zcore].symbol + self.core = Elements(self.Zcore).symbol #end if self.lmax = lmax self.local = lloc diff --git a/nexus/nexus/pwscf.py b/nexus/nexus/pwscf.py index 33f85ef505..71d4ca34a1 100644 --- a/nexus/nexus/pwscf.py +++ b/nexus/nexus/pwscf.py @@ -18,10 +18,12 @@ import os +import shutil import numpy as np +from .nexus_base import nexus_core from .developer import obj from .physical_system import PhysicalSystem -from .simulation import Simulation +from .simulation import Simulation, DynamicProcess from .pwscf_input import PwscfInput, generate_pwscf_input from .pwscf_analyzer import PwscfAnalyzer from .execute import execute @@ -122,6 +124,9 @@ class Pwscf(Simulation): vdw_table = None + # dynamic workflow support + allowed_requirements = ['none','structure','charge_density','orbitals'] + @staticmethod def settings(vdw_table=None): # van der Waals family of functional require the vdW table generated by @@ -388,11 +393,134 @@ def get_output_files(self): def app_command(self): return self.app_name+' -input '+self.infile #end def app_command + + + # dynamic workflow support + + def fill_produces(self): + calc = 'scf' + if 'calculation' in self.input.control: + calc = self.input.control.calculation.lower() + + # charge density + if calc=='scf': + self.produces.add('charge_density') + self.produces.add('energy') + + # orbitals + if calc=='nscf': + self.produces.add('orbitals') + elif calc=='scf': + k_points = self.input.k_points + nkpoints = 1 + if 'grid' in k_points and k_points.grid==(1,1,1): + nkpoints = 1 + elif 'kpoints' in self.input.k_points: + nkpoints = len(self.input.k_points.kpoints) + nosym = True + if 'nosym' in self.input.system: + nosym = self.input.system.nosym + if nkpoints==1 or not nosym: + self.produces.add('orbitals') + + # structure + if 'relax' in calc: + self.produces.add('structure') + self.produces.add('energy') + #end def fill_produces + + + def fill_products(self): + if not self.filled_products: + self.filled_products = True + else: + self.error('fill_products must be called only once.\nThis is likely a developer error.') + if len(self.produces)==0: + return + analyzer = self.load_analyzer_image() + input = analyzer.input + if 'energy' in self.produces: + self.products.energy = analyzer.E + if 'charge_density' in self.produces: + outdir = input.control.outdir + path = os.path.join(self.locdir,outdir) + self.products.charge_density = path + if 'orbitals' in self.produces: + outdir = input.control.outdir + path = os.path.join(self.locdir,outdir) + self.products.orbitals = path + if 'structure' in self.produces: + pa = analyzer + structs = pa.structures + struct = structs[len(structs)-1].copy() + pos = struct.positions + atoms = struct.atoms + if 'celldm(1)' in self.input.system: + scale = self.input.system['celldm(1)'] + else: + scale = 1.0 + pos = scale*np.array(pos) + structure = self.system.structure.copy() + structure.change_units('B') + structure.set_pos(pos) + structure.set_elem(atoms) + if 'axes' in struct: + structure._set_axes(struct.axes) + self.products.structure = structure + #end def fill_products + + + def receive_charge_density(self,charge_density_path): + if not os.path.isdir(charge_density_path): + self.error('charge density path is not a directory.\nPath provided: {}'.format(charge_density_path)) + c = self.input.control + res_path = os.path.realpath(charge_density_path) + loc_path = os.path.realpath(self.locdir) + if res_path==loc_path: + return # don't need to do anything if in same directory + outdir = os.path.join(self.locdir,c.outdir) + # try shutil copytree, should be ok if never copying over + #command = 'rsync -av {0}/* {1}/'.format(res_path,outdir) + if not os.path.exists(outdir): + os.makedirs(outdir) + sync_record = os.path.join(outdir,'nexus_sync_record') + if not os.path.exists(sync_record): + print(' Copying directory: {}\n this might take a while'.format(outdir)) + #execute(command) + shutil.copytree(res_path, outdir, dirs_exist_ok=True) + print(' directory copy complete') + # fix "permission denied" on some systems + execute('chmod -R a+rw '+outdir) + f = open(sync_record,'w') + f.write('\n') + f.close() + #end def recieve_charge_density + + + def receive_structure(self,struct): + struct.change_units('B') + self.system.structure = struct + self.system.remove_folded() + input = self.input + preserve_kp = 'k_points' in input and 'specifier' in input.k_points and (input.k_points.specifier=='automatic' or input.k_points.specifier=='gamma') + if preserve_kp: + kp = input.k_points.copy() + input.incorporate_system(self.system) + if preserve_kp: + input.k_points = kp + #end def receive_structure + #end class Pwscf def generate_pwscf(**kwargs): + + if nexus_core.dynamic: + dp,dyn_args = DynamicProcess.check_first_gen(kwargs) + if dp is not None: + return dp + sim_args,inp_args = Pwscf.separate_inputs(kwargs) if 'input' not in sim_args: @@ -401,5 +529,8 @@ def generate_pwscf(**kwargs): #end if pwscf = Pwscf(**sim_args) + if nexus_core.dynamic: + pwscf = DynamicProcess(sim=pwscf,**dyn_args) + return pwscf #end def generate_pwscf diff --git a/nexus/nexus/pwscf_analyzer.py b/nexus/nexus/pwscf_analyzer.py index 86da67d672..459d820316 100644 --- a/nexus/nexus/pwscf_analyzer.py +++ b/nexus/nexus/pwscf_analyzer.py @@ -21,17 +21,18 @@ import numpy as np from .developer import obj, unavailable from .unit_converter import convert -from .periodic_table import PeriodicTable +from .periodic_table import Elements from .numerics import simstats, simplestats from .simulation import SimulationAnalyzer, Simulation from .structure import Structure, get_kpath from .pwscf_input import PwscfInput from .pwscf_data_reader import read_qexml from .fileio import TextFile +from .utilities import path_string from . import numpy_extensions as npe -pt = PeriodicTable() -elements = set(pt.elements.keys()) + +elements = set([e.symbol for e in Elements]) def is_number(s): @@ -88,7 +89,7 @@ def __init__(self,arg0=None,infile_name=None,outfile_name=None,pw2c_outfile_name outfile_name= sim.outfile self.input_structure = sim.system.structure elif arg0 is not None: - path = arg0 + path = path_string(arg0) if not os.path.exists(path): self.error('path to QE data does not exist\npath provided: {}'.format(path)) #end if @@ -178,7 +179,8 @@ def analyze(self): #end try try: - lines = open(outfile,'r').read().splitlines() + with open(outfile, "r") as f: + lines = f.read().splitlines() except: nx+=1 if self.info.warn: @@ -622,7 +624,8 @@ def analyze(self): try: if pw2c_outfile_name is not None: - lines = open(os.path.join(path,pw2c_outfile_name),'r').readlines() + with open(os.path.join(path,pw2c_outfile_name), "r") as out: + lines = out.readlines() for l in lines: if l.find('Kinetic')!=-1: tokens = l.split() diff --git a/nexus/nexus/pwscf_data_reader.py b/nexus/nexus/pwscf_data_reader.py index 5153132633..0acd058aaa 100644 --- a/nexus/nexus/pwscf_data_reader.py +++ b/nexus/nexus/pwscf_data_reader.py @@ -124,7 +124,8 @@ def read_qexml(inp): if isinstance(inp,list): rawlines = inp elif isinstance(inp,str):# and os.path.exists(inp): - rawlines = open(inp,'r').read().splitlines() + with open(inp, "r") as f: + rawlines = f.read().splitlines() else: print('read_qexml error: input can only be filename or list of lines') print(' input received: ',inp) diff --git a/nexus/nexus/pwscf_input.py b/nexus/nexus/pwscf_input.py index c5979a0979..544d29f7dc 100644 --- a/nexus/nexus/pwscf_input.py +++ b/nexus/nexus/pwscf_input.py @@ -45,13 +45,14 @@ import os +import sys import inspect from copy import deepcopy import numpy as np from numpy import pi from numpy.linalg import inv from .unit_converter import convert -from .periodic_table import is_element +from .periodic_table import Elements from .structure import Structure, kmesh from .physical_system import PhysicalSystem from .developer import DevBase, obj, log, warn, error @@ -904,7 +905,6 @@ class ee(Section): #end for -exit_ = exit def check_new_variables(exit=True): sections = section_classes msg = '' @@ -925,7 +925,7 @@ def check_new_variables(exit=True): log('section checks of new variables passed') #end if if exit: - exit_() + sys.exit() #end if #end def check_new_variables #check_new_variables() @@ -970,7 +970,7 @@ def check_section_classes(exit=True): log('pwscf input checks passed') #end if if exit: - exit_() + sys.exit() #end if #end def check_section_classes #check_section_classes() @@ -2210,9 +2210,9 @@ def generate_any_pwscf_input(**kwargs): pp = pw.atomic_species.pseudopotentials for atom in pw.atomic_species.atoms: if atom not in pp: - iselem,symbol = is_element(atom,symbol=True) - if iselem and symbol in pp: - pp[atom] = str(pp[symbol]) + iselem, element = Elements.is_element(atom, return_element=True) + if iselem and element.symbol in pp: + pp[atom] = str(pp[element.symbol]) #end if #end if #end for diff --git a/nexus/nexus/pwscf_postprocessors.py b/nexus/nexus/pwscf_postprocessors.py index 4926720eb1..c15a6c4fd4 100644 --- a/nexus/nexus/pwscf_postprocessors.py +++ b/nexus/nexus/pwscf_postprocessors.py @@ -760,7 +760,8 @@ def write_lowdin(self,filepath=None,sum=None,tot=None,pol=None,up=None,down=None #end if #end for if filepath is not None: - open(filepath,'w').write(text) + with open(filepath, "w") as f: + f.write(text) #end if return text #end def write_lowdin diff --git a/nexus/nexus/qmcpack.py b/nexus/nexus/qmcpack.py index 78057a8697..5e7348987c 100644 --- a/nexus/nexus/qmcpack.py +++ b/nexus/nexus/qmcpack.py @@ -601,6 +601,8 @@ class Qmcpack(Simulation): application_properties = set(['serial','omp','mpi']) application_results = set(['jastrow','cuspcorr','wavefunction']) + # dynamic workflow support + allowed_requirements = ['none','pwscf_orbitals','jastrow','wavefunction'] def has_afqmc_input(self): afqmc_input = False @@ -1580,6 +1582,176 @@ def read_bandinfo_dat(self): #end for return edata #end def read_bandinfo_dat + + + # dynamic worfklow support + + def fill_produces(self): + calctypes = self.input.get_output_info('calctypes') + if 'opt' in calctypes: + if self.input.has_jastrows(): + self.produces.add('jastrows') + self.produces.add('wavefunction') + #end def fill_produces + + + def fill_products(self): + if len(self.produces)==0: + return + if 'jastrow' in self.produces or 'wavefunction' in self.produces: + analyzer = self.load_analyzer_image() + if 'results' not in analyzer or 'optimization' not in analyzer.results: + self.error('analyzer did not compute results required to determine jastrow or wavefunction') + opt_file = str(analyzer.results.optimization.optimal_file) + opt_file = os.path.join(self.locdir,opt_file) + if 'jastrow' in self.produces: + self.products.jastrow = opt_file + if 'wavefunction' in self.produces: + self.products.wavefunction = opt_file + #end def fill_products + + + def receive_structure(self,struct): + struct.change_units('B') + self.system.structure = struct + self.system.remove_folded() + self.input.incorporate_system(self.system) + #end def receive_structure + + + def receive_pwscf_orbitals(self,orb_file): + if not orb_file.endswith('.h5'): + self.error('pwscf orbitals must be in hdf5 (.h5) file.\nFile provided: {}'.format(orb_file)) + input = self.input + system = self.system + h5file = orb_file + wavefunction = input.get('wavefunction') + if isinstance(wavefunction,collection): + wavefunction = wavefunction.get_single('psi0') + wf = wavefunction + if 'sposet_builder' in wf and wf.sposet_builder.type=='bspline': + orb_elem = wf.sposet_builder + elif 'sposet_builders' in wf and 'bspline' in wf.sposet_builders: + orb_elem = wf.sposet_builders.bspline + elif 'sposet_builders' in wf and 'einspline' in wf.sposet_builders: + orb_elem = wf.sposet_builders.einspline + elif 'determinantset' in wf and wf.determinantset.type in ('bspline','einspline'): + orb_elem = wf.determinantset + else: + self.error('Could not incorporate pw2qmcpack orbitals.\nbspline sposet_builder and determinantset are both missing.') + if 'href' in orb_elem and isinstance(orb_elem.href,str) and os.path.exists(orb_elem.href): + # user specified h5 file for orbitals, bypass orbital dependency + orb_elem.href = os.path.relpath(orb_elem.href,self.locdir) + else: + orb_elem.href = os.path.relpath(h5file,self.locdir) + if system.structure.folded_structure is not None: + orb_elem.tilematrix = np.array(system.structure.tmatrix) + defs = obj( + #twistnum = 0, + meshfactor = 1.0 + ) + for var,val in defs.items(): + if var not in orb_elem: + orb_elem[var] = val + has_twist = 'twist' in orb_elem + has_twistnum = 'twistnum' in orb_elem + if not has_twist and not has_twistnum: + orb_elem.twistnum = 0 + + structure = system.structure + nkpoints = len(structure.kpoints) + if nkpoints==0: + self.error('system must have kpoints to assign twistnums') + + twistnums = list(range(len(structure.kpoints))) + if self.should_twist_average: + self.twist_average(twistnums) + elif not has_twist and orb_elem.twistnum is None: + orb_elem.twistnum = twistnums[0] + + #end def receive_pwscf_orbitals + + + def receive_jastrow(self,jastrow_file): + opt_file = jastrow_file + opt = QmcpackInput(opt_file) + wavefunction = input.get('wavefunction') + optwf = opt.qmcsystem.wavefunction + # handle spinor case + spinor = input.get('spinor') + if spinor is not None and spinor: + # remove u-d term from optmized jastrow + # also set correct cusp condition + J2 = optwf.get('J2') + if J2 is not None: + corr = J2.get('correlation') + if 'ud' in corr: + del corr.ud + if 'uu' in corr: + corr.uu.cusp = -0.5 + J3 = optwf.get('J3') + if J3 is not None: + corr = J3.get('correlation') + if hasattr(corr, 'coefficients'): + # For single-species systems, the data structure changes. + # In this case, the only J3 term should be 'uu'. + # Otherwise, the user might be trying to do something strange. + assert 'uu' in corr.coefficients.id, 'Only uu J3 terms are allowed in SOC calculations.' + else: + j3_ids = [] + for j3_term in corr: + j3_id = j3_term.coefficients.id + j3_ids.append(j3_id) + for j3_id in j3_ids: + if 'ud' in j3_id: + delattr(corr, j3_id) + def process_jastrow(wf): + if 'jastrow' in wf: + js = [wf.jastrow] + elif 'jastrows' in wf: + js = list(wf.jastrows.values()) + else: + js = [] + jd = dict() + for j in js: + jtype = j.type.lower().replace('-','_').replace(' ','_') + key = jtype + # take care of multiple jastrows of the same type + if key in jd: # use name to distinguish + key += j.name + if key in jd: # if still duplicate then error out + msg = 'duplicate jastrow in '+self.__class__.__name__ + self.error(msg) + jd[key] = j + return jd + #end def process_jastrow + if wavefunction is None: + qs = input.get('qmcsystem') + qs.wavefunction = optwf.copy() + else: + jold = process_jastrow(wavefunction) + jopt = process_jastrow(optwf) + jnew = list(jopt.values()) + for jtype in jold.keys(): + if jtype not in jopt: + jnew.append(jold[jtype]) + if len(jnew)==1: + wavefunction.jastrow = jnew[0].copy() + else: + wavefunction.jastrows = collection(jnew) + #end def receive_jastrow + + + def receive_wavefunction(self,wf_file): + opt = QmcpackInput(wf_file) + qs = input.get('qmcsystem') + wfn = opt.qmcsystem.wavefunction.copy() + ovp = 'override_variational_parameters' # name is too long + if ovp in wfn: + wfn[ovp].href = os.path.relpath(wfn[ovp].href,self.locdir) + qs.wavefunction = wfn + #end def receive_wavefunction + #end class Qmcpack diff --git a/nexus/nexus/qmcpack_analyzer.py b/nexus/nexus/qmcpack_analyzer.py index 6d3b8ed456..8951055b69 100644 --- a/nexus/nexus/qmcpack_analyzer.py +++ b/nexus/nexus/qmcpack_analyzer.py @@ -25,6 +25,7 @@ import os import sys import traceback +from pathlib import Path import numpy as np #custom library imports from .developer import obj, unavailable @@ -117,7 +118,7 @@ def __init__(self,source=None,destination=None,savefile='', output=set(['averages','samples']), ndmc_blocks=1000,equilibration=None,group_num=None, traces=False,dm_settings=None): - self.source = source + self.source = source if not isinstance(source, Path) else str(source.resolve()) self.destination = destination self.savefile = str(savefile) self.output = set(output) @@ -241,7 +242,7 @@ def __init__(self,arg0=None,**kwargs): #end if elif isinstance(arg0,QmcpackAnalysisRequest): request = arg0 - elif isinstance(arg0,str): + elif isinstance(arg0, (str, Path)): kwargs['source']=arg0 request = QmcpackAnalysisRequest(**kwargs) else: diff --git a/nexus/nexus/qmcpack_converters.py b/nexus/nexus/qmcpack_converters.py index c757192f76..c1e4ce2a56 100644 --- a/nexus/nexus/qmcpack_converters.py +++ b/nexus/nexus/qmcpack_converters.py @@ -46,7 +46,9 @@ import os import numpy as np from .developer import obj, error +from .nexus_base import nexus_core from .simulation import Simulation, SimulationInput, SimulationAnalyzer +from .simulation import DynamicProcess from .pwscf import Pwscf from .gamess import Gamess from .pyscf_sim import Pyscf @@ -292,6 +294,9 @@ class Pw2qmcpack(Simulation): application_properties = set(['serial']) application_results = set(['orbitals','gc_occupation']) + # dynamic workflow support + allowed_requirements = ['orbitals'] + def check_result(self,result_name,sim): calculating_result = False if result_name=='orbitals': @@ -386,9 +391,8 @@ def incorporate_result(self,result_name,result,sim): def check_sim_status(self): outfile = os.path.join(self.locdir,self.outfile) - fobj = open(outfile,'r') - output = fobj.read() - fobj.close() + with open(outfile, "r") as fobj: + output = fobj.read() inputpp = self.input.inputpp prefix = 'pwscf' outdir = './' @@ -437,12 +441,64 @@ def get_output_files(self): def app_command(self): return self.app_name+'<'+self.infile #end def app_command + + + # dynamic workflow support + + def fill_produces(self): + self.produces.add('orbitals') + #end def fill_produces + + + def fill_products(self): + inputpp = self.input.inputpp + prefix = 'pwscf' + outdir = './' + if 'prefix' in inputpp: + prefix = inputpp.prefix + if 'outdir' in inputpp: + outdir = inputpp.outdir + if outdir.startswith('./'): + outdir = outdir[2:] + orb_file = os.path.join(self.locdir,outdir,prefix+'.pwscf.h5') + self.products.orbitals = orb_file + #end def fill_products + + + def receive_orbitals(self,orb_path): + # This just checks if output paths match. + # Otherwise running pw2qmcpack will fail. + orbdir = os.path.realpath(orb_path) + if not os.path.isdir(orb_path): + self.error('orbitals path is not a directory.\nPath provided: {}'.format(orb_path)) + savedir = None + for d in os.listdir(orbdir): + if d.endswith('.save'): + savedir = d + break + if savedir is None or not os.path.exists(os.path.join(orbdir,savedir)): + self.error('.save directory does not exist at provided orbitals path.\nPath provided: {}'.format(orb_path)) + prefix = savedir.rsplit('.',1) + p2in = self.input.inputpp + if prefix!=p2in.prefix: + self.error('pw2qmcpack must have same prefix as pwscf run\npwscf prefix: {}\npw2qmcpack prefix: {}'.format(prefix,p2in.prefix)) + p2dir = os.path.realpath(os.path.join(self.locdir,p2in.outdir)) + if p2dir!=orbdir: + self.error('pwscf orbital location does not match pw2qmcpack.\npwscf location: {}\npw2qmcpack location: {}'.format(orbdir,p2dir)) + #end def receive_orbitals + #end class Pw2qmcpack def generate_pw2qmcpack(**kwargs): + + if nexus_core.dynamic: + dp,dyn_args = DynamicProcess.check_first_gen(kwargs) + if dp is not None: + return dp + sim_args,inp_args = Simulation.separate_inputs(kwargs) if 'input' not in sim_args: @@ -450,6 +506,9 @@ def generate_pw2qmcpack(**kwargs): #end if pw2qmcpack = Pw2qmcpack(**sim_args) + if nexus_core.dynamic: + pw2qmcpack = DynamicProcess(sim=pw2qmcpack,**dyn_args) + return pw2qmcpack #end def generate_pw2qmcpack @@ -856,7 +915,8 @@ def incorporate_result(self,result_name,result,sim): def check_sim_status(self): - output = open(os.path.join(self.locdir,self.outfile),'r').read() + with open(os.path.join(self.locdir,self.outfile), "r") as out: + output = out.read() #errors = open(os.path.join(self.locdir,self.errfile),'r').read() # Recent versions of convert4qmc no longer produce the orbs.h5 file. @@ -1348,7 +1408,8 @@ def incorporate_result(self,result_name,result,sim): def check_sim_status(self): - output = open(os.path.join(self.locdir,self.outfile),'r').read() + with open(os.path.join(self.locdir,self.outfile), "r") as out: + output = out.read() success = '# Finished.' in output success &= os.path.exists(os.path.join(self.locdir,self.input.output)) diff --git a/nexus/nexus/qmcpack_input.py b/nexus/nexus/qmcpack_input.py index 1cac450bd3..258f92b2af 100644 --- a/nexus/nexus/qmcpack_input.py +++ b/nexus/nexus/qmcpack_input.py @@ -134,17 +134,19 @@ import os +from pathlib import Path import inspect import keyword import numpy as np from .numpy_extensions import reshape_inplace from .xmlreader import XMLreader, XMLelement from .developer import DevBase, obj, hidden, error -from .periodic_table import is_element +from .periodic_table import Elements from .structure import Structure, Jellium, get_kpath from .physical_system import PhysicalSystem from .simulation import SimulationInput, SimulationInputTemplate from .pwscf_input import array_to_string as pwscf_array_string +from .utilities import path_string from . import numpy_extensions as npe yesno_dict = {True:'yes' ,False:'no'} @@ -3166,8 +3168,8 @@ def __init__(self,arg0=None,arg1=None): element = None if arg0 is None and arg1 is None: None - elif isinstance(arg0,str) and arg1 is None: - filepath = arg0 + elif isinstance(arg0,(str, Path)) and arg1 is None: + filepath = path_string(arg0) elif isinstance(arg0,QIxml) and arg1 is None: element = arg0 elif isinstance(arg0,meta) and isinstance(arg1,QIxml): @@ -4540,482 +4542,506 @@ def modify(self, qmc = None, **gen_calcs ): - """ - Modify the parameters and xml elements of a QMCPACK input file. + """Modify the parameters and xml elements of a QMCPACK input file. Parameters ---------- - driver : {'batched', 'legacy', None}, default = None - Sets `driver_version` in QMCPACK input. If None, 'batched' is assumed. - remove_system : bool, default = False - Removes `` and `'. - change_system : PhysicalSystem (such as from `generate_physical_system` - Updates physical system information in `` and `' - to match the contents of the PhysicalSystem object. - remove_jastrows: bool, default = False - Removes all `` elements. - remove_J1: bool, default = False - Remove only the one-body jastrow, `` - remove_J2: bool, default = False - Remove only the two-body jastrow, `` - remove_J3: bool, default = False - Remove only the three-body jastrow, `` - remove_determinants: bool, default = False - Removes `` - remove_multidet: bool, default = False - Removes `` - remove_calculations: bool, default = False - Removes all `` and ` elements. - optimize: {bool, None}, default = None - Sets `optimize` parameter in all wavefunction components. - If `True` or `False` `optimize` is set accordingly. - If `None` no changes are made. - jastrow_opt: {bool, None}, default = None - Sets `optimize` parameters in all `` elements. - Logic is identical to `optimize`. - orbitals_h5: {str, None} + driver : {'batched', 'legacy'} or None, default=None + Sets ``driver_version`` in QMCPACK input. If ``None``, ``'batched'`` + is assumed. + remove_system : bool, default=False + Removes ```` and ````. + change_system : PhysicalSystem (such as from `generate_physical_system`) + Updates physical system information in ```` and + ```` to match the contents of the ``PhysicalSystem`` + object. + remove_jastrows : bool, default=False + Removes all ```` elements. + remove_J1 : bool, default=False + Remove only the one-body jastrow, ```` + remove_J2 : bool, default=False + Remove only the two-body jastrow, ```` + remove_J3 : bool, default=False + Remove only the three-body jastrow, ```` + remove_determinants : bool, default=False + Removes ```` + remove_multidet : bool, default=False + Removes ```` + remove_calculations : bool, default=False + Removes all ```` and ```` elements. + optimize : bool or None, default=None + Sets ``optimize`` parameter in all wavefunction components. + If ``True`` or ``False`` ``optimize`` is set accordingly. + If ``None`` no changes are made. + jastrow_opt : bool or None, default=None + Sets ``optimize`` parameters in all ```` elements. + Logic is identical to ``optimize``. + orbitals_h5 : str or None Sets path to an HDF5 file containing single particle orbitals. - If type `str`, `href` is set in `' or - `' if present and in `' + If type ``str``, ``href`` is set in ```` or + ```` if present and in ```` otherwise. - If `None`, no action is taken. - multidet_h5: {bool, None}, default = None + If ``None``, no action is taken. + multidet_h5 : bool or None, default=None Set path to an HDF5 file containing multideterminat coefficents. - If type `str`, `href` is set in ``. - If `None`, no action is taken. - multidet_cutoff: {float, None}, default = None - Sets the multideterminant coefficient cutoff, which itself - determints to include based on their magnitude relative to + If type ``str``, ``href`` is set in ````. + If ``None``, no action is taken. + multidet_cutoff : float or None, default=None + Sets the multideterminant coefficient cutoff, which itself + determints to include based on their magnitude relative to the cutoff. - If type `float`, `cutoff` in `` is set. - If `None`, no action is taken. - pseudo_files: **kwargs, default = **{} + If type ``float``, ``cutoff`` in ```` is set. + If ``None``, no action is taken. + pseudo_files : dict of str:str, default={} Sets paths to pseudopotential files. - Any atomic species as keywords and pseudopotential filepaths as - values. - For example: + Any atomic species as keywords and pseudopotential filepaths + as values. + For example: + + .. code-block:: python + qi.modify( pseudo_files = dict( Mo = 'Mo.ccECP.xml', S = 'S.ccECP.xml')) + Atomic species matching is case insensitive. - calculations: `None` or list of `qmc` or `loop` objects - Overwrite all `' or `' elements with those provided. - If `None`, no action is taken. + calculations : None or list of qmc or loop objects + Overwrite all ```` or ```` elements with those provided. + If ``None``, no action is taken. + + Notes + ----- + The remaining input parameters are broken into sections based on + what part of the input file they modify. Jastrow Generation Parameters - ----------------------------- - Generate Jastrow factors based on the parameters given. Existing - Jastrows are overwritten. - - The parameter signature is identical to `generate_jastrows_alt` - called both here and by `generate_qmcpack_input` or - `generate_qmcpack`. - - J1: bool, default False - Creates a one-body B-spline Jastrow if `True`. - If no other `J1_` parameters are given, sensible defaults are set: - cutoff set to the Wigner-Seitz radius for periodic systems or to + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + + Generate Jastrow factors based on the parameters given. Existing + Jastrows are overwritten. The parameter signature is identical + to ``generate_jastrows_alt`` called both here and by + ``generate_qmcpack_input`` or ``generate_qmcpack``. + + J1 : bool, default=False + Creates a one-body B-spline Jastrow if ``True``. + If no other ``J1_`` parameters are given, sensible defaults are set: + cutoff set to the Wigner-Seitz radius for periodic systems or to 5 Bohr for open boundary conditions. By default, one knot is placed every 0.5 Bohr up to the cutoff. - J2: bool, default False. - Creates both one-body and two-body B-spline Jastrows if `True`. - If no other `J2_` parameters are given, sensible defaults are set: - cutoff set to the Wigner-Seitz radius for periodic systems or to + J2 : bool, default=False. + Creates both one-body and two-body B-spline Jastrows if ``True``. + If no other ``J2_`` parameters are given, sensible defaults are set: + cutoff set to the Wigner-Seitz radius for periodic systems or to 10 Bohr for open boundary conditions. By default, one knot is placed every 0.5 Bohr up to the cutoff. - J3: bool, default False. - Creates one-, two-, and three-body B-spline Jastrows if `True`. - If no other `J3_` parameters are given, sensible defaults are set: - cutoff set to 5 Bohr, `isize=3`, esize=3`. - J1_rcut: {float, None}, default = None - Sets the cutoff (`rcut`) in the one-body Jastrow. - If `None`, the Wigner-Seitz radius is used for periodic systems, - or the value of `J1_rcut_open` for open boundary conditions. - J1_rcut_open: float, default = 5.0 - Sets the cutoff (`rcut`) in the one-body Jastrow for open systems.. - J1_size: {int, None}, default = None + J3 : bool, default=False. + Creates one-, two-, and three-body B-spline Jastrows if ``True``. + If no other ``J3_`` parameters are given, sensible defaults are set: + cutoff set to 5 Bohr, ``isize=3``, ``esize=3``. + J1_rcut : float or None, default=None + Sets the cutoff (``rcut``) in the one-body Jastrow. + If ``None``, the Wigner-Seitz radius is used for periodic systems, + or the value of ``J1_rcut_open`` for open boundary conditions. + J1_rcut_open : float, default=5.0 + Sets the cutoff (``rcut``) in the one-body Jastrow for open systems. + J1_size : int or None, default=None Sets the number of knots in the one-body B-spline Jastrow. - If `int`, knots are placed up to the cutoff. - If `None`, `J1_dr` is used instead. - J1_dr: float, default = 0.5 - Sets B-spline knots every `J1_dr` up to the cutoff. - J1_opt: {True, False, None}, default = None - If `bool`, sets `optimize` flag in the one-body Jastrow. - If `None`, no action is taken. - J2_rcut: {float, None}, default = None - Sets the cutoff (`rcut`) in the two-body Jastrow. - If `None`, the Wigner-Seitz radius is used for periodic systems, - or the value of `J2_rcut_open` for open boundary conditions. - J2_rcut_open: float, default = 10.0 - Sets the cutoff (`rcut`) in the two-body Jastrow for open systems. - J2_size: {int, None}, default = None + If ``int``, knots are placed up to the cutoff. + If ``None``, ``J1_dr`` is used instead. + J1_dr : float, default=0.5 + Sets B-spline knots every ``J1_dr`` up to the cutoff. + J1_opt : bool or None, default=None + If ``bool``, sets ``optimize`` flag in the one-body Jastrow. + If ``None``, no action is taken. + J2_rcut : float or None, default=None + Sets the cutoff (``rcut``) in the two-body Jastrow. + If ``None``, the Wigner-Seitz radius is used for periodic systems, + or the value of ``J2_rcut_open`` for open boundary conditions. + J2_rcut_open : float, default=10.0 + Sets the cutoff (``rcut``) in the two-body Jastrow for open systems. + J2_size : int or None, default=None Sets the number of knots in the one-body B-spline Jastrow. - If `int`, knots are placed up to the cutoff. - If `None`, `J2_dr` is used instead. - J2_dr: float, default = 0.5 - Sets B-spline knots every `J2_dr` up to the cutoff. - J2_opt: {True, False, None}, default = None - If `bool`, sets `optimize` flag in the two-body Jastrow. - If `None`, no action is taken. - J2_init: {'zero', 'rpa'}, default = 'zero' - If `zero`, set all B-spline coefficients to 0.0. - If `rpa`, set B-spline coefficents based on the RPA Jastrow for - a homogeneous electron gas with the same electron density as the + If ``int``, knots are placed up to the cutoff. + If ``None``, ``J2_dr`` is used instead. + J2_dr : float, default=0.5 + Sets B-spline knots every ``J2_dr`` up to the cutoff. + J2_opt : bool or None, default=None + If ``bool``, sets ``optimize`` flag in the two-body Jastrow. + If ``None``, no action is taken. + J2_init : {'zero', 'rpa'}, default='zero' + If ``zero``, set all B-spline coefficients to 0.0. + If ``rpa``, set B-spline coefficents based on the RPA Jastrow for + a homogeneous electron gas with the same electron density as the current atomic system. - For an open system only 'zero' is allowed. - J1k: bool, default False - Creates a one-body k-space Jastrow with defaults below if `True`. - J1k_kcut: float, default 5.0 + For an open system only ``'zero'`` is allowed. + J1k : bool, default=False + Creates a one-body k-space Jastrow with defaults below if ``True``. + J1k_kcut : float, default=5.0 Sets the k-space cutoff which determines how many plane-waves and coefficients are used. - J1k_symm: {'crystal', 'isotropic', 'none'} + J1k_symm : {'crystal', 'isotropic', 'none'} Whether to use symmetries to constrain the plane-wave coefficients. - If 'crystal', enforce translation symmetries. - If 'isotropic', impose symmetry based on identical |k|. - If 'none', the coefficients are fully unconstrained. - J1k_opt: {True, False, None}, default = None - If `bool`, sets `optimize` flag in the one-body k-space Jastrow. - If `None`, no action is taken. - J2k: bool, default False - Creates a two-body k-space Jastrow with defaults below if `True`. - J2k_kcut: float, default 5.0 + If ``'crystal'``, enforce translation symmetries. + If ``'isotropic'``, impose symmetry based on identical :math:`|k|`. + If ``'none'``, the coefficients are fully unconstrained. + J1k_opt : bool or None, default=None + If ``bool``, sets ``optimize`` flag in the one-body k-space Jastrow. + If ``None``, no action is taken. + J2k : bool, default=False + Creates a two-body k-space Jastrow with defaults below if ``True``. + J2k_kcut : float, default=5.0 Sets the k-space cutoff which determines how many plane-waves and coefficients are used. - J2k_symm: {'crystal', 'isotropic', 'none'} + J2k_symm : {'crystal', 'isotropic', 'none'} Whether to use symmetries to constrain the plane-wave coefficients. - If 'crystal', enforce translation symmetries. - If 'isotropic', impose symmetry based on identical |k-k'|. - If 'none', the coefficients are fully unconstrained. - J2k_opt: {True, False, None}, default = None - If `bool`, sets `optimize` flag in the two-body k-space Jastrow. - If `None`, no action is taken. + If ``'crystal'``, enforce translation symmetries. + If ``'isotropic'``, impose symmetry based on identical :math:`|k-k'|`. + If ``'none'``, the coefficients are fully unconstrained. + J2k_opt : bool or None, default=None + If ``bool``, sets ``optimize`` flag in the two-body k-space Jastrow. + If ``None``, no action is taken. QMC Calculation Generation Parameters - ------------------------------------- - Generate `` and/or `` elements. Any existing elements - are overwritten + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + + Generate ```` and/or ```` elements. Any existing elements + are overwritten. - The number of input parameters depends on the value of `qmc` and - are given as keyword inputs represented by **gen_calcs. + The number of input parameters depends on the value of ``qmc`` and + are given as keyword inputs represented by ``gen_calcs``. Only inputs for batched drivers are described below. - Parameters at the top are shared by nearly all `qmc` methods. + Parameters at the top are shared by nearly all ``qmc`` methods. - qmc: {'vmc', 'vmc_test', 'vmc_noJ', 'dmc', 'dmc_test', 'dmc_noJ', - 'opt', None} - If `None`, no action is taken. + qmc : {'vmc', 'vmc_test', 'vmc_noJ', 'dmc', 'dmc_test', 'dmc_noJ', 'opt'} or None + If ``None``, no action is taken. Otherwise calculations are generated as detailed below. Shared Parameters - ----------------- - total_walkers: {None, int}, default None - If not `None`, set the `total_walkers` parameter, which is the - number of independent walker configuration trajectories across + ^^^^^^^^^^^^^^^^^ + + total_walkers : int or None, default=None + If not ``None``, set the ``total_walkers`` parameter, which is the + number of independent walker configuration trajectories across within each VMC sampling. If using MPI or threads, the walkers will be divided roughly evenly between each MPI rank/thread. - walkers_per_rank: {None, int}, default = None - If not `None`, set the `walkers_per_rank` parameter, which is - the number of independent walker configuration trajectories - within each MPI rank. In this case, the total number of - walkers is #MPI_ranks*`walkers_per_rank`. - Only one of {`walkers_per_rank`, `total_walkers`} should be + walkers_per_rank : int or None, default=None + If not ``None``, set the ``walkers_per_rank`` parameter, which is + the number of independent walker configuration trajectories + within each MPI rank. In this case, the total number of + walkers is ``#MPI_ranks*walkers_per_rank``. + Only one of {``walkers_per_rank``, ``total_walkers``} should be provided. - warmupsteps: int + warmupsteps : int Number of VMC steps used to move the walker population toward - the equilibrium distribution before sampling estimators + the equilibrium distribution before sampling estimators such as the total energy. - blocks: int - Sets `blocks` parameter, the outer loop in the VMC/DMC + blocks : int + Sets ``blocks`` parameter, the outer loop in the VMC/DMC sampling process. - steps: {int, None}, default = None - If not None, set the `steps` parameter, the inner loop in - the VMC/DMC sampling. The resulting number of samples per - walker is `blocks`*`steps`. - Only one of {`samples`, `steps`} should be provided. - substeps: int - Sets the `substeps` parameter, which is the number of VMC - steps in between the generation of each sample. Used to - decorrelate walker configurations between the collection of - each sample (energy evaluation). Does not apply to DMC + steps : int or None, default=None + If not None, set the ``steps`` parameter, the inner loop in + the VMC/DMC sampling. The resulting number of samples per + walker is ``blocks*steps``. + Only one of {``samples``, ``steps``} should be provided. + substeps : int + Sets the ``substeps`` parameter, which is the number of VMC + steps in between the generation of each sample. Used to + decorrelate walker configurations between the collection of + each sample (energy evaluation). Does not apply to DMC calculations. - timestep: float - Sets the `timestep` parameter, which is the width of the - gaussian used to generate the next configuration in each - walker's configuration trajectory. Affects the acceptance - ratio, and hence the efficiency of the sampling. In production - DMC a small value should be used (e.g. 0.01) to prioritize the - accuracy of the solution (minimize timestep) over apparent + timestep : float + Sets the ``timestep`` parameter, which is the width of the + gaussian used to generate the next configuration in each + walker's configuration trajectory. Affects the acceptance + ratio, and hence the efficiency of the sampling. In production + DMC a small value should be used (e.g. 0.01) to prioritize the + accuracy of the solution (minimize timestep) over apparent gains in efficiency. - usedrift: bool - Sets the `usedrift` parameter. - If `True`, use the logarithmic gradient to shift the gaussian + usedrift : bool + Sets the ``usedrift`` parameter. + If ``True``, use the logarithmic gradient to shift the gaussian center for a more efficient sampling (higher acceptance ratio). Used only in VMC. - checkpoint: {int, None}, default = None - If not `None`, set the `checkpoint` parameter. A checkpoint - HDF5 file will be written every `checkpoint` blocks. - maxcpusecs: {float, None} - If not `None`, set the `maxcpusecs` parameter. QMCPACK will + checkpoint : int or None, default=None + If not ``None``, set the ``checkpoint`` parameter. A checkpoint + HDF5 file will be written every ``checkpoint`` blocks. + maxcpusecs : float or None + If not ``None``, set the ``maxcpusecs`` parameter. QMCPACK will terminate gracefully if the walltime exceeds this value. - crowds: {int, None}, default = None - If not `None`, set the `crowds` parameter, which controls - the partitioning of walkers for parallel (thread/gpu) + crowds : int or None, default=None + If not ``None``, set the ``crowds`` parameter, which controls + the partitioning of walkers for parallel (thread/gpu) execution. - spinmass: {float, None}, default = None - If not `None`, set the `spinmass` parameter. Generally only + spinmass : float or None, default=None + If not ``None``, set the ``spinmass`` parameter. Generally only used in calculations including spin-orbit coupling. - Case `qmc='vmc'` - ---------------- + Case ``qmc='vmc'`` + ^^^^^^^^^^^^^^^^^^ + As in "Shared Parameters" above, but with the defaults below. - warmupsteps: int, default = 50 - blocks: int, default = 800 - steps: int, default = 10 - substeps: int, default = 3 - timestep: float, default = 0.3 - usedrift: bool, default = False - - Case `qmc='vmc_test'` - ------------------- - As in `qmc='vmc'`, but with the defaults below. Intended to - make a quick test run to check for successful execution or to + - ``warmupsteps : int, default=50`` + - ``blocks : int, default=800`` + - ``steps : int, default=10`` + - ``substeps : int, default=3`` + - ``timestep : float, default=0.3`` + - ``usedrift : bool, default=False`` + + Case ``qmc='vmc_test'`` + ^^^^^^^^^^^^^^^^^^^^^^^ + + As in ``qmc='vmc'``, but with the defaults below. Intended to + make a quick test run to check for successful execution or to obtain timing estimates to design production runs. - Case `qmc='vmc_noJ'` - ------------------- - As in `qmc='vmc'`, but with the defaults below. Uses increased - sampling intended to better deal with the increased variance + Case ``qmc='vmc_noJ'`` + ^^^^^^^^^^^^^^^^^^^^^^ + + As in ``qmc='vmc'``, but with the defaults below. Uses increased + sampling intended to better deal with the increased variance present in Jastrow-free runs. - - warmupsteps: int, default = 200 - blocks: int, default = 800 - steps: int, default = 100 - - Case `qmc='dmc'` - --------------- + + - ``warmupsteps : int, default=200`` + - ``blocks : int, default=800`` + - ``steps : int, default=100`` + + Case ``qmc='dmc'`` + ^^^^^^^^^^^^^^^^^^ + As in "Shared Parameters" above, but with the defaults below. These parameter names and defaults refer to the DMC sections. - - warmupsteps: int, default = 20 - blocks: int, default = 200 - steps: int, default = 10 - timestep: float, default = 0.01 - nonlocalmoves: {None, True, False, 'v0', 'v1', 'v3'}, default = None + - ``warmupsteps : int, default=20`` + - ``blocks : int, default=200`` + - ``steps : int, default=10`` + - ``timestep : float, default=0.01`` + + nonlocalmoves : {'v0', 'v1', 'v3'} or bool or None, default=None Perform T-moves or the locality approximation. - If None, use QMCPACK's default (locality approx) - If False, use the locality approximation. - If True or 'v0', use the first developed T-moves algorithm. - If 'v1', use the second developed T-moves algorithm. - If 'v3', use a modified T-moves algorithm, courtesy Ye Luo. - branching_cutoff_scheme: + If ``None``, use QMCPACK's default (locality approx) + If ``False``, use the locality approximation. + If ``True`` or ``'v0'``, use the first developed T-moves algorithm. + If ``'v1'``, use the second developed T-moves algorithm. + If ``'v3'``, use a modified T-moves algorithm, courtesy Ye Luo. + branching_cutoff_scheme See QMCPACK manual. - crowd_serialize_walkers: + crowd_serialize_walkers See QMCPACK manual. - reconfiguration: + reconfiguration See QMCPACK manual. - maxage: + maxage See QMCPACK manual. - feedback: + feedback See QMCPACK manual. - sigmabound: + sigmabound See QMCPACK manual. - - vmc_warmupsteps: int, default = 30 - Set `warmupsteps` in the VMC block executed prior to DMC. + vmc_warmupsteps : int, default=30 + Set ``warmupsteps`` in the VMC block executed prior to DMC. The parameters below set the respective params in VMC. - vmc_blocks: int, default = 40 - vmc_steps: int, default = 10 - vmc_substeps: int, default = 3 - vmc_timestep: float, default = 0.3 - vmc_usedrift: bool, default = False - vmc_checkpoint: {int, None}, default = None - vmc_spin_mass: {float, None}, default = None - - eq_dmc: bool, default = False + + vmc_blocks : int, default=40 + vmc_steps : int, default=10 + vmc_substeps : int, default=3 + vmc_timestep : float, default=0.3 + vmc_usedrift : bool, default=False + vmc_checkpoint : int or None, default=None + vmc_spin_mass : float or None, default=None + + eq_dmc : bool, default=False Insert a DMC block following VMC for the purpose of rapid equilibration prior to the subsequent production DMC sections. - eq_warmupsteps: int, default = 20 - eq_blocks: int, default = 20 - eq_steps: int, default = 5 - eq_timestep: float, default = 0.02 - The timestep should be greater than or equal to the ones used - in the subsequent DMC sections. - eq_checkpoint: {int, None}, default = None - - ntimesteps: int, default = 1 - If greater than one, create a sequence of `ntimesteps` DMC - sections with successively smaller timesteps. Intended for - DMC timestep extrapolation. - timestep_factor: float, default = 0.5 - The first timestep is given by `timestep`, the following ones - are reduced by successive multiplication of `timestep_factor`. - - Case `qmc='dmc_test'` - ------------------- - As in `qmc='dmc', but with the defaults below. Intended to - make a quick test run to check for successful execution or to + + eq_warmupsteps : int, default=20 + eq_blocks : int, default=20 + eq_steps : int, default=5 + + eq_timestep : float, default=0.02 + The timestep should be greater than or equal to the ones used + in the subsequent DMC sections. + + eq_checkpoint : int or None, default=None + + ntimesteps : int, default=1 + If greater than one, create a sequence of ``ntimesteps`` DMC + sections with successively smaller timesteps. Intended for + DMC timestep extrapolation. + timestep_factor : float, default=0.5 + The first timestep is given by ``timestep``, the following ones + are reduced by successive multiplication of ``timestep_factor``. + + Case ``qmc='dmc_test'`` + ^^^^^^^^^^^^^^^^^^^^^^^ + + As in ``qmc='dmc'``, but with the defaults below. Intended to + make a quick test run to check for successful execution or to obtain timing estimates to design production runs. - warmupsteps: int, default = 2 - blocks: int, default = 10 - steps: int, default = 2 - vmc_warmupsteps: int, default = 10 - vmc_blocks: int, default = 4 - eq_dmc: bool, default = False - eq_warmupsteps: int, default = 2 - eq_blocks: int, default = 5 - eq_steps: int, default = 2 - - Case `qmc='dmc_noJ'` - ------------------ - As in `qmc='dmc'`, but with the defaults below. Uses increased - sampling intended to better deal with the increased variance - present in Jastrow-free runs. Note that Jastrow-free runs are - much more likely to be unstable due to large fluctations in the + - ``warmupsteps : int, default=2`` + - ``blocks : int, default=10`` + - ``steps : int, default=2`` + - ``vmc_warmupsteps : int, default=10`` + - ``vmc_blocks : int, default=4`` + - ``eq_dmc : bool, default=False`` + - ``eq_warmupsteps : int, default=2`` + - ``eq_blocks : int, default=5`` + - ``eq_steps : int, default=2`` + + Case ``qmc='dmc_noJ'`` + ^^^^^^^^^^^^^^^^^^^^^^ + + As in ``qmc='dmc'``, but with the defaults below. Uses increased + sampling intended to better deal with the increased variance + present in Jastrow-free runs. Note that Jastrow-free runs are + much more likely to be unstable due to large fluctations in the branching weights. - warmupsteps: int, default = 40 - blocks: int, default = 400 - steps: int, default = 20 - - Case `qmc='opt'` - --------------- + - ``warmupsteps : int, default=40`` + - ``blocks : int, default=400`` + - ``steps : int, default=20`` + + Case ``qmc='opt'`` + ^^^^^^^^^^^^^^^^^^ + Generate calculation elements for wavefunction optimization. - The parameter signature is identical to `generate_opt_calculations`, - which depends on the value of `method` and `minmethod`. + The parameter signature is identical to ``generate_opt_calculations``, + which depends on the value of ``method`` and ``minmethod``. - method: {'linear', 'cslinear'}, default = 'linear' - If `linear`, use one of the versions of the linear method. - If 'cslinear', use the correlated sampling linear method. + method : {'linear', 'cslinear'}, default='linear' + If ``'linear'``, use one of the versions of the linear method. + If ``'cslinear'``, use the correlated sampling linear method. - minmethod: {'quartic' , 'rescale' , 'linemin', - 'adaptive', 'oneshift', 'sr_cg' } - default = 'quartic' + minmethod : {'quartic' , 'rescale' , 'linemin', 'adaptive', 'oneshift', 'sr_cg'}, default='quartic' - minwalkers: float, default = 0.3 - Minimum threshold to accept a parameter update based on the + minwalkers : float, default=0.3 + Minimum threshold to accept a parameter update based on the ratio of wavefunction values between internal sub-iterations. - The value of `minwalkers` should be given in the range (0,1]. - A small value of `minwalkers` will easily accept parameter + The value of ``minwalkers`` should be given in the range (0,1]. + A small value of ``minwalkers`` will easily accept parameter updates, likely resulting in an unstable run. - cost: {'energy','variance', tuple} - If 'energy', energy minization is performed. - If 'variance', variance minimization is performed. - If length 2 tuple of floats `(we, wv)`, - cost = we*energy + wv*variance - If length 3 tuple of floats `(we, wv, wuv)`, - cost = we*energy + wv*variance + wuv*unreweightedvariance - When `minmethod='oneshift', no cost function is being - minimized, but instead the parameter updates are determined - solely by `minwalkers`. - cycles: int, default = 12 - Number of top level optimization iterations to perform. - Sets `. - samples: {None, int}, default = None - If not `None` set the `samples` parameter, i.e. the total - number of VMC walker configurations to use in each optimization + cost : {'energy', 'variance'} or tuple + If ``'energy'``, energy minization is performed. + If ``'variance'``, variance minimization is performed. + If length 2 tuple of floats ``(we, wv)``, + + ``cost = we*energy + wv*variance`` + + If length 3 tuple of floats ``(we, wv, wuv)``, + + ``cost = we*energy + wv*variance + wuv*unreweightedvariance`` + + When ``minmethod='oneshift'``, no cost function is being + minimized, but instead the parameter updates are determined + solely by ``minwalkers``. + cycles : int, default=12 + Number of top level optimization iterations to perform. + Sets ````. + samples : int or None, default=None + If not ``None`` set the ``samples`` parameter, i.e. the total + number of VMC walker configurations to use in each optimization cycle. - init_cycles: int, default = 0 - If init_cycles>0, introduce a preceding optimization loop of - the same type (same `minmethod`, `cost` and most other - parameters). - Sets ` in this prior loop. - A few parameters can be set to different values from the - subsequent/main loop as listed below. - init_samples: {None, int}, default = None - If not `None` set the `samples` parameter, i.e. the total - number of VMC walker configurations to use in the preceding - optimization loop. - init_steps: {None, int} - If not `None` set the `steps` parameter in the preceding - optimization loop. - init_minwalkers: float, default=0.1 - If not `None` set the `minwalkers` parameter in the preceding - optimization loop. Often set to a smaller value than in the - subsequent/main loop to allow more aggressive parameter updates - in hopes of a faster convergence to the general vicinity - of the cost minimum. - init_line_search: bool, default = False - Only applicable to `minmethod`='sr_cg', see below. - If True, perform a linesearch along the direction of the - parameter gradient using the minimum cost to determine the - parameter stepsize. - init_sr_tau: float, default = 0.1 - Only applicable to `minmethod`='opt_sr', see below. - Set the `sr_tau` parameter appearing in the stochastic - reconfiguration projector. - - Case `qmc='opt'` `method={'linear', 'cslinear'}` - `minmethod={'quartic', 'rescale', 'linemin'}` - ------------------------------------------------- - minmethod: {'quartic', 'rescale', 'linemin'}, default = 'quartic' - Sets `minmethod` parameter. See QMCPACK manual. - usebuffer: bool, default = True - Sets `usebuffer` parameter. See QMCPACK manual. - exp0: float, default = -6 - Sets `exp0` parameter. See QMCPACK manual. - bigchange: float, default = 10.0 - Sets `bigchange` parameter. See QMCPACK manual. - alloweddifference: float, default = 1e-4 - Sets `alloweddifference` parameter. See QMCPACK manual. - stepsize: float, default = 0.15 - Sets `stepsize` parameter. See QMCPACK manual. - nstabilizers: int, default = 1 - Sets `nstabilizers` parameter. See QMCPACK manual. - var_cycles: int, default = 0 - If var_cycles>0, introduce a preceding loop of variance - minmization to obtain a preconditioned starting point, e.g. - to stabilize subsequent energy minimization. - Sets ` in this prior loop. - Uses all other parameters as set for the subsequent/main loop, - perhaps excepting `samples`. - var_samples: {None, int}, default = None - If not `None` set the `samples` parameter, i.e. the total - number of VMC walker configurations to use in the preceding - variance minimization cycle. - - Case `qmc='opt'` `method='linear' `minmethod='oneshift'` - ------------------------------------------------------- - Use the "oneshift" variant of the linear method, courtesy Ye Luo. - - shift_i: float - Set the `shift_i` parameter. See QMCPACK manual. - shift_s: float - Set the `shift_s` parameter. See QMCPACK manual. - - Case `qmc='opt'` `method='linear' `minmethod='adaptive'` - ------------------------------------------------------- - max_relative_change: float, default = 10.0 - Sets `max_relative_change` parameter. See QMCPACK manual. - max_param_change: float, default = 0.3 - Sets `max_param_change` parameter. See QMCPACK manual. - shift_i: float, default = 0.01 - Set the `shift_i` parameter. See QMCPACK manual. - shift_s: float, default = 1.0 - Set the `shift_s` parameter. See QMCPACK manual. - - Case `qmc='opt'` `method='linear' `minmethod='sr_cg'` - ------------------------------------------------------ - Use a preliminary implementation of stochastic reconfiguration, + init_cycles : int, default=0 + If ``init_cycles>0``, introduce a preceding optimization loop of + the same type (same ``minmethod``, ``cost`` and most other + parameters). + Sets ```` in this prior loop. + A few parameters can be set to different values from the + subsequent/main loop as listed below. + init_samples : int or None, default=None + If not ``None`` set the ``samples`` parameter, i.e. the total + number of VMC walker configurations to use in the preceding + optimization loop. + init_steps : int or None + If not ``None`` set the ``steps`` parameter in the preceding + optimization loop. + init_minwalkers : float, default=0.1 + If not ``None`` set the ``minwalkers`` parameter in the preceding + optimization loop. Often set to a smaller value than in the + subsequent/main loop to allow more aggressive parameter updates + in hopes of a faster convergence to the general vicinity + of the cost minimum. + init_line_search : bool, default=False + Only applicable to ``minmethod='sr_cg'``, see below. + If ``True``, perform a linesearch along the direction of the + parameter gradient using the minimum cost to determine the + parameter stepsize. + init_sr_tau : float, default=0.1 + Only applicable to ``minmethod='opt_sr'``, see below. + Set the ``sr_tau`` parameter appearing in the stochastic + reconfiguration projector. + + Case ``qmc='opt'`` ``method={'linear', 'cslinear'}`` ``minmethod={'quartic', 'rescale', 'linemin'}`` + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + + minmethod : {'quartic', 'rescale', 'linemin'}, default='quartic' + Sets ``minmethod`` parameter. See QMCPACK manual. + usebuffer : bool, default=True + Sets ``usebuffer`` parameter. See QMCPACK manual. + exp0 : float, default=-6 + Sets ``exp0`` parameter. See QMCPACK manual. + bigchange : float, default=10.0 + Sets ``bigchange`` parameter. See QMCPACK manual. + alloweddifference : float, default=1e-4 + Sets ``alloweddifference`` parameter. See QMCPACK manual. + stepsize : float, default=0.15 + Sets ``stepsize`` parameter. See QMCPACK manual. + nstabilizers : int, default=1 + Sets ``nstabilizers`` parameter. See QMCPACK manual. + var_cycles : int, default=0 + If ``var_cycles>0``, introduce a preceding loop of variance + minmization to obtain a preconditioned starting point, e.g. + to stabilize subsequent energy minimization. + Sets ```` in this prior loop. + Uses all other parameters as set for the subsequent/main loop, + perhaps excepting ``samples``. + var_samples : int or None, default=None + If not ``None`` set the ``samples`` parameter, i.e. the total + number of VMC walker configurations to use in the preceding + variance minimization cycle. + + Case ``qmc='opt'`` ``method='linear'`` ``minmethod='oneshift'`` + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + + Use the ``"oneshift"`` variant of the linear method, courtesy Ye Luo. + + shift_i : float + Set the ``shift_i`` parameter. See QMCPACK manual. + shift_s : float + Set the ``shift_s`` parameter. See QMCPACK manual. + + Case ``qmc='opt'`` ``method='linear'`` ``minmethod='adaptive'`` + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + + max_relative_change : float, default=10.0 + Sets ``max_relative_change`` parameter. See QMCPACK manual. + max_param_change : float, default=0.3 + Sets ``max_param_change`` parameter. See QMCPACK manual. + shift_i : float, default=0.01 + Set the ``shift_i`` parameter. See QMCPACK manual. + shift_s : float, default=1.0 + Set the ``shift_s`` parameter. See QMCPACK manual. + + Case ``qmc='opt'`` ``method='linear'`` ``minmethod='sr_cg'`` + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + Use a preliminary implementation of stochastic reconfiguration, courtesy Cody Melton. - - sr_tau: float, default = 0.01 - Set the `sr_tau` parameter, which is the timestep in the + + sr_tau : float, default=0.01 + Set the ``sr_tau`` parameter, which is the timestep in the stochastic reconfiguration projector. - sr_tolerance: float, default = 0.001. - Set the `sr_tolerance` parameter. See QMCPACK manual. - sr_regularization: float, default = 0.01. - Set the `sr_regularization` parameter. See QMCPACK manual. - linesearch: bool, default = False - Perform a correlated sampling linesearch to determine tau + sr_tolerance : float, default=0.001. + Set the ``sr_tolerance`` parameter. See QMCPACK manual. + sr_regularization : float, default=0.01. + Set the ``sr_regularization`` parameter. See QMCPACK manual. + linesearch : bool, default=False + Perform a correlated sampling linesearch to determine tau automatically for each iteration. - If `True`, the default for `sr_tau` is 0.1 instead. + If ``True``, the default for ``sr_tau`` is 0.1 instead. """ if optimize is not None: @@ -5310,7 +5336,8 @@ def preprocess(self,contents,filepath=None): include_file = token.replace('href','').replace('=','').replace('"','').strip() include_path = os.path.join(basepath,include_file) if os.path.exists(include_path): - icont = open(include_path,'r').read()+'\n' + with open(include_path, "r") as f: + icont = f.read() + "\n" line = '' for iline in icont.splitlines(): if ' + """Generate ```` - Parameters - ---------- + Parameters + ---------- kc1 : float, optional - kcut for one-body Jastrow, default 0 + kcut for one-body Jastrow. Must provide this and/or ``kc2``. kc2 : float, optional - kcut for two-body Jastrow, default 0 - nk1 : int, optional - number of coefficients for one-body Jastrow, default 0 - nk2 : int, optional - number of coefficients for two-body Jastrow, default 0 - symm1 : str, optional - one of ['crystal', 'isotropic', 'none'], default 'isotropic' - symm2 : str, optional - one of ['crystal', 'isotropic', 'none'], default is 'isotropic' + kcut for two-body Jastrow. Must provide this and/or ``kc1``. + nk1 : int, default=0 + Number of coefficients for one-body Jastrow. + nk2 : int, default=0 + Number of coefficients for two-body Jastrow. + symm1 : {'crystal', 'isotropic', 'none'}, default='isotropic' + Impose specified symmetry on 1-body Jastrow coefficients. + See Notes for description. + symm2 : {'crystal', 'isotropic', 'none'}, default='isotropic' + Impose specified symmetry on 2-body Jastrow coefficients. + See Notes for description. coeff1 : list, optional - one-body Jastrow coefficients, default None + One-body Jastrow coefficients, optional. coeff2 : list, optional - list, optional two-body Jastrow coefficients, default None - Returns - ------- - jk: QIxml - kspace_jastrow qmcpack_input element - """ - J1k = kc1 is not None - J2k = kc2 is not None - if not J1k and not J2k: - QmcpackInput.class_error('must have at least one term', 'generate_kspace_jastrow') - #end if - if coeff1 is None: coeff1 = [0]*nk1 - if coeff2 is None: coeff2 = [0]*nk2 - if len(coeff1) != nk1: - QmcpackInput.class_error('coeff1 mismatch', 'generate_kspace_jastrow') - #end if - if len(coeff2) != nk2: - QmcpackInput.class_error('coeff2 mismatch', 'generate_kspace_jastrow') - #end if - - corrs = [] - if J1k: - corr1 = correlation( - type = 'One-Body', - symmetry = symm1, - kc = kc1, - coefficients = section(id='cG1', type='Array', coeff=coeff1), - ) - if opt1 is not None: - corr1.coefficients.optimize = bool(opt1) - corrs.append(corr1) - #end if - if J2k: - corr2 = correlation( - type = 'Two-Body', - symmetry = symm2, - kc = kc2, - coefficients = section(id='cG2', type='Array', coeff=coeff2), - ) - if opt2 is not None: - corr2.coefficients.optimize = bool(opt2) - corrs.append(corr2) - #end if - jk = kspace_jastrow( - type = 'kSpace', - name = 'Jk', - source = 'ion0', - correlations = collection(corrs), - ) - return jk + Two-body Jastrow coefficients, optional. + opt1 : bool or None, default=None + Set whether or not the one-body Jastrow coefficients are optimizable. + See Notes for more information. + opt2 : bool or None, default=None + Set whether or not the two-body Jastrow coefficients are optimizable. + See Notes for more information. + + Returns + ------- + jk : QIxml + ``kspace_jastrow`` qmcpack_input element + + Notes + ----- + The ``symm1`` and ``symm2`` parameters yield the following behavior: + + ``"crystal"`` + Impose crystal symmetry on coefficients according to the + structure factor. + + ``"isotropic"`` + Impose spherical symmetry on coefficients according to G-vector + magnitude. + + ``"none"`` + Impose no symmetry on the coefficients. + + The parameters ``opt1`` and ``opt2`` are not necessarily guaranteed + to control the behavior of QMCPACK. See QMCPACK's documentation on + `k-space Jastrow`_. + + .. _k-space Jastrow: https://qmcpack.readthedocs.io/en/develop/intro_wavefunction.html#long-ranged-jastrow-k-space-jastrow + """ + J1k = kc1 is not None + J2k = kc2 is not None + if not J1k and not J2k: + QmcpackInput.class_error('must have at least one term', 'generate_kspace_jastrow') + #end if + if coeff1 is None: + coeff1 = [0]*nk1 + if coeff2 is None: + coeff2 = [0]*nk2 + + if len(coeff1) != nk1: + QmcpackInput.class_error('coeff1 mismatch', 'generate_kspace_jastrow') + #end if + if len(coeff2) != nk2: + QmcpackInput.class_error('coeff2 mismatch', 'generate_kspace_jastrow') + #end if + + corrs = [] + if J1k: + corr1 = correlation( + type = 'One-Body', + symmetry = symm1, + kc = kc1, + coefficients = section(id='cG1', type='Array', coeff=coeff1), + ) + if opt1 is not None: + corr1.coefficients.optimize = bool(opt1) + corrs.append(corr1) + #end if + if J2k: + corr2 = correlation( + type = 'Two-Body', + symmetry = symm2, + kc = kc2, + coefficients = section(id='cG2', type='Array', coeff=coeff2), + ) + if opt2 is not None: + corr2.coefficients.optimize = bool(opt2) + corrs.append(corr2) + #end if + jk = kspace_jastrow( + type = 'kSpace', + name = 'Jk', + source = 'ion0', + correlations = collection(corrs), + ) + return jk # end def generate_kspace_jastrow @@ -8232,7 +8292,7 @@ def generate_batched_vmc_calculations( optional_vmc_inputs = obj( total_walkers = total_walkers, walkers_per_rank = walkers_per_rank, - #checkpoint = checkpoint, # no checkpointing support yet + checkpoint = checkpoint, maxcpusecs = maxcpusecs, crowds = crowds, spin_mass = spin_mass, @@ -8306,8 +8366,8 @@ def generate_batched_dmc_calculations( total_walkers = total_walkers, walkers_per_rank = walkers_per_rank, crowds = crowds, - spin_mass = vmc_spin_mass, - #checkpoint = vmc_checkpoint, # not supported yet + spin_mass = vmc_spin_mass, + checkpoint = vmc_checkpoint, ) for name,value in optional_vmc_inputs.items(): if value is not None: @@ -8325,7 +8385,6 @@ def generate_batched_dmc_calculations( blocks = eq_blocks, steps = eq_steps, timestep = eq_timestep, - #checkpoint = eq_checkpoint, # not supported yet ) ) #end if @@ -8338,7 +8397,6 @@ def generate_batched_dmc_calculations( blocks = blocks, steps = int(sfac*steps), timestep = tfac*timestep, - #checkpoint = checkpoint, # not supported yet ) ) tfac *= timestep_factor @@ -8357,6 +8415,7 @@ def generate_batched_dmc_calculations( feedback = feedback, sigmabound = sigmabound, spin_mass = spin_mass, + checkpoint = checkpoint, ) for calc in dmc_calcs: if isinstance(calc,dmc): diff --git a/nexus/nexus/quantum_package.py b/nexus/nexus/quantum_package.py index 8fd1c1f717..6190a960fc 100644 --- a/nexus/nexus/quantum_package.py +++ b/nexus/nexus/quantum_package.py @@ -18,6 +18,7 @@ import os +from pathlib import Path from .developer import obj from .execute import execute from .nexus_base import nexus_core @@ -48,7 +49,11 @@ class QuantumPackage(Simulation): @staticmethod def settings(qprc=None): # path to quantum_package.rc file - QuantumPackage.qprc = qprc + if isinstance(qprc, Path): + QuantumPackage.qprc = str(qprc.resolve()) + else: + QuantumPackage.qprc = qprc + if qprc is not None and not nexus_core.status_only: if not isinstance(qprc,str): QuantumPackage.class_error('settings input "qprc" must be a path\nreceived type: {0}\nwith value: {1}'.format(qprc.__class__.__name__,qprc)) diff --git a/nexus/nexus/quantum_package_input.py b/nexus/nexus/quantum_package_input.py index 68194b4ade..b24ece13d1 100644 --- a/nexus/nexus/quantum_package_input.py +++ b/nexus/nexus/quantum_package_input.py @@ -405,7 +405,7 @@ def restore_added_keys(self,extra): def read(self,filepath): - epath = filepath.rstrip('/') + epath = str(filepath).rstrip('/') if not os.path.exists(epath): self.error('cannot read input\nprovided ezfio directory does not exist\ndirectory provided: {0}'.format(epath)) elif not os.path.isdir(epath): @@ -438,7 +438,7 @@ def write(self,filepath=None): #end if # get the ezfio path - epath = filepath.rstrip('/') + epath = str(filepath).rstrip('/') # check that write can occur if not epath.endswith('.ezfio'): diff --git a/nexus/nexus/simulation.py b/nexus/nexus/simulation.py index e23a43d898..a4ff718980 100644 --- a/nexus/nexus/simulation.py +++ b/nexus/nexus/simulation.py @@ -68,14 +68,17 @@ import os import sys import shutil +from pathlib import Path from string import Template from subprocess import Popen import tempfile -from .developer import obj, unavailable +from .developer import obj, unavailable, DevBase +from .structure import Structure, read_structure from .physical_system import PhysicalSystem -from .machines import Job +from .machines import Job, Workstation, get_machine from .pseudopotential import ppset -from .nexus_base import NexusCore, nexus_core +from .nexus_base import NexusCore, nexus_core, dynamic_storage +from .utilities import path_string class SimulationInput(NexusCore): @@ -101,6 +104,7 @@ def write_file_text(self,filepath,text): #end def write_file_text def read(self,filepath): + filepath = path_string(filepath) tokens = filepath.split(None,1) if len(tokens)>1: text = filepath @@ -114,6 +118,7 @@ def read(self,filepath): def write(self,filepath=None): text = self.write_text(filepath) if filepath is not None: + filepath = path_string(filepath) self.write_file_text(filepath,text) #end if return text @@ -268,7 +273,6 @@ class Simulation(NexusCore): sim_directories = dict() all_sims = [] - @classmethod def clear_all_sims(cls): cls.sim_directories.clear() @@ -425,6 +429,22 @@ def __init__(self,**kwargs): self.post_init() Simulation.all_sims.append(self) + + # dynamic workflow support + if nexus_core.dynamic: + assert self.simid not in dynamic_storage.simulation_ids + self.produces = set() + self.products = obj() + self.filled_products = False + self.fill_produces() + for prod in self.produces: + self.products[prod] = None + dynamic_storage.simulations[self.simid] = self + dynamic_storage.simulation_ids.add(self.simid) + # instantly restore image/state data from disk + self.reconstruct_cascade() + if self.finished: + self.fill_products() #end def __init__ @@ -471,21 +491,25 @@ def set(self,**kw): self[name] = kw[name] #end for if 'path' in allowed: - p = self.path - if not isinstance(p,str): - self.error('path must be a string, you provided {0} (type {1})'.format(p,p.__class__.__name__)) + if not isinstance(self.path, str | Path): + self.error('path must be a string or Path, you provided {0} (type {1})'.format(self.path,self.path.__class__.__name__)) + else: + self.path = path_string(self.path) + p = self.path + #end if if p.startswith('./'): p = p[2:] #end if ld = nexus_core.local_directory + if p.startswith(ld): p = p.split(ld)[1].lstrip('/') #end if self.path = p #end if if 'files' in allowed: - self.files = set(self.files) + self.files = set([path_string(f) for f in self.files]) #end if if not isinstance(self.input,(self.input_type,GenericSimulationInput)): self.error('input must be of type {0}\nreceived {1}\nplease provide input appropriate to {2}'.format(self.input_type.__name__,self.input.__class__.__name__,self.__class__.__name__)) @@ -703,6 +727,8 @@ def create_directories(self): def depends(self,*dependencies): + if nexus_core.dynamic: + self.error('dynamic workflows do not allow explicit dependencies between simulations') if len(dependencies)==0: return #end if @@ -1178,6 +1204,10 @@ def analyze(self): #end if self.analyzed = True self.save_image() + + # support dynamic workflows + if nexus_core.dynamic: + self.fill_products() #end if #end def analyze @@ -1315,6 +1345,13 @@ def reconstruct_cascade(self): self.load_image() # continue from interruption if self.submitted and not self.finished and self.process_id is not None: + if nexus_core.dynamic: + machine = get_machine(Job.machine) + if isinstance(machine,Workstation): + # fully rerun following interrupt + self.save_attempt() + self.reset_indicators() + self.job.system_id = self.process_id # load process id of job self.job.reenter_queue() #end if @@ -1421,6 +1458,17 @@ def show_input(self,exit=True): exit_call() #end if #end def show_input + + + # dynamic workflow support + + def fill_produces(self): + self.not_implemented('fill_produces') + #end def fill_produces + + def fill_products(self): + self.not_implemented('fill_products') + #end def fill_products #end class Simulation @@ -1830,3 +1878,361 @@ def graph_sims(sims=None,savefile=None,useid=False,exit=True,quants=True,display #end def graph_sims + + +class DynamicProcess(DevBase): + '''Enables dynamic workflows execution + + Basic DP contains a single simulation. + Derived classes may perform more elaborate processes, + i.e. recovery for failed jobs, resetting the primary + simulation object (sim data member) to point at the + final sim in the process. + + Takes the place of Simulation in user scripts. All + generate_* simulation functions return DP's when + executing dynamic workflows. + ''' + + all_dynamic_processes = obj() + + allowed_requirements = set([ + 'none', + 'structure', + 'charge_density', + 'orbitals', + 'jastrow', + 'wavefunction', + 'pwscf_orbitals', # explicit QE + ]) + + @classmethod + def check_first_gen(cls,kw): + nc_loc = nexus_core.local_directory + runs = nexus_core.runs + path = kw['path'] + identifier = kw['identifier'] + locdir = os.path.join(nc_loc,runs,path) + if 'dynamic_id' not in kw: + cls.class_error('dynamic_id is required for dynamic workflows in a generate_* function.\nSimulation run location: {}\nSimulation identifier : {}'.format(locdir,identifier)) + dynamic_id = kw.pop('dynamic_id') + dpid = (locdir,identifier,dynamic_id) + if dpid in DynamicProcess.all_dynamic_processes: + dp = DynamicProcess.all_dynamic_processes[dpid] + return dp,None + else: + dp = None + if 'requires' not in kw: + cls.class_error('dependency requirements must be given via the "requires" keyword for dynamic workflows') + requires = kw.pop('requires') + dyn_args = obj(dpid=dpid,requires=requires) + return dp,dyn_args + #end def check_first_gen + + + def __init__(self,dpid,sim,requires): + # check dynamic id + if dpid in self.all_dynamic_processes: + self.error('dynamic process created with overlapping id. Provided id: {}'.format(dpid)) + + # check simulation type + if not isinstance(sim,Simulation): + self.error('expected Simulation type but received type {}'.format(sim.__class__.__name__)) + + # check requires + if isinstance(requires,str): + requires = [requires] + elif not isinstance(requires,(tuple,list,set)): + self.error('keyword "requires" must be a tuple, list or set of requirements') + for req in requires: + if not isinstance(req,str): + self.error('each requirement in "requires" must be given as a string.\nType received: {}\nValue received: {}'.format(req.__class__.__name__,req)) + requires = set(requires) + invalid_reqs = requires-self.allowed_requirements + if len(invalid_reqs)>0: + self.error('invalid requirements provided.\nAllowed requirements: {}\nRequirements provided: {}'.format(list(self.allowed_requirements),list(invalid_reqs))) + if len(requires)==0: + self.error("every simulation dynamic process must specify least one dependency requirement.\nIf there are no dependencies/requirements, set requires='none'") + if 'none' in requires: + requires.remove('none') + + # check produces + produces = sim.produces + if isinstance(produces,str): + produces = [produces] + if not isinstance(produces,(tuple,list,set)): + self.error('keyword "requires" must be a tuple, list or set of products') + for prod in produces: + if not isinstance(req,str): + self.error('each product in "produces" must be given as a string.\nType received: {}\nValue received: {}'.format(req.__class__.__name__,req)) + produces = set(produces) + + # initial values + self.dpid = dpid # unique identifier, str + self.sim = sim # wrapped Simulation object + self.requires = requires # replaces dependencies + self.unmet_reqs = set(requires) + self.req_values = obj() + self.reqs_met = False + self.produces = produces + + # store references in global registries + self.all_dynamic_processes[dpid] = self + dynamic_storage.dynamic_processes[dpid] = self + dynamic_storage.dynamic_process_ids.add(dpid) + #end def __init__ + + + def requirements_met(self): + '''Check if all input/dependency requirements are met''' + if self.reqs_met: + return True + reqs_met = True + reqs_met &= len(self.unmet_reqs)==0 + reqs_met &= len(self.requires-set(self.req_values))==0 + if reqs_met: + self.reqs_met = reqs_met + return reqs_met + #end def requirements_met + + def _check_get_product(self,prod_name): + '''Support product getter functions + + Note that requirements are a subset of products + ''' + sim = self.sim + msg = None + if prod_name not in sim.produces: + msg = 'simulation does not produce "{}"'.format(prod_name) + elif not sim.finished: + msg = 'Simulation is not finished\nProduct "{}" not yet computed'.format(prod_name) + elif not sim.analyzed: + msg = 'simulation has not been analyzed, requested prod_name "{}" has not been computed yet'.format(prod_name) + elif prod_name not in sim.products: + msg = 'simulation products have not been handled correctly. This is a developer error' + if msg is not None: + self.error(msg+'\nSimulation type : {}\nSimulation id : {}\nSimulation directory: {}\nDynamic process id : {}'.format(sim.__class__.__name__,sim.simid,sim.locdir,self.dpid)) + return sim.products[prod_name] + #end def _check_get_product + + + def _check_set_requirement(self, + req_name, + req_value = None, + req_type = str, + is_path = False, + ): + '''Support requirement setter functions''' + # check supported requirement value types + if not isinstance(req_value,req_type): + if not isinstance(req_type,tuple): + ts = req_type.__name__ + else: + ts = [t.__name__ for t in req_type] + self.error('product "{}" must be of type "{}".\nReceived type: {}'.format(req_name,ts,req_value.__class__.__name__)) + # check if requirement value has already been set + if req_name not in self.req_values: + self.req_values[req_name] = req_value + already_set = False + elif isinstance(req_value,(str,int)) and req_value!=self.req_values[req_name]: + self.error('attempted assignment of required parameter "{}" with value differing from the original.\nOriginal value: {}\nValue received: {}'.format(req_name,self.req_values[req_name],req_value)) + elif id(req_value)!=id(self.req_values[req_name]): + self.error('attempted assignment of required parameter "{}" with python id differing from the original.\nOriginal id: {}\nid received: {}'.format(req_name,id(self.req_values[req_name]),id(req_value))) + else: + already_set = True + # if already set, return + if already_set: + return already_set + # proceed with incorporation + # ensure requirement is one of the supported options in general + if req_name not in self.sim.allowed_requirements: + self.error('incorporating "{}" into simulation type {} is not supported.'.format(req_name,self.sim.__class__.__name__)) + elif is_path and isinstance(req_value,str) and not os.path.exists(req_value): + self.error('"{}" path does not exist.\nPath provided: {}'.format(req_name,req_value)) + # mark the requirement as fulfilled + self.unmet_reqs.remove(req_name) + return already_set + #end def _check_set_requirement + + + # general access to product info + #@property + #def produces(self): + # return self.sim.produces + + @property + def products(self): + return self.sim.products + + # getters for all possible requirements (subset of products) + @property + def structure(self): + return self._check_get_product('structure') + + @property + def charge_density(self): + return self._check_get_product('charge_density') + + @property + def orbitals(self): + return self._check_get_product('orbitals') + + @property + def jastrow(self): + return self._check_get_product('jastrow') + + @property + def wavefunction(self): + return self._check_get_product('wavefunction') + + @property + def pwscf_orbitals(self): + return self._check_get_product('pwscf_orbitals') + + + # setters for all possible requirements + @structure.setter + def structure(self,struct): + already_set = self._check_set_requirement( + 'structure',struct,req_type=(str,Structure),is_path=True) + if already_set: + return + if isinstance(struct,str): + struct = read_structure(struct) + else: + struct = struct.copy() + self.sim.receive_structure(struct) + #end def structure + + @charge_density.setter + def charge_density(self,charge_density): + already_set = self._check_set_requirement( + 'charge_density',charge_density,is_path=True) + if already_set: + return + self.sim.receive_charge_density(charge_density) + #end def charge_density + + @orbitals.setter + def orbitals(self,orbitals): + already_set = self._check_set_requirement( + 'orbitals',orbitals,is_path=True) + if already_set: + return + self.sim.receive_orbitals(orbitals) + #end def orbitals + + @jastrow.setter + def jastrow(self,jastrow): + already_set = self._check_set_requirement( + 'jastrow',jastrow,is_path=True) + if already_set: + return + self.sim.receive_jastrow(jastrow) + #end def jastrow + + @wavefunction.setter + def wavefunction(self,wavefunction): + already_set = self._check_set_requirement( + 'wavefunction',wavefunction,is_path=True) + if already_set: + return + self.sim.receive_wavefunction(wavefunction) + #end def wavefunction + + @pwscf_orbitals.setter + def pwscf_orbitals(self,pwscf_orbitals): + already_set = self._check_set_requirement( + 'pwscf_orbitals',pwscf_orbitals,is_path=True) + if already_set: + return + self.sim.receive_pwscf_orbitals(pwscf_orbitals) + #end def pwscf_orbitals + + + # preserve Simulation UI + # data fields and functions + @property + def simid(self): + return self.sim.simid + + @property + def identifier(self): + return self.sim.identifier + + @property + def job(self): + return self.sim.job + + @property + def input(self): + return self.sim.input + + @input.setter + def input(self,input): + self.sim.input = input + + def show_input(self): + self.sim.show_input() + + @property + def system(self): + return self.sim.system + + @property + def analyzer_image(self): + return self.sim.analyzer_image + + # status_flags + @property + def setup(self): + return self.sim.setup + + @property + def sent_files(self): + return self.sim.sent_files + + @property + def submitted(self): + return self.sim.submitted + + @property + def finished(self): + return self.sim.finished + + @property + def got_output(self): + return self.sim.got_output + + @property + def analyzed(self): + return self.sim.analyzed + + @property + def failed(self): + return self.sim.failed + + # execution modification + @property + def skip_submit(self): + return self.sim.skip_submit + + @property + def block(self): + return self.sim.block + + + # try on new user-facing status properties + @property + def done(self): + return self.sim.finished + + @property + def succ(self): + return self.sim.finished and not self.sim.failed + + @property + def fail(self): + return self.sim.failed + #return self.sim.finished and self.sim.failed +#end class DynamicProcess diff --git a/nexus/nexus/structure.py b/nexus/nexus/structure.py index 930d3174fa..d7b8f391f3 100644 --- a/nexus/nexus/structure.py +++ b/nexus/nexus/structure.py @@ -117,6 +117,7 @@ """ import os +from pathlib import Path import numpy as np from copy import deepcopy from random import randint @@ -130,12 +131,13 @@ sqrt, ) from numpy.linalg import inv, det, norm +import numpy.typing as npt from .unit_converter import convert from .numerics import nearest_neighbors, convex_hull, voronoi_neighbors -from .periodic_table import is_element -from .periodic_table import pt as ptable +from .periodic_table import Elements from .fileio import XsfFile, PoscarFile from .developer import DevBase, obj, unavailable, error +from .utilities import path_string from . import numpy_extensions as npe try: @@ -498,8 +500,8 @@ def recenter_points(pos, center, axes): pos : NDArray Array of positions centered around the given center - Note - ---- + Notes + ----- This function also ensures that points close (within 1e-12) to the minimum edge (-0.5) of the cell are placed exactly on that edge. The intent here is to make sure that atoms close to or on the leading edge (+0.5) are wrapped around to retain periodicity. @@ -1143,8 +1145,33 @@ def has_folded_structure(self): #end def has_folded_structure - # test needed - def group_atoms(self,folded=True): + def group_atoms(self, folded=True) -> None: + """Group the atoms by their element type, sorting in alphabetical order. + + Parameters + ---------- + folded : bool, default=True + Optionally sort the folded structure, if it exists. + + Examples + -------- + >>> structure = Structure( + ... elem = ["Be", "N", "C", "Be", "C", "O"], + ... pos = np.array([ + ... [0, 0, 0], + ... [0, 0, 0], + ... [0, 0, 0], + ... [0, 0, 0], + ... [0, 0, 0], + ... [0, 0, 0], + ... ], dtype=np.float64), + ... ) + >>> print(structure.elem) + ['Be' 'N' 'C' 'Be' 'C' 'O'] + >>> structure.group_atoms() + >>> print(structure.elem) + ['Be' 'Be' 'C' 'C' 'N' 'O'] + """ if len(self.elem)>0: order = self.elem.argsort() if (self.elem!=self.elem[order]).any(): @@ -1158,8 +1185,35 @@ def group_atoms(self,folded=True): #end def group_atoms - # test needed - def rename(self,folded=True,**name_pairs): + def rename(self, folded=True, **name_pairs) -> None: + """Rename element names in a structure. + + Parameters + ---------- + folded : bool, default=True + Rename elements in folded structure as well as tiled structure + (if there is no folded structure then this does nothing) + **name_pairs : dict[str] + A dictionary containing key:value pairs where the key is the old + element name and the value is the new element name. + + Examples + -------- + >>> structure = Structure( + ... elem = ["N", "C", "O", "H"], + ... pos = np.array([ + ... [0, 0, 0], + ... [0, 0, 0], + ... [0, 0, 0], + ... [0, 0, 0], + ... ], dtype=np.float64), + ... ) + >>> print(structure.elem) + ['N' 'C' 'O' 'H'] + >>> structure.rename(N="Dy", C="Er") + >>> print(structure.elem) + ['Dy' 'Er' 'O' 'H'] + """ elem = self.elem for old,new in name_pairs.items(): for i in range(len(self.elem)): @@ -1174,8 +1228,77 @@ def rename(self,folded=True,**name_pairs): #end def rename - # test needed - def reset_axes(self,axes=None): + def reset_axes(self, axes: npt.ArrayLike | None = None) -> None: + """Reset the structure's axes, k-space axes, and center. + + Notes + ----- + If ``axes`` is given, this function will remove the previous folded + structure (as new axes could invalidate the tiling) and then set + ``self.axes`` to the new axes, update the k-space axes, and set the + center of the cell to be the (0.5, 0.5, 0.5) point. + + If ``axes`` are not given (e.g. ``axes=None``, the default), then this + function will reuse the same axes as the current structure, reset the + k-space axes, and set the cell center at the (0.5, 0.5, 0.5) point. + + Examples + -------- + Providing axes will also make sure ``kaxes`` and ``center`` are consistent. + + >>> structure = Structure( + ... axes = np.array([ + ... [6.0, 0.0, 0.0], + ... [0.0, 6.0, 0.0], + ... [0.0, 0.0, 6.0], + ... ]), + ... ) + >>> print(structure.axes) + [[6. 0. 0.] + [0. 6. 0.] + [0. 0. 6.]] + >>> print(structure.kaxes) + [[1.04719755 0. 0. ] + [0. 1.04719755 0. ] + [0. 0. 1.04719755]] + >>> print(structure.center) + [3. 3. 3.] + + >>> structure.reset_axes(np.array([ + ... [12.0, 0.0, 0.0], + ... [ 0.0, 12.0, 0.0], + ... [ 0.0, 0.0, 12.0], + ... ])) + >>> print(structure.axes) + [[12. 0. 0.] + [ 0. 12. 0.] + [ 0. 0. 12.]] + >>> print(structure.kaxes) + [[0.52359878 0. 0. ] + [0. 0.52359878 0. ] + [0. 0. 0.52359878]] + >>> print(structure.center) + [6. 6. 6.] + + Alternatively, if you don't provide ``axes`` you can ensure that the + ``kaxes`` and ``center`` of the structure are correct. Here we set + ``center`` to be at the origin, then use ``reset_axes`` to correct it. + + >>> structure = Structure( + ... axes = np.array([ + ... [6.0, 0.0, 0.0], + ... [0.0, 6.0, 0.0], + ... [0.0, 0.0, 6.0], + ... ]), + ... center = np.array([0.0, 0.0, 0.0]), + ... ) + >>> print(structure.center) + [0. 0. 0.] + + >>> structure.reset_axes() + >>> print(structure.center) + [3. 3. 3.] + """ if axes is None: axes = self.axes else: @@ -1217,7 +1340,11 @@ def reshape_axes(self,reshaping): #end def reshape_axes - def write_axes(self): + def write_axes(self) -> str: + """Write the unit cell axes as a string. + + Only implemented for ``self.dim=3``. + """ c = '' for a in self.axes: c+='{0:12.8f} {1:12.8f} {2:12.8f}\n'.format(a[0],a[1],a[2]) @@ -1225,8 +1352,12 @@ def write_axes(self): return c #end def write_axes - - def corners(self): + + def corners(self) -> npt.NDArray[np.float64]: + """Calculate vectors corresponding to the 8 corners of the unit cell. + + Only implemented for ``self.dim=3``. + """ a = self.axes c = np.array([(0,0,0), a[0], @@ -1334,8 +1465,8 @@ def center_molecule(self, rmin_edge = 1e-8): rmin_edge : float-like or array-like, default=1e-8 Minimum acceptable distance from the cell edges to any atom in the molecule, potentially specified per-axis. - Note - ---- + Notes + ----- The default rmin_edge of 1e-8 is designed to just barely contain the molecule. It is important to ensure that for larger, non-periodic molecular systems or atoms that the unit cell size is sufficiently large to contain the charge density otherwise the molecular system @@ -1752,45 +1883,45 @@ def stretch(self,s1,s2,s3): # test needed def rotate(self,r,rp=None,passive=False,units="radians",check=True): - """ - Arbitrary rotation of the structure. + """Arbitrary rotation of the structure. + Parameters ---------- - r : `array_like, float, shape (3,3)` or `array_like, float, shape (3,)` or `str` - If a 3x3 matrix, then code executes rotation consistent with this matrix -- - it is assumed that the matrix acts on a column-major vector (eg, v'=Rv) - If a three-dimensional array, then the operation of the function depends - on the input type of rp in the following ways: - 1. If rp is a scalar, then rp is assumed to be an angle and a rotation - of rp is made about the axis defined by r - 2. If rp is a vector, then rp is assumed to be an axis and a rotation is made - such that r aligns with rp - 3. If rp is a str, then the rotation is such that r aligns with the - axis given by the str ('x', 'y', 'z', 'a0', 'a1', or 'a2') - If a str then the axis, r, is defined by the input label (e.g. 'x', 'y', 'z', 'a1', 'a2', or 'a3') - and the operation of the function depends on the input type of rp in the following - ways (same as above): - 1. If rp is a scalar, then rp is assumed to be an angle and a rotation - of rp is made about the axis defined by r - 2. If rp is a vector, then rp is assumed to be an axis and a rotation is made - such that r aligns with rp - 3. If rp is a str, then the rotation is such that r aligns with the - axis given by the str ('x', 'y', 'z', 'a0', 'a1', or 'a2') - rp : `array_like, float, shape (3), optional` or `str, optional` - If a 3-dimensional vector is given, then rp is assumed to be an axis and a rotation is made - such that the axis r is aligned with rp. - If a str, then rp is assumed to be an angle and a rotation about the axis defined by r - is made by an angle rp - If a str is given, then rp is assumed to be an axis defined by the given label - (e.g. 'x', 'y', 'z', 'a1', 'a2', or 'a3') and a rotation is made such that the axis r - is aligned with rp. - passive : `bool, optional, default False` - If `True`, perform a passive rotation - If `False`, perform an active rotation - units : `str, optional, default "radians"` - Units of rp, if rp is given as an angle (scalar) - check : `bool, optional, default True` - Perform a check to verify rotation matrix is orthogonal + r : array_like of float with shape (3,3) or array_like of float shape (3,) or str + If a 3x3 matrix, then code executes rotation consistent with this + matrix -- it is assumed that the matrix acts on a column-major + vector (eg, v'=Rv). If a three-dimensional array, then the operation + of the function depends on the input type of ``rp`` in the + following ways: + + 1. If ``rp`` is a scalar, then ``rp`` is assumed to be an angle and + a rotation of ``rp`` is made about the axis defined by ``r``. + 2. If ``rp`` is a vector, then ``rp`` is assumed to be an axis and a + rotation is made such that ``r`` aligns with ``rp``. + 3. If ``rp`` is a ``str``, then the rotation is such that ``r`` + aligns with the axis given by the str + ``('x', 'y', 'z', 'a0', 'a1', or 'a2')``. + + If a ``str`` then the axis, ``r``, is defined by the input label + (e.g. 'x', 'y', 'z', 'a1', 'a2', or 'a3') and the operation of the + function depends on the input type of ``rp`` in the same ways as + above. + rp : array_like of float with shape (3) or str, optional + If a 3-dimensional vector is given, then ``rp`` is assumed to be an + axis and a rotation is made such that the axis ``r`` is aligned with + ``rp``. + If a str, then ``rp`` is assumed to be an angle and a + rotation about the axis defined by ``r`` is made by an angle ``rp``. + If a str is given, then ``rp`` is assumed to be an axis defined by + the given label (e.g. 'x', 'y', 'z', 'a1', 'a2', or 'a3') and a + rotation is made such that the axis ``r`` is aligned with ``rp``. + passive : bool, default=False + If ``True``, perform a passive rotation. + If ``False``, perform an active rotation. + units : {"radians", "rad", "degrees", "deg"}, default="radians" + Units of ``rp``, if ``rp`` is given as an angle (scalar). + check : bool, default=True + Perform a check to verify rotation matrix is orthogonal. """ if rp is not None: dirmap = dict(x=[1,0,0],y=[0,1,0],z=[0,0,1]) @@ -2394,8 +2525,8 @@ def species(self,symbol=False): species_labels = set(self.elem) species = set() for e in species_labels: - is_elem,symbol = is_element(e,symbol=True) - species.add(symbol) + is_elem, element = Elements.is_element(e, return_element=True) + species.add(element.symbol) #end for return species_labels,species #end if @@ -2418,7 +2549,8 @@ def ordered_species(self,symbol=False): species = [] spec_set = set() for e in self.elem: - is_elem,symbol = is_element(e,symbol=True) + is_elem, element = Elements.is_element(e, return_element=True) + symbol = element.symbol if e not in speclab_set: speclab_set.add(e) species_labels.append(e) @@ -3482,17 +3614,17 @@ def recenter_k(self,kpoints=None,kaxes=None,kcenter=None,remove_duplicates=False # test needed def recorner(self, center = None): - """Center atoms around the origin of the cell - + """Center atoms around the origin of the cell. + Parameters ---------- center : NDArray, default = self.center Position of the center of the cell. - - Note - ---- - If the user supplies `center`, then this will modify `self.center` to reflect - that change. + + Notes + ----- + If the user supplies ``center``, then this will modify + ``self.center`` to reflect that change. """ if center is not None: self.center = np.array(center, dtype=float) @@ -4892,6 +5024,7 @@ def makov_payne(self,q=1,eps=1.0,units='Ha',order=1): def read(self,filepath,format=None,elem=None,block=None,grammar='1.1',cell='prim',contents=False): if os.path.exists(filepath): + filepath = path_string(filepath) path,file = os.path.split(filepath) if format is None: if '.' in file: @@ -4940,7 +5073,8 @@ def read_xyz(self,filepath): elem = [] pos = [] if os.path.exists(filepath): - lines = open(filepath,'r').read().strip().splitlines() + with open(filepath, "r") as f: + lines = f.read().strip().splitlines() else: lines = filepath.strip().splitlines() # "filepath" is file contents #end if @@ -5008,7 +5142,7 @@ def read_xsf(self,filepath): if isinstance(n,str): elem.append(n) else: - elem.append(ptable.simple_elements[n].symbol) + elem.append(Elements(n).symbol) #end if #end for self.dim = 3 @@ -5021,7 +5155,8 @@ def read_xsf(self,filepath): def read_poscar(self,filepath,elem=None): if os.path.exists(filepath): - lines = open(filepath,'r').read().splitlines() + with open(filepath, "r") as f: + lines = f.read().splitlines() else: lines = filepath.splitlines() # "filepath" is file contents #end if @@ -5141,7 +5276,8 @@ def read_cif(self,filepath,block=None,grammar='1.1',cell='prim'): # test needed def read_fhi_aims(self,filepath): if os.path.exists(filepath): - lines = open(filepath,'r').read().splitlines() + with open(filepath, "r") as f: + lines = f.read().splitlines() else: lines = filepath.splitlines() # "filepath" is contents #end if @@ -5199,7 +5335,9 @@ def write(self,filepath=None,format=None): if filepath is None and format is None: self.error('please specify either the filepath or format arguments to write()') elif format is None: - if '.' in filepath: + if isinstance(filepath, Path): + format = filepath.suffix.lstrip(".") + elif '.' in filepath: format = filepath.split('.')[-1] else: self.error( @@ -5237,10 +5375,10 @@ def pos_to_str(self, units: str = "A", with_elem: bool = False): Notes ----- This function will write the positions in the format - (in this case using `with_elem=True`) - ```python + (in this case using ``with_elem=True``) + .. code-block:: python + "{element:2} {dim1:12.8f} {dim2:12.8f} ... {dimN:12.8f}\\n" - ``` """ s = self.copy() s.change_units(units) @@ -5263,8 +5401,8 @@ def pos_to_str(self, units: str = "A", with_elem: bool = False): def write_xyz(self, filepath=None): - """Write a `Structure` object to an XYZ file - + """Write a ``Structure`` object to an XYZ file + Parameters ---------- filepath : PathLike or None, default=None @@ -5277,9 +5415,9 @@ def write_xyz(self, filepath=None): xyz : str The text that was or would have been written to the XYZ file. - Note - ---- - To get a string of only the atomic positions, use `pos_to_str()` instead. + Notes + ----- + To get a string of only the atomic positions, use ``pos_to_str()`` instead. """ if self.dim!=3: self.error('write_xyz is currently only implemented for 3 dimensions') @@ -5297,7 +5435,8 @@ def write_xyz(self, filepath=None): #end for if filepath is not None: - open(filepath,'w').write(c) + with open(filepath, "w") as f: + f.write(c) #end if return c #end def write_xyz @@ -5318,27 +5457,20 @@ def write_xsf(self,filepath=None): c += ' {0} 1\n'.format(len(s.elem)) for i in range(len(s.elem)): e = s.elem[i] - identified = e in ptable.elements - if not identified: - if len(e)>2: - e = e[0:2] - elif len(e)==2: - e = e[0:1] - #end if - identified = e in ptable.elements - #end if + identified, element = Elements.is_element(e, return_element=True) if not identified: self.error( "{0} is not an element\n" "xsf file cannot be written".format(e) ) #end if - enum = ptable.elements[e].atomic_number + enum = element.atomic_number r = s.pos[i] c += ' {0:>3} {1:12.8f} {2:12.8f} {3:12.8f}\n'.format(enum,r[0],r[1],r[2]) #end for if filepath is not None: - open(filepath,'w').write(c) + with open(filepath, "w") as f: + f.write(c) #end if return c #end def write_xsf @@ -5357,7 +5489,8 @@ def write_poscar(self,filepath=None): poscar.pos = s.pos c = poscar.write_text() if filepath is not None: - open(filepath,'w').write(c) + with open(filepath, "w") as f: + f.write(c) #end if return c #end def write_poscar @@ -5377,7 +5510,8 @@ def write_fhi_aims(self,filepath=None): c += 'atom_frac {0: 12.8f} {1: 12.8f} {2: 12.8f} {3}\n'.format(p[0],p[1],p[2],e) #end for if filepath is not None: - open(filepath,'w').write(c) + with open(filepath, "w") as f: + f.write(c) #end if return c #end def write_fhi_aims @@ -5503,11 +5637,11 @@ def get_number_of_atoms(self): def get_atomic_numbers(self): an = [] for e in self.elem: - iselem,esymb = is_element(e,symbol=True) + iselem, element = Elements.is_element(e, return_element=True) if not iselem: - self.error('Atomic symbol, {}, not recognized'.format(esymb)) + self.error('Atomic symbol, {}, not recognized'.format(element)) else: - an.append(ptable[esymb].atomic_number) + an.append(element.atomic_number) #end if #end for return np.array(an,dtype='intc') @@ -5674,11 +5808,11 @@ def equivalent_atoms(self): # collect sets of species labels species_by_specnum = obj() for e,sn in zip(self.elem,ds.equivalent_atoms): - is_elem,es = is_element(e,symbol=True) + is_elem,element = Elements.is_element(e, return_element=True) if sn not in species_by_specnum: species_by_specnum[sn] = set() #end if - species_by_specnum[sn].add(es) + species_by_specnum[sn].add(element.symbol) #end for for sn,sset in species_by_specnum.items(): if len(sset)>1: @@ -5965,10 +6099,7 @@ def get_conventional_cell( bcharge = structure.background_charge*volfac pos = dot(posd,axes) sout = structure.copy() - elem = np.empty(len(enumbers), dtype='str') - for el in ptable.elements.items(): - elem[enumbers==el[1].atomic_number]=el[0] - #end for + elem = np.array([Elements(i).symbol for i in enumbers], dtype=str) if abs(bcharge-int(bcharge)) > 1E-6: raise ValueError("Invalid background charge for conventional structure") #end if @@ -5991,10 +6122,7 @@ def get_primitive_cell( bcharge = structure.background_charge*volfac pos = dot(posd,axes) sout = structure.copy() - elem = np.array(enumbers, dtype='str') - for el in ptable.elements.items(): - elem[enumbers==el[1].atomic_number]=el[0] - #end for + elem = np.array([Elements(i).symbol for i in enumbers], dtype=str) return {'structure' : Structure(axes=axes, elem=elem, pos=pos, background_charge=bcharge, units='A'), 'T' : seekpathout['primitive_transformation_matrix']} #end def get_primitive_cell diff --git a/nexus/nexus/template_simulation.py b/nexus/nexus/template_simulation.py index 748883ee9c..0498505e43 100644 --- a/nexus/nexus/template_simulation.py +++ b/nexus/nexus/template_simulation.py @@ -318,8 +318,11 @@ def check_sim_status(self): # read output/error files to check whether simulation has # completed successfully # one could also check whether all output files exist - output = open(os.path.join(self.locdir,self.outfile),'r').read() - errors = open(os.path.join(self.locdir,self.errfile),'r').read() + with open(os.path.join(self.locdir,self.outfile), "r") as out: + output = out.read() + + with open(os.path.join(self.locdir,self.errfile), "r") as err: + errors = err.read() success = False # check output and errors diff --git a/nexus/nexus/testing.py b/nexus/nexus/testing.py index ea0b7791a9..b3351d1256 100644 --- a/nexus/nexus/testing.py +++ b/nexus/nexus/testing.py @@ -276,339 +276,6 @@ def text_eq(*args,**kwargs): #end def text_eq -# find the path to the Nexus directory and other internal paths -def nexus_path(append=None,location=None): - import os - testing_path = os.path.realpath(__file__) - - assert(isinstance(testing_path,str)) - assert(len(testing_path)>0) - assert('/' in testing_path) - - tokens = testing_path.split('/') - - assert(len(tokens)>=3) - assert(tokens[-1].startswith('testing.py')) - assert(tokens[-2]=='nexus') - - path = os.path.dirname(testing_path) - - assert(path.endswith('/nexus')) - - if location is not None: - if location=='unit': - append = 'tests' - elif location=='bin': - append = 'bin' - else: - print('nexus location "{}" is unknown'.format(location)) - raise ValueError - #end if - #end if - if append is not None: - path = os.path.join(path,append) - #end if - - assert(os.path.exists(path)) - - return path -#end def nexus_path - - - -# find the path to a file associated with a unit test -def unit_test_file_path(test,file=None): - import os - unit_path = nexus_path(location='unit') - files_dir = 'test_{}_files'.format(test) - path = os.path.join(unit_path,files_dir) - if file is not None: - path = os.path.join(path,file) - #end if - assert(os.path.exists(path)) - return path -#end def unit_test_file_path - - - -# collect paths to all files associated with a unit test -def collect_unit_test_file_paths(test,storage): - import os - if len(storage)==0: - test_files_dir = unit_test_file_path(test) - files = os.listdir(test_files_dir) - for file in files: - if not file.startswith('.'): - filepath = os.path.join(test_files_dir,file) - assert(os.path.exists(filepath)) - storage[file] = filepath - #end if - #end for - #end if - return storage -#end def collect_unit_test_file_paths - - - -# find the output path for a test -def unit_test_output_path(test,subtest=None): - import os - unit_path = nexus_path(location='unit') - files_dir = 'test_{}_output'.format(test) - path = os.path.join(unit_path,files_dir) - if subtest is not None: - path = os.path.join(path,("nexus."+"test."+subtest)) - #end if - return path -#end def unit_test_output_path - - - -# setup the output directory for a test -def setup_unit_test_output_directory(test,subtest,divert=False,file_sets=None,pseudo_dir=None,pseudo_files=None,pseudo_files_create=None): - import os - import shutil - from subprocess import Popen,PIPE - - divert |= pseudo_dir is not None - - path = unit_test_output_path(test,subtest) - assert('nexus' in path) - assert('nexus/tests' in path) - assert(os.path.basename(path).startswith('nexus.test.test_')) - assert(path.endswith('/nexus.test.'+subtest)) - if os.path.exists(path): - shutil.rmtree(path) - #end if - os.makedirs(path) - assert(os.path.exists(path)) - - # divert nexus paths and output, if requested - if divert: - from .nexus_base import nexus_core - divert_nexus() - nexus_core.local_directory = path - nexus_core.remote_directory = path - nexus_core.file_locations = nexus_core.file_locations + [path] - #end if - - # transfer files into output directory, if requested - if file_sets is not None: - if isinstance(file_sets,list): - file_sets = {'':file_sets} - #end if - assert(isinstance(file_sets,dict)) - filepaths = dict() - collect_unit_test_file_paths(test,filepaths) - for fpath,filenames in file_sets.items(): - assert(len(set(filenames)-set(filepaths.keys()))==0) - dest_path = path - if fpath is not None: - dest_path = os.path.join(dest_path,fpath) - if not os.path.exists(dest_path): - os.makedirs(dest_path) - #end if - #end if - assert(os.path.exists(dest_path)) - for filename in filenames: - source_filepath = filepaths[filename] - if os.path.isdir(source_filepath): - command = 'rsync -a {} {}'.format(source_filepath,dest_path) - process = Popen(command,shell=True,stdout=PIPE,stderr=PIPE,close_fds=True) - out,err = process.communicate() - else: - shutil.copy2(source_filepath,dest_path) - #end if - assert(os.path.exists(dest_path)) - #end for - #end for - #end if - - # create pseudopotential directory and set internal nexus data structures - if pseudo_dir is not None: - from .nexus_base import nexus_noncore - pseudo_path = os.path.join(path,pseudo_dir) - if not os.path.exists(pseudo_path): - os.makedirs(pseudo_path) - #end if - assert(os.path.exists(pseudo_path)) - pseudo_filepaths = [] - if pseudo_files is not None: - assert(isinstance(pseudo_files,list)) - for src_file in pseudo_files: - assert(os.path.exists(src_file)) - assert(os.path.isfile(src_file)) - pp_filename = os.path.basename(src_file) - pp_file = os.path.join(pseudo_path,pp_filename) - shutil.copy2(src_file,pseudo_path) - assert(os.path.exists(pp_file)) - assert(os.path.isfile(pp_file)) - pseudo_filepaths.append(pp_file) - #end for - #end if - if pseudo_files_create is not None: - assert(isinstance(pseudo_files_create,list)) - for pp_filename in pseudo_files_create: - pp_contents = '' - if isinstance(pp_filename,tuple): - pp_filename,pp_contents = pp_filename - #end if - pp_file = os.path.join(pseudo_path,pp_filename) - f = open(pp_file,'w') - f.write(pp_contents) - f.close() - assert(os.path.exists(pp_file)) - assert(os.path.isfile(pp_file)) - pseudo_filepaths.append(pp_file) - #end for - #end if - if len(pseudo_filepaths)>0: - from .pseudopotential import Pseudopotentials - for pp_file in pseudo_filepaths: - assert(os.path.exists(pp_file)) - assert(os.path.isfile(pp_file)) - #end for - pps = Pseudopotentials(pseudo_filepaths) - nexus_core.pseudopotentials = pps - nexus_noncore.pseudopotentials = pps - #end if - nexus_core.pseudo_dir = pseudo_path - nexus_noncore.pseudo_dir = pseudo_path - #end if - - return path -#end def setup_unit_test_output_directory - - - -# class used to divert log output when desired -class FakeLog: - def __init__(self): - self.reset() - #end def __init__ - - def reset(self): - self.s = '' - #end def reset - - def write(self,s): - self.s+=s - #end def write - - def close(self): - None - #end def close - - def contents(self): - return self.s - #end def contents -#end class FakeLog - - -# dict to temporarily store logger when log output is diverted -logging_storage = dict() - -# dict to temporarily store nexus core attributes when diverted -nexus_core_storage = dict() -nexus_noncore_storage = dict() - - -# divert nexus log output -def divert_nexus_log(): - from .generic import generic_settings,object_interface - assert(len(logging_storage)==0) - logging_storage['devlog'] = generic_settings.devlog - logging_storage['objlog'] = object_interface._logfile - logfile = FakeLog() - generic_settings.devlog = logfile - object_interface._logfile = logfile - return logfile -#end def divert_nexus_log - - -# restore nexus log output -def restore_nexus_log(): - from .generic import generic_settings,object_interface - assert(set(logging_storage.keys())==set(['devlog','objlog'])) - generic_settings.devlog = logging_storage.pop('devlog') - object_interface._logfile = logging_storage.pop('objlog') - assert(len(logging_storage)==0) -#end def restore_nexus_log - - -core_keys = [ - 'local_directory', - 'remote_directory', - 'mode', - 'stages', - 'stages_set', - 'status', - 'sleep', - 'file_locations', - 'pseudo_dir', - 'pseudopotentials', - 'runs', - 'results', - ] -noncore_keys = [ - 'pseudo_dir', - 'pseudopotentials', - ] - -# divert nexus core attributes -def divert_nexus_core(): - from .nexus_base import nexus_core,nexus_noncore - assert(len(nexus_core_storage)==0) - for key in core_keys: - nexus_core_storage[key] = nexus_core[key] - #end for - assert(len(nexus_noncore_storage)==0) - for key in noncore_keys: - if key in nexus_noncore: - nexus_noncore_storage[key] = nexus_noncore[key] - #end if - #end for -#end def divert_nexus_core - - -# restore nexus core attributes -def restore_nexus_core(): - from .nexus_base import nexus_core,nexus_noncore,nexus_core_noncore - from .nexus_base import nexus_noncore_defaults - for key in core_keys: - nexus_core[key] = nexus_core_storage.pop(key) - #end for - assert(len(nexus_core_storage)==0) - for key in noncore_keys: - if key in nexus_noncore_storage: - nexus_noncore[key] = nexus_noncore_storage.pop(key) - elif key in nexus_noncore: - del nexus_noncore[key] - #end if - #end for - for key in list(nexus_noncore.keys()): - if key not in nexus_noncore_defaults: - del nexus_noncore[key] - #end if - #end for - nexus_core_noncore.pseudopotentials = None - assert(len(nexus_noncore_storage)==0) -#end def restore_nexus_core - - -def divert_nexus(): - divert_nexus_log() - divert_nexus_core() -#end def divert_nexus - - -def restore_nexus(): - restore_nexus_log() - restore_nexus_core() -#end def restore_nexus - - - # declare test failure # useful inside try/except blocks def failed(msg='Test failed.'): @@ -627,12 +294,6 @@ class FailedTest(Exception): ) -def divert_nexus_errors(): - from .generic import generic_settings - generic_settings.raise_error = True -#end def divert_nexus_errors - - def clear_all_sims(): from .simulation import Simulation Simulation.clear_all_sims() @@ -662,46 +323,6 @@ def check_final_state(): -def executable_path(exe_name): - import os - # nexus bin directory - nexus_bin = nexus_path(location='bin') - # path to exe - exe_path = os.path.join(nexus_bin,exe_name) - # exe file exists - assert(os.path.isfile(exe_path)) - # exe file is executable - assert(os.access(exe_path,os.X_OK)) - return exe_path -#end def executable_path - - - -def create_file(filename,path,contents=''): - import os - filepath = os.path.join(path,filename) - f = open(filepath,'w') - f.write(contents) - f.close() - assert(os.path.isfile(filepath)) - return filepath -#end def create_file - - - -def create_path(path,basepath=None): - import os - if basepath is not None: - path = os.path.join(basepath,path) - #end if - if not os.path.exists(path): - os.makedirs(path) - #end if - assert(os.path.isdir(path)) -#end def create_path - - - def execute(command): from .execute import execute as nexus_execute import os diff --git a/nexus/nexus/tests/CMakeLists.txt b/nexus/nexus/tests/CMakeLists.txt index 272c3df2f7..6c0be26427 100644 --- a/nexus/nexus/tests/CMakeLists.txt +++ b/nexus/nexus/tests/CMakeLists.txt @@ -2,56 +2,65 @@ include("${PROJECT_SOURCE_DIR}/CMake/test_labels.cmake") include("${PROJECT_SOURCE_DIR}/CMake/python.cmake") -check_python_reqs(numpy "nexus base" ADD_TEST) +check_python_reqs("numpy;pytest" "Nexus" ADD_TEST) if(ADD_TEST) - file(TIMESTAMP ${qmcpack_SOURCE_DIR}/nexus/nexus/bin/nxs-test NEXUS_TESTLIST_TIMESTAMP) - if(NOT "${NEXUS_TESTLIST_TIMESTAMP}" STREQUAL "${CACHE_NEXUS_TESTLIST_TIMESTAMP}") - message("Generating Nexus test list for the first time or after a nxs-test time stamp change") - execute_process(COMMAND ${Python3_EXECUTABLE} ${qmcpack_SOURCE_DIR}/nexus/nexus/bin/nxs-test --ctestlist - RESULT_VARIABLE NEXUS_TESTLIST_RESULT OUTPUT_VARIABLE NEXUS_TESTLIST) - if(NOT NEXUS_TESTLIST_RESULT EQUAL 0) - message(FATAL_ERROR "Command line '${Python3_EXECUTABLE} ${qmcpack_SOURCE_DIR}/nexus/nexus/bin/nxs-test --ctestlist' failed!") - endif() - - set(CACHE_NEXUS_TESTLIST - ${NEXUS_TESTLIST} - CACHE INTERNAL "NEXUS_TESTLIST cache variable" FORCE) - set(CACHE_NEXUS_TESTLIST_TIMESTAMP - ${NEXUS_TESTLIST_TIMESTAMP} - CACHE INTERNAL "Timestamp used to validate NEXUS_TESTLIST cache variables" FORCE) - else() - message("nxs-test time stamp remains unchanged. Using cached Nexus test list") - set(NEXUS_TESTLIST ${CACHE_NEXUS_TESTLIST}) + message("Generating Nexus test list") + execute_process(COMMAND ${Python3_EXECUTABLE} -m pytest --collect-only -qq --disable-warnings ${qmcpack_SOURCE_DIR}/nexus/nexus/tests + RESULT_VARIABLE NEXUS_TESTLIST_RESULT OUTPUT_VARIABLE NEXUS_TESTLIST) + if(NOT NEXUS_TESTLIST_RESULT EQUAL 0) + message(FATAL_ERROR "Command line ' ${Python3_EXECUTABLE} -m pytest --collect-only -qq ${qmcpack_SOURCE_DIR}/nexus/nexus/tests ' failed!") endif() + + string(REPLACE "\n" ";" NEXUS_TESTLIST "${NEXUS_TESTLIST}") # Join into a single line with semicolon separators + list(REMOVE_ITEM NEXUS_TESTLIST "") # remove empty entries + set(CACHE_NEXUS_TESTLIST + ${NEXUS_TESTLIST} + CACHE INTERNAL "NEXUS_TESTLIST cache variable" FORCE) if(NEXUS_TESTLIST) message("Adding Nexus tests") else() message("Nexus test list is empty. No Nexus tests added.") endif() - foreach(TESTNAME ${NEXUS_TESTLIST}) - #message("Adding test ntest_nexus_${TESTNAME}") - set(NTEST "${qmcpack_SOURCE_DIR}/nexus/nexus/bin/nxs-test") - IF(ENABLE_PYCOV) - add_test(NAME ntest_nexus_${TESTNAME} COMMAND ${PYTHON_COVERAGE_EXECUTABLE} run -p ${NTEST} -R ${TESTNAME}\$ --ctest - --pythonpath=${PROJECT_SOURCE_DIR}/nexus:$ENV{PYTHONPATH}) - - ELSE() - add_test(NAME ntest_nexus_${TESTNAME} COMMAND ${Python3_EXECUTABLE} ${NTEST} -R ${TESTNAME}\$ --ctest - --pythonpath=${PROJECT_SOURCE_DIR}/nexus:$ENV{PYTHONPATH}) - ENDIF() - set_tests_properties(ntest_nexus_${TESTNAME} PROPERTIES ENVIRONMENT PYTHONPATH=$ENV{PYTHONPATH}) + set(NTEST "pytest") + if(ENABLE_PYCOV) + add_test(NAME ntest_nexus_coverage_all + COMMAND ${Python3_EXECUTABLE} -m ${NTEST} ${qmcpack_SOURCE_DIR}/nexus/nexus/tests -c ${qmcpack_SOURCE_DIR}/nexus/pyproject.toml + --cov + --cov-report=xml + --cov-config=${qmcpack_SOURCE_DIR}/nexus/pyproject.toml + --basetemp=${qmcpack_BINARY_DIR}/nexus-test-tmp-dir/ + ) + set_tests_properties(ntest_nexus_coverage_all PROPERTIES ENVIRONMENT PYTHONPATH=$ENV{PYTHONPATH}) set_property( - TEST ntest_nexus_${TESTNAME} + TEST ntest_nexus_coverage_all APPEND PROPERTY LABELS "nexus;deterministic") set(TEST_LABELS "") - add_test_labels(ntest_nexus_${TESTNAME} TEST_LABELS) - # Use a resource lock to avoid potential race condition in copying example inputs - if(${TESTNAME} MATCHES ".*example.*") - set_tests_properties(ntest_nexus_${TESTNAME} PROPERTIES RESOURCE_LOCK nexus_examples_resource) - endif() - endforeach() -else() - message("Skipping Nexus tests because numpy is not present in python installation") + add_test_labels(ntest_nexus_coverage_all TEST_LABELS) + else() + foreach(TESTFILE IN LISTS NEXUS_TESTLIST) + string(REGEX REPLACE "\.py:.*[0-9]" "" TESTFILE "${TESTFILE}") + string(REPLACE "nexus/tests/test_" "" TESTNAME "${TESTFILE}") + #message("Adding test ntest_nexus_${TESTNAME}") + set(NEXUS_TEST_DIR ${qmcpack_BINARY_DIR}/nexus-test-tmp-dir/test_${TESTNAME}_output) + make_directory(${NEXUS_TEST_DIR}) + add_test(NAME ntest_nexus_${TESTNAME} + COMMAND ${Python3_EXECUTABLE} -m ${NTEST} ${qmcpack_SOURCE_DIR}/nexus/${TESTFILE}.py + -c ${qmcpack_SOURCE_DIR}/nexus/pyproject.toml + --basetemp=${NEXUS_TEST_DIR} + ) + set_tests_properties(ntest_nexus_${TESTNAME} PROPERTIES ENVIRONMENT PYTHONPATH=$ENV{PYTHONPATH}) + set_property( + TEST ntest_nexus_${TESTNAME} + APPEND + PROPERTY LABELS "nexus;deterministic") + set(TEST_LABELS "") + add_test_labels(ntest_nexus_${TESTNAME} TEST_LABELS) + # Use a resource lock to avoid potential race condition in copying example inputs + if(${TESTNAME} MATCHES ".*example.*") + set_tests_properties(ntest_nexus_${TESTNAME} PROPERTIES RESOURCE_LOCK nexus_examples_resource) + endif() + endforeach() + endif() endif() diff --git a/nexus/nexus/tests/__init__.py b/nexus/nexus/tests/__init__.py index e69de29bb2..afb82da2e2 100644 --- a/nexus/nexus/tests/__init__.py +++ b/nexus/nexus/tests/__init__.py @@ -0,0 +1,261 @@ +from inspect import signature +from enum import IntEnum, auto +from pathlib import Path +from copy import deepcopy +import functools +from nexus.nexus_base import nexus_core, nexus_noncore, nexus_core_noncore, nexus_noncore_defaults +from nexus.generic import generic_settings, object_interface +from nexus.pseudopotential import Pseudopotentials +from nexus.simulation import Simulation + +# qmcpack/nexus/nexus/tests/ +TEST_DIR = Path(__file__).resolve().parent + +NEXUS_CORE_KEYS = ( + "local_directory", + "remote_directory", + "mode", + "stages", + "stages_set", + "status", + "sleep", + "file_locations", + "pseudo_dir", + "pseudopotentials", + "runs", + "results", + ) +NEXUS_NONCORE_KEYS = ( + "pseudo_dir", + "pseudopotentials", + ) + +def divert_nexus_core(): + """Store Nexus's core and noncore keys and return them.""" + nexus_core_storage = {} + for key in NEXUS_CORE_KEYS: + nexus_core_storage[key] = nexus_core[key] + nexus_core[key] = deepcopy(nexus_core[key]) + + nexus_noncore_storage = {} + for key in NEXUS_NONCORE_KEYS: + if key in nexus_noncore: + nexus_noncore_storage[key] = nexus_noncore[key] + nexus_noncore[key] = deepcopy(nexus_noncore[key]) + + return nexus_core_storage, nexus_noncore_storage + + +def restore_nexus_core(nexus_core_storage: dict, nexus_noncore_storage: dict): + """Use the keys in ``nexus_core_storage`` and ``nexus_noncore_storage`` to restore state.""" + + for key in NEXUS_CORE_KEYS: + nexus_core[key] = nexus_core_storage.pop(key) + + for key in NEXUS_NONCORE_KEYS: + if key in nexus_noncore_storage: + nexus_noncore[key] = nexus_noncore_storage.pop(key) + elif key in nexus_noncore: + del nexus_noncore[key] + + for key in list(nexus_noncore.keys()): + if key not in nexus_noncore_defaults: + del nexus_noncore[key] + + nexus_core_noncore.pseudopotentials = None + + assert len(nexus_noncore_storage) == 0, "Nexus Core keys have not been properly reset!" + assert len(nexus_core_storage) == 0, "Nexus NonCore keys have not been properly reset!" + + +class FakeLog: + def __init__(self): + self.reset() + + def reset(self): + self.s = "" + + def write(self,s): + self.s += s + + def close(self): + None + + def contents(self): + return self.s + + +def divert_nexus_log(): + """Create a fake logging object to divert Nexus's output.""" + logging_storage = { + 'devlog': generic_settings.devlog, + 'objlog': object_interface._logfile, + } + logfile = FakeLog() + generic_settings.devlog = logfile + object_interface._logfile = logfile + return logfile, logging_storage + + +def restore_nexus_log(logging_storage: dict): + """Restore Nexus's logging to the state stored in ``logging_storage``.""" + generic_settings.devlog = logging_storage.pop('devlog') + object_interface._logfile = logging_storage.pop('objlog') + + +def isolate_nexus_core(test_func = None): + """Isolate changes in ``nexus_core`` for a test function.""" + + needs_tmp_path = "tmp_path" in str(signature(test_func)) + + @functools.wraps(test_func) + def wrap_path(tmp_path): + nexus_core_storage, nexus_noncore_storage = divert_nexus_core() + logfile, logging_storage = divert_nexus_log() + try: + test_func(tmp_path) + test_err = None + except Exception as err: + test_err = err + + restore_nexus_core(nexus_core_storage, nexus_noncore_storage) + restore_nexus_log(logging_storage) + Simulation.clear_all_sims() + if test_err is not None: + raise test_err + + @functools.wraps(test_func) + def wrap(): + nexus_core_storage, nexus_noncore_storage = divert_nexus_core() + logfile, logging_storage = divert_nexus_log() + try: + test_func() + test_err = None + except Exception as err: + test_err = err + + restore_nexus_core(nexus_core_storage, nexus_noncore_storage) + restore_nexus_log(logging_storage) + Simulation.clear_all_sims() + if test_err is not None: + raise test_err + + if needs_tmp_path: + return wrap_path + else: + return wrap + + +def create_pseudo_files( + tmp_dir: Path, + pseudos: list[str], + pseudo_strs: list[str | None] | None = None + ): + """Create pseudopotential files and add them to the global pseudopotentials. + + This function must be called in a function that has been decorated + with ``@isolate_nexus_core(needs_tmp_path=True)``. + + Parameters + ---------- + tmp_dir : Path + Path to the temporary directory of a test. + pseudos : list of str + List of pseudopotential name(s). These are created at the path + ``tmp_dir/pseudopotential/``. + pseudo_strs : list of str or None, optional + Text to write into the pseudopotential file(s). Must have the + same length as ``pseudos``. + """ + + if pseudo_strs is None: + pseudo_strs = [""] * len(pseudos) + elif len(pseudo_strs) != len(pseudos): + raise ValueError( + "Test improperly written!\n" + "Must have pseudo text or `None` for every pseudo file!" + ) + + pseudo_dir = tmp_dir / "pseudopotentials" + pseudo_dir.mkdir(parents=True) + + new_pseudos = [] + for pseudo, text in zip(pseudos, pseudo_strs): + pseudo_file = pseudo_dir / pseudo + pseudo_file.write_text(text) + new_pseudos.append(pseudo_file) + + + pseudopotentials = Pseudopotentials(new_pseudos) + nexus_core.pseudopotentials = pseudopotentials + nexus_noncore.pseudopotentials = pseudopotentials + nexus_core.pseudo_dir = str(pseudo_dir) + nexus_noncore.pseudo_dir = str(pseudo_dir) + + +class NexusTestOrder(IntEnum): + """Test order for Nexus testing. + + This dictates the order that the tests are run in, reflecting the + inheritance hierarchy that Nexus has, so the first tests to fail are + going to be indicative of where the actual root problem is. + """ + + TESTING = auto() + EXECUTE = auto() + MEMORY = auto() + UTILITIES = auto() + GENERIC_OPERATION = auto() + DEVELOPER = auto() + UNIT_CONVERTER = auto() + PERIODIC_TABLE = auto() + NUMERICS = auto() + GRID_FUNCTIONS = auto() + FILEIO = auto() + HDFREADER = auto() + XMLREADER = auto() + STRUCTURE = auto() + PHYSICAL_SYSTEM = auto() + BASISSET = auto() + PSEUDOPOTENTIAL = auto() + NEXUS_BASE = auto() + MACHINES = auto() + SIMULATION = auto() + BUNDLE = auto() + PROJECT_MANAGER = auto() + SETTINGS_OPERATION = auto() + VASP_INPUT = auto() + PWSCF_INPUT = auto() + PWSCF_POSTPROCESSOR_INPUT = auto() + GAMESS_INPUT = auto() + PYSCF_INPUT = auto() + QUANTUM_PACKAGE_INPUT = auto() + RMG_INPUT = auto() + QMCPACK_CONVERTER_INPUT = auto() + QMCPACK_INPUT = auto() + VASP_ANALYZER = auto() + PWSCF_ANALYZER = auto() + PWSCF_POSTPROCESSOR_ANALYZERS = auto() + GAMESS_ANALYZER = auto() + PYSCF_ANALYZER = auto() + QUANTUM_PACKAGE_ANALYZER = auto() + RMG_ANALYZER = auto() + QMCPACK_CONVERTER_ANALYZERS = auto() + QMCPACK_ANALYZER = auto() + VASP_SIMULATION = auto() + PWSCF_SIMULATION = auto() + GAMESS_SIMULATION = auto() + PYSCF_SIMULATION = auto() + QUANTUM_PACKAGE_SIMULATION = auto() + RMG_SIMULATION = auto() + PWSCF_POSTPROCESSOR_SIMULATIONS = auto() + QMCPACK_CONVERTER_SIMULATIONS = auto() + QMCPACK_SIMULATION = auto() + OBSERVABLES = auto() + NXS_REDO = auto() + NXS_SIM = auto() + QMC_FIT = auto() + QDENS = auto() + QDENS_RADIAL = auto() + QMCA = auto() + USER_EXAMPLES = auto() diff --git a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/dmc.in.xml b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/dmc.in.xml index 87d030f48a..41ad584e75 100644 --- a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/dmc.in.xml +++ b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/dmc.in.xml @@ -35,11 +35,11 @@ 4.05580089 4.05580089 3.00901473 - + 1 1 1 - 1837.36221934 + 1837.47159264 4.05580089 1.35193363 5.10258705 4.05580089 6.75966815 5.10258705 diff --git a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/opt.in.xml b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/opt.in.xml index 7452d0529b..31f59bfcf0 100644 --- a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/opt.in.xml +++ b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/opt.in.xml @@ -35,11 +35,11 @@ 4.05580089 4.05580089 3.00901473 - + 1 1 1 - 1837.36221934 + 1837.47159264 4.05580089 1.35193363 5.10258705 4.05580089 6.75966815 5.10258705 diff --git a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/scf.in b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/scf.in index f69e53bf03..81315687b8 100644 --- a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/scf.in +++ b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/H2O/runs/scf.in @@ -35,7 +35,7 @@ ATOMIC_SPECIES - H 1.00794 H.BFD.upf + H 1.008 H.BFD.upf O 15.999 O.BFD.upf ATOMIC_POSITIONS bohr diff --git a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/dmc.in.xml b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/dmc.in.xml index 3c8d0ccbbf..bc4dc652a9 100644 --- a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/dmc.in.xml +++ b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/dmc.in.xml @@ -27,20 +27,20 @@ - + 1 1 3 - 12652.6689728 + 12650.8460843 0.00000000 0.00000000 0.00000000 - + 1 1 1 - 1837.36221934 + 1837.47159264 3.55000000 3.55000000 3.55000000 diff --git a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/nscf.in b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/nscf.in index 20a14cafd7..1d66ce1faa 100644 --- a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/nscf.in +++ b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/nscf.in @@ -35,8 +35,8 @@ ATOMIC_SPECIES - H 1.00794 H.TN-DF.upf - Li 6.941 Li.TN-DF.upf + H 1.008 H.TN-DF.upf + Li 6.94 Li.TN-DF.upf ATOMIC_POSITIONS bohr Li 0.00000000 0.00000000 0.00000000 diff --git a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/opt.in.xml b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/opt.in.xml index 696c01d710..2dd259bb4b 100644 --- a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/opt.in.xml +++ b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/opt.in.xml @@ -27,20 +27,20 @@ - + 1 1 3 - 12652.6689728 + 12650.8460843 0.00000000 0.00000000 0.00000000 - + 1 1 1 - 1837.36221934 + 1837.47159264 3.55000000 3.55000000 3.55000000 diff --git a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/scf.in b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/scf.in index 562ea39546..f31bad3eb9 100644 --- a/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/scf.in +++ b/nexus/nexus/tests/reference/user_examples/qmcpack/rsqmc_misc/LiH/runs/scf.in @@ -35,8 +35,8 @@ ATOMIC_SPECIES - H 1.00794 H.TN-DF.upf - Li 6.941 Li.TN-DF.upf + H 1.008 H.TN-DF.upf + Li 6.94 Li.TN-DF.upf ATOMIC_POSITIONS bohr Li 0.00000000 0.00000000 0.00000000 diff --git a/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_111/relax.in b/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_111/relax.in index f6673f4805..6913520903 100644 --- a/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_111/relax.in +++ b/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_111/relax.in @@ -41,7 +41,7 @@ ATOMIC_SPECIES - Ge 72.61 Ge.pbe-kjpaw.UPF + Ge 72.63 Ge.pbe-kjpaw.UPF ATOMIC_POSITIONS bohr Ge 5.34792496 5.34792496 5.34792496 diff --git a/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_222/relax.in b/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_222/relax.in index 3be3e4ab30..e4542af830 100644 --- a/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_222/relax.in +++ b/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_222/relax.in @@ -41,7 +41,7 @@ ATOMIC_SPECIES - Ge 72.61 Ge.pbe-kjpaw.UPF + Ge 72.63 Ge.pbe-kjpaw.UPF ATOMIC_POSITIONS bohr Ge 5.34792496 5.34792496 5.34792496 diff --git a/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_444/relax.in b/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_444/relax.in index 76eb629eb7..9a98a28b0c 100644 --- a/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_444/relax.in +++ b/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_444/relax.in @@ -41,7 +41,7 @@ ATOMIC_SPECIES - Ge 72.61 Ge.pbe-kjpaw.UPF + Ge 72.63 Ge.pbe-kjpaw.UPF ATOMIC_POSITIONS bohr Ge 5.34792496 5.34792496 5.34792496 diff --git a/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_666/relax.in b/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_666/relax.in index 5f3044a074..0ae735f56e 100644 --- a/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_666/relax.in +++ b/nexus/nexus/tests/reference/user_examples/quantum_espresso/relax_Ge_T_vs_kpoints/runs/relax/kgrid_666/relax.in @@ -41,7 +41,7 @@ ATOMIC_SPECIES - Ge 72.61 Ge.pbe-kjpaw.UPF + Ge 72.63 Ge.pbe-kjpaw.UPF ATOMIC_POSITIONS bohr Ge 5.34792496 5.34792496 5.34792496 diff --git a/nexus/nexus/tests/test_basisset.py b/nexus/nexus/tests/test_basisset.py index 0f81dbe38c..65b716a7a1 100644 --- a/nexus/nexus/tests/test_basisset.py +++ b/nexus/nexus/tests/test_basisset.py @@ -1,48 +1,27 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.BASISSET) -from .. import testing -from ..testing import value_eq,object_eq -from ..testing import divert_nexus_log,restore_nexus_log +from ..generic import generic_settings +generic_settings.raise_error = True +from . import TEST_DIR +from ..testing import object_eq -associated_files = dict() +TEST_FILES = { + "Fe.aug-cc-pwcv5z-dk.0.bas": TEST_DIR / "test_basisset_files/Fe.aug-cc-pwcv5z-dk.0.bas", + "Fe.aug-cc-pwcv5z-dk.0.gbs": TEST_DIR / "test_basisset_files/Fe.aug-cc-pwcv5z-dk.0.gbs", + "Fe.BFD_VQZ.bas": TEST_DIR / "test_basisset_files/Fe.BFD_VQZ.bas", + "Fe.BFD_VQZ.gbs": TEST_DIR / "test_basisset_files/Fe.BFD_VQZ.gbs", + "Fe.stuttgart_rsc_1997.0.bas": TEST_DIR / "test_basisset_files/Fe.stuttgart_rsc_1997.0.bas", + "Fe.stuttgart_rsc_1997.0.gbs": TEST_DIR / "test_basisset_files/Fe.stuttgart_rsc_1997.0.gbs", + "Fe.stuttgart_rsc_1997_ecp.0.bas": TEST_DIR / "test_basisset_files/Fe.stuttgart_rsc_1997_ecp.0.bas", + "Fe.stuttgart_rsc_1997_ecp.0.gbs": TEST_DIR / "test_basisset_files/Fe.stuttgart_rsc_1997_ecp.0.gbs", + } -def get_filenames(): - filenames = [ - 'Fe.aug-cc-pwcv5z-dk.0.bas', - 'Fe.aug-cc-pwcv5z-dk.0.gbs', - 'Fe.BFD_VQZ.bas', - 'Fe.BFD_VQZ.gbs', - 'Fe.stuttgart_rsc_1997.0.bas', - 'Fe.stuttgart_rsc_1997.0.gbs', - 'Fe.stuttgart_rsc_1997_ecp.0.bas', - 'Fe.stuttgart_rsc_1997_ecp.0.gbs', - ] - return filenames -#end def get_filenames - - -def get_files(): - return testing.collect_unit_test_file_paths('basisset',associated_files) -#end def get_files - - - -def test_files(): - filenames = get_filenames() - files = get_files() - assert(set(files.keys())==set(filenames)) -#end def test_files - - - -def test_import(): - from .. import basisset - from ..basisset import BasisSets - from ..basisset import process_gaussian_text - from ..basisset import GaussianBasisSet -#end def test_import - +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" def test_basissets(): @@ -55,31 +34,24 @@ def test_basissets(): BasisFile() gamessBasisFile() - filenames = get_filenames() - files = get_files() - f = [files[fn] for fn in filenames] - - # standard initialization - divert_nexus_log() - bf = BasisFile(f[1]) - gbf = gamessBasisFile(f[0]) - bs = BasisSets(f[2:]+[bf,gbf]) - restore_nexus_log() - - assert(bf.element=='Fe') - assert(bf.filename=='Fe.aug-cc-pwcv5z-dk.0.gbs') - - assert(gbf.element=='Fe') - assert(gbf.filename=='Fe.aug-cc-pwcv5z-dk.0.bas') - assert(gbf.text.startswith('IRON')) - assert(gbf.text.endswith('1 1.3776500 1.0000000')) - assert(len(gbf.text.strip())==21135) - - for fn in filenames: - assert(fn in bs) - assert(isinstance(bs[fn],BasisFile)) - if fn.endswith('.bas'): - assert(isinstance(bs[fn],gamessBasisFile)) + basis_file = BasisFile(TEST_FILES["Fe.aug-cc-pwcv5z-dk.0.gbs"]) + gamess_basis_file = gamessBasisFile(TEST_FILES["Fe.aug-cc-pwcv5z-dk.0.bas"]) + basis_sets = BasisSets(list(TEST_FILES.values())[2:]+[basis_file,gamess_basis_file]) + + assert(basis_file.element=='Fe') + assert(basis_file.filename=='Fe.aug-cc-pwcv5z-dk.0.gbs') + + assert(gamess_basis_file.element=='Fe') + assert(gamess_basis_file.filename=='Fe.aug-cc-pwcv5z-dk.0.bas') + assert(gamess_basis_file.text.startswith('IRON')) + assert(gamess_basis_file.text.endswith('1 1.3776500 1.0000000')) + assert(len(gamess_basis_file.text.strip())==21135) + + for fn in TEST_FILES.values(): + assert(fn.name in basis_sets) + assert(isinstance(basis_sets[fn.name],BasisFile)) + if fn.suffix == '.bas': + assert(isinstance(basis_sets[fn.name],gamessBasisFile)) #end if #end for #end def test_basissets @@ -89,10 +61,7 @@ def test_basissets(): def test_process_gaussian_text(): from ..basisset import process_gaussian_text - filenames = get_filenames() - files = get_files() - - bs_ref = { + basis_refs = { 'Fe.aug-cc-pwcv5z-dk.0.bas' : 503, 'Fe.aug-cc-pwcv5z-dk.0.gbs' : 503, 'Fe.BFD_VQZ.bas' : 132, @@ -102,7 +71,7 @@ def test_process_gaussian_text(): } - pp_ref = { + pseudo_refs = { 'Fe.BFD_VQZ.bas' : ( 9, 132 ), 'Fe.BFD_VQZ.gbs' : ( 13, 132 ), 'Fe.stuttgart_rsc_1997.0.bas' : ( 13, 38 ), @@ -111,35 +80,31 @@ def test_process_gaussian_text(): 'Fe.stuttgart_rsc_1997_ecp.0.gbs' : ( 17, None ), } - for fn in filenames: + for file in TEST_FILES.values(): - if fn.endswith('.bas'): + if file.suffix == '.bas': format = 'gamess' - elif fn.endswith('.gbs'): + elif file.suffix == '.gbs': format = 'gaussian' else: format = None #end if - f = open(files[fn],'r') - text = f.read() - f.close() + file_text = file.read_text() - bs = process_gaussian_text(text,format,pp=False) + basis_set = process_gaussian_text(file_text,format,pp=False) - if fn in bs_ref: - assert(len(bs)==bs_ref[fn]) + if file.name in basis_refs: + assert(len(basis_set)==basis_refs[file.name]) #end if - pp,bs = process_gaussian_text(text,format) + pseudo, basis_set = process_gaussian_text(file_text,format) - if fn in pp_ref: - ppr,bsr = pp_ref[fn] - assert(len(pp)==ppr) - if bsr is None: - assert(bs is None) - else: - assert(len(bs)==bsr) + if file.name in pseudo_refs: + pseudo_ref, basis_ref = pseudo_refs[file.name] + assert(len(pseudo)==pseudo_ref) + if basis_ref is not None: + assert(len(basis_set)==basis_ref) #end if #end if #end for @@ -151,9 +116,6 @@ def test_process_gaussian_text(): def test_gaussianbasisset(): from ..basisset import GaussianBasisSet - filenames = get_filenames() - files = get_files() - GaussianBasisSet() ref = { @@ -165,21 +127,20 @@ def test_gaussianbasisset(): 'Fe.stuttgart_rsc_1997.0.gbs' : 15, } - gbs = dict() - for fn in filenames: - if 'ecp' not in fn: - if fn.endswith('.bas'): + for file in TEST_FILES.values(): + if 'ecp' not in file.name: + if file.suffix == '.bas': format = 'gamess' - elif fn.endswith('.gbs'): + elif file.suffix == '.gbs': format = 'gaussian' else: format = None #end if - bs = GaussianBasisSet(files[fn],format) + bs = GaussianBasisSet(file,format) assert(bs.name=='Fe') - assert(len(bs.basis)==ref[fn]) + assert(len(bs.basis)==ref[file.name]) text = bs.write(format=format) text = 'header line\n'+text @@ -190,4 +151,3 @@ def test_gaussianbasisset(): #end if #end for #end def test_gaussianbasisset - diff --git a/nexus/nexus/tests/test_bundle.py b/nexus/nexus/tests/test_bundle.py index ab3aae76db..4ff7ee1dea 100644 --- a/nexus/nexus/tests/test_bundle.py +++ b/nexus/nexus/tests/test_bundle.py @@ -1,13 +1,13 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.BUNDLE) + +from ..generic import generic_settings +generic_settings.raise_error = True from .. import testing from ..testing import failed,FailedTest -from ..testing import value_eq,object_eq - - -def test_import(): - from ..bundle import bundle - from ..bundle import SimulationBundle -#end def test_import +from ..testing import object_eq diff --git a/nexus/nexus/tests/test_developer.py b/nexus/nexus/tests/test_developer.py index 5d76039436..8a3e25909d 100644 --- a/nexus/nexus/tests/test_developer.py +++ b/nexus/nexus/tests/test_developer.py @@ -1,14 +1,12 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.DEVELOPER) -from ..testing import failed,FailedTest +from ..generic import generic_settings +generic_settings.raise_error = True -def test_import(): - from ..developer import log,error,warn - from ..developer import ci,interact - from ..developer import DevBase - from ..developer import Void - from ..developer import unavailable,available - from ..developer import valid_variable_name -#end def test_import + +from ..testing import failed,FailedTest diff --git a/nexus/nexus/tests/test_execute.py b/nexus/nexus/tests/test_execute.py index de7e495160..9ce74d5418 100644 --- a/nexus/nexus/tests/test_execute.py +++ b/nexus/nexus/tests/test_execute.py @@ -1,9 +1,9 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.EXECUTE) - -def test_import(): - from ..execute import execute -#end def test_import - +from ..generic import generic_settings +generic_settings.raise_error = True def test_execute(): diff --git a/nexus/nexus/tests/test_fileio.py b/nexus/nexus/tests/test_fileio.py index 55ba47dbf9..1cc9f9e5b1 100644 --- a/nexus/nexus/tests/test_fileio.py +++ b/nexus/nexus/tests/test_fileio.py @@ -1,50 +1,34 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.FILEIO) -from .. import testing -from ..testing import value_eq,object_eq +from ..generic import generic_settings +generic_settings.raise_error = True +from . import TEST_DIR +from ..testing import value_eq, object_eq -associated_files = dict() -def get_files(): - return testing.collect_unit_test_file_paths('fileio',associated_files) -#end def get_files - - - -def test_files(): - filenames = [ - 'scf.in', - 'VO2_R_48.xsf', - 'VO2_R_48.POSCAR', - 'VO2_R_48_dens.xsf', - 'VO2_R_48_dens.CHGCAR', - ] - files = get_files() - assert(set(files.keys())==set(filenames)) -#end def test_files - - - -def test_import(): - from .. import fileio - from ..fileio import TextFile - from ..fileio import XsfFile - from ..fileio import PoscarFile - from ..fileio import ChgcarFile -#end def test_import +TEST_FILES = { + "scf.in": TEST_DIR / "test_fileio_files/scf.in", + "VO2_R_48_dens.CHGCAR": TEST_DIR / "test_fileio_files/VO2_R_48_dens.CHGCAR", + "VO2_R_48_dens.xsf": TEST_DIR / "test_fileio_files/VO2_R_48_dens.xsf", + "VO2_R_48.POSCAR": TEST_DIR / "test_fileio_files/VO2_R_48.POSCAR", + "VO2_R_48.xsf": TEST_DIR / "test_fileio_files/VO2_R_48.xsf", + } +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" def test_textfile(): from ..fileio import TextFile - files = get_files() - # test empty initialization empty = TextFile() # test read - f = TextFile(files['scf.in']) + f = TextFile(TEST_FILES["scf.in"]) assert(len(f.read())==1225) assert(len(f.lines())==55) @@ -65,17 +49,10 @@ def test_textfile(): #end def test_textfile - - -def test_xsffile(): - import os +def test_xsffile(tmp_path): import numpy as np from ..fileio import XsfFile - tpath = testing.setup_unit_test_output_directory('fileio','test_xsffile') - - files = get_files() - # test empty initialization empty = XsfFile() assert(not empty.is_valid()) @@ -147,31 +124,24 @@ def test_xsffile(): assert(ref.is_valid()) # test read - f = XsfFile(files['VO2_R_48.xsf']) + f = XsfFile(TEST_FILES['VO2_R_48.xsf']) assert(f.is_valid()) assert(object_eq(f,ref)) # test write - outfile = os.path.join(tpath,'test.xsf') + outfile = tmp_path / "test.xsf" f.write(outfile) f2 = XsfFile(outfile) assert(f2.is_valid()) assert(object_eq(f2,ref)) - #end def test_xsffile - -def test_xsffile_density(): - import os +def test_xsffile_density(tmp_path): import numpy as np from ..fileio import XsfFile - tpath = testing.setup_unit_test_output_directory('fileio','test_xsffile_density') - - files = get_files() - - ref = XsfFile(files['VO2_R_48.xsf']) + ref = XsfFile(TEST_FILES['VO2_R_48.xsf']) grid = 3,5,7 dens = 0.01*np.arange(np.prod(grid),dtype=float) @@ -180,7 +150,7 @@ def test_xsffile_density(): ref.add_density(ref.primvec,dens,add_ghost=True) assert(ref.is_valid()) - f = XsfFile(files['VO2_R_48_dens.xsf']) + f = XsfFile(TEST_FILES['VO2_R_48_dens.xsf']) assert(f.is_valid()) assert(object_eq(f,ref)) @@ -188,7 +158,7 @@ def test_xsffile_density(): assert(isinstance(d,np.ndarray)) assert(d.shape==(4,6,8)) - outfile = os.path.join(tpath,'test_density.xsf') + outfile = tmp_path / "test_density.xsf" f.write(outfile) f2 = XsfFile(outfile) assert(f2.is_valid()) @@ -197,15 +167,10 @@ def test_xsffile_density(): -def test_poscar_file(): - import os +def test_poscar_file(tmp_path): import numpy as np from ..fileio import PoscarFile - tpath = testing.setup_unit_test_output_directory('fileio','test_poscarfile') - - files = get_files() - # test empty initialization empty = PoscarFile() assert(not empty.is_valid()) @@ -279,12 +244,12 @@ def test_poscar_file(): ) # test read - f = PoscarFile(files['VO2_R_48.POSCAR']) + f = PoscarFile(TEST_FILES['VO2_R_48.POSCAR']) assert(f.is_valid()) assert(object_eq(f,ref)) # test write - outfile = os.path.join(tpath,'test.POSCAR') + outfile = tmp_path / "test.POSCAR" f.write(outfile) f2 = PoscarFile(outfile) assert(f2.is_valid()) @@ -292,7 +257,7 @@ def test_poscar_file(): # test incorporate xsf from ..fileio import XsfFile - x = XsfFile(files['VO2_R_48.xsf']) + x = XsfFile(TEST_FILES['VO2_R_48.xsf']) f = PoscarFile() f.incorporate_xsf(x) assert(f.is_valid()) @@ -301,22 +266,17 @@ def test_poscar_file(): -def test_chgcar_file(): - import os +def test_chgcar_file(tmp_path): from ..fileio import XsfFile from ..fileio import PoscarFile from ..fileio import ChgcarFile - tpath = testing.setup_unit_test_output_directory('fileio','test_chgcarfile') - - files = get_files() - empty = ChgcarFile() assert(not empty.is_valid()) # get reference poscar and xsf files - p = PoscarFile(files['VO2_R_48.POSCAR']) - x = XsfFile(files['VO2_R_48_dens.xsf']) + p = PoscarFile(TEST_FILES['VO2_R_48.POSCAR']) + x = XsfFile(TEST_FILES['VO2_R_48_dens.xsf']) # create and test reference chgcar file ref = ChgcarFile() @@ -325,12 +285,12 @@ def test_chgcar_file(): assert(object_eq(ref.poscar,p)) # test read - f = ChgcarFile(files['VO2_R_48_dens.CHGCAR']) + f = ChgcarFile(TEST_FILES['VO2_R_48_dens.CHGCAR']) assert(f.is_valid()) assert(object_eq(f,ref)) # test write - outfile = os.path.join(tpath,'test.CHGCAR') + outfile = tmp_path / "test.CHGCAR" f.write(outfile) f2 = ChgcarFile(outfile) assert(f2.is_valid()) diff --git a/nexus/nexus/tests/test_gamess_analyzer.py b/nexus/nexus/tests/test_gamess_analyzer.py index cf1961dded..bdc3eb855b 100644 --- a/nexus/nexus/tests/test_gamess_analyzer.py +++ b/nexus/nexus/tests/test_gamess_analyzer.py @@ -1,11 +1,20 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.GAMESS_ANALYZER) -from .. import testing -from ..testing import value_eq,object_eq,text_eq +from ..generic import generic_settings +generic_settings.raise_error = True +from . import TEST_DIR +from ..testing import object_eq -def test_import(): - from ..gamess_analyzer import GamessAnalyzer -#end def test_import +TEST_FILES = { + "gms.inp": TEST_DIR / "test_gamess_analyzer_files/gms.inp", + "gms.out": TEST_DIR / "test_gamess_analyzer_files/gms.out", + } + +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" def test_empty_init(): @@ -17,21 +26,12 @@ def test_empty_init(): def test_analyze(): - import os - from numpy import array,ndarray + from numpy import array from ..developer import obj from ..gamess_analyzer import GamessAnalyzer - tpath = testing.setup_unit_test_output_directory( - test = 'gamess_analyzer', - subtest = 'test_analyze', - file_sets = ['gms.inp','gms.out'], - ) - - outpath = os.path.join(tpath,'gms.inp') - # no analysis - ga = GamessAnalyzer(outpath) + ga = GamessAnalyzer(TEST_FILES["gms.inp"]) del ga.info.input del ga.info.path @@ -133,7 +133,7 @@ def test_analyze(): # full analysis - ga = GamessAnalyzer(outpath,analyze=True) + ga = GamessAnalyzer(TEST_FILES["gms.out"],analyze=True) del ga.info.input del ga.info.path diff --git a/nexus/nexus/tests/test_gamess_input.py b/nexus/nexus/tests/test_gamess_input.py index 6fb084b8ea..dbde7ef970 100644 --- a/nexus/nexus/tests/test_gamess_input.py +++ b/nexus/nexus/tests/test_gamess_input.py @@ -1,16 +1,26 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.GAMESS_INPUT) -from .. import testing -from ..testing import divert_nexus,restore_nexus -from ..testing import divert_nexus_log,restore_nexus_log -from ..testing import value_eq,object_eq +from ..generic import generic_settings +generic_settings.raise_error = True +import shutil +from . import isolate_nexus_core, TEST_DIR +from nexus.nexus_base import nexus_core +from ..testing import object_eq -associated_files = dict() -def get_files(): - return testing.collect_unit_test_file_paths('gamess_input',associated_files) -#end def get_files +TEST_FILES = { + "rhf.inp": TEST_DIR / "test_gamess_input_files/rhf.inp", + "cisd.inp": TEST_DIR / "test_gamess_input_files/cisd.inp", + "cas.inp": TEST_DIR / "test_gamess_input_files/cas.inp", + "H.BFD_V5Z_ANO.gms": TEST_DIR / "test_gamess_input_files/H.BFD_V5Z_ANO.gms", + "O.BFD_V5Z.gms": TEST_DIR / "test_gamess_input_files/O.BFD_V5Z.gms", + } +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" def make_serial_reference(gi): @@ -267,36 +277,11 @@ def check_vs_serial_reference(gi,name): assert(object_eq(sg,sr)) #end def check_vs_serial_reference - - -def test_files(): - filenames = [ - 'rhf.inp', - 'cisd.inp', - 'cas.inp', - 'H.BFD_V5Z_ANO.gms', - 'O.BFD_V5Z.gms', - ] - files = get_files() - assert(set(filenames)==set(files.keys())) -#end def test_files - - - -def test_import(): - from ..gamess_input import GamessInput,generate_gamess_input -#end def test_import - - - +@isolate_nexus_core def test_keyspec_groups(): from ..gamess_input import check_keyspec_groups - divert_nexus_log() - check_keyspec_groups() - - restore_nexus_log() #end def test_keyspec_groups @@ -316,34 +301,26 @@ def test_empty_init(): def test_read(): from ..gamess_input import GamessInput - - files = get_files() input_files = ['rhf.inp','cisd.inp','cas.inp'] for infile in input_files: - gi_read = GamessInput(files[infile]) + gi_read = GamessInput(TEST_FILES[infile]) check_vs_serial_reference(gi_read,infile) #end for - #end def test_read -def test_write(): - import os +def test_write(tmp_path): from ..gamess_input import GamessInput - tpath = testing.setup_unit_test_output_directory('gamess_input','test_write') - - files = get_files() - input_files = ['rhf.inp','cisd.inp','cas.inp'] for infile in input_files: - write_file = os.path.join(tpath,infile) + write_file = tmp_path / infile - gi_read = GamessInput(files[infile]) + gi_read = GamessInput(TEST_FILES[infile]) gi_read.write(write_file) @@ -351,31 +328,32 @@ def test_write(): check_vs_serial_reference(gi_write,infile) #end for - #end def test_write - -def test_generate(): - import os +@isolate_nexus_core +def test_generate(tmp_path): from ..developer import obj from ..nexus_base import nexus_noncore from ..pseudopotential import Pseudopotentials from ..physical_system import generate_physical_system from ..gamess_input import generate_gamess_input - - ppfiles = ['H.BFD_V5Z_ANO.gms','O.BFD_V5Z.gms'] - - tpath = testing.setup_unit_test_output_directory( - test = 'gamess_input', - subtest = 'test_generate', - divert = True, - file_sets = { - 'pseudopotentials':ppfiles - } - ) - ppfiles_full = [os.path.join(tpath,'pseudopotentials',f) for f in ppfiles] + ppfiles = ["H.BFD_V5Z_ANO.gms","O.BFD_V5Z.gms"] + pp_dir = tmp_path / "pseudopotentials" + pp_dir.mkdir() + + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] + ppfiles_full = [] + for file in ppfiles: + pp = TEST_FILES[file] + pp_copied = shutil.copy( + src=pp, + dst=pp_dir / file, + ) + ppfiles_full.append(str(pp_copied)) nexus_noncore.pseudopotentials = Pseudopotentials(ppfiles_full) @@ -475,8 +453,6 @@ def test_generate(): gi = generate_gamess_input(**inputs[infile]) check_vs_serial_reference(gi,infile) #end for - - restore_nexus() #end def test_generate diff --git a/nexus/nexus/tests/test_gamess_simulation.py b/nexus/nexus/tests/test_gamess_simulation.py index b08a988dd6..db266a9bf6 100644 --- a/nexus/nexus/tests/test_gamess_simulation.py +++ b/nexus/nexus/tests/test_gamess_simulation.py @@ -1,8 +1,15 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.GAMESS_SIMULATION) +from ..generic import generic_settings +generic_settings.raise_error = True + +from pathlib import Path +from . import isolate_nexus_core from .. import testing -from ..testing import divert_nexus,restore_nexus from ..testing import failed,FailedTest -from ..testing import value_eq,object_eq,text_eq +from ..testing import object_eq def clear_all_sims(): @@ -17,16 +24,14 @@ def clear_all_sims(): def get_gamess_sim(type='rhf'): from ..machines import job from ..gamess import Gamess,generate_gamess,GamessInput - from .test_gamess_input import get_files + from .test_gamess_input import TEST_FILES sim = None Gamess.ericfmt = '' - files = get_files() - if type=='rhf': - gi_input = GamessInput(files['rhf.inp']) + gi_input = GamessInput(TEST_FILES['rhf.inp']) sim = generate_gamess( identifier = 'rhf', @@ -46,12 +51,6 @@ def get_gamess_sim(type='rhf'): -def test_import(): - from ..gamess import Gamess,generate_gamess -#end def test_import - - - def test_minimal_init(): from ..machines import job from ..gamess import Gamess,generate_gamess @@ -70,7 +69,6 @@ def test_minimal_init(): def test_check_result(): - tpath = testing.setup_unit_test_output_directory('gamess_simulation','test_check_result') sim = get_gamess_sim('rhf') @@ -81,27 +79,25 @@ def test_check_result(): #end def test_check_result - -def test_get_result(): - import os +@isolate_nexus_core +def test_get_result(tmp_path): from ..developer import obj, NexusError from ..nexus_base import nexus_core - tpath = testing.setup_unit_test_output_directory('gamess_simulation','test_get_result',divert=True) - + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] nexus_core.runs = '' sim = get_gamess_sim('rhf') - assert(sim.locdir.rstrip('/')==os.path.join(tpath,'rhf').rstrip('/')) + assert(Path(sim.locdir).resolve()==tmp_path / 'rhf') sim.create_directories() sim.write_inputs() - if not os.path.exists(sim.imresdir): - os.makedirs(sim.imresdir) - #end if + Path(sim.imresdir).resolve().mkdir(exist_ok=True) analyzer = sim.analyzer_type(sim) - analyzer.save(os.path.join(sim.imresdir,sim.analyzer_image)) + analyzer.save(Path(sim.imresdir).resolve() / sim.analyzer_image) try: sim.get_result('unknown',None) @@ -125,22 +121,19 @@ def test_get_result(): vec = None, ) - result.location = result.location.replace(tpath,'').lstrip('/') - result.outfile = result.outfile.replace(tpath,'').lstrip('/') + result.location = result.location.replace(str(tmp_path),'').lstrip('/') + result.outfile = result.outfile.replace(str(tmp_path),'').lstrip('/') assert(object_eq(result,result_ref)) clear_all_sims() - restore_nexus() #end def test_get_result def test_incorporate_result(): - import os - from ..developer import NexusError, obj - tpath = testing.setup_unit_test_output_directory('gamess_simulation','test_incorporate_result') + from ..developer import NexusError, obj sim = get_gamess_sim('rhf') @@ -177,19 +170,18 @@ def test_incorporate_result(): #end def test_incorporate_result - -def test_check_sim_status(): - import os - from ..developer import NexusError, obj +@isolate_nexus_core +def test_check_sim_status(tmp_path): from ..nexus_base import nexus_core - tpath = testing.setup_unit_test_output_directory('gamess_simulation','test_check_sim_status',divert=True) - + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] nexus_core.runs = '' sim = get_gamess_sim('rhf') - assert(sim.locdir.rstrip('/')==os.path.join(tpath,'rhf').rstrip('/')) + assert(Path(sim.locdir).resolve()==tmp_path / 'rhf') assert(not sim.finished) assert(not sim.failed) @@ -204,12 +196,10 @@ def test_check_sim_status(): #end try sim.create_directories() - outfile = os.path.join(sim.locdir,sim.outfile) + outfile = Path(sim.locdir).resolve() / sim.outfile outfile_text = 'EXECUTION OF GAMESS TERMINATED NORMALLY' - out = open(outfile,'w') - out.write(outfile_text) - out.close() - assert(outfile_text in open(outfile,'r').read()) + outfile.write_text(outfile_text) + assert(outfile_text in outfile.read_text()) sim.check_sim_status() @@ -217,5 +207,4 @@ def test_check_sim_status(): assert(not sim.failed) clear_all_sims() - restore_nexus() #end def test_check_sim_status diff --git a/nexus/nexus/tests/test_generic.py b/nexus/nexus/tests/test_generic.py index fc0353a109..4fdaf2805c 100644 --- a/nexus/nexus/tests/test_generic.py +++ b/nexus/nexus/tests/test_generic.py @@ -1,17 +1,27 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.GENERIC_OPERATION) -from .. import testing +from ..generic import generic_settings +generic_settings.raise_error = True + +from pathlib import Path +from . import isolate_nexus_core, FakeLog from ..testing import failed,FailedTest -from ..testing import divert_nexus_log,restore_nexus_log,FakeLog -from ..testing import value_eq,object_eq,object_neq +from ..testing import object_eq,object_neq +TEST_FILES = { + "old_nxs_pwscf_input.p": Path(__file__+"/../test_generic_files/old_nxs_pwscf_input.p").resolve(), + "old_nxs_sim.p": Path(__file__+"/../test_generic_files/old_nxs_sim.p").resolve(), + "old_nxs_pwscf_input_numpy_1.p": Path(__file__+"/../test_generic_files/old_nxs_pwscf_input_numpy_1.p").resolve(), + "old_nxs_sim_numpy_1.p": Path(__file__+"/../test_generic_files/old_nxs_sim_numpy_1.p").resolve(), + } +@isolate_nexus_core def test_logging(): - from ..generic import log,message,warn,error + from ..generic import log,warn,error from ..generic import generic_settings,NexusError - # send messages to object rather than stdout - divert_nexus_log() - logfile = generic_settings.devlog # test log @@ -105,22 +115,17 @@ def test_logging(): except Exception as e: failed(str(e)) #end try - - restore_nexus_log() - #end def test_logging - -def test_intrinsics(): +@isolate_nexus_core +def test_intrinsics(tmp_path): # test object_interface functions import os from ..generic import obj,object_interface from ..generic import generic_settings,NexusError from numpy import array,bool_ - tpath = testing.setup_unit_test_output_directory('generic','test_intrinsics') - # test object set/get # make a simple object o = obj() @@ -283,7 +288,7 @@ def test_intrinsics(): assert('a' not in o2) # test save/load - save_file = os.path.join(tpath,'o.p') + save_file = tmp_path / "o.p" o.save(save_file) o2 = obj() o2.load(save_file) @@ -354,8 +359,7 @@ class objint(object_interface): os.remove('log.out') assert(so==s) - # send messages to object rather than stdout - divert_nexus_log() + logfile = object_interface._logfile # simple message @@ -460,9 +464,6 @@ class DerivedObj(obj): failed(str(e)) #end try - # restore logging function - restore_nexus_log() - #end def test_intrinsics @@ -1125,3 +1126,130 @@ class DerivedObj(obj): #end def test_extensions +def test_old_nexus_unpickle(): + import numpy as np + from ..generic import obj + + sim_obj = obj() + if np.lib.NumpyVersion(np.__version__) >= '2.0.0b1': + sim_obj.load(TEST_FILES["old_nxs_sim.p"]) + else: + sim_obj.load(TEST_FILES["old_nxs_sim_numpy_1.p"]) + + assert(sim_obj.analyzed is True) + assert(sim_obj.analyzer_image == "analyzer.p") + assert(sim_obj.app_name == "pw.x") + assert(set(sim_obj.app_props) == set(["serial", "mpi"])) + assert(sim_obj.block is False) + assert(sim_obj.block_subcascade is False) + assert(sim_obj.errfile == "relax.err") + assert(sim_obj.failed is False) + assert(sim_obj.files == {"Ge.pbe-kjpaw.UPF", "relax.in"}) + assert(sim_obj.finished is True) + assert(sim_obj.got_output is True) + assert(sim_obj.identifier == "relax") + assert(sim_obj.image_dir == "sim_relax") + assert(sim_obj.imlocdir == "./runs/relax/kgrid_111/sim_relax") + assert(sim_obj.imremdir == "./runs/relax/kgrid_111/sim_relax") + assert(sim_obj.imresdir == "./runs/relax/kgrid_111/sim_relax") + assert(sim_obj.infile == "relax.in") + assert(sim_obj.input_image == "input.p") + assert(sim_obj.locdir == "./runs/relax/kgrid_111") + assert(sim_obj.outfile == "relax.out") + assert(sim_obj.outputs is None) + assert(sim_obj.path == "relax/kgrid_111") + assert(sim_obj.process_id == 1) + assert(sim_obj.remdir == "./runs/relax/kgrid_111") + assert(sim_obj.resdir == "./runs/relax/kgrid_111") + assert(sim_obj.sent_files is True) + assert(sim_obj.setup is True) + assert(sim_obj.sim_image == "sim.p") + assert(sim_obj.subcascade_finished is False) + assert(sim_obj.submitted is True) + + + ref_atomic_positions_atoms = [ + "Ge", "Ge", "Ge", "Ge", "Ge", "Ge", "Ge", "Ge", "Ge", + "Ge", "Ge", "Ge", "Ge", "Ge", "Ge", "Ge", "Ge", + ] + + ref_atomic_positions_positions = np.array([ + [ 5.34792496, 5.34792496, 5.34792496], + [ 0. , 0. , 0. ], + [ 2.67396248, 2.67396248, 2.67396248], + [ 5.34792496, 5.34792496, 0. ], + [ 8.02188743, 8.02188743, 2.67396248], + [ 0. , 5.34792496, 5.34792496], + [ 2.67396248, 8.02188743, 8.02188743], + [ 5.34792496, 10.69584991, 5.34792496], + [ 8.02188743, 13.36981239, 8.02188743], + [ 5.34792496, 0. , 5.34792496], + [ 8.02188743, 2.67396248, 8.02188743], + [10.69584991, 5.34792496, 5.34792496], + [13.36981239, 8.02188743, 8.02188743], + [ 5.34792496, 5.34792496, 10.69584991], + [ 8.02188743, 8.02188743, 13.36981239], + [10.69584991, 10.69584991, 10.69584991], + [13.36981239, 13.36981239, 13.36981239], + ], dtype=np.float64) + + ref_cell_parameters_vectors = np.array([ + [10.69584991, 10.69584991, 0. ], + [ 0. , 10.69584991, 10.69584991], + [10.69584991, 0. , 10.69584991], + ], dtype=np.float64) + + inp_obj = obj() + if np.lib.NumpyVersion(np.__version__) >= '2.0.0b1': + inp_obj.load(TEST_FILES["old_nxs_pwscf_input.p"]) + else: + inp_obj.load(TEST_FILES["old_nxs_pwscf_input_numpy_1.p"]) + + assert(inp_obj.atomic_positions.atoms == ref_atomic_positions_atoms) + np.testing.assert_allclose(inp_obj.atomic_positions.positions, ref_atomic_positions_positions, rtol=1e-7) + assert(inp_obj.atomic_positions.specifier == "bohr") + + assert(inp_obj.atomic_species.atoms == ["Ge"]) + assert(inp_obj.atomic_species.specifier == "") + np.testing.assert_allclose(inp_obj.atomic_species.masses.Ge, 72.61, rtol=1e-7) + assert(inp_obj.atomic_species.pseudopotentials.Ge == "Ge.pbe-kjpaw.UPF") + + assert(inp_obj.cell_parameters.specifier == "bohr") + np.testing.assert_allclose(inp_obj.cell_parameters.vectors, ref_cell_parameters_vectors, rtol=1e-7) + + assert(inp_obj.control.calculation == "relax") + assert(inp_obj.control.disk_io == "low") + assert(inp_obj.control.outdir == "pwscf_output") + assert(inp_obj.control.prefix == "pwscf") + assert(inp_obj.control.pseudo_dir == "./") + assert(inp_obj.control.restart_mode == "from_scratch") + assert(inp_obj.control.verbosity == "high") + assert(inp_obj.control.wf_collect == False) + + np.testing.assert_allclose(inp_obj.electrons.conv_thr, 1e-06, rtol=1e-7) + assert(inp_obj.electrons.diagonalization == "david") + assert(inp_obj.electrons.electron_maxstep == 1000) + np.testing.assert_allclose(inp_obj.electrons.mixing_beta, 0.7, rtol=1e-7) + assert(inp_obj.electrons.mixing_mode == "plain") + + assert(inp_obj.ions.ion_dynamics == "bfgs") + assert(inp_obj.ions.pot_extrapolation == "second_order") + assert(inp_obj.ions.upscale == 100) + assert(inp_obj.ions.wfc_extrapolation == "second_order") + + assert(inp_obj.k_points.grid == (1, 1, 1)) + assert(inp_obj.k_points.shift == (1, 1, 1)) + assert(inp_obj.k_points.specifier == "automatic") + + np.testing.assert_allclose(inp_obj.system.degauss, 0.0001, rtol=1e-7) + assert(inp_obj.system.ecutrho == 200) + assert(inp_obj.system.ecutwfc == 50) + assert(inp_obj.system.ibrav == 0) + assert(inp_obj.system.input_dft == "pbe") + assert(inp_obj.system.nat == 17) + assert(inp_obj.system.nosym == True) + assert(inp_obj.system.ntyp == 1) + assert(inp_obj.system.occupations == "smearing") + assert(inp_obj.system.smearing == "fermi-dirac") + assert(inp_obj.system.tot_charge == 0) +#end def test_old_nexus_unpickle \ No newline at end of file diff --git a/nexus/nexus/tests/test_generic_files/old_nxs_pwscf_input.p b/nexus/nexus/tests/test_generic_files/old_nxs_pwscf_input.p new file mode 100644 index 0000000000000000000000000000000000000000..31f7483fc2e92f35f340e238da1e9d45d1e860a9 GIT binary patch literal 1698 zcmb_cL5mzk6rRa!@9gZX?hcZRco0!sm7Rc!c+j{Q*)eIdgat)}&{S7fPgS;U4?d$u!9O5^-n@!GK=kfG1o7-qUw2QjG>vaMB6Br3BzToWgZ!-iKQI#Q-+m^j1qzI&y6pj16kU7 zwbK*=mvtrji7=;;kl=cmoP!(8n2x0pc7f?~F|C}<(}>C}W7NWZ#Jy=2# 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numpy - from .. import testing - from .. import grid_functions -#end def test_imports +from ..generic import generic_settings +generic_settings.raise_error = True def test_coord_conversion(): @@ -492,7 +491,7 @@ def get_props(): def test_grid_initialization(): import numpy as np - from ..testing import object_eq,value_eq + from ..testing import value_eq from ..grid_functions import Grid,StructuredGrid,StructuredGridWithAxes from ..grid_functions import ParallelotopeGrid from ..grid_functions import SpheroidGrid @@ -654,7 +653,6 @@ def test_grid_reset(): def test_grid_set_operations(): import numpy as np - from ..developer import obj from ..testing import value_eq from .. import numpy_extensions as npe @@ -1022,7 +1020,7 @@ def shift_and_test_inside(g,p,upoints,d,sign): def test_grid_project(): import numpy as np - from ..testing import value_eq,object_eq + from ..testing import object_eq from .. import numpy_extensions as npe def make_1d(x): @@ -1306,9 +1304,6 @@ def test_grid_function_initialization(): import numpy as np from ..testing import object_eq from ..grid_functions import unit_grid_points - from ..grid_functions import ParallelotopeGrid - from ..grid_functions import SpheroidGrid - from ..grid_functions import SpheroidSurfaceGrid from ..grid_functions import GridFunction from ..grid_functions import StructuredGridFunction from ..grid_functions import StructuredGridFunctionWithAxes diff --git a/nexus/nexus/tests/test_hdfreader.py b/nexus/nexus/tests/test_hdfreader.py index 3b61bfdb6d..a0984ad5ad 100644 --- a/nexus/nexus/tests/test_hdfreader.py +++ b/nexus/nexus/tests/test_hdfreader.py @@ -1,81 +1,75 @@ - -from nexus.versions import h5py_available -from .. import testing -from ..testing import value_eq,object_eq - - -def test_import(): - from .. import hdfreader - from ..hdfreader import HDFreader,read_hdf -#end def test_import - - -if h5py_available: - def test_read(): - import os - import numpy as np - import h5py - from ..hdfreader import read_hdf - - ds = 'string value' - di = 100 - df = np.pi - das = np.array(tuple('abcdefghijklmnopqrstuvwxyz'),dtype=bytes) - dai = np.arange(20,dtype=np.int64) - daf = 0.1*np.arange(20,dtype=np.float64) - - path = testing.setup_unit_test_output_directory('hdfreader','test_read') - - def add_datasets(g): - g.create_dataset('sdata',data=das) - g.create_dataset('idata',data=dai) - g.create_dataset('fdata',data=daf) - #end def add_datasets - - def add_attrs(g): - g.attrs['sval'] = ds - g.attrs['ival'] = di - g.attrs['fval'] = df - #end def add_attrs - - def add_group(g,label=''): - g = g.create_group('group'+str(label)) - add_attrs(g) - add_datasets(g) - return g - #end def add_group - - testfile = os.path.join(path,'test.h5') - f = h5py.File(testfile,'w') - - add_datasets(f) - g1 = add_group(f,1) - g2 = add_group(f,2) - g11 = add_group(g1,1) - g12 = add_group(g1,2) - g21 = add_group(g2,1) - g22 = add_group(g2,2) - - f.close() - - def check_datasets(g): - assert(value_eq(g.sdata,das)) - assert(value_eq(g.idata,dai)) - assert(value_eq(g.fdata,daf)) - #end def check_datasets - - def check_groups(g): - assert('group1' in g) - assert('group2' in g) - check_datasets(g.group1) - check_datasets(g.group2) - #end def check_groups - - h = read_hdf(testfile) - - check_datasets(h) - check_groups(h) - check_groups(h.group1) - check_groups(h.group2) - #end def test_read -#end if +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.HDFREADER) + +from ..generic import generic_settings +generic_settings.raise_error = True + +from ..testing import value_eq + + +def test_read(tmp_path): + h5py = pytest.importorskip("h5py") + import os + import numpy as np + from ..hdfreader import read_hdf + + ds = 'string value' + di = 100 + df = np.pi + das = np.array(tuple('abcdefghijklmnopqrstuvwxyz'),dtype=bytes) + dai = np.arange(20,dtype=np.int64) + daf = 0.1*np.arange(20,dtype=np.float64) + + def add_datasets(g): + g.create_dataset('sdata',data=das) + g.create_dataset('idata',data=dai) + g.create_dataset('fdata',data=daf) + #end def add_datasets + + def add_attrs(g): + g.attrs['sval'] = ds + g.attrs['ival'] = di + g.attrs['fval'] = df + #end def add_attrs + + def add_group(g,label=''): + g = g.create_group('group'+str(label)) + add_attrs(g) + add_datasets(g) + return g + #end def add_group + + testfile = tmp_path / "test.h5" + f = h5py.File(testfile,'w') + + add_datasets(f) + g1 = add_group(f,1) + g2 = add_group(f,2) + g11 = add_group(g1,1) + g12 = add_group(g1,2) + g21 = add_group(g2,1) + g22 = add_group(g2,2) + + f.close() + + def check_datasets(g): + assert(value_eq(g.sdata,das)) + assert(value_eq(g.idata,dai)) + assert(value_eq(g.fdata,daf)) + #end def check_datasets + + def check_groups(g): + assert('group1' in g) + assert('group2' in g) + check_datasets(g.group1) + check_datasets(g.group2) + #end def check_groups + + h = read_hdf(testfile) + + check_datasets(h) + check_groups(h) + check_groups(h.group1) + check_groups(h.group2) +#end def test_read diff --git a/nexus/nexus/tests/test_machines.py b/nexus/nexus/tests/test_machines.py index 89929dc63a..c319620b47 100644 --- a/nexus/nexus/tests/test_machines.py +++ b/nexus/nexus/tests/test_machines.py @@ -1,8 +1,14 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.MACHINES) -from .. import testing -from ..testing import value_eq,object_eq,failed,FailedTest -from ..testing import divert_nexus_log,restore_nexus_log +from ..generic import generic_settings +generic_settings.raise_error = True +from . import isolate_nexus_core +from .. import testing +from ..testing import object_eq,object_diff,failed,FailedTest +from ..utilities import path_string all_machines = [] machines_data = dict() @@ -50,15 +56,6 @@ def get_supercomputers(): - -def test_import(): - from ..machines import Machine,Workstation,InteractiveCluster,Supercomputer - from ..machines import Job,job - from ..machines import get_machine,get_machine_name -#end def test_import - - - def test_cpu_count(): from ..machines import cpu_count assert(isinstance(cpu_count(),int)) @@ -490,7 +487,7 @@ def init_job(j, ): import os identifier = id - directory = dir + directory = path_string(dir) j.set_id() j.identifier = identifier j.directory = directory @@ -506,18 +503,15 @@ def init_job(j, #end def init_job - -def test_workstation_scheduling(): +@isolate_nexus_core +def test_workstation_scheduling(tmp_path): import time from ..machines import Workstation from ..machines import job,Job - tpath = testing.setup_unit_test_output_directory('machines','test_workstation_scheduling') - # create workstation for testing ws = Workstation('wss',16,'mpirun') - # test process_job(), process_job_options(), write_job() j = job(machine=ws.name,cores=4,threads=2,local=True) assert(j.machine==ws.name) @@ -527,7 +521,7 @@ def test_workstation_scheduling(): assert(j.processes==2) assert(j.run_options.np=='-np 2') assert(j.batch_mode==False) - init_job(j,dir=tpath) # imitate interaction w/ simulation object + init_job(j,dir=tmp_path) # imitate interaction w/ simulation object assert(ws.write_job(j)=='export OMP_NUM_THREADS=2\nmpirun -np 2 echo run') j = job(machine=ws.name,serial=True) @@ -538,7 +532,7 @@ def test_workstation_scheduling(): assert(j.processes==1) assert(j.run_options.np=='-np 1') assert(j.batch_mode==False) - init_job(j,dir=tpath) # imitate interaction w/ simulation object + init_job(j,dir=tmp_path) # imitate interaction w/ simulation object assert(ws.write_job(j)=='export OMP_NUM_THREADS=1\necho run') @@ -557,7 +551,6 @@ def test_workstation_scheduling(): # test submit_jobs() and submit_job() - divert_nexus_log() assert(j.system_id is None) assert(len(ws.running)==0) assert(len(ws.processes)==0) @@ -573,7 +566,6 @@ def test_workstation_scheduling(): assert(p.popen.pid==j.system_id) assert(id(p.job)==id(j)) assert(set(ws.jobs.keys())==set([j.internal_id])) - restore_nexus_log() # allow a moment for all system calls to resolve time.sleep(0.1) @@ -637,16 +629,14 @@ class ThetaInit(Theta): #end def test_supercomputer_init - -def test_supercomputer_scheduling(): +@isolate_nexus_core +def test_supercomputer_scheduling(tmp_path): import os import time from ..developer import obj from ..machines import Theta from ..machines import job,Job - tpath = testing.setup_unit_test_output_directory('machines','test_supercomputer_scheduling') - # create supercomputer for testing class ThetaSched(Theta): name = 'theta_sched' @@ -679,7 +669,7 @@ class ThetaSched(Theta): # test write_job() - init_job(j,id='123',dir=tpath) # imitate interaction w/ simulation object + init_job(j,id='123',dir=tmp_path) # imitate interaction w/ simulation object ref_wj = '''#!/bin/bash #COBALT -q default #COBALT -A ABC123 @@ -719,7 +709,7 @@ def scomp(s): # test write_job() to file sc.write_job(j,file=True) - subfile_path = os.path.join(tpath,j.subfile) + subfile_path = os.path.join(tmp_path,j.subfile) assert(os.path.exists(subfile_path)) wj = open(subfile_path,'r').read().strip() assert('aprun ' in wj) @@ -735,7 +725,6 @@ def scomp(s): # test submit_jobs() and submit_job() - divert_nexus_log() assert(j.system_id is None) sc.submit_jobs() # will call system echo @@ -746,7 +735,6 @@ def scomp(s): assert(sc.running==set([j.internal_id])) assert(set(sc.processes.keys())==set([123])) assert(set(sc.jobs.keys())==set([j.internal_id])) - restore_nexus_log() # allow a moment for all system calls to resolve diff --git a/nexus/nexus/tests/test_memory.py b/nexus/nexus/tests/test_memory.py index e88bd042b7..d2afb52d3a 100644 --- a/nexus/nexus/tests/test_memory.py +++ b/nexus/nexus/tests/test_memory.py @@ -1,9 +1,9 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.MEMORY) - -def test_import(): - from ..memory import memory,resident,stacksize -#end def test_import - +from ..generic import generic_settings +generic_settings.raise_error = True def test_memory(): diff --git a/nexus/nexus/tests/test_nexus_base.py b/nexus/nexus/tests/test_nexus_base.py index 73df40238b..b719eb1457 100644 --- a/nexus/nexus/tests/test_nexus_base.py +++ b/nexus/nexus/tests/test_nexus_base.py @@ -1,14 +1,12 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.NEXUS_BASE) -from .. import testing -from ..testing import value_eq,object_eq -from ..testing import divert_nexus_log,restore_nexus_log +from ..generic import generic_settings +generic_settings.raise_error = True - -def test_import(): - from .. import nexus_base - from ..nexus_base import nexus_core,nexus_noncore,nexus_core_noncore - from ..nexus_base import NexusCore -#end def test_import +from . import isolate_nexus_core +from ..testing import object_eq @@ -34,41 +32,36 @@ def test_empty_init(): #end def test_empty_init - +@isolate_nexus_core def test_write_splash(): from ..nexus_base import NexusCore - log = divert_nexus_log() + + log = generic_settings.devlog nc = NexusCore() assert(not nc.wrote_splash) nc.write_splash() assert('Nexus' in log.contents()) assert('Please cite:' in log.contents()) assert(nc.wrote_splash) - restore_nexus_log() #end def test_write_splash - -def test_enter_leave(): +@isolate_nexus_core +def test_enter_leave(tmp_path): import os from ..nexus_base import NexusCore - - tpath = testing.setup_unit_test_output_directory('nexus_base','test_enter_leave') - cwd = os.getcwd() - log = divert_nexus_log() + log = generic_settings.devlog nc = NexusCore() - nc.enter(tpath) + nc.enter(tmp_path) tcwd = os.getcwd() - assert(tcwd==tpath) + assert(tcwd==str(tmp_path)) assert('Entering' in log.contents()) - assert(tpath in log.contents()) + assert(str(tmp_path) in log.contents()) nc.leave() assert(os.getcwd()==cwd) - - restore_nexus_log() #end def test_enter_leave diff --git a/nexus/nexus/tests/test_nexus_imports.py b/nexus/nexus/tests/test_nexus_imports.py deleted file mode 100644 index 0a5a36e1b9..0000000000 --- a/nexus/nexus/tests/test_nexus_imports.py +++ /dev/null @@ -1,88 +0,0 @@ - - -def test_imports(): - import nexus - from nexus import settings,job,run_project - from nexus import ppset - from nexus import read_structure,read_input - from nexus import generate_structure - from nexus import generate_physical_system - from nexus import generate_qmcpack,generate_convert4qmc - from nexus import generate_pwscf,generate_pw2qmcpack - from nexus import generate_gamess - from nexus import generate_pyscf - from nexus import generate_quantum_package - from nexus import generate_vasp - from nexus import ci,error - - import nexus.versions - import nexus.nexus_base - import nexus.testing - import nexus.execute - import nexus.memory - import nexus.generic - import nexus.developer - import nexus.unit_converter - import nexus.periodic_table - import nexus.numerics - import nexus.grid_functions - import nexus.fileio - import nexus.hdfreader - import nexus.structure - import nexus.physical_system - import nexus.basisset - import nexus.pseudopotential - import nexus.machines - import nexus.simulation - import nexus.bundle - import nexus.project_manager - import nexus.vasp_input - import nexus.pwscf_input - import nexus.pwscf_postprocessors - import nexus.gamess_input - import nexus.pyscf_input - import nexus.quantum_package_input - import nexus.rmg_input - import nexus.qmcpack_converters - import nexus.qmcpack_input - import nexus.vasp_analyzer - import nexus.pwscf_analyzer - import nexus.pwscf_postprocessors - import nexus.gamess_analyzer - import nexus.pyscf_analyzer - import nexus.quantum_package_analyzer - import nexus.rmg_analyzer - import nexus.qmcpack_converters - import nexus.qmcpack_analyzer - import nexus.vasp - import nexus.pwscf - import nexus.gamess - import nexus.pyscf_sim - import nexus.quantum_package - import nexus.rmg - import nexus.pwscf_postprocessors - import nexus.qmcpack_converters - import nexus.qmcpack - import nexus.observables - - - from nexus import settings - from nexus.machines import job - from nexus import run_project - from nexus.pseudopotential import ppset - from nexus.structure import read_structure - from nexus import read_input - from nexus.structure import generate_structure - from nexus.physical_system import generate_physical_system - from nexus.qmcpack import generate_qmcpack - from nexus.qmcpack_converters import generate_convert4qmc - from nexus.qmcpack_converters import generate_pw2qmcpack - from nexus.pwscf import generate_pwscf - from nexus.gamess import generate_gamess - from nexus.pyscf_sim import generate_pyscf - from nexus.quantum_package import generate_quantum_package - from nexus.vasp import generate_vasp - from nexus.developer import ci,error - from nexus import read_structure - -#end def test_imports diff --git a/nexus/nexus/tests/test_numerics.py b/nexus/nexus/tests/test_numerics.py index 9ff398dc87..6a544b55f5 100644 --- a/nexus/nexus/tests/test_numerics.py +++ b/nexus/nexus/tests/test_numerics.py @@ -1,30 +1,11 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.NUMERICS) -from nexus.versions import scipy_available - - -def test_import(): - from .. import numerics - from ..numerics import curve_fit - from ..numerics import morse,morse_re,morse_a,morse_De,morse_Einf,morse_width - from ..numerics import morse_depth,morse_Ee,morse_k,morse_params - from ..numerics import morse_reduced_mass,morse_freq,morse_w,morse_wX - from ..numerics import morse_En,morse_zero_point,morse_harmfreq - from ..numerics import morse_harmonic_potential,morse_spect_fit - from ..numerics import morse_rDw_fit,morse_fit,morse_fit_fine - from ..numerics import murnaghan,birch,vinet - from ..numerics import murnaghan_pressure,birch_pressure,vinet_pressure - from ..numerics import eos_param,eos_eval,eos_fit,eos_Einf,eos_V,eos_B,eos_Bp - from ..numerics import jackknife,jackknife_aux,check_jackknife_inputs - from ..numerics import ndgrid - from ..numerics import simstats,simplestats,equilibration_length,ttest - from ..numerics import surface_normals,simple_surface - from ..numerics import func_fit - from ..numerics import distance_table,nearest_neighbors,voronoi_neighbors - from ..numerics import convex_hull - -#end def test_import - +from ..generic import generic_settings +generic_settings.raise_error = True +from importlib.util import find_spec def test_ndgrid(): import numpy as np @@ -189,7 +170,7 @@ def check_nn(nn): check_nn(nn) assert(value_eq(dist,dist_ref)) - if scipy_available: + if find_spec("scipy") is not None: nn = nearest_neighbors(3,plow,phigh) check_nn(nn) @@ -202,101 +183,100 @@ def check_nn(nn): -if scipy_available: - def test_voronoi_neighbors(): - import numpy as np - from ..testing import value_eq - from ..numerics import voronoi_neighbors - - points = [ - [0,0,0], - [1,0,0], - [0,1,0], - [1,1,0], - [0,0,1], - [1,0,1], - [0,1,1], - [1,1,1], - ] - points = np.array(points,dtype=float) - - joggle = np.array( - [[0.60801892, 0.68024807, 0.09037058], - [0.95800898, 0.43112463, 0.52981569], - [0.08862067, 0.69084511, 0.35177345], - [0.37363091, 0.57409599, 0.95654043], - [0.8310818 , 0.17146777, 0.90490215], - [0.17600223, 0.89772462, 0.75582196], - [0.7408217 , 0.22768522, 0.64564984], - [0.71678216, 0.6409734 , 0.53354209]]) - joggle *= 1e-8 - - points += joggle - - nn_pairs_ref = [[0,1], - [0,2], - [0,4], - [0,3], - [0,6], - [0,5], - [7,3], - [7,5], - [7,6], - [3,1], - [3,2], - [3,6], - [3,5], - [1,5], - [5,4], - [5,6], - [6,4], - [6,2]] - nn_pairs_ref = np.array(nn_pairs_ref,dtype=int) - - d1 = 1.0 - d2 = float(np.sqrt(2.)) - - nn_pairs = voronoi_neighbors(points) - - dist_ref = 3*[d1]+3*[d2]+5*[d1]+2*[d2]+2*[d1]+[d2]+2*[d1] - - assert(isinstance(nn_pairs,np.ndarray)) - nn_pairs = np.array(nn_pairs,dtype=int) - assert(value_eq(nn_pairs,nn_pairs_ref)) - - for n,(i,j) in enumerate(nn_pairs): - d = np.linalg.norm(points[i]-points[j]) - assert(value_eq(float(d),dist_ref[n])) - #end for +def test_voronoi_neighbors(): + _ = pytest.importorskip("scipy") + import numpy as np + from ..testing import value_eq + from ..numerics import voronoi_neighbors - #end def test_voronoi_neighbors + points = [ + [0,0,0], + [1,0,0], + [0,1,0], + [1,1,0], + [0,0,1], + [1,0,1], + [0,1,1], + [1,1,1], + ] + points = np.array(points,dtype=float) + + joggle = np.array( + [[0.60801892, 0.68024807, 0.09037058], + [0.95800898, 0.43112463, 0.52981569], + [0.08862067, 0.69084511, 0.35177345], + [0.37363091, 0.57409599, 0.95654043], + [0.8310818 , 0.17146777, 0.90490215], + [0.17600223, 0.89772462, 0.75582196], + [0.7408217 , 0.22768522, 0.64564984], + [0.71678216, 0.6409734 , 0.53354209]]) + joggle *= 1e-8 + + points += joggle + + nn_pairs_ref = [[0,1], + [0,2], + [0,4], + [0,3], + [0,6], + [0,5], + [7,3], + [7,5], + [7,6], + [3,1], + [3,2], + [3,6], + [3,5], + [1,5], + [5,4], + [5,6], + [6,4], + [6,2]] + nn_pairs_ref = np.array(nn_pairs_ref,dtype=int) + + d1 = 1.0 + d2 = float(np.sqrt(2.)) + + nn_pairs = voronoi_neighbors(points) + + dist_ref = 3*[d1]+3*[d2]+5*[d1]+2*[d2]+2*[d1]+[d2]+2*[d1] + + assert(isinstance(nn_pairs,np.ndarray)) + nn_pairs = np.array(nn_pairs,dtype=int) + assert(value_eq(nn_pairs,nn_pairs_ref)) + + for n,(i,j) in enumerate(nn_pairs): + d = np.linalg.norm(points[i]-points[j]) + assert(value_eq(float(d),dist_ref[n])) + #end for +#end def test_voronoi_neighbors - def test_convex_hull(): - import numpy as np - from ..testing import value_eq - from ..numerics import convex_hull - points = [ - [0,0,0], - [1,0,0], - [0,1,0], - [1,1,0], - [0,0,1], - [1,0,1], - [0,1,1], - [1,1,1], - ] - points = np.array(points,dtype=float)-0.5 - - points = np.append(2*points,points,axis=0) +def test_convex_hull(): + _ = pytest.importorskip("scipy") + import numpy as np + from ..numerics import convex_hull + + points = [ + [0,0,0], + [1,0,0], + [0,1,0], + [1,1,0], + [0,0,1], + [1,0,1], + [0,1,1], + [1,1,1], + ] + points = np.array(points,dtype=float)-0.5 + + points = np.append(2*points,points,axis=0) - hull = convex_hull(points) + hull = convex_hull(points) - assert(hull==list(range(8))) - #end def test_convex_hull -#end if + assert(hull==list(range(8))) +#end def test_convex_hull @@ -392,19 +372,17 @@ def test_equilibration_length(): -if scipy_available: - def test_ttest(): - import numpy as np - from ..testing import value_eq - from ..numerics import ttest +def test_ttest(): + _ = pytest.importorskip("scipy") + from ..testing import value_eq + from ..numerics import ttest - p = ttest(0.,1.,100,0.,1.,100) - assert(value_eq(float(p),1.0)) + p = ttest(0.,1.,100,0.,1.,100) + assert(value_eq(float(p),1.0)) - p = ttest(0.,1.,10000,1.,1.,10000) - assert(value_eq(float(p),0.479508361523)) - #end def test_ttest -#end if + p = ttest(0.,1.,10000,1.,1.,10000) + assert(value_eq(float(p),0.479508361523)) +#end def test_ttest @@ -432,13 +410,12 @@ def test_morse(): from ..unit_converter import convert from ..numerics import morse,morse_re,morse_a,morse_De,morse_Einf,morse_width from ..numerics import morse_depth,morse_Ee,morse_k,morse_params - from ..numerics import morse_reduced_mass,morse_freq,morse_w,morse_wX + from ..numerics import morse_reduced_mass,morse_freq,morse_w from ..numerics import morse_E0,morse_En,morse_zero_point,morse_harmfreq - from ..numerics import morse_harmonic_potential,morse_spect_fit - from ..numerics import morse_rDw_fit,morse_fit,morse_fit_fine + from ..numerics import morse_rDw_fit rm = morse_reduced_mass('Ti','O') - assert(value_eq(rm,21862.2266134)) + assert(value_eq(rm, 21858.453534035318)) r_ref,D_ref,w_ref = 1.620,6.87,1009.18 r_ref_A = r_ref @@ -456,7 +433,7 @@ def test_morse(): assert(value_eq(float(w),w_ref)) assert(value_eq(float(Einf),0.0)) - width_ref = 1.0451690611 + width_ref = 1.0452592627174173 width = morse_width(p) assert(value_eq(float(width),width_ref)) @@ -469,7 +446,7 @@ def test_morse(): Ee = morse_Ee(p) assert(value_eq(float(Ee),-D_ref)) - k_ref = 0.462235185922 + k_ref = 0.46215541133767707 k = morse_k(p) assert(value_eq(float(k),k_ref)) @@ -516,38 +493,36 @@ def test_morse(): -if scipy_available: - def test_morse_fit(): - import numpy as np - from ..testing import value_eq - from ..unit_converter import convert - from ..numerics import morse - from ..numerics import morse_rDw_fit,morse_fit,morse_fit_fine - - r_ref,D_ref,w_ref = 1.620,6.87,1009.18 - r_ref_A = r_ref - p = morse_rDw_fit(r_ref,D_ref,w_ref,'Ti','O',Dunit='eV') +def test_morse_fit(): + _ = pytest.importorskip("scipy") + import numpy as np + from ..testing import value_eq + from ..unit_converter import convert + from ..numerics import morse + from ..numerics import morse_rDw_fit,morse_fit,morse_fit_fine - r_ref = convert(r_ref,'A','B') + r_ref,D_ref,w_ref = 1.620,6.87,1009.18 + r_ref_A = r_ref + p = morse_rDw_fit(r_ref,D_ref,w_ref,'Ti','O',Dunit='eV') + r_ref = convert(r_ref,'A','B') - rfine = np.linspace(0.8*r_ref,1.2*r_ref,100) - Efine = morse(p,rfine) - pf = morse_fit(rfine,Efine,p) + rfine = np.linspace(0.8*r_ref,1.2*r_ref,100) + Efine = morse(p,rfine) - pref = tuple(np.array(p,dtype=float)) - pf = tuple(np.array(pf,dtype=float)) + pf = morse_fit(rfine,Efine,p) - assert(value_eq(pf,pref)) + pref = tuple(np.array(p,dtype=float)) + pf = tuple(np.array(pf,dtype=float)) - pf,Ef = morse_fit_fine(rfine,Efine,p,rfine,both=True) - pf = tuple(np.array(pf,dtype=float)) - assert(value_eq(pf,pref)) - assert(value_eq(Ef,Efine)) - #end def test_morse_fit -#end if + assert(value_eq(pf,pref)) + pf,Ef = morse_fit_fine(rfine,Efine,p,rfine,both=True) + pf = tuple(np.array(pf,dtype=float)) + assert(value_eq(pf,pref)) + assert(value_eq(Ef,Efine)) +#end def test_morse_fit @@ -555,7 +530,7 @@ def test_eos(): import numpy as np from ..testing import value_eq from ..unit_converter import convert - from ..numerics import eos_fit,eos_eval,eos_param + from ..numerics import eos_eval,eos_param data = np.array([ [0.875, -83.31851261], @@ -597,48 +572,47 @@ def test_eos(): -if scipy_available: - def test_eos_fit(): - import numpy as np - from ..testing import value_eq - from ..unit_converter import convert - from ..numerics import eos_fit,eos_eval,eos_param +def test_eos_fit(): + _ = pytest.importorskip("scipy") + import numpy as np + from ..testing import value_eq + from ..unit_converter import convert + from ..numerics import eos_fit,eos_eval - data = np.array([ - [0.875, -83.31851261], - [0.900, -83.38085214], - [0.925, -83.42172843], - [0.950, -83.44502216], - [0.975, -83.45476035], - [1.025, -83.44564229], - [1.050, -83.43127254], - [1.000, -83.45412846], - [1.100, -83.39070714], - [1.125, -83.36663810], - ]) + data = np.array([ + [0.875, -83.31851261], + [0.900, -83.38085214], + [0.925, -83.42172843], + [0.950, -83.44502216], + [0.975, -83.45476035], + [1.025, -83.44564229], + [1.050, -83.43127254], + [1.000, -83.45412846], + [1.100, -83.39070714], + [1.125, -83.36663810], + ]) - a = 5.539 # lattice constant + a = 5.539 # lattice constant - V = (a*data[:,0])**3 - E = convert(data[:,1],'Ry','eV') + V = (a*data[:,0])**3 + E = convert(data[:,1],'Ry','eV') - # done originally to get params below - #pf = eos_fit(V,E,'vinet') + # done originally to get params below + #pf = eos_fit(V,E,'vinet') - Einf = -1.13547294e+03 - V0 = 1.62708941e+02 - B0 = 1.34467867e-01 - Bp0 = 4.55846963e+00 + Einf = -1.13547294e+03 + V0 = 1.62708941e+02 + B0 = 1.34467867e-01 + Bp0 = 4.55846963e+00 - pf = Einf,V0,B0,Bp0 + pf = Einf,V0,B0,Bp0 - Ef = eos_eval(pf,V,'vinet') + Ef = eos_eval(pf,V,'vinet') - pf2 = eos_fit(V,Ef,'vinet') + pf2 = eos_fit(V,Ef,'vinet') - pf = np.array(pf,dtype=float) - pf2 = np.array(pf2,dtype=float) + pf = np.array(pf,dtype=float) + pf2 = np.array(pf2,dtype=float) - assert(value_eq(pf,pf2,atol=1e-3)) - #end def test_eos_fit -#end if + assert(value_eq(pf,pf2,atol=1e-3)) +#end def test_eos_fit diff --git a/nexus/nexus/tests/test_nxs_redo.py b/nexus/nexus/tests/test_nxs_redo.py index f5f0f8a038..1450156abd 100644 --- a/nexus/nexus/tests/test_nxs_redo.py +++ b/nexus/nexus/tests/test_nxs_redo.py @@ -1,20 +1,23 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.NXS_REDO) -from .. import testing -from ..testing import create_file,create_path,execute +from ..generic import generic_settings +generic_settings.raise_error = True +from . import TEST_DIR +from ..testing import execute -def test_redo(): - import os - tpath = testing.setup_unit_test_output_directory('nxs_redo','test_redo') - - exe = testing.executable_path('nxs-redo') +def test_redo(tmp_path): - command = '{} {}'.format(exe,tpath) + exe = TEST_DIR.parent / "bin/nxs-redo" + + command = '{} {}'.format(exe,tmp_path) # empty directory - assert(os.listdir(tpath)==[]) + assert(list(tmp_path.iterdir())==[]) out,err,rc = execute(command) @@ -22,32 +25,32 @@ def test_redo(): # directory w/ files, but not nexus simulation directory - create_file('qmc.in.xml',tpath) + (tmp_path / "qmc.in.xml").touch() out,err,rc = execute(command) assert('no simulation directories found' in out) - assert(set(os.listdir(tpath))==set(['qmc.in.xml'])) + assert(set(tmp_path.iterdir())==set([tmp_path / 'qmc.in.xml'])) # nexus simulation directory - create_path('sim_qmc',tpath) + (tmp_path / "sim_qmc").mkdir() - assert(set(os.listdir(tpath))==set(['qmc.in.xml','sim_qmc'])) + assert(set(tmp_path.iterdir())==set([tmp_path / 'qmc.in.xml', tmp_path / 'sim_qmc'])) out,err,rc = execute(command) - assert(set(os.listdir(tpath))==set(['attempt1'])) + assert(set(tmp_path.iterdir())==set([tmp_path / 'attempt1'])) # nexus simulation directory w/ prior attempt - create_file('qmc.in.xml',tpath) - create_path('sim_qmc',tpath) + (tmp_path / "qmc.in.xml").touch() + (tmp_path / "sim_qmc").mkdir() - assert(set(os.listdir(tpath))==set(['attempt1','qmc.in.xml','sim_qmc'])) + assert(set(tmp_path.iterdir())==set([tmp_path / 'attempt1',tmp_path / 'qmc.in.xml',tmp_path / 'sim_qmc'])) out,err,rc = execute(command) - assert(set(os.listdir(tpath))==set(['attempt1','attempt2'])) + assert(set(tmp_path.iterdir())==set([tmp_path / 'attempt1',tmp_path / 'attempt2'])) #end def test_redo diff --git a/nexus/nexus/tests/test_nxs_sim.py b/nexus/nexus/tests/test_nxs_sim.py index 46a56f72ce..cedd8ad0f9 100644 --- a/nexus/nexus/tests/test_nxs_sim.py +++ b/nexus/nexus/tests/test_nxs_sim.py @@ -1,22 +1,29 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.NXS_SIM) + +from ..generic import generic_settings +generic_settings.raise_error = True import sys -from .. import testing -from ..testing import divert_nexus,restore_nexus,clear_all_sims +from . import isolate_nexus_core, TEST_DIR +from ..testing import clear_all_sims from ..testing import execute,text_eq - -def test_sim(): - import os +@isolate_nexus_core +def test_sim(tmp_path): from ..nexus_base import nexus_core from .test_simulation_module import get_sim - tpath = testing.setup_unit_test_output_directory('nxs_sim','test_sim',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] nexus_core.runs = '' nexus_core.results = '' - exe = testing.executable_path('nxs-sim') + exe = TEST_DIR.parent / "bin/nxs-sim" sim = get_sim() @@ -24,8 +31,8 @@ def test_sim(): sim.save_image() - simp_path = os.path.join(tpath,sim.imlocdir,'sim.p') - assert(os.path.isfile(simp_path)) + simp_path = (tmp_path / sim.imlocdir / 'sim.p').resolve() + assert(simp_path.is_file()) # initial simulation state @@ -114,5 +121,4 @@ def test_sim(): assert(text_eq(out,out_ref)) clear_all_sims() - restore_nexus() #end def test_sim diff --git a/nexus/nexus/tests/test_observables.py b/nexus/nexus/tests/test_observables.py index 243f4ca65f..10c97b7c6e 100644 --- a/nexus/nexus/tests/test_observables.py +++ b/nexus/nexus/tests/test_observables.py @@ -1,15 +1,12 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.OBSERVABLES) -from .. import testing -from ..testing import value_eq,object_eq,text_eq,check_object_eq -from ..testing import FailedTest,failed - +from ..generic import generic_settings +generic_settings.raise_error = True -def test_import(): - from .. import observables - from ..observables import AttributeProperties,DefinedAttributeBase - from ..observables import Observable - from ..observables import MomentumDistribution -#end def test_import +from ..testing import check_object_eq +from ..testing import FailedTest,failed diff --git a/nexus/nexus/tests/test_optional_dependencies.py b/nexus/nexus/tests/test_optional_dependencies.py deleted file mode 100644 index 47b6d17fbf..0000000000 --- a/nexus/nexus/tests/test_optional_dependencies.py +++ /dev/null @@ -1,42 +0,0 @@ - - -def test_scipy_available(): - from .. import versions - assert(versions.scipy_available) -#end def test_scipy_available - - -def test_h5py_available(): - from .. import versions - assert(versions.h5py_available) -#end def test_h5py_available - - -def test_matplotlib_available(): - from .. import versions - assert(versions.matplotlib_available) -#end def test_matplotlib_available - - -def test_pydot_available(): - from .. import versions - assert(versions.pydot_available) -#end def test_pydot_available - - -def test_spglib_available(): - from .. import versions - assert(versions.spglib_available) -#end def test_spglib_available - - -def test_pycifrw_available(): - from .. import versions - assert(versions.pycifrw_available) -#end def test_pycifrw_available - - -def test_seekpath_available(): - from .. import versions - assert(versions.seekpath_available) -#end def test_seekpath_available diff --git a/nexus/nexus/tests/test_periodic_table.py b/nexus/nexus/tests/test_periodic_table.py index 5b2dca1b19..2b96300f29 100644 --- a/nexus/nexus/tests/test_periodic_table.py +++ b/nexus/nexus/tests/test_periodic_table.py @@ -1,134 +1,283 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PERIODIC_TABLE) +from ..generic import generic_settings +generic_settings.raise_error = True -def test_import(): - from .. import periodic_table - from ..periodic_table import pt,is_element -#end def test_import +def test_periodic_table(): + from ..periodic_table import Elements + ref_element_symbols = ( + "Xx", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", + "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", + "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", + "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", + "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", + "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", + "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", + "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", + "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", + "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", + "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", + "Ds", "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og", + ) -def test_periodic_table(): - from ..testing import value_eq - from ..periodic_table import pt - - elements = set(''' - H He - Li Be B C N O F Ne - Na Mg Al Si P S Cl Ar - K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr - Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe - Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn - Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr - '''.split()) - - atomic_numbers = set(range(1,len(elements)+1)) - - missing = elements - set(pt.keys()) - assert(len(missing)==0) + ref_atomic_numbers = tuple(range(0,len(ref_element_symbols))) + + element_symbols = [e.symbol for e in Elements] + atomic_numbers = [e.atomic_number for e in Elements] + + assert(len(element_symbols) == len(ref_element_symbols)) + assert(len(atomic_numbers) == len(ref_atomic_numbers)) + + for elem in element_symbols: + assert(elem in ref_element_symbols) + + for number in atomic_numbers: + assert(number in ref_atomic_numbers) - missing = elements - set(pt.elements.keys()) - assert(len(missing)==0) - - missing = atomic_numbers - set(pt.simple_elements.keys()) - assert(len(missing)==0) - - fields = ''' - atomic_weight - atomic_radius - nuclear_charge - electron_affinity - ionization_energy - ionic_radius - thermal_cond - melting_point - boiling_point - '''.split() - - for e in elements: - elem = pt.elements[e] - assert(id(elem)==id(pt[e])) - selem = pt.simple_elements[elem.atomic_number] - for f in fields: - assert(value_eq(selem[f],elem[f].orig)) - #end for - #end for + ref_carbon_name = "Carbon" + ref_carbon_symbol = "C" + ref_carbon_number = 6 + ref_carbon_weight = 12.011 + ref_carbon_group = 14 + ref_carbon_isotopes = {12:12.0000000, 13:13.00335483507, 14:14.0032419884} - C = pt.C - assert(C.atomic_number==6) - assert(C.symbol=='C') - assert(value_eq(C.atomic_radius.pm ,77.2)) - assert(value_eq(C.atomic_weight.amu ,12.011)) - assert(value_eq(C.boiling_point.degC ,4827.0)) - assert(value_eq(C.electron_affinity.kJ_mol,121.9)) - assert(value_eq(C.ionic_radius.pm,260.0)) - assert(value_eq(C.ionization_energy.eV,11.26)) - assert(value_eq(C.melting_point.degC,3550.0)) - assert(value_eq(C.nuclear_charge.e,3.25)) - assert(value_eq(C.thermal_cond.W_mK,1960.0)) + assert(Elements.Carbon.name == ref_carbon_name) + assert(Elements.Carbon.symbol == ref_carbon_symbol) + assert(str(Elements.Carbon) == ref_carbon_symbol) + assert(Elements.Carbon.atomic_number == ref_carbon_number) + assert(Elements.Carbon.atomic_weight == ref_carbon_weight) + assert(Elements.Carbon.group == ref_carbon_group) + assert(Elements.Carbon.isotopes == ref_carbon_isotopes) + assert(Elements.C.name == ref_carbon_name) + assert(Elements.C.symbol == ref_carbon_symbol) + assert(str(Elements.C) == ref_carbon_symbol) + assert(Elements.C.atomic_number == ref_carbon_number) + assert(Elements.C.atomic_weight == ref_carbon_weight) + assert(Elements.C.group == ref_carbon_group) + assert(Elements.C.isotopes == ref_carbon_isotopes) + + assert(Elements.Carbon is Elements.C) + + assert(Elements.num_elements() == 118) #end def test_periodic_table +def test_call_elements(): + from ..periodic_table import Elements + + # Good calls + assert(Elements("Hydrogen") is Elements.Hydrogen) + assert(Elements("H") is Elements.Hydrogen) + assert(Elements(1) is Elements.Hydrogen) + + # Calls that need to go through `_missing_` + # Improper case + assert(Elements("hydrogen") is Elements.Hydrogen) + assert(Elements("h") is Elements.Hydrogen) + # Trailing and leading whitespace + assert(Elements("Hydrogen ") is Elements.Hydrogen) + assert(Elements(" H") is Elements.Hydrogen) + # One step from good + assert(Elements("1") is Elements.Hydrogen) + assert(Elements(1.0) is Elements.Hydrogen) + + # Another spot check, same situations + assert(Elements("Ruthenium") is Elements.Ruthenium) + assert(Elements("Ru") is Elements.Ruthenium) + assert(Elements(44) is Elements.Ruthenium) + + assert(Elements("ruthenium") is Elements.Ruthenium) + assert(Elements("ru") is Elements.Ruthenium) + assert(Elements("Ruthenium ") is Elements.Ruthenium) + assert(Elements(" Ru") is Elements.Ruthenium) + assert(Elements("44") is Elements.Ruthenium) + assert(Elements(44.0) is Elements.Ruthenium) +#end def test_call_elements + def test_is_element(): - from ..periodic_table import is_element - - elements = ''' - H He - Li Be B C N O F Ne - Na Mg Al Si P S Cl Ar - K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr - Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe - Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn - Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr - '''.split() - - - for e in elements: - assert(is_element(e)) - is_elem,symbol = is_element(e,symbol=True) + from ..periodic_table import Elements + + ref_symbols = ( + "Xx", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", + "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", + "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", + "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", + "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", + "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", + "Nd", "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", + "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", + "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", + "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", + "Fm", "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", + "Ds", "Rg", "Cn", "Nh", "Fl", "Mc", "Lv", "Ts", "Og", + ) + + ref_elements = ( + Elements.Xx, + Elements.H, Elements.He, Elements.Li, Elements.Be, Elements.B, + Elements.C, Elements.N, Elements.O, Elements.F, Elements.Ne, + Elements.Na, Elements.Mg, Elements.Al, Elements.Si, Elements.P, + Elements.S, Elements.Cl, Elements.Ar, Elements.K, Elements.Ca, + Elements.Sc, Elements.Ti, Elements.V, Elements.Cr, Elements.Mn, + Elements.Fe, Elements.Co, Elements.Ni, Elements.Cu, Elements.Zn, + Elements.Ga, Elements.Ge, Elements.As, Elements.Se, Elements.Br, + Elements.Kr, Elements.Rb, Elements.Sr, Elements.Y, Elements.Zr, + Elements.Nb, Elements.Mo, Elements.Tc, Elements.Ru, Elements.Rh, + Elements.Pd, Elements.Ag, Elements.Cd, Elements.In, Elements.Sn, + Elements.Sb, Elements.Te, Elements.I, Elements.Xe, Elements.Cs, + Elements.Ba, Elements.La, Elements.Ce, Elements.Pr, Elements.Nd, + Elements.Pm, Elements.Sm, Elements.Eu, Elements.Gd, Elements.Tb, + Elements.Dy, Elements.Ho, Elements.Er, Elements.Tm, Elements.Yb, + Elements.Lu, Elements.Hf, Elements.Ta, Elements.W, Elements.Re, + Elements.Os, Elements.Ir, Elements.Pt, Elements.Au, Elements.Hg, + Elements.Tl, Elements.Pb, Elements.Bi, Elements.Po, Elements.At, + Elements.Rn, Elements.Fr, Elements.Ra, Elements.Ac, Elements.Th, + Elements.Pa, Elements.U, Elements.Np, Elements.Pu, Elements.Am, + Elements.Cm, Elements.Bk, Elements.Cf, Elements.Es, Elements.Fm, + Elements.Md, Elements.No, Elements.Lr, Elements.Rf, Elements.Db, + Elements.Sg, Elements.Bh, Elements.Hs, Elements.Mt, Elements.Ds, + Elements.Rg, Elements.Cn, Elements.Nh, Elements.Fl, Elements.Mc, + Elements.Lv, Elements.Ts, Elements.Og, + ) + + for symbol, element in zip(ref_symbols, ref_elements): + assert(Elements.is_element(symbol)) # True for symbols + assert(Elements.is_element(element)) # True for members + + is_elem, elem = Elements.is_element(element, return_element=True) + assert(is_elem) + assert(elem.symbol is symbol) + assert(elem is element) + is_elem, elem = Elements.is_element(symbol, return_element=True) assert(is_elem) - assert(symbol==e) + assert(elem.symbol is symbol) + assert(elem is element) #end for - valid = ''' - C - C1 - C2 - C12 - C123 - C_1 - C_2 - C_12 - C_123 - C_a - C_abc - '''.split() - for e in valid: - assert(is_element(e)) - is_elem,symbol = is_element(e,symbol=True) + carbon_strs = ( + "C", + "C1", + "C2", + "C12", + "C123", + "C_1", + "C_2", + "C_12", + "C_123", + "C_a", + "C_abc", + "C-1", + "C-2", + "C-12", + "C-123", + "C-a", + "C-abc", + "c", + "c1", + "c2", + "c12", + "c123", + "c_1", + "c_2", + "c_12", + "c_123", + "c_a", + "c_abc", + "c-1", + "c-2", + "c-12", + "c-123", + "c-a", + "c-abc", + ) + + for string in carbon_strs: + assert(Elements.is_element(string)) + + is_elem, elem = Elements.is_element(string, return_element=True) assert(is_elem) - assert(symbol=='C') + assert(elem is Elements.Carbon) + assert(elem.symbol == "C") + assert(elem.name == "Carbon") #end for - - valid = ''' - Co - Co1 - Co2 - Co12 - Co123 - Co_1 - Co_2 - Co_12 - Co_123 - Co_a - Co_abc - '''.split() - for e in valid: - assert(is_element(e)) - is_elem,symbol = is_element(e,symbol=True) + + cobalt_strs = [ + "Co", + "Co1", + "Co2", + "Co12", + "Co123", + "Co_1", + "Co_2", + "Co_12", + "Co_123", + "Co_a", + "Co_abc", + "Co-1", + "Co-2", + "Co-12", + "Co-123", + "Co-a", + "Co-abc", + "co", + "co1", + "co2", + "co12", + "co123", + "co_1", + "co_2", + "co_12", + "co_123", + "co_a", + "co_abc", + "co-1", + "co-2", + "co-12", + "co-123", + "co-a", + "co-abc", + ] + for string in cobalt_strs: + assert(Elements.is_element(string)) + + is_elem, element = Elements.is_element(string, return_element=True) assert(is_elem) - assert(symbol=='Co') + assert(element is Elements.Cobalt) + assert(element.symbol == "Co") + assert(element.name == "Cobalt") #end for - #end def test_is_element + + +def test_element_set(): + from ..periodic_table import Elements + ref_set = set([ + Elements.Xx, + Elements.H, + Elements.Dy, + Elements.U, + Elements.Nh, + ]) + + element_set = set([ + Elements.Xx, + Elements.H, Elements.H, Elements.H, + Elements.Dy, + Elements.U, Elements.U, Elements.U, Elements.U, Elements.U, + Elements.Nh, Elements.Nh, Elements.Nh, Elements.Nh, + ]) + + assert(ref_set == element_set) + + +def test_representation(): + from ..periodic_table import Elements + + ref_repr = "" + assert(repr(Elements.Carbon) == ref_repr) diff --git a/nexus/nexus/tests/test_physical_system.py b/nexus/nexus/tests/test_physical_system.py index ce91b9a2c7..fd438f1545 100644 --- a/nexus/nexus/tests/test_physical_system.py +++ b/nexus/nexus/tests/test_physical_system.py @@ -1,8 +1,13 @@ -#! /usr/bin/env python3 +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PHYSICAL_SYSTEM) + +from ..generic import generic_settings +generic_settings.raise_error = True import numpy as np from .. import testing -from ..testing import value_eq,object_eq,object_diff,print_diff +from ..testing import value_eq,object_eq from .test_structure import structure_same @@ -27,19 +32,8 @@ def system_same(s1,s2,pseudized=True,tiled=False): #end def system_same - -def test_import(): - from .. import physical_system - from ..physical_system import Matter,Particle,Ion,PseudoIon,Particles - from ..physical_system import PhysicalSystem,generate_physical_system -#end def test_import - - - def test_particle_initialization(): - from ..developer import obj from ..physical_system import Matter,Particle,Ion,PseudoIon,Particles - from ..physical_system import PhysicalSystem,generate_physical_system # empty initialization Matter() @@ -65,7 +59,7 @@ def check_none(v,vfields): # matter elements = Matter.elements - assert(len(elements)==103) + assert(len(elements)==119) assert('Si' in elements) pc = Matter.particle_collection @@ -89,7 +83,8 @@ def check_none(v,vfields): si = pc.Si assert(si.name=='Si') - assert(value_eq(si.mass,51197.6459833)) + print(si.mass) + assert(value_eq(si.mass,51195.82309476658)) assert(si.charge==14) assert(si.protons==14) assert(si.neutrons==14) @@ -104,27 +99,25 @@ def check_none(v,vfields): -def test_physical_system_initialization(): +def test_physical_system_initialization(tmp_path): import os from ..developer import obj from ..structure import generate_structure from ..physical_system import generate_physical_system from ..physical_system import PhysicalSystem - - tpath = testing.setup_unit_test_output_directory('physical_system','test_physical_system_initialization') d2 = generate_structure( structure = 'diamond', cell = 'prim', ) - d2_path = os.path.join(tpath,'diamond2.xsf') + d2_path = tmp_path / 'diamond2.xsf' d2.write(d2_path) d8 = generate_structure( structure = 'diamond', cell = 'conv', ) - d8_path = os.path.join(tpath,'diamond8.xsf') + d8_path = tmp_path / 'diamond8.xsf' d8.write(d8_path) @@ -372,7 +365,7 @@ def test_physical_system_initialization(): # test load for i,sys in enumerate(systems): - path = os.path.join(tpath,'system_{}'.format(i)) + path = tmp_path / 'system_{}'.format(i) sys.save(path) sys2 = PhysicalSystem() sys2.load(path) diff --git a/nexus/nexus/tests/test_project_manager.py b/nexus/nexus/tests/test_project_manager.py index b6bb9a9ab3..f90b085eea 100644 --- a/nexus/nexus/tests/test_project_manager.py +++ b/nexus/nexus/tests/test_project_manager.py @@ -1,15 +1,13 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PROJECT_MANAGER) -from .. import testing -from ..testing import value_eq,object_eq -from ..testing import failed,FailedTest -from ..testing import divert_nexus_log,restore_nexus_log -from ..testing import divert_nexus,restore_nexus - - -def test_import(): - from ..project_manager import ProjectManager -#end def test_import +from ..generic import generic_settings +generic_settings.raise_error = True +from . import isolate_nexus_core +from ..testing import value_eq +from ..testing import failed,FailedTest def test_init(): @@ -143,7 +141,7 @@ def test_screen_fake_sims(): #end def test_screen_fake_sims - +@isolate_nexus_core def test_resolve_file_collisions(): from ..developer import NexusError from ..simulation import Simulation @@ -151,8 +149,6 @@ def test_resolve_file_collisions(): from .test_simulation_module import get_test_workflow,n_test_workflows - divert_nexus_log() - sims = [] for n in range(n_test_workflows): sims.extend(get_test_workflow(n).list()) @@ -180,15 +176,12 @@ def test_resolve_file_collisions(): failed(str(e)) #end try - restore_nexus_log() - Simulation.clear_all_sims() #end def test_resolve_file_collisions def test_propagate_blockages(): - from ..developer import NexusError from ..simulation import Simulation from ..project_manager import ProjectManager @@ -268,8 +261,6 @@ def test_check_dependencies(): from .test_simulation_module import get_test_workflow - divert_nexus_log() - sims = get_test_workflow(1) pm = ProjectManager() @@ -280,13 +271,11 @@ def test_check_dependencies(): pm.check_dependencies() - restore_nexus_log() - Simulation.clear_all_sims() #end def test_check_dependencies - +@isolate_nexus_core def test_write_simulation_status(): from ..generic import generic_settings from ..nexus_base import nexus_core @@ -295,8 +284,6 @@ def test_write_simulation_status(): from .test_simulation_module import get_test_workflow - divert_nexus() - log = generic_settings.devlog sims = get_test_workflow(3) @@ -355,14 +342,12 @@ def status_log(): ''' assert(status_log().strip()==status_ref.strip()) - restore_nexus() - Simulation.clear_all_sims() #end def test_write_simulation_status - -def test_run_project(): +@isolate_nexus_core +def test_run_project(tmp_path): from ..generic import generic_settings from ..nexus_base import nexus_core from ..simulation import Simulation,input_template @@ -370,7 +355,10 @@ def test_run_project(): from .test_simulation_module import get_test_workflow,n_test_workflows - tpath = testing.setup_unit_test_output_directory('project_manager','test_run_project',divert=True) + # divert_nexus() + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] assert(nexus_core.mode==nexus_core.modes.stages) assert(len(nexus_core.stages)==0) @@ -442,7 +430,7 @@ def empty(s): assert(finished(s)) #end for - restore_nexus() + # restore_nexus() Simulation.clear_all_sims() #end def test_run_project diff --git a/nexus/nexus/tests/test_pseudopotential.py b/nexus/nexus/tests/test_pseudopotential.py index ce95142c8a..3480417df5 100644 --- a/nexus/nexus/tests/test_pseudopotential.py +++ b/nexus/nexus/tests/test_pseudopotential.py @@ -1,48 +1,22 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PSEUDOPOTENTIAL) -from .. import testing -from ..testing import value_eq,object_eq -from ..testing import divert_nexus_log,restore_nexus_log - - -associated_files = dict() - - -def get_filenames(): - filenames = [ - 'C.BFD.gms', - 'C.BFD.upf', - 'C.BFD.xml', - ] - return filenames -#end def get_filenames +from ..generic import generic_settings +generic_settings.raise_error = True - -def get_files(): - return testing.collect_unit_test_file_paths('pseudopotential',associated_files) -#end def get_files - - - -def test_files(): - filenames = get_filenames() - files = get_files() - assert(set(files.keys())==set(filenames)) -#end def test_files +from . import isolate_nexus_core, TEST_DIR +from ..testing import value_eq,object_eq -def test_import(): - from .. import pseudopotential - from ..pseudopotential import Pseudopotentials - from ..pseudopotential import PseudoFile - from ..pseudopotential import gamessPPFile - from ..pseudopotential import PPset - from ..pseudopotential import Pseudopotential - from ..pseudopotential import SemilocalPP - from ..pseudopotential import GaussianPP - from ..pseudopotential import QmcpackPP - from ..pseudopotential import CasinoPP -#end def test_import +TEST_FILES = { + "C.BFD.gms": TEST_DIR / "test_pseudopotential_files/C.BFD.gms", + "C.BFD.upf": TEST_DIR / "../examples/qmcpack/pseudopotentials/C.BFD.upf", + "C.BFD.xml": TEST_DIR / "../examples/qmcpack/pseudopotentials/C.BFD.xml", + } +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" def test_pp_elem_label(): @@ -69,28 +43,22 @@ def test_pp_elem_label(): #end def test_pp_elem_label - +@isolate_nexus_core def test_pseudopotentials(): from ..pseudopotential import Pseudopotentials from ..pseudopotential import PseudoFile from ..pseudopotential import gamessPPFile - filenames = get_filenames() - files = get_files() - - filepaths = [files[fn] for fn in filenames] - # empty initialization Pseudopotentials() PseudoFile() gamessPPFile() # standard initialization - divert_nexus_log() - pps = Pseudopotentials(filepaths) - restore_nexus_log() + file_paths = list(TEST_FILES.values()) + pps = Pseudopotentials(file_paths) - for fn in filenames: + for fn in TEST_FILES.keys(): assert(fn in pps) pp = pps[fn] assert(isinstance(pp,PseudoFile)) @@ -213,31 +181,20 @@ def test_ppset(): -def test_pseudopotential_classes(): - import os +def test_pseudopotential_classes(tmp_path): import numpy as np from ..pseudopotential import SemilocalPP from ..pseudopotential import GaussianPP from ..pseudopotential import QmcpackPP from ..pseudopotential import CasinoPP - tpath = testing.setup_unit_test_output_directory('pseudopotential','test_pseudopotential_classes') - - files = get_files() - # empty initialization SemilocalPP() GaussianPP() QmcpackPP() CasinoPP() - f = open(files['C.BFD.xml'],'r') - pp_relpath = f.read().strip() - pp_path = os.path.split(files['C.BFD.xml'])[0] - filepath = os.path.realpath(os.path.join(pp_path,pp_relpath)) - f.close() - - qpp = QmcpackPP(filepath) + qpp = QmcpackPP(TEST_FILES['C.BFD.xml']) # SemilocalPP attributes/methods assert(qpp.name is None) @@ -375,7 +332,7 @@ def test_pseudopotential_classes(): # tests for GaussianPP - gpp = GaussianPP(files['C.BFD.gms'],format='gamess') + gpp = GaussianPP(TEST_FILES['C.BFD.gms'],format='gamess') assert(gpp.Zcore == 2 ) assert(gpp.Zval == 4 ) assert(gpp.core == 'He') @@ -402,16 +359,16 @@ def test_pseudopotential_classes(): assert(value_eq(gpp.components.p[1].expon,4.48361888)) # check cross-format write/read - gamess_file = os.path.join(tpath,'C.BFD.gamess') + gamess_file = tmp_path / 'C.BFD.gamess' gpp.write(gamess_file,format='gamess') - gaussian_file = os.path.join(tpath,'C.BFD.gaussian') + gaussian_file = tmp_path / 'C.BFD.gaussian' gpp.write(gaussian_file,format='gaussian') - qmcpack_file = os.path.join(tpath,'C.BFD.qmcpack') + qmcpack_file = tmp_path / 'C.BFD.qmcpack' gpp.write(qmcpack_file,format='qmcpack') - casino_file = os.path.join(tpath,'C.BFD.casino') + casino_file = tmp_path / 'C.BFD.casino' gpp.write(casino_file,format='casino') @@ -434,7 +391,7 @@ def test_pseudopotential_classes(): del qo.rmax assert(object_eq(co,qo,atol=1e-12)) - qmcpack_from_casino_file = os.path.join(tpath,'C.BFD.qmcpack_from_casino') + qmcpack_from_casino_file = tmp_path / 'C.BFD.qmcpack_from_casino' cpp.write_qmcpack(qmcpack_from_casino_file) qpp_casino = QmcpackPP(qmcpack_from_casino_file) diff --git a/nexus/nexus/tests/test_pwscf_analyzer.py b/nexus/nexus/tests/test_pwscf_analyzer.py index ca634a1de9..0d996f438e 100644 --- a/nexus/nexus/tests/test_pwscf_analyzer.py +++ b/nexus/nexus/tests/test_pwscf_analyzer.py @@ -1,12 +1,13 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PWSCF_ANALYZER) -from .. import testing -from ..testing import value_eq,object_eq,text_eq +from ..generic import generic_settings +generic_settings.raise_error = True -def test_import(): - from ..pwscf_analyzer import PwscfAnalyzer -#end def test_import - +from . import TEST_DIR +from ..testing import object_eq def test_empty_init(): @@ -16,22 +17,14 @@ def test_empty_init(): #end def test_empty_init - def test_analyze(): - import os - from numpy import array,ndarray + from numpy import array from ..developer import obj from ..pwscf_analyzer import PwscfAnalyzer - tpath = testing.setup_unit_test_output_directory( - test = 'pwscf_analyzer', - subtest = 'test_analyze', - file_sets = ['scf_output','relax_output','nscf_output'], - ) - - scf_path = os.path.join(tpath,'scf_output') - relax_path = os.path.join(tpath,'relax_output') - nscf_path = os.path.join(tpath,'nscf_output') + scf_path = TEST_DIR / "test_pwscf_analyzer_files/scf_output" + relax_path = TEST_DIR / "test_pwscf_analyzer_files/relax_output" + nscf_path = TEST_DIR / "test_pwscf_analyzer_files/nscf_output" # scf w/o actual analysis pa = PwscfAnalyzer(scf_path,'scf.in','scf.out') diff --git a/nexus/nexus/tests/test_pwscf_input.py b/nexus/nexus/tests/test_pwscf_input.py index 457dfadf70..be90dffeb0 100644 --- a/nexus/nexus/tests/test_pwscf_input.py +++ b/nexus/nexus/tests/test_pwscf_input.py @@ -1,76 +1,46 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PWSCF_INPUT) -from .. import testing -from ..testing import failed -from ..testing import divert_nexus_log,restore_nexus_log -from ..testing import value_eq,object_eq - - -associated_files = dict() - -input_files = [ - 'Cr_noncolin.in', - 'Fe_start_ns_eig.in', - 'LiI_vc_relax.in', - 'Ni_surface.in', - 'TiO2_band_structure.in', - 'TiO2_relax_freeze.in', - 'VO2_M1_afm.in', - 'WSe2_band_structure.in', - ] - -structure_files = [ - 'VO2_M1_afm.xsf', - ] - -other_files = [ - 'README', - ] - +from ..generic import generic_settings +generic_settings.raise_error = True -def get_files(): - return testing.collect_unit_test_file_paths('pwscf_input',associated_files) -#end def get_files - - -def test_files(): - filenames = input_files + structure_files + other_files - files = get_files() - assert(set(files.keys())==set(filenames)) -#end def test_files - - - -def test_import(): - from ..pwscf_input import check_new_variables,check_section_classes - from ..pwscf_input import PwscfInput,generate_pwscf_input -#end def test_import - - - -def test_input(): +from . import isolate_nexus_core, TEST_DIR +from ..testing import failed +from ..testing import object_eq,object_diff + + +TEST_FILES = { + "Cr_noncolin.in": TEST_DIR / "test_pwscf_input_files/Cr_noncolin.in", + "Fe_start_ns_eig.in": TEST_DIR / "test_pwscf_input_files/Fe_start_ns_eig.in", + "LiI_vc_relax.in": TEST_DIR / "test_pwscf_input_files/LiI_vc_relax.in", + "Ni_surface.in": TEST_DIR / "test_pwscf_input_files/Ni_surface.in", + "TiO2_band_structure.in": TEST_DIR / "test_pwscf_input_files/TiO2_band_structure.in", + "TiO2_relax_freeze.in": TEST_DIR / "test_pwscf_input_files/TiO2_relax_freeze.in", + "VO2_M1_afm.in": TEST_DIR / "test_pwscf_input_files/VO2_M1_afm.in", + "VO2_M1_afm.xsf": TEST_DIR / "test_pwscf_input_files/VO2_M1_afm.xsf", + "WSe2_band_structure.in": TEST_DIR / "test_pwscf_input_files/WSe2_band_structure.in", + "README": TEST_DIR / "test_pwscf_input_files/README", + } + +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" + +@isolate_nexus_core +def test_input(tmp_path): # imports - import os import numpy as np - from .. import pwscf_input as pwi from ..developer import obj from ..structure import read_structure from ..physical_system import generate_physical_system from ..pwscf_input import check_new_variables,check_section_classes from ..pwscf_input import PwscfInput,generate_pwscf_input - - # directories - tpath = testing.setup_unit_test_output_directory('pwscf_input','test_input') - - # files - files = get_files() - - # divert logging function - divert_nexus_log() # definitions def check_pw_same(pw1_,pw2_,l1='pw1',l2='pw2'): - pw_same = object_eq(pw1_,pw2_,int_as_float=True) + pw_same = object_eq(pw1_, pw2_, int_as_float=True, atol=5e-4) + if not pw_same: d,d1,d2 = object_diff(pw1_,pw2_,full=True,int_as_float=True) diff = obj({l1:obj(d1),l2:obj(d2)}) @@ -154,14 +124,14 @@ def check_pw_same(pw1_,pw2_,l1='pw1',l2='pw2'): # test read - pwr = PwscfInput(files['Fe_start_ns_eig.in']) + pwr = PwscfInput(TEST_FILES['Fe_start_ns_eig.in']) pwc = pw.copy() pwc.standardize_types() check_pw_same(pwc,pwr,'compose','read') # test write - infile = os.path.join(tpath,'pwscf.in') + infile = tmp_path / 'pwscf.in' pw.write(infile) pw2 = PwscfInput() pw2.read(infile) @@ -170,17 +140,16 @@ def check_pw_same(pw1_,pw2_,l1='pw1',l2='pw2'): # test read/write/read reads = obj() - for infile in input_files: - read_path = files[infile] - write_path = os.path.join(tpath,infile) - if os.path.exists(write_path): - os.remove(write_path) - #end if + for input_file, file_path in TEST_FILES.items(): + if file_path.suffix != ".in": + continue + read_path = file_path + write_path = tmp_path / input_file pw = PwscfInput(read_path) pw.write(write_path) pw2 = PwscfInput(write_path) check_pw_same(pw,pw2,'read','write/read') - reads[infile] = pw + reads[input_file] = pw #end for @@ -189,9 +158,9 @@ def check_pw_same(pw1_,pw2_,l1='pw1',l2='pw2'): # based on sample_inputs/VO2_M1_afm.in infile = 'VO2_M1_afm.in' - struct_file = files['VO2_M1_afm.xsf'] - read_path = files[infile] - write_path = os.path.join(tpath,infile) + struct_file = TEST_FILES['VO2_M1_afm.xsf'] + read_path = TEST_FILES[infile] + write_path = tmp_path / infile s = read_structure(struct_file) s.elem[0] = 'V1' @@ -238,9 +207,6 @@ def check_pw_same(pw1_,pw2_,l1='pw1',l2='pw2'): generations[infile] = pw - if os.path.exists(write_path): - os.remove(write_path) - #end if pw.write(write_path) pw2 = PwscfInput(read_path) pw3 = PwscfInput(write_path) @@ -248,8 +214,8 @@ def check_pw_same(pw1_,pw2_,l1='pw1',l2='pw2'): # based on sample_inputs/Fe_start_ns_eig.in infile = 'Fe_start_ns_eig.in' - read_path = files[infile] - write_path = os.path.join(tpath,infile) + read_path = TEST_FILES[infile] + write_path = tmp_path / infile pw = generate_pwscf_input( selector = 'generic', @@ -303,16 +269,12 @@ def check_pw_same(pw1_,pw2_,l1='pw1',l2='pw2'): pw2 = compositions[infile] check_pw_same(pw,pw2,'generate','compose') - if os.path.exists(write_path): - os.remove(write_path) - #end if pw.write(write_path) pw3 = PwscfInput(write_path) pw4 = reads[infile] check_pw_same(pw3,pw4,'generate','read') - # based on sample_inputs/Fe_start_ns_eig.in # variant that uses direct pwscf array input pw = generate_pwscf_input( @@ -371,14 +333,7 @@ def check_pw_same(pw1_,pw2_,l1='pw1',l2='pw2'): check_pw_same(pwg,pw2,'generate','compose') pw3 = reads[infile] check_pw_same(pwg,pw3,'generate','read') - if os.path.exists(write_path): - os.remove(write_path) - #end if pw.write(write_path) pw4 = PwscfInput(write_path) check_pw_same(pwg,pw3,'generate','write') - - - # restore logging function - restore_nexus_log() #end def test_input diff --git a/nexus/nexus/tests/test_pwscf_postprocessor_analyzers.py b/nexus/nexus/tests/test_pwscf_postprocessor_analyzers.py index 5fa1957a43..7f4cc5c86c 100644 --- a/nexus/nexus/tests/test_pwscf_postprocessor_analyzers.py +++ b/nexus/nexus/tests/test_pwscf_postprocessor_analyzers.py @@ -1,18 +1,21 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PWSCF_POSTPROCESSOR_ANALYZERS) -from .. import testing -from ..testing import value_eq,object_eq,text_eq +from ..generic import generic_settings +generic_settings.raise_error = True +from . import TEST_DIR +from ..testing import object_eq,text_eq -def test_import(): - from ..pwscf_postprocessors import PPAnalyzer - from ..pwscf_postprocessors import DosAnalyzer - from ..pwscf_postprocessors import BandsAnalyzer - from ..pwscf_postprocessors import ProjwfcAnalyzer - from ..pwscf_postprocessors import CpppAnalyzer - from ..pwscf_postprocessors import PwexportAnalyzer -#end def test_import +TEST_FILES = { + "pwf.in": TEST_DIR / "test_pwscf_postprocessor_analyzers_files/pwf.in", + "pwf.out": TEST_DIR / "test_pwscf_postprocessor_analyzers_files/pwf.out", + } +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" def test_empty_init(): @@ -32,19 +35,11 @@ def test_empty_init(): #end def test_empty_init - -def test_projwfc_analyzer(): - import os +def test_projwfc_analyzer(tmp_path): from ..developer import obj from ..pwscf_postprocessors import ProjwfcAnalyzer - tpath = testing.setup_unit_test_output_directory( - test = 'pwscf_postprocessor_analyzers', - subtest = 'test_projwfc_analyzer', - file_sets = ['pwf.in','pwf.out'], - ) - - projwfc_in = os.path.join(tpath,'pwf.in') + projwfc_in = TEST_FILES["pwf.in"] pa = ProjwfcAnalyzer(projwfc_in) @@ -158,11 +153,11 @@ def test_projwfc_analyzer(): assert(object_eq(pa.to_obj(),pa_ref)) - lowdin_file = os.path.join(tpath,'pwf.lowdin') + lowdin_file = tmp_path / 'pwf.lowdin' pa.write_lowdin(lowdin_file) - text = open(lowdin_file,'r').read() + text = lowdin_file.read_text() text_ref = ''' nup+ndn = 5.9977 @@ -191,11 +186,11 @@ def process_text(t): assert(text_eq(text,text_ref)) - lowdin_file = os.path.join(tpath,'pwf.lowdin_long') + lowdin_file = tmp_path / 'pwf.lowdin_long' pa.write_lowdin(lowdin_file,long=True) - text = open(lowdin_file,'r').read() + text = lowdin_file.read_text() text_ref = ''' nup+ndn = 5.9977 diff --git a/nexus/nexus/tests/test_pwscf_postprocessor_input.py b/nexus/nexus/tests/test_pwscf_postprocessor_input.py index 4f69c90af3..e1acebab0d 100644 --- a/nexus/nexus/tests/test_pwscf_postprocessor_input.py +++ b/nexus/nexus/tests/test_pwscf_postprocessor_input.py @@ -1,6 +1,11 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PWSCF_POSTPROCESSOR_INPUT) -from .. import testing -from ..testing import value_eq,object_eq,text_eq +from ..generic import generic_settings +generic_settings.raise_error = True + +from ..testing import object_eq projwfc_in = '''&projwfc @@ -11,17 +16,6 @@ -def test_import(): - from ..pwscf_postprocessors import PPInput,generate_pp_input - from ..pwscf_postprocessors import DosInput,generate_dos_input - from ..pwscf_postprocessors import BandsInput,generate_bands_input - from ..pwscf_postprocessors import ProjwfcInput,generate_projwfc_input - from ..pwscf_postprocessors import CpppInput,generate_cppp_input - from ..pwscf_postprocessors import PwexportInput,generate_pwexport_input -#end def test_import - - - def test_empty_init(): from ..pwscf_postprocessors import PPInput,generate_pp_input from ..pwscf_postprocessors import DosInput,generate_dos_input @@ -52,15 +46,12 @@ def test_empty_init(): -def test_read(): - import os +def test_read(tmp_path): from ..developer import obj from ..pwscf_postprocessors import ProjwfcInput - tpath = testing.setup_unit_test_output_directory('pwscf_postprocessor_input','test_read') - - infile_path = os.path.join(tpath,'projwfc.in') - open(infile_path,'w').write(projwfc_in) + infile_path = tmp_path / 'projwfc.in' + infile_path.write_text(projwfc_in) pi = ProjwfcInput(infile_path) @@ -76,17 +67,14 @@ def test_read(): -def test_write(): - import os +def test_write(tmp_path): from ..developer import obj from ..pwscf_postprocessors import ProjwfcInput - tpath = testing.setup_unit_test_output_directory('pwscf_postprocessor_input','test_write') - - infile_path = os.path.join(tpath,'projwfc.in') - open(infile_path,'w').write(projwfc_in) + infile_path = tmp_path / 'projwfc.in' + infile_path.write_text(projwfc_in) - write_path = os.path.join(tpath,'projwfc_write.in') + write_path = tmp_path / 'projwfc_write.in' pi_write = ProjwfcInput(infile_path) pi_write.write(write_path) diff --git a/nexus/nexus/tests/test_pwscf_postprocessor_simulations.py b/nexus/nexus/tests/test_pwscf_postprocessor_simulations.py index 4493ae41a2..1f63bef0ec 100644 --- a/nexus/nexus/tests/test_pwscf_postprocessor_simulations.py +++ b/nexus/nexus/tests/test_pwscf_postprocessor_simulations.py @@ -1,8 +1,12 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PWSCF_POSTPROCESSOR_SIMULATIONS) -from .. import testing -from ..testing import divert_nexus,restore_nexus,clear_all_sims +from ..generic import generic_settings +generic_settings.raise_error = True + +from ..testing import clear_all_sims from ..testing import failed,FailedTest -from ..testing import value_eq,object_eq,text_eq def get_class_generators(): @@ -27,17 +31,6 @@ def get_class_generators(): -def test_import(): - from ..pwscf_postprocessors import PP,generate_pp - from ..pwscf_postprocessors import Dos,generate_dos - from ..pwscf_postprocessors import Bands,generate_bands - from ..pwscf_postprocessors import Projwfc,generate_projwfc - from ..pwscf_postprocessors import Cppp,generate_cppp - from ..pwscf_postprocessors import Pwexport,generate_pwexport -#end def test_import - - - def test_minimal_init(): from ..machines import job diff --git a/nexus/nexus/tests/test_pwscf_simulation.py b/nexus/nexus/tests/test_pwscf_simulation.py index a29d35cf62..b3c6fe7161 100644 --- a/nexus/nexus/tests/test_pwscf_simulation.py +++ b/nexus/nexus/tests/test_pwscf_simulation.py @@ -1,15 +1,17 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PWSCF_SIMULATION) -from .. import testing -from ..testing import divert_nexus,restore_nexus,clear_all_sims -from ..testing import failed,FailedTest -from ..testing import value_eq,object_eq,text_eq - +from ..generic import generic_settings +generic_settings.raise_error = True +from pathlib import Path -pseudo_inputs = dict( - pseudo_dir = 'pseudopotentials', - pseudo_files_create = ['C.BFD.upf'], - ) +from . import isolate_nexus_core, create_pseudo_files +from nexus.nexus_base import nexus_core +from ..testing import clear_all_sims +from ..testing import failed,FailedTest +from ..testing import value_eq,object_eq def get_system(): @@ -49,13 +51,13 @@ def get_pwscf_sim(type='scf'): job = job(machine='ws1',cores=1), input_type = 'generic', calculation = 'scf', - input_dft = 'lda', - ecutwfc = 200, - conv_thr = 1e-8, + input_dft = 'lda', + ecutwfc = 200, + conv_thr = 1e-8, nosym = True, wf_collect = True, system = get_system(), - pseudos = ['C.BFD.upf'], + pseudos = ['C.BFD.upf'], nogamma = True, ) else: @@ -70,12 +72,6 @@ def get_pwscf_sim(type='scf'): -def test_import(): - from ..pwscf import Pwscf,generate_pwscf -#end def test_import - - - def test_minimal_init(): from ..machines import job from ..pwscf import Pwscf,generate_pwscf @@ -91,12 +87,17 @@ def test_minimal_init(): #end def test_minimal_init +@isolate_nexus_core +def test_check_result(tmp_path): -def test_check_result(): - tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_check_result',**pseudo_inputs) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] + + create_pseudo_files(tmp_path, ["C.BFD.upf"]) sim = get_pwscf_sim('scf') - + assert(not sim.check_result('unknown',None)) assert(sim.check_result('charge_density',None)) assert(sim.check_result('restart',None)) @@ -104,15 +105,18 @@ def test_check_result(): assert(not sim.check_result('structure',None)) clear_all_sims() - restore_nexus() #end def test_check_result - -def test_get_result(): +@isolate_nexus_core +def test_get_result(tmp_path): from ..developer import NexusError - tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_get_result',**pseudo_inputs) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] + + create_pseudo_files(tmp_path, ["C.BFD.upf"]) sim = get_pwscf_sim('scf') @@ -141,7 +145,7 @@ def test_get_result(): assert(set(result.keys())==set(result_ref.keys())) for k,path in result.items(): - path = path.replace(tpath,'').lstrip('/') + path = path.replace(str(tmp_path),'').lstrip('/') assert(path==result_ref[k]) #end for @@ -153,19 +157,23 @@ def test_get_result(): assert(set(result.keys())==set(result_ref.keys())) for k,path in result.items(): - path = path.replace(tpath,'').lstrip('/') + path = path.replace(str(tmp_path),'').lstrip('/') assert(path==result_ref[k]) #end for clear_all_sims() - restore_nexus() #end def test_get_result - -def test_incorporate_result(): +@isolate_nexus_core +def test_incorporate_result(tmp_path): from ..developer import obj - tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_incorporate_result',**pseudo_inputs) + + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] + + create_pseudo_files(tmp_path, ["C.BFD.upf"]) sim = get_pwscf_sim('scf') @@ -189,7 +197,7 @@ def test_incorporate_result(): assert(c.restart_mode=='restart') del c.restart_mode assert(object_eq(sim.to_obj(),sim_start)) - + # structure altered_structure = sim.system.structure.copy() altered_structure.pos += 0.1 @@ -212,21 +220,23 @@ def test_incorporate_result(): assert(object_eq(sim.to_obj(),sim_ref)) clear_all_sims() - restore_nexus() #end def test_incorporate_result +@isolate_nexus_core +def test_check_sim_status(tmp_path): + + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] -def test_check_sim_status(): - import os - tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_check_sim_status',**pseudo_inputs) + create_pseudo_files(tmp_path, ["C.BFD.upf"]) sim = get_pwscf_sim('scf') - assert(sim.locdir.rstrip('/')==os.path.join(tpath,'scf').rstrip('/')) - if not os.path.exists(sim.locdir): - os.makedirs(sim.locdir) - #end if + sim_dir = Path(sim.locdir).resolve() + assert(sim_dir == (tmp_path / 'scf').resolve()) + sim_dir.mkdir() assert(not sim.finished) @@ -240,23 +250,17 @@ def test_check_sim_status(): assert(not sim.finished) - out_path = os.path.join(tpath,'scf',sim.outfile) - - out_text = '' - outfile = open(out_path,'w') - outfile.write(out_text) - outfile.close() - assert(os.path.exists(out_path)) + out_path = sim_dir / sim.outfile + out_path.touch() + assert(out_path.exists()) sim.check_sim_status() assert(not sim.finished) - out_text = 'JOB DONE' - outfile = open(out_path,'w') - outfile.write(out_text) - outfile.close() - assert(out_text in open(out_path,'r').read()) + out_text = "JOB DONE" + out_path.write_text(out_text) + assert(out_text in out_path.read_text()) sim.check_sim_status() @@ -264,6 +268,5 @@ def test_check_sim_status(): assert(not sim.failed) clear_all_sims() - restore_nexus() #end def test_check_sim_status diff --git a/nexus/nexus/tests/test_pyscf_analyzer.py b/nexus/nexus/tests/test_pyscf_analyzer.py index 4f9e61b7f4..735417d7f5 100644 --- a/nexus/nexus/tests/test_pyscf_analyzer.py +++ b/nexus/nexus/tests/test_pyscf_analyzer.py @@ -1,8 +1,9 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PYSCF_ANALYZER) - -def test_import(): - from ..pyscf_analyzer import PyscfAnalyzer -#end def test_import +from ..generic import generic_settings +generic_settings.raise_error = True diff --git a/nexus/nexus/tests/test_pyscf_input.py b/nexus/nexus/tests/test_pyscf_input.py index 3b57b67f07..34091f1210 100644 --- a/nexus/nexus/tests/test_pyscf_input.py +++ b/nexus/nexus/tests/test_pyscf_input.py @@ -1,6 +1,11 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PYSCF_INPUT) -from .. import testing -from ..testing import value_eq,object_eq,text_eq +from ..generic import generic_settings +generic_settings.raise_error = True + +from ..testing import object_eq,text_eq mno_poscar = '''MnO Crystal @@ -40,11 +45,6 @@ ''' -def test_import(): - from ..pyscf_input import PyscfInput,generate_pyscf_input -#end def test_import - - def test_empty_init(): from ..developer import obj from ..pyscf_input import PyscfInput,generate_pyscf_input @@ -70,20 +70,17 @@ def test_empty_init(): -def test_generate(): - import os +def test_generate(tmp_path): from ..developer import obj from ..physical_system import generate_physical_system from ..pyscf_input import generate_pyscf_input - tpath = testing.setup_unit_test_output_directory('pyscf_input','test_generate') - # water molecule - xyz_path = os.path.join(tpath,'H2O.xyz') - template_path = os.path.join(tpath,'scf_template.py') + xyz_path = tmp_path / 'H2O.xyz' + template_path = tmp_path / 'scf_template.py' - open(xyz_path,'w').write(h2o_xyz) - open(template_path,'w').write(scf_template) + xyz_path.write_text(h2o_xyz) + template_path.write_text(scf_template) system = generate_physical_system( structure = xyz_path, @@ -198,9 +195,9 @@ def test_generate(): assert(object_eq(pi.to_obj(),ref_internal)) # water molecule without template - xyz_path = os.path.join(tpath,'H2O.xyz') + xyz_path = tmp_path / 'H2O.xyz' - open(xyz_path,'w').write(h2o_xyz) + xyz_path.write_text(h2o_xyz) system = generate_physical_system( structure = xyz_path, @@ -277,9 +274,9 @@ def test_generate(): # MnO crystal without template - poscar_path = os.path.join(tpath,'MnO.POSCAR') + poscar_path = tmp_path / 'MnO.POSCAR' - open(poscar_path,'w').write(mno_poscar) + poscar_path.write_text(mno_poscar) system = generate_physical_system( structure = poscar_path, @@ -395,26 +392,21 @@ def test_generate(): del pi.calculation del pi.template assert(object_eq(pi.to_obj(),ref_internal)) - - #end def test_generate -def test_write(): - import os +def test_write(tmp_path): from ..developer import obj from ..physical_system import generate_physical_system from ..pyscf_input import generate_pyscf_input - tpath = testing.setup_unit_test_output_directory('pyscf_input','test_write') - # water molecule - xyz_path = os.path.join(tpath,'H2O.xyz') - template_path = os.path.join(tpath,'scf_template.py') + xyz_path = tmp_path / 'H2O.xyz' + template_path = tmp_path / 'scf_template.py' - open(xyz_path,'w').write(h2o_xyz) - open(template_path,'w').write(scf_template) + xyz_path.write_text(h2o_xyz) + template_path.write_text(scf_template) system = generate_physical_system( structure = xyz_path, @@ -432,13 +424,13 @@ def test_write(): save_qmc = True, ) - write_path = os.path.join(tpath,'h2o.py') + write_path = tmp_path / 'h2o.py' pi.write(write_path) - assert(os.path.exists(write_path)) + assert(write_path.exists()) - text = open(write_path,'r').read().strip() + text = write_path.read_text().strip() ref_text = ''' #! /usr/bin/env python3 @@ -506,13 +498,13 @@ def test_write(): save_qmc = True, ) - write_path = os.path.join(tpath,'diamond.py') + write_path = tmp_path / 'diamond.py' pi.write(write_path) - assert(os.path.exists(write_path)) + assert(write_path.exists()) - text = open(write_path,'r').read() + text = write_path.read_text() ref_text = ''' #! /usr/bin/env python3 diff --git a/nexus/nexus/tests/test_pyscf_simulation.py b/nexus/nexus/tests/test_pyscf_simulation.py index 94f8be49f9..3100f7bda1 100644 --- a/nexus/nexus/tests/test_pyscf_simulation.py +++ b/nexus/nexus/tests/test_pyscf_simulation.py @@ -1,7 +1,13 @@ -from .. import testing -from ..testing import divert_nexus,restore_nexus,clear_all_sims +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.PYSCF_SIMULATION) + +from ..generic import generic_settings +generic_settings.raise_error = True + +from . import isolate_nexus_core +from ..testing import clear_all_sims from ..testing import failed,FailedTest -from ..testing import value_eq,object_eq,text_eq def get_pyscf_sim(**kwargs): @@ -20,12 +26,6 @@ def get_pyscf_sim(**kwargs): -def test_import(): - from ..pyscf_sim import Pyscf,generate_pyscf -#end def test_import - - - def test_minimal_init(): from ..machines import job from ..pyscf_sim import Pyscf,generate_pyscf @@ -65,22 +65,21 @@ def test_check_result(): #end def test_check_result - -def test_get_result(): - import os - from ..developer import NexusError, obj +@isolate_nexus_core +def test_get_result(tmp_path): + from ..developer import NexusError from ..nexus_base import nexus_core - tpath = testing.setup_unit_test_output_directory('pyscf_simulation','test_get_result',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] nexus_core.runs = '' template_file = 'scf_template.py' template_text = 'template $chkfile' - template_filepath = os.path.join(tpath,template_file) - f = open(template_filepath,'w') - f.write(template_text) - f.close() + template_filepath = tmp_path / template_file + template_filepath.write_text(template_text) sim = get_pyscf_sim( prefix = 'scf', @@ -101,14 +100,13 @@ def test_get_result(): result = sim.get_result('orbitals',None) - assert(result.h5_file.replace(tpath,'').lstrip('/')=='scf.h5') + assert(result.h5_file.replace(str(tmp_path),'').lstrip('/')=='scf.h5') result = sim.get_result('wavefunction',None) - assert(result.chkfile.replace(tpath,'').lstrip('/')=='scf.chk') + assert(result.chkfile.replace(str(tmp_path),'').lstrip('/')=='scf.chk') clear_all_sims() - restore_nexus() #end def test_get_result diff --git a/nexus/nexus/tests/test_qdens.py b/nexus/nexus/tests/test_qdens.py index 36a6a8652b..c2ee0fbc0a 100644 --- a/nexus/nexus/tests/test_qdens.py +++ b/nexus/nexus/tests/test_qdens.py @@ -1,155 +1,191 @@ - -from .. import versions -from .. import testing -from ..testing import execute,text_eq,check_value_eq - - -if versions.h5py_available: - def test_density(): - import os - - tpath = testing.setup_unit_test_output_directory('qdens','test_density') - - exe = testing.executable_path('qdens') - - qa_files_path = testing.unit_test_file_path('qmcpack_analyzer','diamond_gamma/dmc') - command = 'rsync -a {} {}'.format(qa_files_path,tpath) - out,err,rc = execute(command) - assert(rc==0) - dmc_path = os.path.join(tpath,'dmc') - dmc_infile = os.path.join(dmc_path,'dmc.in.xml') - assert(os.path.exists(dmc_infile)) - - files_bef = ''' - dmc.err dmc.s000.scalar.dat dmc.s001.stat.h5 dmc.s003.scalar.dat - dmc.in.xml dmc.s000.stat.h5 dmc.s002.scalar.dat dmc.s003.stat.h5 - dmc.out dmc.s001.scalar.dat dmc.s002.stat.h5 - '''.split() - - assert(check_value_eq(set(os.listdir(dmc_path)),set(files_bef))) - - command = '{0} -v -e 4 -f xsf -i {1}/dmc.in.xml {1}/*stat.h5'.format(exe,dmc_path) - - out,err,rc = execute(command) - - files_aft = ''' - dmc.err dmc.s001.stat.h5 - dmc.in.xml dmc.s002.scalar.dat - dmc.out dmc.s002.SpinDensity_d-err.xsf - dmc.s000.scalar.dat dmc.s002.SpinDensity_d+err.xsf - dmc.s000.SpinDensity_d-err.xsf dmc.s002.SpinDensity_d.xsf - dmc.s000.SpinDensity_d+err.xsf dmc.s002.SpinDensity_u-d-err.xsf - dmc.s000.SpinDensity_d.xsf dmc.s002.SpinDensity_u-d+err.xsf - dmc.s000.SpinDensity_u-d-err.xsf dmc.s002.SpinDensity_u+d-err.xsf - dmc.s000.SpinDensity_u-d+err.xsf dmc.s002.SpinDensity_u+d+err.xsf - dmc.s000.SpinDensity_u+d-err.xsf dmc.s002.SpinDensity_u-d.xsf - dmc.s000.SpinDensity_u+d+err.xsf dmc.s002.SpinDensity_u+d.xsf - dmc.s000.SpinDensity_u-d.xsf dmc.s002.SpinDensity_u-err.xsf - dmc.s000.SpinDensity_u+d.xsf dmc.s002.SpinDensity_u+err.xsf - dmc.s000.SpinDensity_u-err.xsf dmc.s002.SpinDensity_u.xsf - dmc.s000.SpinDensity_u+err.xsf dmc.s002.stat.h5 - dmc.s000.SpinDensity_u.xsf dmc.s003.scalar.dat - dmc.s000.stat.h5 dmc.s003.SpinDensity_d-err.xsf - dmc.s001.scalar.dat dmc.s003.SpinDensity_d+err.xsf - dmc.s001.SpinDensity_d-err.xsf dmc.s003.SpinDensity_d.xsf - dmc.s001.SpinDensity_d+err.xsf dmc.s003.SpinDensity_u-d-err.xsf - dmc.s001.SpinDensity_d.xsf dmc.s003.SpinDensity_u-d+err.xsf - dmc.s001.SpinDensity_u-d-err.xsf dmc.s003.SpinDensity_u+d-err.xsf - dmc.s001.SpinDensity_u-d+err.xsf dmc.s003.SpinDensity_u+d+err.xsf - dmc.s001.SpinDensity_u+d-err.xsf dmc.s003.SpinDensity_u-d.xsf - dmc.s001.SpinDensity_u+d+err.xsf dmc.s003.SpinDensity_u+d.xsf - dmc.s001.SpinDensity_u-d.xsf dmc.s003.SpinDensity_u-err.xsf - dmc.s001.SpinDensity_u+d.xsf dmc.s003.SpinDensity_u+err.xsf - dmc.s001.SpinDensity_u-err.xsf dmc.s003.SpinDensity_u.xsf - dmc.s001.SpinDensity_u+err.xsf dmc.s003.stat.h5 - dmc.s001.SpinDensity_u.xsf - '''.split() - - assert(check_value_eq(set(os.listdir(dmc_path)),set(files_aft),verbose=True)) - - tot_file = os.path.join(dmc_path,'dmc.s003.SpinDensity_u+d.xsf') - pol_file = os.path.join(dmc_path,'dmc.s003.SpinDensity_u-d.xsf') - - tot = open(tot_file,'r').read() - pol = open(pol_file,'r').read() - - tot_ref = ''' - CRYSTAL - PRIMVEC - 1.78500000 1.78500000 0.00000000 - -0.00000000 1.78500000 1.78500000 - 1.78500000 -0.00000000 1.78500000 - PRIMCOORD - 2 1 - 6 0.00000000 0.00000000 0.00000000 - 6 0.89250000 0.89250000 0.89250000 - BEGIN_BLOCK_DATAGRID_3D - density - BEGIN_DATAGRID_3D_density - 4 4 4 - 0.59500000 0.59500000 0.59500000 - 1.78500000 1.78500000 0.00000000 - -0.00000000 1.78500000 1.78500000 - 1.78500000 -0.00000000 1.78500000 - 0.73126076 0.62407496 0.51676366 0.73126076 - 0.62575089 0.19225114 0.18686389 0.62575089 - 0.51847569 0.18457799 0.42203355 0.51847569 - 0.73126076 0.62407496 0.51676366 0.73126076 - 0.62659840 0.19325900 0.18422995 0.62659840 - 0.19219866 0.04873728 0.13184395 0.19219866 - 0.18474638 0.13013188 0.10227670 0.18474638 - 0.62659840 0.19325900 0.18422995 0.62659840 - 0.51793019 0.18615766 0.41806405 0.51793019 - 0.18425005 0.13092538 0.10088238 0.18425005 - 0.41967003 0.10133434 0.14471118 0.41967003 - 0.51793019 0.18615766 0.41806405 0.51793019 - 0.73126076 0.62407496 0.51676366 0.73126076 - 0.62575089 0.19225114 0.18686389 0.62575089 - 0.51847569 0.18457799 0.42203355 0.51847569 - 0.73126076 0.62407496 0.51676366 0.73126076 - END_DATAGRID_3D_density - END_BLOCK_DATAGRID_3D - ''' - - pol_ref = ''' - CRYSTAL - PRIMVEC - 1.78500000 1.78500000 0.00000000 - -0.00000000 1.78500000 1.78500000 - 1.78500000 -0.00000000 1.78500000 - PRIMCOORD - 2 1 - 6 0.00000000 0.00000000 0.00000000 - 6 0.89250000 0.89250000 0.89250000 - BEGIN_BLOCK_DATAGRID_3D - density - BEGIN_DATAGRID_3D_density - 4 4 4 - 0.59500000 0.59500000 0.59500000 - 1.78500000 1.78500000 0.00000000 - -0.00000000 1.78500000 1.78500000 - 1.78500000 -0.00000000 1.78500000 - 0.00106753 0.00015792 -0.00122859 0.00106753 - -0.00003402 0.00018762 -0.00051347 -0.00003402 - 0.00154254 0.00067654 0.00073434 0.00154254 - 0.00106753 0.00015792 -0.00122859 0.00106753 - 0.00263956 0.00079744 -0.00118289 0.00263956 - -0.00039348 -0.00026396 -0.00069392 -0.00039348 - 0.00087929 0.00000719 0.00113934 0.00087929 - 0.00263956 0.00079744 -0.00118289 0.00263956 - -0.00013655 -0.00041508 -0.00235212 -0.00013655 - 0.00003805 -0.00025962 -0.00133495 0.00003805 - 0.00040692 0.00051699 -0.00198263 0.00040692 - -0.00013655 -0.00041508 -0.00235212 -0.00013655 - 0.00106753 0.00015792 -0.00122859 0.00106753 - -0.00003402 0.00018762 -0.00051347 -0.00003402 - 0.00154254 0.00067654 0.00073434 0.00154254 - 0.00106753 0.00015792 -0.00122859 0.00106753 - END_DATAGRID_3D_density - END_BLOCK_DATAGRID_3D - ''' - - assert(text_eq(tot,tot_ref,atol=1e-7)) - assert(text_eq(pol,pol_ref,atol=1e-7)) - #end def test_density -#end if +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QDENS) + +from ..generic import generic_settings +generic_settings.raise_error = True + + +from . import TEST_DIR +import shutil +from ..testing import execute, text_eq + + +def test_density(tmp_path): + + exe = TEST_DIR.parent / "bin/qdens" + + qa_files_path = TEST_DIR / "test_qmcpack_analyzer_files/diamond_gamma" + shutil.copytree(qa_files_path, tmp_path, dirs_exist_ok=True) + + dmc_path = tmp_path / 'dmc' + + files_bef = ( + dmc_path / "dmc.s000.stat.h5", + dmc_path / "dmc.s000.scalar.dat", + dmc_path / "dmc.s001.stat.h5", + dmc_path / "dmc.s001.scalar.dat", + dmc_path / "dmc.s002.stat.h5", + dmc_path / "dmc.s002.scalar.dat", + dmc_path / "dmc.s003.stat.h5", + dmc_path / "dmc.s003.scalar.dat", + dmc_path / "dmc.in.xml", + dmc_path / "dmc.out", + dmc_path / "dmc.err", + ) + + assert(set(dmc_path.iterdir()) == set(files_bef)) + + command = f'{exe} -v -e 4 -f xsf -i {dmc_path}/dmc.in.xml {dmc_path}/*stat.h5' + + out,err,rc = execute(command) + + files_aft = ( + tmp_path / "dmc/dmc.err", + tmp_path / "dmc/dmc.in.xml", + tmp_path / "dmc/dmc.out", + tmp_path / "dmc/dmc.s000.scalar.dat", + tmp_path / "dmc/dmc.s000.SpinDensity_d+err.xsf", + tmp_path / "dmc/dmc.s000.SpinDensity_d-err.xsf", + tmp_path / "dmc/dmc.s000.SpinDensity_d.xsf", + tmp_path / "dmc/dmc.s000.SpinDensity_u+d+err.xsf", + tmp_path / "dmc/dmc.s000.SpinDensity_u+d-err.xsf", + tmp_path / "dmc/dmc.s000.SpinDensity_u-d+err.xsf", + tmp_path / "dmc/dmc.s000.SpinDensity_u-d-err.xsf", + tmp_path / "dmc/dmc.s000.SpinDensity_u+d.xsf", + tmp_path / "dmc/dmc.s000.SpinDensity_u-d.xsf", + tmp_path / "dmc/dmc.s000.SpinDensity_u+err.xsf", + tmp_path / "dmc/dmc.s000.SpinDensity_u-err.xsf", + tmp_path / "dmc/dmc.s000.SpinDensity_u.xsf", + tmp_path / "dmc/dmc.s000.stat.h5", + tmp_path / "dmc/dmc.s001.scalar.dat", + tmp_path / "dmc/dmc.s001.SpinDensity_d+err.xsf", + tmp_path / "dmc/dmc.s001.SpinDensity_d-err.xsf", + tmp_path / "dmc/dmc.s001.SpinDensity_d.xsf", + tmp_path / "dmc/dmc.s001.SpinDensity_u+d+err.xsf", + tmp_path / "dmc/dmc.s001.SpinDensity_u+d-err.xsf", + tmp_path / "dmc/dmc.s001.SpinDensity_u-d+err.xsf", + tmp_path / "dmc/dmc.s001.SpinDensity_u-d-err.xsf", + tmp_path / "dmc/dmc.s001.SpinDensity_u+d.xsf", + tmp_path / "dmc/dmc.s001.SpinDensity_u-d.xsf", + tmp_path / "dmc/dmc.s001.SpinDensity_u+err.xsf", + tmp_path / "dmc/dmc.s001.SpinDensity_u-err.xsf", + tmp_path / "dmc/dmc.s001.SpinDensity_u.xsf", + tmp_path / "dmc/dmc.s001.stat.h5", + tmp_path / "dmc/dmc.s002.scalar.dat", + tmp_path / "dmc/dmc.s002.SpinDensity_d+err.xsf", + tmp_path / "dmc/dmc.s002.SpinDensity_d-err.xsf", + tmp_path / "dmc/dmc.s002.SpinDensity_d.xsf", + tmp_path / "dmc/dmc.s002.SpinDensity_u+d+err.xsf", + tmp_path / "dmc/dmc.s002.SpinDensity_u+d-err.xsf", + tmp_path / "dmc/dmc.s002.SpinDensity_u-d+err.xsf", + tmp_path / "dmc/dmc.s002.SpinDensity_u-d-err.xsf", + tmp_path / "dmc/dmc.s002.SpinDensity_u+d.xsf", + tmp_path / "dmc/dmc.s002.SpinDensity_u-d.xsf", + tmp_path / "dmc/dmc.s002.SpinDensity_u+err.xsf", + tmp_path / "dmc/dmc.s002.SpinDensity_u-err.xsf", + tmp_path / "dmc/dmc.s002.SpinDensity_u.xsf", + tmp_path / "dmc/dmc.s002.stat.h5", + tmp_path / "dmc/dmc.s003.scalar.dat", + tmp_path / "dmc/dmc.s003.SpinDensity_d+err.xsf", + tmp_path / "dmc/dmc.s003.SpinDensity_d-err.xsf", + tmp_path / "dmc/dmc.s003.SpinDensity_d.xsf", + tmp_path / "dmc/dmc.s003.SpinDensity_u+d+err.xsf", + tmp_path / "dmc/dmc.s003.SpinDensity_u+d-err.xsf", + tmp_path / "dmc/dmc.s003.SpinDensity_u-d+err.xsf", + tmp_path / "dmc/dmc.s003.SpinDensity_u-d-err.xsf", + tmp_path / "dmc/dmc.s003.SpinDensity_u+d.xsf", + tmp_path / "dmc/dmc.s003.SpinDensity_u-d.xsf", + tmp_path / "dmc/dmc.s003.SpinDensity_u+err.xsf", + tmp_path / "dmc/dmc.s003.SpinDensity_u-err.xsf", + tmp_path / "dmc/dmc.s003.SpinDensity_u.xsf", + tmp_path / "dmc/dmc.s003.stat.h5", + ) + + assert(set(dmc_path.iterdir()) == set(files_aft)) + + tot_file = dmc_path / 'dmc.s003.SpinDensity_u+d.xsf' + pol_file = dmc_path / 'dmc.s003.SpinDensity_u-d.xsf' + + tot = tot_file.read_text() + pol = pol_file.read_text() + + tot_ref = ''' + CRYSTAL + PRIMVEC + 1.78500000 1.78500000 0.00000000 + -0.00000000 1.78500000 1.78500000 + 1.78500000 -0.00000000 1.78500000 + PRIMCOORD + 2 1 + 6 0.00000000 0.00000000 0.00000000 + 6 0.89250000 0.89250000 0.89250000 + BEGIN_BLOCK_DATAGRID_3D + density + BEGIN_DATAGRID_3D_density + 4 4 4 + 0.59500000 0.59500000 0.59500000 + 1.78500000 1.78500000 0.00000000 + -0.00000000 1.78500000 1.78500000 + 1.78500000 -0.00000000 1.78500000 + 0.73126076 0.62407496 0.51676366 0.73126076 + 0.62575089 0.19225114 0.18686389 0.62575089 + 0.51847569 0.18457799 0.42203355 0.51847569 + 0.73126076 0.62407496 0.51676366 0.73126076 + 0.62659840 0.19325900 0.18422995 0.62659840 + 0.19219866 0.04873728 0.13184395 0.19219866 + 0.18474638 0.13013188 0.10227670 0.18474638 + 0.62659840 0.19325900 0.18422995 0.62659840 + 0.51793019 0.18615766 0.41806405 0.51793019 + 0.18425005 0.13092538 0.10088238 0.18425005 + 0.41967003 0.10133434 0.14471118 0.41967003 + 0.51793019 0.18615766 0.41806405 0.51793019 + 0.73126076 0.62407496 0.51676366 0.73126076 + 0.62575089 0.19225114 0.18686389 0.62575089 + 0.51847569 0.18457799 0.42203355 0.51847569 + 0.73126076 0.62407496 0.51676366 0.73126076 + END_DATAGRID_3D_density + END_BLOCK_DATAGRID_3D + ''' + + pol_ref = ''' + CRYSTAL + PRIMVEC + 1.78500000 1.78500000 0.00000000 + -0.00000000 1.78500000 1.78500000 + 1.78500000 -0.00000000 1.78500000 + PRIMCOORD + 2 1 + 6 0.00000000 0.00000000 0.00000000 + 6 0.89250000 0.89250000 0.89250000 + BEGIN_BLOCK_DATAGRID_3D + density + BEGIN_DATAGRID_3D_density + 4 4 4 + 0.59500000 0.59500000 0.59500000 + 1.78500000 1.78500000 0.00000000 + -0.00000000 1.78500000 1.78500000 + 1.78500000 -0.00000000 1.78500000 + 0.00106753 0.00015792 -0.00122859 0.00106753 + -0.00003402 0.00018762 -0.00051347 -0.00003402 + 0.00154254 0.00067654 0.00073434 0.00154254 + 0.00106753 0.00015792 -0.00122859 0.00106753 + 0.00263956 0.00079744 -0.00118289 0.00263956 + -0.00039348 -0.00026396 -0.00069392 -0.00039348 + 0.00087929 0.00000719 0.00113934 0.00087929 + 0.00263956 0.00079744 -0.00118289 0.00263956 + -0.00013655 -0.00041508 -0.00235212 -0.00013655 + 0.00003805 -0.00025962 -0.00133495 0.00003805 + 0.00040692 0.00051699 -0.00198263 0.00040692 + -0.00013655 -0.00041508 -0.00235212 -0.00013655 + 0.00106753 0.00015792 -0.00122859 0.00106753 + -0.00003402 0.00018762 -0.00051347 -0.00003402 + 0.00154254 0.00067654 0.00073434 0.00154254 + 0.00106753 0.00015792 -0.00122859 0.00106753 + END_DATAGRID_3D_density + END_BLOCK_DATAGRID_3D + ''' + + assert(text_eq(tot,tot_ref,atol=1e-7)) + assert(text_eq(pol,pol_ref,atol=1e-7)) +#end def test_density diff --git a/nexus/nexus/tests/test_qdens_radial.py b/nexus/nexus/tests/test_qdens_radial.py index 663eb1c974..4128943cbc 100644 --- a/nexus/nexus/tests/test_qdens_radial.py +++ b/nexus/nexus/tests/test_qdens_radial.py @@ -1,146 +1,146 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QDENS_RADIAL) -from .. import versions -from .. import testing +from ..generic import generic_settings +generic_settings.raise_error = True + +from . import TEST_DIR from ..testing import execute,text_eq,check_value_eq -if versions.spglib_available: - def test_radial_density(): - import os - - tpath = testing.setup_unit_test_output_directory('qdens_radial','test_radial_density') - - exe = testing.executable_path('qdens-radial') - - qr_vmc_files_path = testing.unit_test_file_path('qdens_radial','diamond_twist/vmc') - command = 'rsync -a {} {}'.format(qr_vmc_files_path,tpath) - out,err,rc = execute(command) - assert(rc==0) - vmc_path = os.path.join(tpath,'vmc') - vmc_infile = os.path.join(vmc_path,'vmc.g000.twistnum_0.in.xml') - assert(os.path.exists(vmc_infile)) - vmc_infile = os.path.join(vmc_path,'vmc.g001.twistnum_1.in.xml') - assert(os.path.exists(vmc_infile)) - vmc_infile = os.path.join(vmc_path,'vmc.g002.twistnum_2.in.xml') - assert(os.path.exists(vmc_infile)) - vmc_infile = os.path.join(vmc_path,'vmc.g003.twistnum_3.in.xml') - assert(os.path.exists(vmc_infile)) - - files_bef = ''' - vmc.avg.s000.SpinDensity_u+d+err.xsf vmc.avg.s000.SpinDensity_u+d-err.xsf - vmc.avg.s000.SpinDensity_u+d.xsf vmc.g000.twistnum_0.in.xml - vmc.g000.s000.scalar.dat vmc.g001.s000.scalar.dat - vmc.g000.twistnum_0.in.g000.qmc vmc.g001.twistnum_1.in.g001.qmc - vmc.g001.twistnum_1.in.xml vmc.g002.twistnum_2.in.xml - vmc.g002.s000.scalar.dat vmc.g003.s000.scalar.dat - vmc.g002.twistnum_2.in.g002.qmc vmc.g003.twistnum_3.in.g003.qmc - vmc.g003.twistnum_3.in.xml vmc.out - vmc.in vmc.info.xml - '''.split() - - qr_dmc_files_path = testing.unit_test_file_path('qdens_radial','diamond_twist/dmc') - command = 'rsync -a {} {}'.format(qr_dmc_files_path,tpath) - out,err,rc = execute(command) - assert(rc==0) - dmc_path = os.path.join(tpath,'dmc') - dmc_infile = os.path.join(dmc_path,'dmc.g000.twistnum_0.in.xml') - assert(os.path.exists(dmc_infile)) - dmc_infile = os.path.join(dmc_path,'dmc.g001.twistnum_1.in.xml') - assert(os.path.exists(dmc_infile)) - dmc_infile = os.path.join(dmc_path,'dmc.g002.twistnum_2.in.xml') - assert(os.path.exists(dmc_infile)) - dmc_infile = os.path.join(dmc_path,'dmc.g003.twistnum_3.in.xml') - assert(os.path.exists(dmc_infile)) - - files_bef = ''' - dmc.avg.s001.SpinDensity_u+d+err.xsf dmc.avg.s001.SpinDensity_u+d-err.xsf - dmc.avg.s001.SpinDensity_u+d.xsf dmc.g001.s001.scalar.dat - dmc.g000.s000.scalar.dat dmc.g000.s001.scalar.dat - dmc.g000.twistnum_0.in.g000.qmc dmc.g001.twistnum_1.in.g001.qmc - dmc.g000.twistnum_0.in.xml dmc.g001.twistnum_1.in.xml - dmc.g001.s000.scalar.dat dmc.g002.s000.scalar.dat - dmc.g002.s001.scalar.dat dmc.g003.s001.scalar.dat - dmc.g002.twistnum_2.in.g002.qmc dmc.g003.twistnum_3.in.g003.qmc - dmc.g002.twistnum_2.in.xml dmc.g003.twistnum_3.in.xml - dmc.g003.s000.scalar.dat dmc.in - dmc.out - '''.split() - - assert(check_value_eq(set(os.listdir(dmc_path)),set(files_bef))) +def test_radial_density(): + _ = pytest.importorskip("spglib") + import os + + exe = TEST_DIR.parent / "bin/qdens-radial" + + vmc_path = TEST_DIR / "test_qdens_radial_files/diamond_twist/vmc" + + vmc_files_bef = ( + vmc_path / "vmc.avg.s000.SpinDensity_u+d+err.xsf", + vmc_path / "vmc.avg.s000.SpinDensity_u+d-err.xsf", + vmc_path / "vmc.avg.s000.SpinDensity_u+d.xsf", + vmc_path / "vmc.g000.s000.scalar.dat", + vmc_path / "vmc.g001.s000.scalar.dat", + vmc_path / "vmc.g002.s000.scalar.dat", + vmc_path / "vmc.g003.s000.scalar.dat", + vmc_path / "vmc.g000.twistnum_0.in.g000.qmc", + vmc_path / "vmc.g001.twistnum_1.in.g001.qmc", + vmc_path / "vmc.g002.twistnum_2.in.g002.qmc", + vmc_path / "vmc.g003.twistnum_3.in.g003.qmc", + vmc_path / "vmc.g000.twistnum_0.in.xml", + vmc_path / "vmc.g001.twistnum_1.in.xml", + vmc_path / "vmc.g002.twistnum_2.in.xml", + vmc_path / "vmc.g003.twistnum_3.in.xml", + vmc_path / "vmc.in", + vmc_path / "vmc.out", + vmc_path / "vmc.info.xml", + ) + + assert(check_value_eq(set(vmc_path.iterdir()),set(vmc_files_bef))) + + dmc_path = TEST_DIR / "test_qdens_radial_files/diamond_twist/dmc" + + dmc_files_bef = ( + dmc_path / "dmc.avg.s001.SpinDensity_u+d+err.xsf", + dmc_path / "dmc.avg.s001.SpinDensity_u+d-err.xsf", + dmc_path / "dmc.avg.s001.SpinDensity_u+d.xsf", + dmc_path / "dmc.g000.s000.scalar.dat", + dmc_path / "dmc.g000.s001.scalar.dat", + dmc_path / "dmc.g001.s000.scalar.dat", + dmc_path / "dmc.g001.s001.scalar.dat", + dmc_path / "dmc.g002.s000.scalar.dat", + dmc_path / "dmc.g002.s001.scalar.dat", + dmc_path / "dmc.g003.s000.scalar.dat", + dmc_path / "dmc.g003.s001.scalar.dat", + dmc_path / "dmc.g000.twistnum_0.in.g000.qmc", + dmc_path / "dmc.g001.twistnum_1.in.g001.qmc", + dmc_path / "dmc.g002.twistnum_2.in.g002.qmc", + dmc_path / "dmc.g003.twistnum_3.in.g003.qmc", + dmc_path / "dmc.g000.twistnum_0.in.xml", + dmc_path / "dmc.g001.twistnum_1.in.xml", + dmc_path / "dmc.g002.twistnum_2.in.xml", + dmc_path / "dmc.g003.twistnum_3.in.xml", + dmc_path / "dmc.in", + dmc_path / "dmc.out", + ) + + assert(check_value_eq(set(dmc_path.iterdir()),set(dmc_files_bef))) # VMC non-cumulative - command = '{0} -s C -r 0.6 {1}/vmc.avg.s000.SpinDensity_u+d.xsf'.format(exe,vmc_path) - out,err,rc = execute(command) + command = f'{exe} -s C -r 0.6 {vmc_path}/vmc.avg.s000.SpinDensity_u+d.xsf' + out,err,rc = execute(command) - # Assert that return code is 0 - assert(rc==0) + # Assert that return code is 0 + assert(rc==0) - # Assert that output is consistent with reference - out_ref = ''' + # Assert that output is consistent with reference + out_ref = ''' Norm: tot = 8.00000003 - + Non-Cumulative Value of C Species at Cutoff 0.6 is: 4.77326491 ''' - assert(text_eq(out,out_ref)) + assert(text_eq(out,out_ref)) # VMC cumulative - command = '{0} -s C -r 0.6 -c {1}/vmc.avg.s000.SpinDensity_u+d.xsf'.format(exe,vmc_path) - out,err,rc = execute(command) + command = f'{exe} -s C -r 0.6 -c {vmc_path}/vmc.avg.s000.SpinDensity_u+d.xsf' + out,err,rc = execute(command) - # Assert that return code is 0 - assert(rc==0) + # Assert that return code is 0 + assert(rc==0) - # Assert that output is consistent with reference - out_ref = ''' + # Assert that output is consistent with reference + out_ref = ''' Norm: tot = 8.00000003 - + Cumulative Value of C Species at Cutoff 0.6 is: 1.06842486 ''' # DMC extrapolated non-cumulative - command = '{0} -s C -r 0.6 --vmc={1}/vmc.avg.s000.SpinDensity_u+d.xsf {2}/dmc.avg.s001.SpinDensity_u+d.xsf'.format(exe,vmc_path,dmc_path) - out,err,rc = execute(command) + command = f'{exe} -s C -r 0.6 --vmc={vmc_path}/vmc.avg.s000.SpinDensity_u+d.xsf {dmc_path}/dmc.avg.s001.SpinDensity_u+d.xsf' + out,err,rc = execute(command) - # Assert that return code is 0 - assert(rc==0) + # Assert that return code is 0 + assert(rc==0) - # Assert that output is consistent with reference - out_ref = ''' + # Assert that output is consistent with reference + out_ref = ''' Extrapolating from VMC and DMC densities... Norm: tot = 7.999999969999998 - + Non-Cumulative Value of C Species at Cutoff 0.6 is: 4.91009396 ''' - assert(text_eq(out,out_ref)) + assert(text_eq(out,out_ref)) # DMC extrapolated cumulative - command = '{0} -s C -r 0.6 -c --vmc={1}/vmc.avg.s000.SpinDensity_u+d.xsf {2}/dmc.avg.s001.SpinDensity_u+d.xsf'.format(exe,vmc_path,dmc_path) - out,err,rc = execute(command) + command = f'{exe} -s C -r 0.6 -c --vmc={vmc_path}/vmc.avg.s000.SpinDensity_u+d.xsf {dmc_path}/dmc.avg.s001.SpinDensity_u+d.xsf' + out,err,rc = execute(command) - # Assert that return code is 0 - assert(rc==0) + # Assert that return code is 0 + assert(rc==0) - # Assert that output is consistent with reference - out_ref = ''' + # Assert that output is consistent with reference + out_ref = ''' Extrapolating from VMC and DMC densities... Norm: tot = 7.999999969999998 - + Cumulative Value of C Species at Cutoff 0.6 is: 1.10782675 ''' - assert(text_eq(out,out_ref)) + assert(text_eq(out,out_ref)) # DMC extrapolated cumulative with error bar - command = '{0} -s C -r 0.6 -c -n 3 --seed=0 --vmc={1}/vmc.avg.s000.SpinDensity_u+d.xsf --vmcerr={1}/vmc.avg.s000.SpinDensity_u+d+err.xsf --dmcerr={2}/dmc.avg.s001.SpinDensity_u+d+err.xsf {2}/dmc.avg.s001.SpinDensity_u+d.xsf'.format(exe,vmc_path,dmc_path) - out,err,rc = execute(command) + command = f'{exe} -s C -r 0.6 -c -n 3 --seed=0 --vmc={vmc_path}/vmc.avg.s000.SpinDensity_u+d.xsf --vmcerr={vmc_path}/vmc.avg.s000.SpinDensity_u+d+err.xsf --dmcerr={dmc_path}/dmc.avg.s001.SpinDensity_u+d+err.xsf {dmc_path}/dmc.avg.s001.SpinDensity_u+d.xsf' + out,err,rc = execute(command) - # Assert that return code is 0 - assert(rc==0) + # Assert that return code is 0 + assert(rc==0) - # Assert that output is consistent with reference - out_ref = ''' + # Assert that output is consistent with reference + out_ref = ''' Extrapolating from VMC and DMC densities... Resampling to obtain error bar (NOTE: This can be slow)... Will compute 3 samples... @@ -149,9 +149,8 @@ def test_radial_density(): sample: 2 Norm: tot = 7.999999969999998 - + Cumulative Value of C Species at Cutoff 0.6 is: 1.10782675 +/- 0.00160665 ''' - assert(text_eq(out,out_ref,atol=1e-8)) - #end def test_radial_density -#end if + assert(text_eq(out,out_ref,atol=1e-8)) +#end def test_radial_density diff --git a/nexus/nexus/tests/test_qmc_fit.py b/nexus/nexus/tests/test_qmc_fit.py index 3dc764f768..e5c37e0d1a 100644 --- a/nexus/nexus/tests/test_qmc_fit.py +++ b/nexus/nexus/tests/test_qmc_fit.py @@ -1,44 +1,42 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QMC_FIT) -from .. import versions -from .. import testing +from ..generic import generic_settings +generic_settings.raise_error = True + +from . import TEST_DIR from ..testing import execute,text_eq -if versions.scipy_available: - def test_fit(): - import os +def test_fit(tmp_path): + _ = pytest.importorskip("scipy") + import os - tpath = testing.setup_unit_test_output_directory('qmc_fit','test_fit') + exe = TEST_DIR.parent / "bin/qmc-fit" + dmc_path = TEST_DIR / "test_qmcpack_analyzer_files/diamond_gamma/dmc" - exe = testing.executable_path('qmc-fit') - - qa_files_path = testing.unit_test_file_path('qmcpack_analyzer','diamond_gamma/dmc') - command = 'rsync -a {} {}'.format(qa_files_path,tpath) - out,err,rc = execute(command) - assert(rc==0) - dmc_path = os.path.join(tpath,'dmc') - dmc_infile = os.path.join(dmc_path,'dmc.in.xml') - assert(os.path.exists(dmc_infile)) + dmc_infile = dmc_path / 'dmc.in.xml' + assert(dmc_infile.exists()) - command = "{} ts --noplot -e 10 -s 1 -t '0.02 0.01 0.005' -f linear {}/*scalar*".format(exe,dmc_path) + command = f"{exe} ts --noplot -e 10 -s 1 -t '0.02 0.01 0.005' -f linear {dmc_path}/*scalar*" - out,err,rc = execute(command) + out,err,rc = execute(command) - out_ref = ''' - fit function : linear - fitted formula: (-10.5271 +/- 0.0021) + (-0.28 +/- 0.17)*t - intercept : -10.5271 +/- 0.0021 Ha - ''' - - def process_text(t): - return t.replace('(',' ( ').replace(')',' ) ') - #end def process_text + out_ref = ''' + fit function : linear + fitted formula: (-10.5271 +/- 0.0021) + (-0.28 +/- 0.17)*t + intercept : -10.5271 +/- 0.0021 Ha + ''' + + def process_text(t): + return t.replace('(',' ( ').replace(')',' ) ') + #end def process_text - out = process_text(out) - out_ref = process_text(out_ref) + out = process_text(out) + out_ref = process_text(out_ref) - assert(text_eq(out,out_ref,atol=1e-2,rtol=1e-2)) + assert(text_eq(out,out_ref,atol=1e-2,rtol=1e-2)) - #end def test_fit -#end if +#end def test_fit diff --git a/nexus/nexus/tests/test_qmca.py b/nexus/nexus/tests/test_qmca.py index 668ac46d3e..a1f64bf5bd 100644 --- a/nexus/nexus/tests/test_qmca.py +++ b/nexus/nexus/tests/test_qmca.py @@ -1,87 +1,37 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QMCA) + +from ..generic import generic_settings +generic_settings.raise_error = True import sys -from .. import testing +import os +from pathlib import Path +from . import TEST_DIR from ..testing import execute,text_eq -test_info = dict() -directories = dict() - - -def get_test_info(): - if len(test_info)==0: - import os - - tpath = testing.setup_unit_test_output_directory('qmca','test_qmca') - - exe = testing.executable_path('qmca') - - dirs = ['diamond_gamma','diamond_twist'] - - for dir in dirs: - qa_files_path = testing.unit_test_file_path('qmcpack_analyzer',dir) - command = 'rsync -a {} {}'.format(qa_files_path,tpath) - out,err,rc = execute(command) - assert(rc==0) - data_path = os.path.join(tpath,dir) - assert(os.path.exists(data_path)) - #end for - - paths = dict( - vmc = 'diamond_gamma/vmc', - opt = 'diamond_gamma/opt', - dmc = 'diamond_gamma/dmc', - vmc_twist = 'diamond_twist/vmc', - multi = 'diamond_gamma', - ) - - test_info['tpath'] = tpath - test_info['exe'] = exe - for name,path in paths.items(): - directories[name] = os.path.join(tpath,path) - #end for - #end if -#end def get_test_info - - -def get_exe(): - get_test_info() - return test_info['exe'] -#end def get_exe - - -def enter(path_name): - import os - assert(path_name in directories) - path = directories[path_name] - assert(os.path.exists(path)) - assert('cwd' not in directories) - directories['cwd'] = os.getcwd() - assert('cwd' in directories) - os.chdir(path) -#end def enter - - -def leave(): - import os - assert('cwd' in directories) - cwd = directories.pop('cwd') - assert(not 'cwd' in directories) - os.chdir(cwd) -#end def leave +QMCA_EXE = TEST_DIR.parent / "bin/qmca" +QA_PATHS = { + "vmc": TEST_DIR / "test_qmcpack_analyzer_files/diamond_gamma/vmc", + "opt": TEST_DIR / "test_qmcpack_analyzer_files/diamond_gamma/opt", + "dmc": TEST_DIR / "test_qmcpack_analyzer_files/diamond_gamma/dmc", + "vmc_twist": TEST_DIR / "test_qmcpack_analyzer_files/diamond_twist/vmc", + "multi": TEST_DIR / "test_qmcpack_analyzer_files/diamond_gamma", + } def test_help(): - exe = get_exe() help_text = 'Usage: qmca' - command = sys.executable+' {}'.format(exe) + command = f'{sys.executable} {QMCA_EXE}' out,err,rc = execute(command) assert(help_text in out) - command = sys.executable+' {} -h'.format(exe) + command = f'{sys.executable} {QMCA_EXE} -h' out,err,rc = execute(command) assert(help_text in out) #end def test_help @@ -89,11 +39,10 @@ def test_help(): def test_examples(): - exe = get_exe() example_text = 'QMCA examples' - command = sys.executable+' {} -x'.format(exe) + command = f'{sys.executable} {QMCA_EXE} -x' out,err,rc = execute(command) assert(example_text in out) #end def test_examples @@ -101,11 +50,11 @@ def test_examples(): def test_unit_conversion(): - exe = get_exe() - enter('vmc') + cwd = Path.cwd() + os.chdir(QA_PATHS["vmc"]) - command = sys.executable+' {} -e 5 -q e -u eV --fp=16.8f *scalar*'.format(exe) + command = f'{sys.executable} {QMCA_EXE} -e 5 -q e -u eV --fp=16.8f *scalar*' out,err,rc = execute(command) out_ref = ''' @@ -114,17 +63,17 @@ def test_unit_conversion(): assert(text_eq(out,out_ref)) - leave() + os.chdir(cwd) #end def test_unit_conversion def test_selected_quantities(): - exe = get_exe() - enter('vmc') + cwd = Path.cwd() + os.chdir(QA_PATHS["vmc"]) - command = sys.executable+" {} -e 5 -q 'e k p' --fp=16.8f *scalar*".format(exe) + command = f"{sys.executable} {QMCA_EXE} -e 5 -q 'e k p' --fp=16.8f *scalar*" out,err,rc = execute(command) out_ref = ''' @@ -136,17 +85,17 @@ def test_selected_quantities(): assert(text_eq(out,out_ref)) - leave() + os.chdir(cwd) #end def test_selected_quantities def test_all_quantities(): - exe = get_exe() - enter('vmc') + cwd = Path.cwd() + os.chdir(QA_PATHS["vmc"]) - command = sys.executable+" {} -e 5 --fp=16.8f *scalar*".format(exe) + command = f"{sys.executable} {QMCA_EXE} -e 5 --fp=16.8f *scalar*" out,err,rc = execute(command) out_ref = ''' @@ -173,17 +122,17 @@ def test_all_quantities(): assert(text_eq(out,out_ref)) - leave() + os.chdir(cwd) #end def test_all_quantities def test_energy_variance(): - exe = get_exe() - enter('opt') + cwd = Path.cwd() + os.chdir(QA_PATHS["opt"]) - command = sys.executable+" {} -e 5 -q ev --fp=16.8f *scalar*".format(exe) + command = f"{sys.executable} {QMCA_EXE} -e 5 -q ev --fp=16.8f *scalar*" out,err,rc = execute(command) out_ref = ''' @@ -198,17 +147,17 @@ def test_energy_variance(): assert(text_eq(out,out_ref)) - leave() + os.chdir(cwd) #end def test_energy_variance def test_multiple_equilibration(): - exe = get_exe() - enter('dmc') + cwd = Path.cwd() + os.chdir(QA_PATHS["dmc"]) - command = sys.executable+" {} -e '5 10 15 20' -q ev --fp=16.8f *scalar*".format(exe) + command = f"{sys.executable} {QMCA_EXE} -e '5 10 15 20' -q ev --fp=16.8f *scalar*" out,err,rc = execute(command) out_ref = ''' @@ -221,17 +170,17 @@ def test_multiple_equilibration(): assert(text_eq(out,out_ref)) - leave() + os.chdir(cwd) #end def test_multiple_equilibration def test_join(): - exe = get_exe() - enter('dmc') + cwd = Path.cwd() + os.chdir(QA_PATHS["dmc"]) - command = sys.executable+" {} -e 5 -j '1 3' -q ev --fp=16.8f *scalar*".format(exe) + command = f"{sys.executable} {QMCA_EXE} -e 5 -j '1 3' -q ev --fp=16.8f *scalar*" out,err,rc = execute(command) out_ref = ''' @@ -242,17 +191,17 @@ def test_join(): assert(text_eq(out,out_ref)) - leave() + os.chdir(cwd) #end def test_join def test_multiple_directories(): - exe = get_exe() - enter('multi') + cwd = Path.cwd() + os.chdir(QA_PATHS["multi"]) - command = sys.executable+" {} -e 5 -q ev --fp=16.8f */*scalar*".format(exe) + command = f"{sys.executable} {QMCA_EXE} -e 5 -q ev --fp=16.8f */*scalar*" out,err,rc = execute(command) out_ref = ''' @@ -274,17 +223,17 @@ def test_multiple_directories(): assert(text_eq(out,out_ref)) - leave() + os.chdir(cwd) #end def test_multiple_directories def test_twist_average(): - exe = get_exe() - enter('vmc_twist') + cwd = Path.cwd() + os.chdir(QA_PATHS["vmc_twist"]) - command = sys.executable+" {} -a -e 5 -q ev --fp=16.8f *scalar*".format(exe) + command = f"{sys.executable} {QMCA_EXE} -a -e 5 -q ev --fp=16.8f *scalar*" out,err,rc = execute(command) out_ref = ''' @@ -294,17 +243,17 @@ def test_twist_average(): assert(text_eq(out,out_ref)) - leave() + os.chdir(cwd) #end def test_twist_average def test_weighted_twist_average(): - exe = get_exe() - enter('vmc_twist') + cwd = Path.cwd() + os.chdir(QA_PATHS["vmc_twist"]) - command = sys.executable+" {} -a -w '1 3 3 1' -e 5 -q ev --fp=16.8f *scalar*".format(exe) + command = f"{sys.executable} {QMCA_EXE} -a -w '1 3 3 1' -e 5 -q ev --fp=16.8f *scalar*" out,err,rc = execute(command) out_ref = ''' @@ -314,6 +263,6 @@ def test_weighted_twist_average(): assert(text_eq(out,out_ref)) - leave() + os.chdir(cwd) #end def test_weighted_twist_average diff --git a/nexus/nexus/tests/test_qmcpack_analyzer.py b/nexus/nexus/tests/test_qmcpack_analyzer.py index 459da7b90e..474cbe0035 100644 --- a/nexus/nexus/tests/test_qmcpack_analyzer.py +++ b/nexus/nexus/tests/test_qmcpack_analyzer.py @@ -1,14 +1,12 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QMCPACK_ANALYZER) -from .. import versions -from .. import testing -from ..testing import divert_nexus_log,restore_nexus_log -from ..testing import value_eq,object_eq,text_eq,print_diff - - -def test_import(): - from ..qmcpack_analyzer import QmcpackAnalyzer -#end def test_import +from ..generic import generic_settings +generic_settings.raise_error = True +from . import isolate_nexus_core, TEST_DIR +from ..testing import value_eq,object_eq,text_eq def test_empty_init(): @@ -65,18 +63,13 @@ def test_empty_init(): def test_vmc_dmc_analysis(): - import os from ..developer import obj from ..qmcpack_analyzer import QmcpackAnalyzer - tpath = testing.setup_unit_test_output_directory( - test = 'qmcpack_analyzer', - subtest = 'test_vmc_dmc_analysis', - file_sets = ['diamond_gamma'], - ) + test_files = TEST_DIR / "test_qmcpack_analyzer_files/diamond_gamma" # test load of vmc data - infile = os.path.join(tpath,'diamond_gamma/vmc/vmc.in.xml') + infile = test_files / 'vmc/vmc.in.xml' qa = QmcpackAnalyzer(infile) @@ -210,7 +203,7 @@ def test_vmc_dmc_analysis(): # test analysis of dmc data - infile = os.path.join(tpath,'diamond_gamma/dmc/dmc.in.xml') + infile = test_files / 'dmc/dmc.in.xml' qa = QmcpackAnalyzer(infile,analyze=True,equilibration=5) @@ -231,26 +224,16 @@ def test_vmc_dmc_analysis(): }) assert(object_eq(le,le_ref)) - #end def test_vmc_dmc_analysis - +@isolate_nexus_core def test_optimization_analysis(): - import os from numpy import array from ..developer import obj from ..qmcpack_analyzer import QmcpackAnalyzer - - tpath = testing.setup_unit_test_output_directory( - test = 'qmcpack_analyzer', - subtest = 'test_optimization_analysis', - file_sets = ['diamond_gamma'], - ) - divert_nexus_log() - - infile = os.path.join(tpath,'diamond_gamma/opt/opt.in.xml') + infile = TEST_DIR / "test_qmcpack_analyzer_files/diamond_gamma/opt/opt.in.xml" qa = QmcpackAnalyzer(infile,analyze=True,equilibration=5) @@ -376,25 +359,15 @@ def test_optimization_analysis(): ) assert(object_eq(opt.to_obj(),opt_ref,atol=1e-8)) - - restore_nexus_log() #end def test_optimization_analysis def test_twist_average_analysis(): - import os from ..developer import obj from ..qmcpack_analyzer import QmcpackAnalyzer - tpath = testing.setup_unit_test_output_directory( - test = 'qmcpack_analyzer', - subtest = 'test_twist_average_analysis', - file_sets = ['diamond_twist'], - ) - - # test analysis of twist averaged vmc data - infile = os.path.join(tpath,'diamond_twist/vmc/vmc.in') + infile = TEST_DIR / "test_qmcpack_analyzer_files/diamond_twist/vmc/vmc.in" qa = QmcpackAnalyzer(infile,analyze=True,equilibration=5) @@ -429,59 +402,48 @@ def test_twist_average_analysis(): le_avg = qa.qmc[0].scalars.LocalEnergy.mean le_avg_ref = -11.343673354655264 assert(value_eq(le_avg,le_avg_ref)) - #end def test_twist_average_analysis -if versions.h5py_available: - def test_density_analysis(): - import os - from numpy import array - from ..developer import obj - from ..qmcpack_analyzer import QmcpackAnalyzer - - tpath = testing.setup_unit_test_output_directory( - test = 'qmcpack_analyzer', - subtest = 'test_density_analysis', - file_sets = ['diamond_gamma'], - ) - - infile = os.path.join(tpath,'diamond_gamma/dmc/dmc.in.xml') - - qa = QmcpackAnalyzer(infile,analyze=True,equilibration=5) +def test_density_analysis(): + _ = pytest.importorskip("h5py") + import os + from numpy import array + from ..qmcpack_analyzer import QmcpackAnalyzer - qmc = qa.qmc[0] + infile = TEST_DIR / "test_qmcpack_analyzer_files/diamond_gamma/dmc/dmc.in.xml" + qa = QmcpackAnalyzer(infile,analyze=True,equilibration=5) - qmc_keys = 'info data scalars scalars_hdf SpinDensity'.split() - assert(set(qmc.keys())==set(qmc_keys)) + qmc = qa.qmc[0] - sd = qmc.SpinDensity + qmc_keys = 'info data scalars scalars_hdf SpinDensity'.split() + assert(set(qmc.keys())==set(qmc_keys)) - sd_keys = 'info method_info data u d'.split() - assert(set(sd.keys())==set(sd_keys)) + sd = qmc.SpinDensity - d_keys = 'mean error'.split() - assert(set(sd.u.keys())==set(d_keys)) - assert(set(sd.d.keys())==set(d_keys)) + sd_keys = 'info method_info data u d'.split() + assert(set(sd.keys())==set(sd_keys)) - d_mean = sd.u.mean + sd.d.mean + d_keys = 'mean error'.split() + assert(set(sd.u.keys())==set(d_keys)) + assert(set(sd.d.keys())==set(d_keys)) - d_mean_ref = array( - [[[0.72833333, 0.604 , 0.514 ], - [0.63666667, 0.19533333, 0.19683333], - [0.51166667, 0.19183333, 0.4175 ]], - [[0.6065 , 0.19533333, 0.19 ], - [0.19066667, 0.052 , 0.129 ], - [0.18783333, 0.13433333, 0.10483333]], - [[0.50633333, 0.19633333, 0.42483333], - [0.1775 , 0.12966667, 0.09983333], - [0.417 , 0.106 , 0.15583333]]], - dtype=float) + d_mean = sd.u.mean + sd.d.mean - assert(d_mean.shape==(3,3,3)) - assert(value_eq(d_mean,d_mean_ref)) + d_mean_ref = array( + [[[0.72833333, 0.604 , 0.514 ], + [0.63666667, 0.19533333, 0.19683333], + [0.51166667, 0.19183333, 0.4175 ]], + [[0.6065 , 0.19533333, 0.19 ], + [0.19066667, 0.052 , 0.129 ], + [0.18783333, 0.13433333, 0.10483333]], + [[0.50633333, 0.19633333, 0.42483333], + [0.1775 , 0.12966667, 0.09983333], + [0.417 , 0.106 , 0.15583333]]], + dtype=float) - #end def test_density_analysis -#end if + assert(d_mean.shape==(3,3,3)) + assert(value_eq(d_mean,d_mean_ref)) +#end def test_density_analysis diff --git a/nexus/nexus/tests/test_qmcpack_converter_analyzers.py b/nexus/nexus/tests/test_qmcpack_converter_analyzers.py index 7fe12ddec7..7733e8fda7 100644 --- a/nexus/nexus/tests/test_qmcpack_converter_analyzers.py +++ b/nexus/nexus/tests/test_qmcpack_converter_analyzers.py @@ -1,11 +1,9 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QMCPACK_CONVERTER_ANALYZERS) - - -def test_import(): - from ..qmcpack_converters import Pw2qmcpackAnalyzer - from ..qmcpack_converters import Convert4qmcAnalyzer - from ..qmcpack_converters import PyscfToAfqmcAnalyzer -#end def import +from ..generic import generic_settings +generic_settings.raise_error = True diff --git a/nexus/nexus/tests/test_qmcpack_converter_input.py b/nexus/nexus/tests/test_qmcpack_converter_input.py index af18461410..b26b77359e 100644 --- a/nexus/nexus/tests/test_qmcpack_converter_input.py +++ b/nexus/nexus/tests/test_qmcpack_converter_input.py @@ -1,20 +1,12 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QMCPACK_CONVERTER_INPUT) -from .. import testing -from ..testing import value_eq,object_eq,text_eq - - - -def test_import(): - from ..qmcpack_converters import Pw2qmcpackInput - from ..qmcpack_converters import generate_pw2qmcpack_input - - from ..qmcpack_converters import Convert4qmcInput - from ..qmcpack_converters import generate_convert4qmc_input - - from ..qmcpack_converters import PyscfToAfqmcInput - from ..qmcpack_converters import generate_pyscf_to_afqmc_input -#end def test_import +from ..generic import generic_settings +generic_settings.raise_error = True +from .. import testing +from ..testing import value_eq,object_eq @@ -36,15 +28,12 @@ def test_pw2qmcpack_input_empty_init(): -def test_pw2qmcpack_input_read(): - import os +def test_pw2qmcpack_input_read(tmp_path): from ..developer import obj from ..qmcpack_converters import Pw2qmcpackInput - tpath = testing.setup_unit_test_output_directory('qmcpack_converter_input','test_pw2qmcpack_input_read') - - infile_path = os.path.join(tpath,'p2q.in') - open(infile_path,'w').write(pw2qmcpack_in) + infile_path = tmp_path / 'p2q.in' + infile_path.write_text(pw2qmcpack_in) pi = Pw2qmcpackInput(infile_path) @@ -60,17 +49,14 @@ def test_pw2qmcpack_input_read(): -def test_pw2qmcpack_input_write(): - import os +def test_pw2qmcpack_input_write(tmp_path): from ..developer import obj from ..qmcpack_converters import Pw2qmcpackInput - tpath = testing.setup_unit_test_output_directory('qmcpack_converter_input','test_pw2qmcpack_input_write') - - infile_path = os.path.join(tpath,'p2q.in') - open(infile_path,'w').write(pw2qmcpack_in) + infile_path = tmp_path / 'p2q.in' + infile_path.write_text(pw2qmcpack_in) - write_path = os.path.join(tpath,'p2q_write.in') + write_path = tmp_path / 'p2q_write.in' pi_write = Pw2qmcpackInput(infile_path) pi_write.write(write_path) diff --git a/nexus/nexus/tests/test_qmcpack_converter_simulations.py b/nexus/nexus/tests/test_qmcpack_converter_simulations.py index 6387946696..9abf0e8d86 100644 --- a/nexus/nexus/tests/test_qmcpack_converter_simulations.py +++ b/nexus/nexus/tests/test_qmcpack_converter_simulations.py @@ -1,8 +1,17 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QMCPACK_CONVERTER_SIMULATIONS) -from .. import testing -from ..testing import divert_nexus,restore_nexus,clear_all_sims +from ..generic import generic_settings +generic_settings.raise_error = True + +from pathlib import Path + +from . import isolate_nexus_core, create_pseudo_files +from nexus.nexus_base import nexus_core +from ..testing import clear_all_sims from ..testing import failed,FailedTest -from ..testing import value_eq,object_eq,text_eq +from ..testing import object_eq #====================================================================# @@ -25,12 +34,6 @@ def get_pw2qmcpack_sim(**kwargs): -def test_pw2qmcpack_import(): - from ..qmcpack_converters import Pw2qmcpack,generate_pw2qmcpack -#end def test_pw2qmcpack_import - - - def test_pw2qmcpack_minimal_init(): from ..machines import job from ..qmcpack_converters import Pw2qmcpack,generate_pw2qmcpack @@ -87,13 +90,17 @@ def test_pw2qmcpack_get_result(): #end def test_pw2qmcpack_get_result - -def test_pw2qmcpack_incorporate_result(): - from ..developer import NexusError, obj +@isolate_nexus_core +def test_pw2qmcpack_incorporate_result(tmp_path): + from ..developer import NexusError from ..simulation import Simulation - from .test_pwscf_simulation import pseudo_inputs,get_pwscf_sim + from .test_pwscf_simulation import get_pwscf_sim - tpath = testing.setup_unit_test_output_directory('pwscf_simulation','test_check_result',**pseudo_inputs) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] + + create_pseudo_files(tmp_path, ["C.BFD.upf"]) other = Simulation() @@ -103,7 +110,7 @@ def test_pw2qmcpack_incorporate_result(): try: sim.incorporate_result('unknown',None,other) - raise TestFailed + raise FailedTest except NexusError: None except FailedTest: @@ -115,23 +122,21 @@ def test_pw2qmcpack_incorporate_result(): sim.incorporate_result('orbitals',None,scf) clear_all_sims() - restore_nexus() #end def test_pw2qmcpack_incorporate_result - -def test_pw2qmcpack_check_sim_status(): - import os - from ..developer import NexusError, obj +@isolate_nexus_core +def test_pw2qmcpack_check_sim_status(tmp_path): from ..nexus_base import nexus_core - tpath = testing.setup_unit_test_output_directory('qmcpack_converter_simulations','test_pw2qmcpack_check_sim_status',divert=True) - nexus_core.runs = '' + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] sim = get_pw2qmcpack_sim() - assert(sim.locdir.rstrip('/')==tpath.rstrip('/')) + assert(Path(sim.locdir).resolve() == tmp_path) assert(not sim.finished) assert(not sim.failed) @@ -146,25 +151,20 @@ def test_pw2qmcpack_check_sim_status(): #end try sim.create_directories() - outfile = os.path.join(sim.locdir,sim.outfile) + outfile = Path(sim.locdir) / sim.outfile outfile_text = 'JOB DONE' - out = open(outfile,'w') - out.write(outfile_text) - out.close() - assert(outfile_text in open(outfile,'r').read()) + outfile.write_text(outfile_text) + assert(outfile_text in outfile.read_text()) prefix = sim.input.inputpp.prefix outdir = sim.input.inputpp.outdir - outdir_path = os.path.join(tpath,outdir) - if not os.path.exists(outdir_path): - os.makedirs(outdir_path) - #end if + outdir_path = tmp_path / outdir + outdir_path.mkdir(parents=True) + filenames = [prefix+'.pwscf.h5',prefix+'.ptcl.xml',prefix+'.wfs.xml'] for filename in filenames: - filepath = os.path.join(tpath,outdir,filename) - f = open(filepath,'w') - f.write('') - f.close() - assert(os.path.exists(filepath)) + filepath = outdir_path / filename + filepath.touch() + assert(filepath.exists()) #end for sim.job.finished = True @@ -174,7 +174,6 @@ def test_pw2qmcpack_check_sim_status(): assert(not sim.failed) clear_all_sims() - restore_nexus() #end def test_pw2qmcpack_check_sim_status @@ -198,12 +197,6 @@ def get_convert4qmc_sim(**kwargs): -def test_convert4qmc_import(): - from ..qmcpack_converters import Convert4qmc,generate_convert4qmc -#end def test_convert4qmc_import - - - def test_convert4qmc_minimal_init(): from ..machines import job from ..qmcpack_converters import Convert4qmc,generate_convert4qmc @@ -273,7 +266,6 @@ def test_convert4qmc_incorporate_result(): from ..developer import NexusError, obj from ..simulation import Simulation from ..gamess import Gamess - from ..pyscf_sim import Pyscf from ..quantum_package import QuantumPackage from .test_gamess_simulation import get_gamess_sim from .test_pyscf_simulation import get_pyscf_sim @@ -308,7 +300,7 @@ def test_convert4qmc_incorporate_result(): sim = sim_start.copy() try: sim.incorporate_result('unknown',None,other) - raise TestFailed + raise FailedTest except NexusError: None except FailedTest: @@ -357,19 +349,18 @@ def test_convert4qmc_incorporate_result(): #end def test_convert4qmc_incorporate_result - -def test_convert4qmc_check_sim_status(): - import os - from ..developer import NexusError, obj +@isolate_nexus_core +def test_convert4qmc_check_sim_status(tmp_path): from ..nexus_base import nexus_core - tpath = testing.setup_unit_test_output_directory('qmcpack_converter_simulations','test_convert4qmc_check_sim_status',divert=True) - nexus_core.runs = '' + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] sim = get_convert4qmc_sim() - assert(sim.locdir.rstrip('/')==tpath.rstrip('/')) + assert(Path(sim.locdir).resolve() == tmp_path) assert(not sim.finished) assert(not sim.failed) @@ -384,18 +375,16 @@ def test_convert4qmc_check_sim_status(): #end try sim.create_directories() - outfile = os.path.join(sim.locdir,sim.outfile) + + outfile = Path(sim.locdir).resolve() / sim.outfile outfile_text = 'QMCGaussianParserBase::dump' - out = open(outfile,'w') - out.write(outfile_text) - out.close() + outfile.write_text(outfile_text) + assert(outfile_text in open(outfile,'r').read()) for filename in sim.list_output_files(): - filepath = os.path.join(sim.locdir,filename) - f = open(filepath,'w') - f.write('') - f.close() - assert(os.path.exists(filepath)) + filepath = Path(sim.locdir).resolve() / filename + filepath.touch() + assert(filepath.exists()) #end for sim.job.finished = True @@ -405,7 +394,6 @@ def test_convert4qmc_check_sim_status(): assert(not sim.failed) clear_all_sims() - restore_nexus() #end def test_convert4qmc_check_sim_status @@ -430,12 +418,6 @@ def get_pyscf_to_afqmc_sim(**kwargs): -def test_pyscf_to_afqmc_import(): - from ..qmcpack_converters import PyscfToAfqmc,generate_pyscf_to_afqmc -#end def test_pyscf_to_afqmc_import - - - def test_pyscf_to_afqmc_minimal_init(): from ..machines import job from ..qmcpack_converters import PyscfToAfqmc,generate_pyscf_to_afqmc @@ -517,7 +499,7 @@ def test_pyscf_to_afqmc_incorporate_result(): try: sim.incorporate_result('unknown',None,other) - raise TestFailed + raise FailedTest except NexusError: None except FailedTest: @@ -540,19 +522,18 @@ def test_pyscf_to_afqmc_incorporate_result(): #end def test_pyscf_to_afqmc_incorporate_result - -def test_pyscf_to_afqmc_check_sim_status(): - import os - from ..developer import NexusError, obj +@isolate_nexus_core +def test_pyscf_to_afqmc_check_sim_status(tmp_path): from ..nexus_base import nexus_core - tpath = testing.setup_unit_test_output_directory('qmcpack_converter_simulations','test_pyscf_to_afqmc_check_sim_status',divert=True) - nexus_core.runs = '' + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] sim = get_pyscf_to_afqmc_sim() - assert(sim.locdir.rstrip('/')==tpath.rstrip('/')) + assert(Path(sim.locdir).resolve()==tmp_path) assert(not sim.finished) assert(not sim.failed) @@ -569,17 +550,14 @@ def test_pyscf_to_afqmc_check_sim_status(): sim.input.output = 'afqmc.h5' sim.create_directories() - outfile = os.path.join(sim.locdir,sim.outfile) + outfile = Path(sim.locdir).resolve() / sim.outfile outfile_text = '# Finished.' - out = open(outfile,'w') - out.write(outfile_text) - out.close() - assert(outfile_text in open(outfile,'r').read()) - output_file = os.path.join(sim.locdir,sim.input.output) - f = open(output_file,'w') - f.write('') - f.close() - assert(os.path.exists(output_file)) + outfile.write_text(outfile_text) + + assert(outfile_text in outfile.read_text()) + output_file = Path(sim.locdir).resolve() / sim.input.output + output_file.touch() + assert(output_file.exists()) sim.job.finished = True sim.check_sim_status() @@ -588,5 +566,4 @@ def test_pyscf_to_afqmc_check_sim_status(): assert(not sim.failed) clear_all_sims() - restore_nexus() #end def test_pyscf_to_afqmc_check_sim_status diff --git a/nexus/nexus/tests/test_qmcpack_input.py b/nexus/nexus/tests/test_qmcpack_input.py index fbac3ea30d..eb7b69137d 100644 --- a/nexus/nexus/tests/test_qmcpack_input.py +++ b/nexus/nexus/tests/test_qmcpack_input.py @@ -1,14 +1,21 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QMCPACK_INPUT) -from .. import versions -from .. import testing -from ..testing import divert_nexus_log,restore_nexus_log +from ..generic import generic_settings +generic_settings.raise_error = True + +from . import isolate_nexus_core, TEST_DIR from ..testing import value_eq,object_eq,check_object_eq -associated_files = dict() +TEST_FILES = { + "CH4_afqmc.in.xml": TEST_DIR / "test_qmcpack_input_files/CH4_afqmc.in.xml", + "OH_mixed_pos.in.xml": TEST_DIR / "test_qmcpack_input_files/OH_mixed_pos.in.xml", + "VO2_M1_afm.in.xml": TEST_DIR / "test_qmcpack_input_files/VO2_M1_afm.in.xml", + } -def get_files(): - return testing.collect_unit_test_file_paths('qmcpack_input',associated_files) -#end def get_files +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" def format_value(v): @@ -180,7 +187,7 @@ def generate_serial_references(): 'simulation/qmcsystem/particlesets/ion0/groups/O/valence' : 6, 'simulation/qmcsystem/particlesets/ion0/groups/V/atomicnumber' : 23, 'simulation/qmcsystem/particlesets/ion0/groups/V/charge' : 13, - 'simulation/qmcsystem/particlesets/ion0/groups/V/mass' : 92861.5851912, + 'simulation/qmcsystem/particlesets/ion0/groups/V/mass' : 92860.6737469, 'simulation/qmcsystem/particlesets/ion0/groups/V/name' : 'V', 'simulation/qmcsystem/particlesets/ion0/groups/V/position' : np.array([ [2.45778327, 8.39460555, 0.22661828], @@ -538,26 +545,6 @@ def remove_metadata(s): #end def check_vs_serial_reference - -def test_files(): - filenames = [ - 'VO2_M1_afm.in.xml', - 'CH4_afqmc.in.xml', - 'OH_mixed_pos.in.xml', - ] - files = get_files() - assert(set(filenames)==set(files.keys())) -#end def test_files - - - -def test_import(): - from ..qmcpack_input import QmcpackInput - from ..qmcpack_input import simulation,meta,section -#end def test_import - - - def test_qixml_class_init(): from ..developer import obj from ..qmcpack_input import classes @@ -687,7 +674,7 @@ def test_compose(): charge = 13, valence = 13, atomicnumber = 23, - mass = 92861.5851912, + mass = 92860.6737469, position = np.array([ [ 2.45778327, 8.39460555, 0.22661828], [ 8.41192147, 8.75579295, -0.22661828], @@ -1393,9 +1380,7 @@ def test_read(): import numpy as np from ..qmcpack_input import QmcpackInput - files = get_files() - - qi_read = QmcpackInput(files['VO2_M1_afm.in.xml']) + qi_read = QmcpackInput(TEST_FILES['VO2_M1_afm.in.xml']) assert(not qi_read.is_afqmc_input()) qi_read.pluralize() assert(not qi_read.is_afqmc_input()) @@ -1417,14 +1402,14 @@ def test_read(): # test read for afqmc input file - qi = QmcpackInput(files['CH4_afqmc.in.xml']) + qi = QmcpackInput(TEST_FILES['CH4_afqmc.in.xml']) assert(qi.is_afqmc_input()) check_vs_serial_reference(qi,'CH4_afqmc.in.xml read') # test reading mixed integer/float positions - qi = QmcpackInput(files['OH_mixed_pos.in.xml']) + qi = QmcpackInput(TEST_FILES['OH_mixed_pos.in.xml']) pos = qi.qmcsystem.particlesets.ion0.position assert pos.dtype==float pos_ref = np.array( @@ -1436,19 +1421,14 @@ def test_read(): -def test_write(): - import os +def test_write(tmp_path): from ..qmcpack_input import QmcpackInput - tpath = testing.setup_unit_test_output_directory('qmcpack_input','test_write') - - files = get_files() - # test write real space qmc input file ref_file = 'VO2_M1_afm.in.xml' - write_file = os.path.join(tpath,'write_'+ref_file) + write_file = tmp_path / ('write_'+ref_file) - qi_read = QmcpackInput(files[ref_file]) + qi_read = QmcpackInput(TEST_FILES[ref_file]) text = qi_read.write() assert('' in text) @@ -1499,9 +1479,9 @@ def test_write(): # test write for afqmc input file ref_file = 'CH4_afqmc.in.xml' - write_file = os.path.join(tpath,'write_'+ref_file) + write_file = tmp_path / ('write_'+ref_file) - qi_read = QmcpackInput(files[ref_file]) + qi_read = QmcpackInput(TEST_FILES[ref_file]) text = qi_read.write() assert(' + qmc_optical = generate_qmcpack_input( + det_format = 'old', + input_type = 'basic', + spin_polarized = True, + system = dia, + excitation = ['up', 'gamma vb x cb'], + jastrows = [], + qmc = 'vmc', + ) + + expect = ''' 0 5 3 6 @@ -2190,21 +2165,21 @@ def test_symbolic_excited_state(): '''.strip() - text = qmc_optical.get('slaterdeterminant').write().strip() - assert(text==expect) - - - qmc_optical = generate_qmcpack_input( - det_format = 'old', - input_type = 'basic', - spin_polarized = True, - system = dia, - excitation = ['up', 'gamma vb-1 x cb'], - jastrows = [], - qmc = 'vmc', - ) + text = qmc_optical.get('slaterdeterminant').write().strip() + assert(text==expect) + + + qmc_optical = generate_qmcpack_input( + det_format = 'old', + input_type = 'basic', + spin_polarized = True, + system = dia, + excitation = ['up', 'gamma vb-1 x cb'], + jastrows = [], + qmc = 'vmc', + ) - expect = ''' + expect = ''' 0 4 3 6 @@ -2214,21 +2189,21 @@ def test_symbolic_excited_state(): '''.strip() - text = qmc_optical.get('slaterdeterminant').write().strip() - assert(text==expect) - - - qmc_optical = generate_qmcpack_input( - det_format = 'old', - input_type = 'basic', - spin_polarized = True, - system = dia, - excitation = ['up', 'gamma vb x cb+1'], - jastrows = [], - qmc = 'vmc', - ) + text = qmc_optical.get('slaterdeterminant').write().strip() + assert(text==expect) + - expect = ''' + qmc_optical = generate_qmcpack_input( + det_format = 'old', + input_type = 'basic', + spin_polarized = True, + system = dia, + excitation = ['up', 'gamma vb x cb+1'], + jastrows = [], + qmc = 'vmc', + ) + + expect = ''' 0 5 3 7 @@ -2238,9 +2213,7 @@ def test_symbolic_excited_state(): '''.strip() - text = qmc_optical.get('slaterdeterminant').write().strip() - assert(text==expect) - - #end def test_symbolic_excited_state -#end if + text = qmc_optical.get('slaterdeterminant').write().strip() + assert(text==expect) +#end def test_symbolic_excited_state diff --git a/nexus/nexus/tests/test_qmcpack_input_files/VO2_M1_afm.in.xml b/nexus/nexus/tests/test_qmcpack_input_files/VO2_M1_afm.in.xml index 003768146c..2800171285 100644 --- a/nexus/nexus/tests/test_qmcpack_input_files/VO2_M1_afm.in.xml +++ b/nexus/nexus/tests/test_qmcpack_input_files/VO2_M1_afm.in.xml @@ -26,11 +26,11 @@ - + 13 13 23 - 92861.5851912 + 92860.6737469 2.45778327 8.39460555 0.22661828 8.41192147 8.75579295 -0.22661828 diff --git a/nexus/nexus/tests/test_qmcpack_simulation.py b/nexus/nexus/tests/test_qmcpack_simulation.py index 40d2bcfe8d..26a07dc344 100644 --- a/nexus/nexus/tests/test_qmcpack_simulation.py +++ b/nexus/nexus/tests/test_qmcpack_simulation.py @@ -1,8 +1,17 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QMCPACK_SIMULATION) -from .. import testing -from ..testing import divert_nexus,restore_nexus,clear_all_sims +from ..generic import generic_settings +generic_settings.raise_error = True + +from pathlib import Path + +from . import isolate_nexus_core, create_pseudo_files, TEST_DIR + +from ..testing import clear_all_sims from ..testing import failed,FailedTest -from ..testing import value_eq,object_eq,text_eq +from ..testing import value_eq,text_eq @@ -57,12 +66,6 @@ def get_qmcpack_sim(type='rsqmc',**kwargs): -def test_import(): - from ..qmcpack import Qmcpack,generate_qmcpack -#end def test_import - - - def test_minimal_init(): from ..machines import job from ..qmcpack import Qmcpack,generate_qmcpack @@ -112,22 +115,21 @@ def test_check_result(): #end def test_check_result - -def test_get_result(): - import os - from subprocess import Popen,PIPE +@isolate_nexus_core +def test_get_result(tmp_path): from ..developer import NexusError, obj from ..nexus_base import nexus_core from ..qmcpack_analyzer import QmcpackAnalyzer - tpath = testing.setup_unit_test_output_directory('qmcpack_simulation','test_get_result',divert=True) - nexus_core.runs = '' nexus_core.results = '' + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] sim = get_qmcpack_sim() - assert(sim.locdir.rstrip('/')==tpath.rstrip('/')) + assert(Path(sim.locdir).resolve() == tmp_path) try: sim.get_result('unknown',None) @@ -151,16 +153,11 @@ def test_get_result(): assert(set(result.keys())==set(result_ref.keys())) for k,v in result.items(): - assert(v.replace(tpath,'').lstrip('/')==result_ref[k]) + assert(Path(v).relative_to(tmp_path)==Path(result_ref[k])) #end for - qa_files_path = testing.unit_test_file_path('qmcpack_analyzer','diamond_gamma/opt') - command = 'rsync -a {} {}'.format(qa_files_path,tpath) - process = Popen(command,shell=True,stdout=PIPE,stderr=PIPE,close_fds=True) - out,err = process.communicate() - opt_path = os.path.join(tpath,'opt') - opt_infile = os.path.join(opt_path,'opt.in.xml') - assert(os.path.exists(opt_infile)) + opt_infile = TEST_DIR / "test_qmcpack_analyzer_files/diamond_gamma/opt/opt.in.xml" + assert(opt_infile.exists()) qa = QmcpackAnalyzer(opt_infile,analyze=True,equilibration=5) @@ -168,7 +165,7 @@ def test_get_result(): sim.create_directories() - qa.save(os.path.join(sim.imresdir,sim.analyzer_image)) + qa.save(Path(sim.imresdir).resolve() / sim.analyzer_image) result = sim.get_result('jastrow',None) @@ -178,46 +175,53 @@ def test_get_result(): assert(set(result.keys())==set(result_ref.keys())) for k,v in result.items(): - assert(v.replace(tpath,'').lstrip('/')==result_ref[k]) + assert(Path(v).relative_to(tmp_path)==Path(result_ref[k])) #end for clear_all_sims() - restore_nexus() #end def test_get_result - -def test_incorporate_result(): - import os +@isolate_nexus_core +def test_incorporate_result(tmp_path): import shutil - from subprocess import Popen,PIPE from numpy import array - from ..developer import NexusError, obj + from ..developer import obj from ..nexus_base import nexus_core from .test_vasp_simulation import setup_vasp_sim as get_vasp_sim - from .test_vasp_simulation import pseudo_inputs as vasp_pseudo_inputs from .test_qmcpack_converter_simulations import get_pw2qmcpack_sim from .test_qmcpack_converter_simulations import get_convert4qmc_sim from .test_qmcpack_converter_simulations import get_pyscf_to_afqmc_sim - pseudo_inputs = obj(vasp_pseudo_inputs) - - tpath = testing.setup_unit_test_output_directory('qmcpack_simulation','test_incorporate_result',**pseudo_inputs) - nexus_core.runs = '' nexus_core.results = '' - + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] + + create_pseudo_files( + tmp_dir=tmp_path, + pseudos=["C.POTCAR"], + pseudo_strs=[( + "This is not a real POTCAR file.\n" + "\n" + "End of Dataset\n" + )] + ) # incorporate vasp structure sim = get_qmcpack_sim(identifier='qmc_vasp_structure',tiling=(2,2,2)) - vasp_struct = get_vasp_sim(tpath,identifier='vasp_structure',files=True) + vasp_struct = get_vasp_sim(tmp_path,identifier='vasp_structure',copy_files=True) - assert(sim.locdir.strip('/')==tpath.strip('/')) + assert(Path(sim.locdir).resolve()==tmp_path) pc_file = 'diamond_POSCAR' cc_file = vasp_struct.identifier+'.CONTCAR' - shutil.copy2(os.path.join(tpath,pc_file),os.path.join(tpath,cc_file)) + shutil.copy2( + src = tmp_path / pc_file, + dst = tmp_path / cc_file, + ) result = vasp_struct.get_result('structure',None) @@ -247,15 +251,12 @@ def test_incorporate_result(): result = p2q_orb.get_result('orbitals',None) - p2q_output_path = os.path.join(tpath,'pwscf_output') - if not os.path.exists(p2q_output_path): - os.makedirs(p2q_output_path) - #end if - p2q_h5file = os.path.join(p2q_output_path,'pwscf.pwscf.h5') - f = open(p2q_h5file,'w') - f.write('') - f.close() - assert(os.path.exists(p2q_h5file)) + p2q_output_path = tmp_path / 'pwscf_output' + p2q_output_path.mkdir() + + p2q_h5file = p2q_output_path / 'pwscf.pwscf.h5' + p2q_h5file.touch() + assert(p2q_h5file.exists()) spo = sim.input.get('bspline') assert(spo.href=='MISSING.h5') @@ -272,8 +273,8 @@ def test_incorporate_result(): result = c4q_orb.get_result('orbitals',None) - wfn_file = os.path.join(tpath,'c4q_orbitals.wfj.xml') - wfn_file2 = os.path.join(tpath,'c4q_orbitals.orbs.h5') + wfn_file = tmp_path / 'c4q_orbitals.wfj.xml' + wfn_file2 = tmp_path / 'c4q_orbitals.orbs.h5' input = sim.input.copy() dset = input.get('determinantset') dset.href = 'orbs.h5' @@ -281,9 +282,9 @@ def test_incorporate_result(): del input.simulation input.qmcsystem = qs input.write(wfn_file) - assert(os.path.exists(wfn_file)) - open(wfn_file2,'w').write('fake') - assert(os.path.exists(wfn_file2)) + assert(wfn_file.exists()) + wfn_file2.write_text('fake') + assert(wfn_file2.exists()) from ..qmcpack_input import QmcpackInput inp = QmcpackInput(wfn_file) @@ -300,15 +301,11 @@ def test_incorporate_result(): # incorporate qmcpack jastrow sim = get_qmcpack_sim(identifier='qmc_jastrow') - qa_files_path = testing.unit_test_file_path('qmcpack_analyzer','diamond_gamma/opt') - command = 'rsync -a {} {}'.format(qa_files_path,tpath) - process = Popen(command,shell=True,stdout=PIPE,stderr=PIPE,close_fds=True) - out,err = process.communicate() - opt_path = os.path.join(tpath,'opt') - opt_infile = os.path.join(opt_path,'opt.in.xml') - assert(os.path.exists(opt_infile)) - opt_file = os.path.join(opt_path,'opt.s004.opt.xml') - assert(os.path.exists(opt_file)) + opt_path = TEST_DIR / "test_qmcpack_analyzer_files/diamond_gamma/opt" + opt_infile = opt_path / 'opt.in.xml' + assert(opt_infile.exists()) + opt_file = opt_path / 'opt.s004.opt.xml' + assert(opt_file.exists()) result = obj(opt_file=opt_file) @@ -371,22 +368,21 @@ def test_incorporate_result(): assert(ham.filename=='p2a_wavefunction.afqmc.h5') clear_all_sims() - restore_nexus() #end def test_incorporate_result() - -def test_check_sim_status(): - import os +@isolate_nexus_core +def test_check_sim_status(tmp_path): from ..nexus_base import nexus_core - tpath = testing.setup_unit_test_output_directory('qmcpack_simulation','test_check_sim_status',divert=True) - nexus_core.runs = '' + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] sim = get_qmcpack_sim(identifier='qmc') - assert(sim.locdir.rstrip('/')==tpath.rstrip('/')) + assert(Path(sim.locdir).resolve()==tmp_path) assert(not sim.finished) assert(not sim.failed) @@ -400,18 +396,14 @@ def test_check_sim_status(): assert(not sim.finished) assert(not sim.failed) - outfile = os.path.join(tpath,sim.outfile) + outfile = tmp_path / sim.outfile out_text = 'Total Execution' - out = open(outfile,'w') - out.write(out_text) - out.close() - assert(os.path.exists(outfile)) - assert(out_text in open(outfile,'r').read()) - errfile = os.path.join(tpath,sim.errfile) - err = open(errfile,'w') - err.write('') - err.close() - assert(os.path.exists(errfile)) + outfile.write_text(out_text) + assert(outfile.exists()) + assert(out_text in outfile.read_text()) + errfile = tmp_path / sim.errfile + errfile.touch() + assert(errfile.exists()) sim.check_sim_status() @@ -419,6 +411,5 @@ def test_check_sim_status(): assert(not sim.failed) clear_all_sims() - restore_nexus() #end def test_check_sim_status() diff --git a/nexus/nexus/tests/test_quantum_package_analyzer.py b/nexus/nexus/tests/test_quantum_package_analyzer.py index d948f94e10..8b36078349 100644 --- a/nexus/nexus/tests/test_quantum_package_analyzer.py +++ b/nexus/nexus/tests/test_quantum_package_analyzer.py @@ -1,8 +1,9 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QUANTUM_PACKAGE_ANALYZER) - -def test_import(): - from ..quantum_package_analyzer import QuantumPackageAnalyzer -#end def test_import +from ..generic import generic_settings +generic_settings.raise_error = True diff --git a/nexus/nexus/tests/test_quantum_package_input.py b/nexus/nexus/tests/test_quantum_package_input.py index f1d3f171f1..aec81389ad 100644 --- a/nexus/nexus/tests/test_quantum_package_input.py +++ b/nexus/nexus/tests/test_quantum_package_input.py @@ -1,6 +1,14 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QUANTUM_PACKAGE_INPUT) + +from ..generic import generic_settings +generic_settings.raise_error = True + +from pathlib import Path from .. import testing -from ..testing import value_eq,object_eq,text_eq,check_object_eq +from ..testing import object_eq def format_value(v): @@ -242,16 +250,9 @@ def check_vs_serial_reference(qi,name): ''' -def test_import(): - from ..quantum_package_input import QuantumPackageInput - from ..quantum_package_input import generate_quantum_package_input -#end def test_import - - def test_empty_init(): from ..quantum_package_input import QuantumPackageInput - from ..quantum_package_input import generate_quantum_package_input qi = QuantumPackageInput() @@ -260,12 +261,9 @@ def test_empty_init(): def test_read(): - import os from ..quantum_package_input import QuantumPackageInput - tpath = testing.setup_unit_test_output_directory('quantum_package_input','test_generate',file_sets=['h2o.ezfio']) - - ezfio = os.path.join(tpath,'h2o.ezfio') + ezfio = Path(__file__+"/../test_quantum_package_input_files/h2o.ezfio").resolve() qi = QuantumPackageInput(ezfio) @@ -274,17 +272,14 @@ def test_read(): -def test_generate(): +def test_generate(tmp_path): import os - from ..developer import obj from ..physical_system import generate_physical_system from ..quantum_package_input import generate_quantum_package_input - tpath = testing.setup_unit_test_output_directory('quantum_package_input','test_generate') - # water molecule rhf - xyz_path = os.path.join(tpath,'H2O.xyz') - open(xyz_path,'w').write(h2o_xyz) + xyz_path = tmp_path / 'H2O.xyz' + xyz_path.write_text(h2o_xyz) system = generate_physical_system( structure = xyz_path, @@ -303,8 +298,8 @@ def test_generate(): # O2 molecule selci - xyz_path = os.path.join(tpath,'O2.xyz') - open(xyz_path,'w').write(o2_xyz) + xyz_path = tmp_path / 'O2.xyz' + xyz_path.write_text(o2_xyz) system = generate_physical_system( structure = xyz_path, diff --git a/nexus/nexus/tests/test_quantum_package_simulation.py b/nexus/nexus/tests/test_quantum_package_simulation.py index 04f6157055..1175d19cad 100644 --- a/nexus/nexus/tests/test_quantum_package_simulation.py +++ b/nexus/nexus/tests/test_quantum_package_simulation.py @@ -1,16 +1,23 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.QUANTUM_PACKAGE_SIMULATION) + +from ..generic import generic_settings +generic_settings.raise_error = True + +from pathlib import Path +from . import isolate_nexus_core -from .. import testing -from ..testing import divert_nexus,restore_nexus from ..testing import failed,FailedTest -from ..testing import value_eq,object_eq,text_eq +from ..testing import object_eq def clear_all_sims(): from ..quantum_package import QuantumPackage - + from nexus.simulation import Simulation QuantumPackage.qprc = None - testing.clear_all_sims() + Simulation.clear_all_sims() #end def clear_all_sims @@ -44,12 +51,6 @@ def get_quantum_package_sim(**kwargs): -def test_import(): - from ..quantum_package import QuantumPackage,generate_quantum_package -#end def test_import - - - def test_minimal_init(): sim = get_quantum_package_sim() @@ -105,7 +106,7 @@ def test_get_result(): def test_incorporate_result(): - from ..developer import NexusError, obj + from ..developer import NexusError from ..machines import job from ..simulation import Simulation from ..gamess import generate_gamess,Gamess @@ -148,19 +149,19 @@ def test_incorporate_result(): #end def test_incorporate_result - -def test_check_sim_status(): +@isolate_nexus_core +def test_check_sim_status(tmp_path): import os - from ..developer import NexusError, obj from ..nexus_base import nexus_core - tpath = testing.setup_unit_test_output_directory('quantum_package_simulation','test_check_sim_status',divert=True) - nexus_core.runs = '' + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] sim = get_quantum_package_sim() - assert(sim.locdir.rstrip('/')==tpath.rstrip('/')) + assert(Path(sim.locdir).resolve()==tmp_path) assert(not sim.finished) assert(not sim.failed) @@ -175,12 +176,10 @@ def test_check_sim_status(): #end try sim.create_directories() - outfile = os.path.join(sim.locdir,sim.outfile) + outfile = Path(sim.locdir).resolve() / sim.outfile outfile_text = '* SCF energy' - out = open(outfile,'w') - out.write(outfile_text) - out.close() - assert(outfile_text in open(outfile,'r').read()) + outfile.write_text(outfile_text) + assert(outfile_text in outfile.read_text()) sim.job.finished = True sim.check_sim_status() @@ -189,5 +188,4 @@ def test_check_sim_status(): assert(not sim.failed) clear_all_sims() - restore_nexus() #end def test_check_sim_status diff --git a/nexus/nexus/tests/test_required_dependencies.py b/nexus/nexus/tests/test_required_dependencies.py deleted file mode 100644 index 236d367cf3..0000000000 --- a/nexus/nexus/tests/test_required_dependencies.py +++ /dev/null @@ -1,14 +0,0 @@ - -def test_numpy_available(): - from .. import versions - assert(versions.numpy_available) -#end def test_numpy_available - - -# skip this since the rest of the test set actually tells you if it is supported -#def test_numpy_supported(): -# from .. import versions -# if versions.numpy_available: -# assert(versions.numpy_supported) -# #end if -##end def test_numpy_supported diff --git a/nexus/nexus/tests/test_rmg_analyzer.py b/nexus/nexus/tests/test_rmg_analyzer.py index ab606dbac3..92e21d0f75 100644 --- a/nexus/nexus/tests/test_rmg_analyzer.py +++ b/nexus/nexus/tests/test_rmg_analyzer.py @@ -1,11 +1,9 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.RMG_ANALYZER) -from .. import testing -from ..testing import value_eq,object_eq,text_eq - - -def test_import(): - from ..rmg_analyzer import RmgAnalyzer -#end def test_import +from ..generic import generic_settings +generic_settings.raise_error = True diff --git a/nexus/nexus/tests/test_rmg_input.py b/nexus/nexus/tests/test_rmg_input.py index 5d20f0823a..7ff4cb77e6 100644 --- a/nexus/nexus/tests/test_rmg_input.py +++ b/nexus/nexus/tests/test_rmg_input.py @@ -1,51 +1,47 @@ - -from .. import testing -from ..testing import failed -from ..testing import divert_nexus_log,restore_nexus_log -from ..testing import value_eq,object_eq,check_object_eq -from .. import versions - - -associated_files = dict() - -input_files = ''' - AlN32_input - atomO_polarized_input - BlackPhosphorus_Delocalize_both_pp_and_proj_davidson_input - BlackPhosphorus_Delocalize_both_pp_and_proj_multigrid_input - BlackPhosphorus_input - BlackPhosphorus_input_1nongammapoint - BlackPhosphorus_input_band - BlackPhosphorus_Localize_both_pp_and_proj_davidson_input - BlackPhosphorus_Localize_both_pp_and_proj_multigrid_input - BlackPhosphorus_Localize_pp_only_davidson_input - BlackPhosphorus_Localize_pp_only_multigrid_input - BlackPhosphorus_Localize_proj_only_davidson_input - BlackPhosphorus_Localize_proj_only_multigrid_input - C60_input - Diamond16_input - Diamond2_input - Fe_2atom_input - graphite_stress_input - Mg_2atom_input - nanotube_80_input - nanotube_80_input_band - nanotube_80_input_band1 - NiO512_input - NiO8_input - Pt_bulk_spinorbit_input - Pt_bulk_spinorbit_input_band - Si_8atoms_EXX_kpoints_input - U_bulk_spinorbit_RMG_input - '''.split() - - - - -def get_files(): - return testing.collect_unit_test_file_paths('rmg_input',associated_files) -#end def get_files - +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.RMG_INPUT) + +from ..generic import generic_settings +generic_settings.raise_error = True + +from importlib.util import find_spec +from . import TEST_DIR +from ..testing import value_eq,check_object_eq + +TEST_FILES = { + "AlN32_input": TEST_DIR / "test_rmg_input_files/AlN32_input", + "atomO_polarized_input": TEST_DIR / "test_rmg_input_files/atomO_polarized_input", + "BlackPhosphorus_Delocalize_both_pp_and_proj_davidson_input": TEST_DIR / "test_rmg_input_files/BlackPhosphorus_Delocalize_both_pp_and_proj_davidson_input", + "BlackPhosphorus_Delocalize_both_pp_and_proj_multigrid_input": TEST_DIR / "test_rmg_input_files/BlackPhosphorus_Delocalize_both_pp_and_proj_multigrid_input", + "BlackPhosphorus_input": TEST_DIR / "test_rmg_input_files/BlackPhosphorus_input", + "BlackPhosphorus_input_1nongammapoint": TEST_DIR / "test_rmg_input_files/BlackPhosphorus_input_1nongammapoint", + "BlackPhosphorus_input_band": TEST_DIR / "test_rmg_input_files/BlackPhosphorus_input_band", + "BlackPhosphorus_Localize_both_pp_and_proj_davidson_input": TEST_DIR / "test_rmg_input_files/BlackPhosphorus_Localize_both_pp_and_proj_davidson_input", + "BlackPhosphorus_Localize_both_pp_and_proj_multigrid_input": TEST_DIR / "test_rmg_input_files/BlackPhosphorus_Localize_both_pp_and_proj_multigrid_input", + "BlackPhosphorus_Localize_pp_only_davidson_input": TEST_DIR / "test_rmg_input_files/BlackPhosphorus_Localize_pp_only_davidson_input", + "BlackPhosphorus_Localize_pp_only_multigrid_input": TEST_DIR / "test_rmg_input_files/BlackPhosphorus_Localize_pp_only_multigrid_input", + "BlackPhosphorus_Localize_proj_only_davidson_input": TEST_DIR / "test_rmg_input_files/BlackPhosphorus_Localize_proj_only_davidson_input", + "BlackPhosphorus_Localize_proj_only_multigrid_input": TEST_DIR / "test_rmg_input_files/BlackPhosphorus_Localize_proj_only_multigrid_input", + "C60_input": TEST_DIR / "test_rmg_input_files/C60_input", + "Diamond16_input": TEST_DIR / "test_rmg_input_files/Diamond16_input", + "Diamond2_input": TEST_DIR / "test_rmg_input_files/Diamond2_input", + "Fe_2atom_input": TEST_DIR / "test_rmg_input_files/Fe_2atom_input", + "graphite_stress_input": TEST_DIR / "test_rmg_input_files/graphite_stress_input", + "Mg_2atom_input": TEST_DIR / "test_rmg_input_files/Mg_2atom_input", + "nanotube_80_input": TEST_DIR / "test_rmg_input_files/nanotube_80_input", + "nanotube_80_input_band": TEST_DIR / "test_rmg_input_files/nanotube_80_input_band", + "nanotube_80_input_band1": TEST_DIR / "test_rmg_input_files/nanotube_80_input_band1", + "NiO512_input": TEST_DIR / "test_rmg_input_files/NiO512_input", + "NiO8_input": TEST_DIR / "test_rmg_input_files/NiO8_input", + "Pt_bulk_spinorbit_input": TEST_DIR / "test_rmg_input_files/Pt_bulk_spinorbit_input", + "Pt_bulk_spinorbit_input_band": TEST_DIR / "test_rmg_input_files/Pt_bulk_spinorbit_input_band", + "Si_8atoms_EXX_kpoints_input": TEST_DIR / "test_rmg_input_files/Si_8atoms_EXX_kpoints_input", + "U_bulk_spinorbit_RMG_input": TEST_DIR / "test_rmg_input_files/U_bulk_spinorbit_RMG_input", + } + +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" def make_serial_reference(ri): @@ -667,51 +663,34 @@ def check_vs_serial_reference(gi,name): #end def check_vs_serial_reference -def test_files(): - filenames = input_files - files = get_files() - assert(set(files.keys())==set(filenames)) -#end def test_files - - - -def test_import(): - from ..rmg_input import RmgInput -#end def test_import - - - def test_empty_init(): from ..rmg_input import RmgInput ri = RmgInput() #end test_empty_init - def test_read(): from ..rmg_input import RmgInput - - files = get_files() infiles_read = {} - for infile in input_files: - ri_read = RmgInput(files[infile]) + for infile in TEST_FILES: + ri_read = RmgInput(TEST_FILES[infile]) assert(ri_read.is_valid()) infiles_read[infile] = ri_read #end for - input_files_check = ''' - BlackPhosphorus_input - BlackPhosphorus_input_band - BlackPhosphorus_Localize_both_pp_and_proj_multigrid_input - C60_input - Diamond16_input - graphite_stress_input - NiO8_input - Pt_bulk_spinorbit_input - Pt_bulk_spinorbit_input_band - Si_8atoms_EXX_kpoints_input - '''.split() + input_files_check = ( + "BlackPhosphorus_input", + "BlackPhosphorus_input_band", + "BlackPhosphorus_Localize_both_pp_and_proj_multigrid_input", + "C60_input", + "Diamond16_input", + "graphite_stress_input", + "NiO8_input", + "Pt_bulk_spinorbit_input", + "Pt_bulk_spinorbit_input_band", + "Si_8atoms_EXX_kpoints_input", + ) # print out the reference text (used in generate_serial_references) #for infile in input_files_check: @@ -731,18 +710,13 @@ def test_read(): -def test_write(): - import os +def test_write(tmp_path): from ..rmg_input import RmgInput - tpath = testing.setup_unit_test_output_directory('rmg_input','test_write') - - files = get_files() - - for infile in input_files: - write_file = os.path.join(tpath,infile) + for infile in TEST_FILES: + write_file = tmp_path / infile - ri_read = RmgInput(files[infile]) + ri_read = RmgInput(TEST_FILES[infile]) ri_read.write(write_file) @@ -913,7 +887,7 @@ def test_generate(): ) check_vs_serial_reference(ri,infile) - if versions.spglib_available and versions.seekpath_available: + if find_spec("spglib") is not None and find_spec("seekpath") is not None: nio8 = generate_physical_system( units = 'B', axes = 7.8811*np.identity(3), diff --git a/nexus/nexus/tests/test_rmg_simulation.py b/nexus/nexus/tests/test_rmg_simulation.py index b6e7c759ac..a27afd83a4 100644 --- a/nexus/nexus/tests/test_rmg_simulation.py +++ b/nexus/nexus/tests/test_rmg_simulation.py @@ -1,14 +1,11 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.RMG_SIMULATION) -from .. import testing -from ..testing import divert_nexus,restore_nexus,clear_all_sims -from ..testing import failed,FailedTest -from ..testing import value_eq,object_eq,text_eq +from ..generic import generic_settings +generic_settings.raise_error = True - - -def test_import(): - from ..rmg import Rmg,generate_rmg -#end def test_import +from ..testing import clear_all_sims diff --git a/nexus/nexus/tests/test_settings.py b/nexus/nexus/tests/test_settings.py index 33b4594f78..0549fb297a 100644 --- a/nexus/nexus/tests/test_settings.py +++ b/nexus/nexus/tests/test_settings.py @@ -1,15 +1,18 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.SETTINGS_OPERATION) -from .. import testing -from ..testing import divert_nexus,restore_nexus -from ..testing import value_eq,object_eq - +from ..generic import generic_settings +generic_settings.raise_error = True -def test_import(): - from nexus import settings,Settings -#end def test_import +from pathlib import Path +from . import isolate_nexus_core +from .. import testing +from ..testing import object_eq -def test_settings(): +@isolate_nexus_core +def test_settings(tmp_path): # test full imports import os from nexus import settings,Settings,obj @@ -26,11 +29,6 @@ def test_settings(): testing.check_final_state() - tpath = testing.setup_unit_test_output_directory('settings','test_settings') - - # divert logging function - divert_nexus() - def aux_defaults(): # check that Job and ProjectManager settings are at default values assert(Job.machine is None) @@ -51,7 +49,7 @@ def check_settings_core_noncore(): 'primary_modes', 'progress_tty', 'pseudo_dir', 'pseudopotentials', 'remote_directory', 'results', 'runs', 'skip_submit', 'sleep', 'stages', 'stages_set', 'status', - 'status_modes', 'status_only', 'trace', 'verbose' + 'status_modes', 'status_only', 'trace', 'verbose', 'dynamic' ]) nnckeys_check = set([ 'basis_dir', 'basissets', 'pseudo_dir', 'pseudopotentials' @@ -63,7 +61,7 @@ def check_settings_core_noncore(): 'modes', 'monitor', 'primary_modes', 'progress_tty', 'pseudo_dir', 'pseudopotentials', 'remote_directory', 'results', 'runs', 'skip_submit', 'sleep', 'stages', 'stages_set', 'status', - 'status_modes', 'status_only', 'trace', 'verbose' + 'status_modes', 'status_only', 'trace', 'verbose', 'dynamic' ]) setkeys_allowed = setkeys_check | Settings.allowed_vars @@ -88,7 +86,7 @@ def check_settings_core_noncore(): if isinstance(v1,obj): assert(object_eq(v1,v2)) else: - assert(value_eq(v1,v2)) + assert(v1 == v2) #end if #end for #end for @@ -133,8 +131,8 @@ def check_empty_settings(): check_empty_settings() # check that a few basic user settings are applied appropriately - cwd = os.getcwd() - os.chdir(tpath) + cwd = Path.cwd() + os.chdir(tmp_path) dft_pseudos = ['Ni.opt.upf','O.opt.upf'] qmc_pseudos = ['Ni.opt.xml','O.opt.xml'] pseudos = dft_pseudos+qmc_pseudos @@ -142,9 +140,9 @@ def check_empty_settings(): if not os.path.exists(pseudo_path): os.makedirs(pseudo_path) for file in pseudos: - filepath = os.path.join(pseudo_path,file) - if not os.path.exists(filepath): - open(filepath,'w').close() + filepath = Path(pseudo_path) / file + if not filepath.exists(): + filepath.touch() #end if #end for #end if @@ -169,7 +167,4 @@ def check_empty_settings(): # check that a new empty settings works following basic check_empty_settings() - - # restore logging function - restore_nexus() #end def test_settings diff --git a/nexus/nexus/tests/test_simulation_module.py b/nexus/nexus/tests/test_simulation_module.py index 03b26a3182..4925e2e5fd 100644 --- a/nexus/nexus/tests/test_simulation_module.py +++ b/nexus/nexus/tests/test_simulation_module.py @@ -1,19 +1,23 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.SIMULATION) + +from ..generic import generic_settings +generic_settings.raise_error = True + + +from pathlib import Path +from . import isolate_nexus_core +from nexus.nexus_base import nexus_core -from .. import testing from ..testing import value_eq,object_eq from ..testing import FailedTest,failed -from ..testing import divert_nexus_log,restore_nexus_log -from ..testing import divert_nexus,restore_nexus - -from .. import versions from ..developer import obj +from ..machines import Job from ..simulation import Simulation,SimulationInput,SimulationAnalyzer -testing.divert_nexus_errors() - - class SimulationInputForTests(SimulationInput): def __init__(self,*args,**kwargs): SimulationInput.__init__(self,*args,**kwargs) @@ -100,7 +104,6 @@ def incorporate_result(self,result_name,result,sim): def get_sim(**kwargs): from ..machines import job from ..simulation import Simulation - test_job = job(machine='ws1',app_command='test.x') n = len(get_sim_simulations) @@ -372,36 +375,18 @@ def make_network(network,**kwargs): - -def test_import(): - from .. import simulation - from ..simulation import Simulation,SimulationInput,SimulationAnalyzer - from ..simulation import SimulationImage - from ..simulation import NullSimulationInput,NullSimulationAnalyzer - from ..simulation import GenericSimulation - from ..simulation import SimulationInputTemplate - from ..simulation import SimulationInputMultiTemplate - from ..simulation import input_template,multi_input_template - from ..simulation import generate_simulation -#end def test_import - - - -def test_simulation_input(): - import os +def test_simulation_input(tmp_path): from ..developer import NexusError from ..simulation import SimulationInput - tpath = testing.setup_unit_test_output_directory('simulation','test_simulation_input') - # empty init si = SimulationInput() # write - infile = os.path.join(tpath,'sim_input.in') + infile = tmp_path / 'sim_input.in' wtext = 'simulation input' si.write_file_text(infile,wtext) - assert(os.path.exists(infile)) + assert(infile.exists()) # read rtext = si.read_file_text(infile) @@ -437,7 +422,6 @@ def test_simulation_input(): def test_simulation_analyzer(): - import os from ..developer import NexusError from ..simulation import SimulationAnalyzer @@ -466,8 +450,7 @@ def test_simulation_analyzer(): -def test_simulation_input_template(): - import os +def test_simulation_input_template(tmp_path): from string import Template from ..developer import obj, NexusError from ..simulation import SimulationInput @@ -475,9 +458,6 @@ def test_simulation_input_template(): from ..simulation import SimulationInputTemplate from ..simulation import input_template - tpath = testing.setup_unit_test_output_directory('simulation','test_simulation_input_template') - - # empty init si_empty = input_template() assert(isinstance(si_empty,SimulationInput)) @@ -503,10 +483,9 @@ def test_simulation_input_template(): file2 = "$file.$ext2" ''' - template_filepath = os.path.join(tpath,'template_file.txt') - - open(template_filepath,'w').write(template_text) + template_filepath = tmp_path / 'template_file.txt' + template_filepath.write_text(template_text) # read si_read = input_template(template_filepath) @@ -588,46 +567,42 @@ def try_write(si): text = si_write.write() assert(text==text_ref) - input_filepath = os.path.join(tpath,'input_file.txt') + input_filepath = tmp_path / 'input_file.txt' si_write.write(input_filepath) - assert(open(input_filepath,'r').read()==text_ref) - + assert(input_filepath.read_text()==text_ref) #end def test_simulation_input_template -def test_simulation_input_multi_template(): - import os +def test_simulation_input_multi_template(tmp_path): from string import Template - from ..developer import obj, NexusError + from ..developer import obj from ..simulation import SimulationInput from ..simulation import GenericSimulationInput from ..simulation import SimulationInputMultiTemplate from ..simulation import multi_input_template - tpath = testing.setup_unit_test_output_directory('simulation','test_simulation_input_multi_template') - # make template files - template1_filepath = os.path.join(tpath,'template1.txt') - template2_filepath = os.path.join(tpath,'template2.txt') - template3_filepath = os.path.join(tpath,'template3.txt') + template1_filepath = tmp_path / 'template1.txt' + template2_filepath = tmp_path / 'template2.txt' + template3_filepath = tmp_path / 'template3.txt' - open(template1_filepath,'w').write(''' + template1_filepath.write_text(''' name = "$name" a = $a ''') - open(template2_filepath,'w').write(''' + template2_filepath.write_text(''' name = "$name" b = $b ''') - open(template3_filepath,'w').write(''' + template3_filepath.write_text(''' name = "$name" c = $c ''') - input1_filepath = os.path.join(tpath,'input_file1.txt') - input2_filepath = os.path.join(tpath,'input_file2.txt') - input3_filepath = os.path.join(tpath,'input_file3.txt') + input1_filepath = tmp_path / 'input_file1.txt' + input2_filepath = tmp_path / 'input_file2.txt' + input3_filepath = tmp_path / 'input_file3.txt' # empty init @@ -720,9 +695,9 @@ def test_simulation_input_multi_template(): assert(object_eq(si_write.write(),write_ref)) si_write.write(input1_filepath) - assert(os.path.exists(input1_filepath)) - assert(os.path.exists(input2_filepath)) - assert(os.path.exists(input3_filepath)) + assert(input1_filepath.exists()) + assert(input2_filepath.exists()) + assert(input3_filepath.exists()) # read @@ -743,7 +718,6 @@ def test_simulation_input_multi_template(): assert(sit.allow_not_set==set()) #end for assert(object_eq(si_read.write(),write_ref)) - #end def test_simulation_input_multi_template @@ -1031,12 +1005,14 @@ def complete(sim): #end def test_indicator_checks - -def test_create_directories(): +@isolate_nexus_core +def test_create_directories(tmp_path): import os from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_create_directories',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] s = Simulation() @@ -1050,36 +1026,33 @@ def test_create_directories(): assert(os.path.exists(s.imlocdir)) assert(s.created_directories) - restore_nexus() - Simulation.clear_all_sims() #end def test_create_directories - -def test_file_text(): - import os +@isolate_nexus_core +def test_file_text(tmp_path): from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_create_directories',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] s = Simulation() s.create_directories() - outfile = os.path.join(s.locdir,s.outfile) - errfile = os.path.join(s.locdir,s.errfile) + outfile = Path(s.locdir).resolve() / s.outfile + errfile = Path(s.locdir).resolve() / s.errfile out_text = 'output' err_text = 'error' - open(outfile,'w').write(out_text) - open(errfile,'w').write(err_text) + outfile.write_text(out_text) + errfile.write_text(err_text) assert(s.outfile_text()==out_text) assert(s.errfile_text()==err_text) - restore_nexus() - Simulation.clear_all_sims() #end def test_file_text @@ -1436,7 +1409,7 @@ class GenInput(SimulationInput,GenericSimulationInput): #end def test_has_generic_input - +@isolate_nexus_core def test_check_dependencies(): from ..developer import obj, NexusError from ..simulation import Simulation @@ -1511,7 +1484,6 @@ def test_check_dependencies(): # existent dependency but generic input - divert_nexus_log() class GenInput(SimulationInput,GenericSimulationInput): None #end class GenInput @@ -1538,7 +1510,6 @@ class GenInput(SimulationInput,GenericSimulationInput): except Exception as e: failed(str(e)) #end try - restore_nexus_log() Simulation.clear_all_sims() #end def test_check_dependencies @@ -1575,7 +1546,7 @@ def test_get_dependencies(): s22 = get_test_sim(dependencies=deps) simdeps[s22.simid] = deps - dependencies = [ + deps = [ (s21,'quant1'), (s22,'quant2'), ] @@ -1710,41 +1681,40 @@ def test_downstream_simids(): -def test_copy_file(): +def test_copy_file(tmp_path): import os from ..simulation import Simulation - - tpath = testing.setup_unit_test_output_directory('simulation','test_copy_file') - opath = os.path.join(tpath,'other') + opath = tmp_path / 'other' if not os.path.exists(opath): os.makedirs(opath) #end if - file1 = os.path.join(tpath,'file.txt') - file2 = os.path.join(opath,'file.txt') + file1 = tmp_path / 'file.txt' + file2 = opath / 'file.txt' - open(file1,'w').write('text') - assert(os.path.exists(file1)) + file1.write_text('text') + assert(file1.exists()) s = get_sim() s.copy_file(file1,opath) - assert(os.path.exists(file2)) - assert(open(file2,'r').read().strip()=='text') + assert(file2.exists()) + assert(file2.read_text().strip()=='text') Simulation.clear_all_sims() #end def test_copy_file - -def test_save_load_image(): - import os +@isolate_nexus_core +def test_save_load_image(tmp_path): from ..developer import obj from ..simulation import Simulation,SimulationImage - tpath = testing.setup_unit_test_output_directory('simulation','test_save_load_image',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] nsave = 30 nload = 22 @@ -1759,8 +1729,8 @@ def test_save_load_image(): sim.save_image() - imagefile = os.path.join(sim.imlocdir,sim.sim_image) - assert(os.path.exists(imagefile)) + imagefile = Path(sim.imlocdir) / sim.sim_image + assert(imagefile.exists()) image = obj() image.load(imagefile) @@ -1782,52 +1752,49 @@ def test_save_load_image(): assert(field in sim) assert(value_eq(sim[field],orig[field])) #end for - - restore_nexus() - Simulation.clear_all_sims() #end def test_save_load_image - -def test_load_analyzer_image(): - import os +@isolate_nexus_core +def test_load_analyzer_image(tmp_path): from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_save_load_analyzer_image',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] sim = get_test_sim() - if not os.path.exists(sim.imresdir): - os.makedirs(sim.imresdir) + if not Path(sim.imresdir).exists(): + Path(sim.imresdir).mkdir(parents=True) #end if - analyzer_file = os.path.join(sim.imresdir,sim.analyzer_image) + analyzer_file = Path(sim.imresdir).resolve() / sim.analyzer_image a = sim.analyzer_type(None) assert(not a.analysis_performed) a.analyze() assert(a.analysis_performed) a.save(analyzer_file) - assert(os.path.exists(analyzer_file)) + assert(Path(analyzer_file).exists()) a2 = sim.load_analyzer_image() assert(isinstance(a2,sim.analyzer_type)) assert(a2.analysis_performed) assert(object_eq(a2,a)) - restore_nexus() - Simulation.clear_all_sims() #end def test_load_analyzer_image - -def test_save_attempt(): - import os +@isolate_nexus_core +def test_save_attempt(tmp_path): from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_save_attempt',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] sim = get_test_sim() @@ -1837,30 +1804,29 @@ def test_save_attempt(): assert(sim.attempt_files()==files) for file in files: - open(os.path.join(sim.locdir,file),'w').write('made an attempt') + (Path(sim.locdir).resolve() / file).write_text('made an attempt') #end for - attempt_dir = os.path.join(sim.locdir,'{}_attempt1'.format(sim.identifier)) - assert(not os.path.exists(attempt_dir)) + attempt_dir = Path(sim.locdir).resolve() / f'{sim.identifier}_attempt1' + assert(not attempt_dir.exists()) sim.save_attempt() - assert(os.path.exists(attempt_dir)) + assert(attempt_dir.exists()) for file in files: - assert(not os.path.exists(os.path.join(sim.locdir,file))) - assert(os.path.exists(os.path.join(attempt_dir,file))) + assert(not (Path(sim.locdir).resolve() / file).exists()) + assert((Path(attempt_dir).resolve() / file).exists()) #end for - restore_nexus() - Simulation.clear_all_sims() #end def test_save_attempt - -def test_write_inputs(): - import os +@isolate_nexus_core +def test_write_inputs(tmp_path): from ..simulation import Simulation,input_template - tpath = testing.setup_unit_test_output_directory('simulation','test_write_inputs',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] template = ''' name = "$name" @@ -1880,49 +1846,47 @@ def test_write_inputs(): ) s.create_directories() - input_file = os.path.join(s.locdir,s.infile) - image_file = os.path.join(s.imlocdir,s.sim_image) - input_image_file = os.path.join(s.imlocdir,s.input_image) + input_file = Path(s.locdir).resolve() / s.infile + image_file = Path(s.imlocdir).resolve() / s.sim_image + input_image_file = Path(s.imlocdir).resolve() / s.input_image assert(not s.setup) - assert(not os.path.exists(input_file)) - assert(not os.path.exists(image_file)) - assert(not os.path.exists(input_image_file)) + assert(not input_file.exists()) + assert(not image_file.exists()) + assert(not input_image_file.exists()) s.write_inputs() assert(s.setup) - assert(os.path.exists(input_file)) - assert(os.path.exists(image_file)) - assert(os.path.exists(input_image_file)) + assert(input_file.exists()) + assert(image_file.exists()) + assert(input_image_file.exists()) - assert(open(input_file,'r').read()==input_ref) + assert(input_file.read_text()==input_ref) s.setup = False s.load_image() assert(s.setup) - restore_nexus() - Simulation.clear_all_sims() - #end def test_write_inputs - -def test_send_files(): - import os +@isolate_nexus_core +def test_send_files(tmp_path): from ..nexus_base import nexus_core from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_send_files',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] # make fake data files data_file1 = 'data_file1.txt' data_file2 = 'data_file2.txt' - open(os.path.join(tpath,data_file1),'w').write('data1') - open(os.path.join(tpath,data_file2),'w').write('data2') + (tmp_path / data_file1).write_text('data1') + (tmp_path / data_file2).write_text('data2') data_files = [data_file1,data_file2] @@ -1936,39 +1900,38 @@ def test_send_files(): s.create_directories() - loc_data_file1 = os.path.join(s.locdir,data_file1) - loc_data_file2 = os.path.join(s.locdir,data_file2) + loc_data_file1 = Path(s.locdir).resolve() / data_file1 + loc_data_file2 = Path(s.locdir).resolve() / data_file2 assert(not s.sent_files) - assert(not os.path.exists(loc_data_file1)) - assert(not os.path.exists(loc_data_file2)) + assert(not loc_data_file1.exists()) + assert(not loc_data_file2.exists()) s.send_files() assert(s.sent_files) - assert(os.path.exists(loc_data_file1)) - assert(os.path.exists(loc_data_file2)) + assert(loc_data_file1.exists()) + assert(loc_data_file2.exists()) - assert(open(loc_data_file1,'r').read()=='data1') - assert(open(loc_data_file2,'r').read()=='data2') + assert(loc_data_file1.read_text()=='data1') + assert(loc_data_file2.read_text()=='data2') s.sent_files = False s.load_image() assert(s.sent_files) - restore_nexus() - Simulation.clear_all_sims() - #end def test_send_files - -def test_submit(): +@isolate_nexus_core +def test_submit(tmp_path): from ..machines import job from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_submit',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] s = get_test_sim( job = job(machine='ws1',app_command='echo run'), @@ -1991,18 +1954,17 @@ def test_submit(): assert(j.internal_id in m.jobs) assert(j.internal_id in m.waiting) - restore_nexus() - Simulation.clear_all_sims() - #end def test_submit - -def test_update_process_id(): +@isolate_nexus_core +def test_update_process_id(tmp_path): from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_update_process_id',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] s = get_test_sim() j = s.job @@ -2024,19 +1986,17 @@ def test_update_process_id(): s.load_image() assert(s.process_id==ref_pid) - restore_nexus() - Simulation.clear_all_sims() - #end def test_update_process_id - -def test_check_status(): - import os +@isolate_nexus_core +def test_check_status(tmp_path): from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_check_status',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] s = get_test_sim() j = s.job @@ -2049,8 +2009,8 @@ def test_check_status(): s.create_directories() - open(os.path.join(s.locdir,s.outfile),'w').write('out') - open(os.path.join(s.locdir,s.errfile),'w').write('err') + (Path(s.locdir).resolve() / s.outfile).write_text('out') + (Path(s.locdir).resolve() / s.errfile).write_text('err') j.finished = True s.check_status() @@ -2061,29 +2021,27 @@ def test_check_status(): s.load_image() assert(s.finished) - restore_nexus() - Simulation.clear_all_sims() - #end def test_check_status - -def test_get_output(): - import os +@isolate_nexus_core +def test_get_output(tmp_path): from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_get_output',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] s = get_test_sim() s.create_directories() - remote_image = os.path.join(s.imremdir,s.sim_image) - results_image = os.path.join(s.imresdir,s.sim_image) + remote_image = Path(s.imremdir).resolve() / s.sim_image + results_image = Path(s.imresdir).resolve() / s.sim_image - assert(not os.path.exists(remote_image)) - assert(not os.path.exists(results_image)) + assert(not remote_image.exists()) + assert(not results_image.exists()) assert(not s.finished) assert(value_eq(s.get_output_files(),[])) @@ -2094,22 +2052,22 @@ def test_get_output(): res_files = [] for file in files: - loc_files.append(os.path.join(s.locdir,file)) - res_files.append(os.path.join(s.resdir,file)) + loc_files.append(Path(s.locdir).resolve() / file) + res_files.append(Path(s.resdir).resolve() / file) #end for for loc_file in loc_files: - open(loc_file,'w').write('contents') + loc_file.write_text('contents') #end for s.finished = True assert(not s.got_output) for loc_file,res_file in zip(loc_files,res_files): - assert(os.path.exists(loc_file)) + assert(loc_file.exists()) if s.resdir!=s.locdir: - assert(not os.path.exists(res_file)) + assert(not res_file.exists()) else: - assert(os.path.exists(res_file)) + assert(res_file.exists()) #end if #end for @@ -2117,27 +2075,25 @@ def test_get_output(): assert(s.got_output) for loc_file,res_file in zip(loc_files,res_files): - assert(os.path.exists(loc_file)) - assert(os.path.exists(res_file)) + assert(loc_file.exists()) + assert(res_file.exists()) #end for s.got_output = False s.load_image() assert(s.got_output) - restore_nexus() - Simulation.clear_all_sims() - #end def test_get_output - -def test_analyze(): - import os +@isolate_nexus_core +def test_analyze(tmp_path): from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_analyze',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] s = get_test_sim() @@ -2146,34 +2102,32 @@ def test_analyze(): assert(not s.finished) s.finished = True - analyzer_image = os.path.join(s.imresdir,s.analyzer_image) + analyzer_image = Path(s.imresdir).resolve() / s.analyzer_image assert(not s.analyzed) - assert(not os.path.exists(analyzer_image)) + assert(not analyzer_image.exists()) s.analyze() assert(s.analyzed) - assert(os.path.exists(analyzer_image)) + assert(analyzer_image.exists()) s.analyzed = False s.load_image() assert(s.analyzed) - restore_nexus() - Simulation.clear_all_sims() - #end def test_analyze - -def test_progress(): - import os +@isolate_nexus_core +def test_progress(tmp_path): from ..nexus_base import nexus_core from ..simulation import Simulation,input_template - tpath = testing.setup_unit_test_output_directory('simulation','test_progress',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] assert(nexus_core.mode==nexus_core.modes.stages) assert(len(nexus_core.stages)==0) @@ -2225,12 +2179,12 @@ def test_progress(): assert(not s.analyzed) assert(s.files==set()) assert(s.job.status==0) - assert(not os.path.exists(s.locdir)) - assert(not os.path.exists(s.remdir)) - assert(not os.path.exists(s.resdir)) - assert(not os.path.exists(s.imlocdir)) - assert(not os.path.exists(s.imremdir)) - assert(not os.path.exists(s.imresdir)) + assert(not Path(s.locdir).exists()) + assert(not Path(s.remdir).exists()) + assert(not Path(s.resdir).exists()) + assert(not Path(s.imlocdir).exists()) + assert(not Path(s.imremdir).exists()) + assert(not Path(s.imresdir).exists()) s.progress() @@ -2244,22 +2198,22 @@ def test_progress(): assert(not s.analyzed) assert(s.files==set([s.infile])) assert(s.job.status==1) - assert(os.path.exists(s.locdir)) - assert(os.path.exists(s.remdir)) - assert(os.path.exists(s.imlocdir)) - assert(os.path.exists(s.imremdir)) - assert(os.path.exists(os.path.join(s.locdir,s.infile))) - assert(os.path.exists(os.path.join(s.imlocdir,s.sim_image))) - assert(os.path.exists(os.path.join(s.imlocdir,s.input_image))) - assert(not os.path.exists(os.path.join(s.locdir,s.outfile))) - assert(not os.path.exists(os.path.join(s.locdir,s.errfile))) - assert(not os.path.exists(os.path.join(s.imlocdir,s.analyzer_image))) + assert(Path(s.locdir).exists()) + assert(Path(s.remdir).exists()) + assert(Path(s.imlocdir).exists()) + assert(Path(s.imremdir).exists()) + assert((Path(s.locdir).resolve() / s.infile).exists()) + assert((Path(s.imlocdir).resolve() / s.sim_image).exists()) + assert((Path(s.imlocdir).resolve() / s.input_image).exists()) + assert(not (Path(s.locdir).resolve() / s.outfile).exists()) + assert(not (Path(s.locdir).resolve() / s.errfile).exists()) + assert(not (Path(s.imlocdir).resolve() / s.analyzer_image).exists()) if s.resdir!=s.locdir: - assert(not os.path.exists(s.resdir)) - assert(not os.path.exists(s.imresdir)) + assert(not Path(s.resdir).exists()) + assert(not Path(s.imresdir).exists()) else: - assert(os.path.exists(s.resdir)) - assert(os.path.exists(s.imresdir)) + assert(Path(s.resdir).exists()) + assert(Path(s.imresdir).exists()) #end if # check image @@ -2278,12 +2232,12 @@ def test_progress(): # simulate job completion # create output and error files # set job status to finished - open(os.path.join(s.locdir,s.outfile),'w').write('out') - open(os.path.join(s.locdir,s.errfile),'w').write('err') + (Path(s.locdir).resolve() / s.outfile).write_text('out') + (Path(s.locdir).resolve() / s.errfile).write_text('err') s.job.finished = True - assert(os.path.exists(os.path.join(s.locdir,s.outfile))) - assert(os.path.exists(os.path.join(s.locdir,s.errfile))) + assert((Path(s.locdir) / s.outfile).exists()) + assert((Path(s.locdir) / s.errfile).exists()) # second progression @@ -2309,18 +2263,18 @@ def test_progress(): assert(s.finished) assert(s.got_output) assert(s.analyzed) - assert(os.path.exists(s.resdir)) - assert(os.path.exists(s.imresdir)) - assert(os.path.exists(os.path.join(s.resdir,s.infile))) - assert(os.path.exists(os.path.join(s.resdir,s.errfile))) - assert(os.path.exists(os.path.join(s.resdir,s.outfile))) - assert(os.path.exists(os.path.join(s.imresdir,s.sim_image))) - assert(os.path.exists(os.path.join(s.imresdir,s.input_image))) - assert(os.path.exists(os.path.join(s.imresdir,s.analyzer_image))) + assert(Path(s.resdir).exists()) + assert(Path(s.imresdir).exists()) + assert((Path(s.resdir) / s.infile).exists()) + assert((Path(s.resdir) / s.errfile).exists()) + assert((Path(s.resdir) / s.outfile).exists()) + assert((Path(s.imresdir) / s.sim_image).exists()) + assert((Path(s.imresdir) / s.input_image).exists()) + assert((Path(s.imresdir) / s.analyzer_image).exists()) if s.resdir!=s.locdir: - assert(not os.path.exists(os.path.join(s.imlocdir,s.analyzer_image))) + assert(not (Path(s.imlocdir) / s.analyzer_image).exists()) else: - assert(os.path.exists(os.path.join(s.imlocdir,s.analyzer_image))) + assert((Path(s.imlocdir) / s.analyzer_image).exists()) #end if # check image @@ -2345,21 +2299,18 @@ def test_progress(): assert(object_eq(s,sbef)) - - restore_nexus() - Simulation.clear_all_sims() - #end def test_progress - -def test_execute(): - import os +@isolate_nexus_core +def test_execute(tmp_path): from ..machines import job from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_execute',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] import shutil serial = shutil.which('mpirun') is None @@ -2370,33 +2321,30 @@ def test_execute(): s.create_directories() - outfile = os.path.join(s.locdir,s.outfile) - errfile = os.path.join(s.locdir,s.errfile) + outfile = Path(s.locdir) / s.outfile + errfile = Path(s.locdir) / s.errfile assert(not s.submitted) assert(not s.job.finished) assert(s.job.status==0) - assert(not os.path.exists(outfile)) - assert(not os.path.exists(errfile)) + assert(not outfile.exists()) + assert(not errfile.exists()) s.execute() assert(s.submitted) assert(s.job.finished) assert(s.job.status==4) - assert(os.path.exists(outfile)) - assert(os.path.exists(errfile)) - assert(open(outfile,'r').read().strip()=='run') - err_contents = open(errfile,'r').read().strip() + assert(outfile.exists()) + assert(errfile.exists()) + assert(outfile.read_text().strip()=='run') + err_contents = errfile.read_text().strip() # Handle spurious error message from OpenMPI # see also: https://github.com/QMCPACK/qmcpack/pull/4339#discussion_r1033813856 err_contents = err_contents.replace('Invalid MIT-MAGIC-COOKIE-1 key','').strip() assert(err_contents=='') - restore_nexus() - Simulation.clear_all_sims() - #end def test_execute @@ -2538,19 +2486,24 @@ def assert_blocked(sim): #end def test_block_dependents - -def test_reconstruct_cascade(): - import os +@isolate_nexus_core +def test_reconstruct_cascade(tmp_path): from ..simulation import Simulation - tpath = testing.setup_unit_test_output_directory('simulation','test_reconstruct_cascade',divert=True) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] sims = get_test_workflow(2) assert(len(sims)==7) + machine_in = Job.machine + Job.machine = sims.s1.job.machine + + for s in sims: - imagefile = os.path.join(s.imlocdir,s.sim_image) - assert(not os.path.exists(imagefile)) + imagefile = Path(s.imlocdir) / s.sim_image + assert(not imagefile.exists()) assert(not s.loaded) assert(not s.submitted) assert(not s.finished) @@ -2564,8 +2517,8 @@ def test_reconstruct_cascade(): #end for for s in sims: - imagefile = os.path.join(s.imlocdir,s.sim_image) - assert(os.path.exists(imagefile)) + imagefile = Path(s.imlocdir) / s.sim_image + assert(imagefile.exists()) assert(not s.loaded) assert(not s.submitted) assert(not s.finished) @@ -2576,8 +2529,8 @@ def test_reconstruct_cascade(): sims.s1.reconstruct_cascade() for s in sims: - imagefile = os.path.join(s.imlocdir,s.sim_image) - assert(os.path.exists(imagefile)) + imagefile = Path(s.imlocdir) / s.sim_image + assert(imagefile.exists()) assert(s.loaded) assert(not s.submitted) assert(not s.finished) @@ -2723,8 +2676,8 @@ def cleared(s): assert(empty(sims.s51)) assert(empty(sims.s52)) - restore_nexus() + Job.machine = machine_in Simulation.clear_all_sims() #end def test_reconstruct_cascade @@ -2788,12 +2741,10 @@ def finish(sim): #end def test_traverse_full_cascade - +@isolate_nexus_core def test_write_dependents(): from ..simulation import Simulation - divert_nexus_log() - for i in range(n_test_workflows): sims = get_test_workflow(i) for s in sims: @@ -2803,8 +2754,6 @@ def test_write_dependents(): #end for #end for - restore_nexus_log() - Simulation.clear_all_sims() #end def test_write_dependents @@ -2834,21 +2783,18 @@ def test_generate_simulation(): #end def test_generate_simulation -def test_generic_simulation(): - import os +def test_generic_simulation(tmp_path): from ..simulation import Simulation,GenericSimulation from ..simulation import generate_simulation,SimulationInputTemplate from ..machines import job - tpath = testing.setup_unit_test_output_directory('simulation','test_generic_simulation') - # Test 1: Create GenericSimulation with string input script_text = 'print("Hello from GenericSimulation")' sim1 = generate_simulation( identifier = 'test_generic_string', - path = os.path.join(tpath,'test1'), + path = str(tmp_path / 'test1'), job = job(machine='ws1', serial=True, app='python3'), - input = script_text, + input = str(script_text), outfiles = ['output.txt'], ) assert(isinstance(sim1,GenericSimulation)) @@ -2865,18 +2811,17 @@ def test_generic_simulation(): assert('python3' in sim1.app_command() or sim1.job.app_name == 'python3') - script_file = os.path.join(tpath,'test_script.py') + script_file = tmp_path / 'test_script.py' script_file_content = 'print("Hello from file")\n' - with open(script_file,'w') as f: - f.write(script_file_content) + script_file.write_text(script_file_content) #end with # Test 2: GenericSimulation with file path input sim2 = generate_simulation( identifier = 'test_generic_file', - path = os.path.join(tpath,'test2'), + path = str(tmp_path / 'test2'), job = job(machine='ws1', serial=True, app='python3'), - input = script_file, + input = str(script_file), outfiles = ['result.txt'], ) assert(isinstance(sim2,GenericSimulation)) @@ -2896,14 +2841,14 @@ def test_generic_simulation(): -if versions.matplotlib_available and versions.pydot_available: - def test_graph_sims(): - from ..simulation import Simulation,graph_sims +def test_graph_sims(): + _ = pytest.importorskip("matplotlib") + _ = pytest.importorskip("pydot") + from ..simulation import Simulation,graph_sims - sims = get_test_workflow(3) + sims = get_test_workflow(3) - graph_sims(sims.list(),display=False,exit=False) + graph_sims(sims.list(),display=False,exit=False) - Simulation.clear_all_sims() - #end def test_graph_sims -#end if + Simulation.clear_all_sims() +#end def test_graph_sims diff --git a/nexus/nexus/tests/test_structure.py b/nexus/nexus/tests/test_structure.py index 504ecfd013..ba7064a741 100644 --- a/nexus/nexus/tests/test_structure.py +++ b/nexus/nexus/tests/test_structure.py @@ -1,11 +1,17 @@ -#!/env/bin/python +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.STRUCTURE) + +from ..generic import generic_settings +generic_settings.raise_error = True import numpy as np -from .. import versions +from . import TEST_DIR from .. import testing from ..testing import value_eq as value_eq_orig from ..testing import object_eq as object_eq_orig from ..testing import object_diff as object_diff_orig +from ..testing import text_eq struct_atol = 1e-10 @@ -32,18 +38,19 @@ def object_diff(*args,**kwargs): #end def object_diff -associated_files = dict() +TEST_FILES = { + 'La2CuO4_ICSD69312.cif': TEST_DIR / "test_structure_files/La2CuO4_ICSD69312.cif", + 'coronene.xyz': TEST_DIR / "test_structure_files/coronene.xyz", + } + +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" + reference_inputs = dict() reference_structures = dict() generated_structures = dict() crystal_structures = dict() - -def get_files(): - return testing.collect_unit_test_file_paths('structure',associated_files) -#end def get_files - - def structure_diff(s1,s2): keys = ('units','elem','pos','axes','kpoints','kweights','kaxes') o1 = s1.obj(keys) @@ -253,26 +260,6 @@ def example_structure_h4(): #end def example_structure_h4 - -def test_files(): - filenames = [ - 'La2CuO4_ICSD69312.cif', - 'coronene.xyz', - ] - files = get_files() - assert(set(files.keys())==set(filenames)) -#end def test_files - - - -def test_import(): - from ..structure import Structure,Crystal - from ..structure import generate_structure - from ..structure import read_structure -#end def test_import - - - def test_empty_init(): from ..structure import Structure from ..structure import generate_structure @@ -284,7 +271,6 @@ def test_empty_init(): def test_reference_inputs(): - from ..developer import obj ref_in = get_reference_inputs() assert(len(ref_in)>0) #end def test_reference_inputs @@ -633,30 +619,27 @@ def test_gen_graphene(): -def test_read_write(): +def test_read_write(tmp_path): """ Write/read conventional diamond cell to/from XYZ, XSF, and POSCAR formats. """ - import os from ..structure import generate_structure, read_structure - tpath = testing.setup_unit_test_output_directory('structure','test_read_write') - d8 = generate_structure( structure = 'diamond', cell = 'conv', ) # Write an XYZ file - xyz_file = os.path.join(tpath,'diamond8.xyz') + xyz_file = tmp_path / 'diamond8.xyz' d8.write(xyz_file) # Write an XSF file - xsf_file = os.path.join(tpath,'diamond8.xsf') + xsf_file = tmp_path / 'diamond8.xsf' d8.write(xsf_file) # Write a POSCAR file - poscar_file = os.path.join(tpath,'diamond8.POSCAR') + poscar_file = tmp_path / 'diamond8.POSCAR' d8.write(poscar_file) # Read an XYZ file @@ -676,44 +659,42 @@ def test_read_write(): -if versions.pycifrw_available and versions.cif2cell_available: - def test_read_cif(): - """ - Read La2CuO4 structure from a CIF file. - """ - from ..structure import read_structure,generate_structure - - files = get_files() +def test_read_cif(): + """ + Read La2CuO4 structure from a CIF file. + """ + _ = pytest.importorskip("cif2cell") + _ = pytest.importorskip("CifFile") + from ..structure import read_structure,generate_structure - # Read from CIF file - s = read_structure(files['La2CuO4_ICSD69312.cif']) + # Read from CIF file + s = read_structure(str(TEST_FILES['La2CuO4_ICSD69312.cif'])) - ref = generate_structure( - units = 'A', - axes = [[ 2.665, 0. , -6.5525], - [ 0. , 5.4126, 0. ], - [ 2.665, 0. , 6.5525]], - elem = 'La La La La Cu Cu O O O O O O O O'.split(), - pos = [[ 2.665 , 5.37038172, -1.8071795 ], - [ 2.665 , 2.74851828, 4.7453205 ], - [ 2.665 , 2.66408172, -4.7453205 ], - [ 2.665 , 0.04221828, 1.8071795 ], - [ 0. , 0. , 0. ], - [ 2.665 , 2.7063 , 0. ], - [ 1.3325, 1.35315 , -0.128429 ], - [ 3.9975, 4.05945 , 0.128429 ], - [ 3.9975, 1.35315 , -0.128429 ], - [ 1.3325, 4.05945 , 0.128429 ], - [ 2.665 , 0.23490684, -4.1398695 ], - [ 2.665 , 2.47139316, 2.4126305 ], - [ 2.665 , 2.94120684, -2.4126305 ], - [ 2.665 , 5.17769316, 4.1398695 ]], - ) + ref = generate_structure( + units = 'A', + axes = [[ 2.665, 0. , -6.5525], + [ 0. , 5.4126, 0. ], + [ 2.665, 0. , 6.5525]], + elem = 'La La La La Cu Cu O O O O O O O O'.split(), + pos = [[ 2.665 , 5.37038172, -1.8071795 ], + [ 2.665 , 2.74851828, 4.7453205 ], + [ 2.665 , 2.66408172, -4.7453205 ], + [ 2.665 , 0.04221828, 1.8071795 ], + [ 0. , 0. , 0. ], + [ 2.665 , 2.7063 , 0. ], + [ 1.3325, 1.35315 , -0.128429 ], + [ 3.9975, 4.05945 , 0.128429 ], + [ 3.9975, 1.35315 , -0.128429 ], + [ 1.3325, 4.05945 , 0.128429 ], + [ 2.665 , 0.23490684, -4.1398695 ], + [ 2.665 , 2.47139316, 2.4126305 ], + [ 2.665 , 2.94120684, -2.4126305 ], + [ 2.665 , 5.17769316, 4.1398695 ]], + ) - assert(structure_same(s,ref)) + assert(structure_same(s,ref)) - #end def test_read_cif -#end if +#end def test_read_cif @@ -721,8 +702,6 @@ def test_bounding_box(): import numpy as np from ..structure import generate_structure,read_structure - files = get_files() - h2o = generate_structure( elem = ['O','H','H'], pos = [[0.000000, 0.000000, 0.000000], @@ -743,7 +722,7 @@ def test_bounding_box(): assert(value_eq(tuple(h2o_auto.pos[-1]),(4.,4.75716,4.29313))) - s = read_structure(files['coronene.xyz']) + s = read_structure(TEST_FILES['coronene.xyz']) # make a bounding box that is at least 5 A from the nearest atom s.bounding_box(mindist=5.0) @@ -782,46 +761,45 @@ def test_opt_tiling(): -if versions.seekpath_available: - def test_primitive_search(): - """ - Find the primitive cell given a supercell. - """ - - from ..structure import generate_structure +def test_primitive_search(): + """ + Find the primitive cell given a supercell. + """ + _ = pytest.importorskip("spglib") + _ = pytest.importorskip("seekpath") + from ..structure import generate_structure - d2 = generate_structure( - structure = 'diamond', - cell = 'prim', - ) + d2 = generate_structure( + structure = 'diamond', + cell = 'prim', + ) - tmatrix = [[ 2, -2, 2], - [ 2, 2, -2], - [-2, 2, 2]] + tmatrix = [[ 2, -2, 2], + [ 2, 2, -2], + [-2, 2, 2]] - d64 = d2.tile(tmatrix) + d64 = d2.tile(tmatrix) - # Remove all traces of the 2 atom cell, supercell is all that remains - d64.remove_folded() - del d2 + # Remove all traces of the 2 atom cell, supercell is all that remains + d64.remove_folded() + del d2 - # Find the primitive cell from the supercell - dprim = d64.primitive() + # Find the primitive cell from the supercell + dprim = d64.primitive() - tmatrix = d64.tilematrix(dprim) + tmatrix = d64.tilematrix(dprim) - axes_ref = np.array([[0. , 1.785, 1.785], - [1.785, 0. , 1.785], - [1.785, 1.785, 0. ]]) - tmatrix_ref = np.array([[-2, 2, 2], - [ 2, -2, 2], - [ 2, 2, -2]]) + axes_ref = np.array([[0. , 1.785, 1.785], + [1.785, 0. , 1.785], + [1.785, 1.785, 0. ]]) + tmatrix_ref = np.array([[-2, 2, 2], + [ 2, -2, 2], + [ 2, 2, -2]]) - assert(value_eq(dprim.axes,axes_ref)) - assert(value_eq(tmatrix,tmatrix_ref)) + assert(value_eq(dprim.axes,axes_ref)) + assert(value_eq(tmatrix,tmatrix_ref)) - #end def test_primitive_search -#end if +#end def test_primitive_search @@ -1081,106 +1059,105 @@ def test_monkhorst_pack_kpoints(): -if versions.spglib_available: - def test_symm_kpoints(): - """ - Add symmetrized Monkhorst-Pack kpoints. - """ - from ..structure import generate_structure +def test_symm_kpoints(): + """ + Add symmetrized Monkhorst-Pack kpoints. + """ + _ = pytest.importorskip("spglib") + from ..structure import generate_structure - # Note: this demo requires spglib + # Note: this demo requires spglib - g44 = generate_structure( - structure = 'graphene', - cell = 'prim', - tiling = (4,4,1), - kgrid = (4,4,1), - kshift = (0,0,0), - symm_kgrid = True, - ) + g44 = generate_structure( + structure = 'graphene', + cell = 'prim', + tiling = (4,4,1), + kgrid = (4,4,1), + kshift = (0,0,0), + symm_kgrid = True, + ) + + g11 = g44.folded_structure + + g44_kw_ref = np.array([1,6,3,6],dtype=float) + + g44_ukp_ref = np.array([ + [ 0.00, 0.00, 0.00 ], + [ 0.25, 0.00, 0.00 ], + [ 0.50, 0.00, 0.00 ], + [ 0.25, 0.25, 0.00 ]]) + + g11_ukp_ref = np.array([ + [ 0.0000, 0.0000, 0.0000 ], + [ 0.0625, 0.0000, 0.0000 ], + [ 0.1250, 0.0000, 0.0000 ], + [ 0.0625, 0.0625, 0.0000 ], + [ 0.2500, 0.0000, 0.0000 ], + [ 0.3125, 0.0000, 0.0000 ], + [ 0.3750, 0.0000, 0.0000 ], + [ 0.3125, 0.0625, 0.0000 ], + [ 0.5000, 0.0000, 0.0000 ], + [ 0.5625, 0.0000, 0.0000 ], + [ 0.6250, 0.0000, 0.0000 ], + [ 0.5625, 0.0625, 0.0000 ], + [ 0.7500, 0.0000, 0.0000 ], + [ 0.8125, 0.0000, 0.0000 ], + [ 0.8750, 0.0000, 0.0000 ], + [ 0.8125, 0.0625, 0.0000 ], + [ 0.0000, 0.2500, 0.0000 ], + [ 0.0625, 0.2500, 0.0000 ], + [ 0.1250, 0.2500, 0.0000 ], + [ 0.0625, 0.3125, 0.0000 ], + [ 0.2500, 0.2500, 0.0000 ], + [ 0.3125, 0.2500, 0.0000 ], + [ 0.3750, 0.2500, 0.0000 ], + [ 0.3125, 0.3125, 0.0000 ], + [ 0.5000, 0.2500, 0.0000 ], + [ 0.5625, 0.2500, 0.0000 ], + [ 0.6250, 0.2500, 0.0000 ], + [ 0.5625, 0.3125, 0.0000 ], + [ 0.7500, 0.2500, 0.0000 ], + [ 0.8125, 0.2500, 0.0000 ], + [ 0.8750, 0.2500, 0.0000 ], + [ 0.8125, 0.3125, 0.0000 ], + [ 0.0000, 0.5000, 0.0000 ], + [ 0.0625, 0.5000, 0.0000 ], + [ 0.1250, 0.5000, 0.0000 ], + [ 0.0625, 0.5625, 0.0000 ], + [ 0.2500, 0.5000, 0.0000 ], + [ 0.3125, 0.5000, 0.0000 ], + [ 0.3750, 0.5000, 0.0000 ], + [ 0.3125, 0.5625, 0.0000 ], + [ 0.5000, 0.5000, 0.0000 ], + [ 0.5625, 0.5000, 0.0000 ], + [ 0.6250, 0.5000, 0.0000 ], + [ 0.5625, 0.5625, 0.0000 ], + [ 0.7500, 0.5000, 0.0000 ], + [ 0.8125, 0.5000, 0.0000 ], + [ 0.8750, 0.5000, 0.0000 ], + [ 0.8125, 0.5625, 0.0000 ], + [ 0.0000, 0.7500, 0.0000 ], + [ 0.0625, 0.7500, 0.0000 ], + [ 0.1250, 0.7500, 0.0000 ], + [ 0.0625, 0.8125, 0.0000 ], + [ 0.2500, 0.7500, 0.0000 ], + [ 0.3125, 0.7500, 0.0000 ], + [ 0.3750, 0.7500, 0.0000 ], + [ 0.3125, 0.8125, 0.0000 ], + [ 0.5000, 0.7500, 0.0000 ], + [ 0.5625, 0.7500, 0.0000 ], + [ 0.6250, 0.7500, 0.0000 ], + [ 0.5625, 0.8125, 0.0000 ], + [ 0.7500, 0.7500, 0.0000 ], + [ 0.8125, 0.7500, 0.0000 ], + [ 0.8750, 0.7500, 0.0000 ], + [ 0.8125, 0.8125, 0.0000 ]]) + + assert(value_eq(g44.kweights,g44_kw_ref)) + assert(value_eq(g44.kpoints_unit(),g44_ukp_ref)) + assert(value_eq(g11.kpoints_unit(),g11_ukp_ref)) - g11 = g44.folded_structure - - g44_kw_ref = np.array([1,6,3,6],dtype=float) - - g44_ukp_ref = np.array([ - [ 0.00, 0.00, 0.00 ], - [ 0.25, 0.00, 0.00 ], - [ 0.50, 0.00, 0.00 ], - [ 0.25, 0.25, 0.00 ]]) - - g11_ukp_ref = np.array([ - [ 0.0000, 0.0000, 0.0000 ], - [ 0.0625, 0.0000, 0.0000 ], - [ 0.1250, 0.0000, 0.0000 ], - [ 0.0625, 0.0625, 0.0000 ], - [ 0.2500, 0.0000, 0.0000 ], - [ 0.3125, 0.0000, 0.0000 ], - [ 0.3750, 0.0000, 0.0000 ], - [ 0.3125, 0.0625, 0.0000 ], - [ 0.5000, 0.0000, 0.0000 ], - [ 0.5625, 0.0000, 0.0000 ], - [ 0.6250, 0.0000, 0.0000 ], - [ 0.5625, 0.0625, 0.0000 ], - [ 0.7500, 0.0000, 0.0000 ], - [ 0.8125, 0.0000, 0.0000 ], - [ 0.8750, 0.0000, 0.0000 ], - [ 0.8125, 0.0625, 0.0000 ], - [ 0.0000, 0.2500, 0.0000 ], - [ 0.0625, 0.2500, 0.0000 ], - [ 0.1250, 0.2500, 0.0000 ], - [ 0.0625, 0.3125, 0.0000 ], - [ 0.2500, 0.2500, 0.0000 ], - [ 0.3125, 0.2500, 0.0000 ], - [ 0.3750, 0.2500, 0.0000 ], - [ 0.3125, 0.3125, 0.0000 ], - [ 0.5000, 0.2500, 0.0000 ], - [ 0.5625, 0.2500, 0.0000 ], - [ 0.6250, 0.2500, 0.0000 ], - [ 0.5625, 0.3125, 0.0000 ], - [ 0.7500, 0.2500, 0.0000 ], - [ 0.8125, 0.2500, 0.0000 ], - [ 0.8750, 0.2500, 0.0000 ], - [ 0.8125, 0.3125, 0.0000 ], - [ 0.0000, 0.5000, 0.0000 ], - [ 0.0625, 0.5000, 0.0000 ], - [ 0.1250, 0.5000, 0.0000 ], - [ 0.0625, 0.5625, 0.0000 ], - [ 0.2500, 0.5000, 0.0000 ], - [ 0.3125, 0.5000, 0.0000 ], - [ 0.3750, 0.5000, 0.0000 ], - [ 0.3125, 0.5625, 0.0000 ], - [ 0.5000, 0.5000, 0.0000 ], - [ 0.5625, 0.5000, 0.0000 ], - [ 0.6250, 0.5000, 0.0000 ], - [ 0.5625, 0.5625, 0.0000 ], - [ 0.7500, 0.5000, 0.0000 ], - [ 0.8125, 0.5000, 0.0000 ], - [ 0.8750, 0.5000, 0.0000 ], - [ 0.8125, 0.5625, 0.0000 ], - [ 0.0000, 0.7500, 0.0000 ], - [ 0.0625, 0.7500, 0.0000 ], - [ 0.1250, 0.7500, 0.0000 ], - [ 0.0625, 0.8125, 0.0000 ], - [ 0.2500, 0.7500, 0.0000 ], - [ 0.3125, 0.7500, 0.0000 ], - [ 0.3750, 0.7500, 0.0000 ], - [ 0.3125, 0.8125, 0.0000 ], - [ 0.5000, 0.7500, 0.0000 ], - [ 0.5625, 0.7500, 0.0000 ], - [ 0.6250, 0.7500, 0.0000 ], - [ 0.5625, 0.8125, 0.0000 ], - [ 0.7500, 0.7500, 0.0000 ], - [ 0.8125, 0.7500, 0.0000 ], - [ 0.8750, 0.7500, 0.0000 ], - [ 0.8125, 0.8125, 0.0000 ]]) - - assert(value_eq(g44.kweights,g44_kw_ref)) - assert(value_eq(g44.kpoints_unit(),g44_ukp_ref)) - assert(value_eq(g11.kpoints_unit(),g11_ukp_ref)) - - #end def test_symm_kpoints -#end if +#end def test_symm_kpoints def test_count_kshells(): @@ -1227,22 +1204,22 @@ def test_volume(): -if versions.scipy_available: - def test_madelung(): - gen = get_generated_structures() - d64 = gen.diamond_64 - assert(value_eq(d64.madelung(),-0.210284756321)) - #end def test_madelung +def test_madelung(): + _ = pytest.importorskip("scipy") + gen = get_generated_structures() + d64 = gen.diamond_64 + assert(value_eq(d64.madelung(),-0.210284756321)) +#end def test_madelung - def test_makov_payne(): - gen = get_generated_structures() - d64 = gen.diamond_64 - assert(value_eq(d64.makov_payne(q=1,eps=5.68),0.0185109820705)) - assert(value_eq(d64.makov_payne(q=2,eps=5.68),0.074043928282)) - #end def test_makov_payne -#end if +def test_makov_payne(): + _ = pytest.importorskip("scipy") + gen = get_generated_structures() + d64 = gen.diamond_64 + assert(value_eq(d64.makov_payne(q=1,eps=5.68),0.0185109820705)) + assert(value_eq(d64.makov_payne(q=2,eps=5.68),0.074043928282)) +#end def test_makov_payne @@ -1351,66 +1328,64 @@ def test_freeze(): -if versions.scipy_available: - def test_embed(): - """ - Embed a "relaxed" structure in a larger pristine cell. - """ - import numpy as np - from ..structure import generate_structure - from .. import numpy_extensions as npe - - center = (0,0,0) +def test_embed(): + """ + Embed a "relaxed" structure in a larger pristine cell. + """ + _ = pytest.importorskip("scipy") + import numpy as np + from ..structure import generate_structure + from .. import numpy_extensions as npe - g = generate_structure( - structure = 'graphene', - cell = 'prim', - tiling = (4,4,1), - ) - g.recenter(center) - - # Represent the "relaxed" cell - gr = g.copy() - npos = len(gr.pos) - dr = gr.min_image_vectors(center) - npe.reshape_inplace(dr, (npos, 3)) - r = np.linalg.norm(dr,axis=1) - dilation = 2*r*np.exp(-r) - for i in range(npos): - if r[i]>0: - gr.pos[i] += dilation[i]/r[i]*dr[i] - #end if - #end for + center = (0,0,0) - # Represent the unrelaxed large cell - gl = generate_structure( - structure = 'graphene', - cell = 'rect', - tiling = (8,4,1), - ) - gl.recenter(center) + g = generate_structure( + structure = 'graphene', + cell = 'prim', + tiling = (4,4,1), + ) + g.recenter(center) + + # Represent the "relaxed" cell + gr = g.copy() + npos = len(gr.pos) + dr = gr.min_image_vectors(center) + npe.reshape_inplace(dr, (npos, 3)) + r = np.linalg.norm(dr,axis=1) + dilation = 2*r*np.exp(-r) + for i in range(npos): + if r[i]>0: + gr.pos[i] += dilation[i]/r[i]*dr[i] + #end if + #end for - # Embed the relaxed cell in the large unrelaxed cell - ge = gl.copy() - ge.embed(gr) + # Represent the unrelaxed large cell + gl = generate_structure( + structure = 'graphene', + cell = 'rect', + tiling = (8,4,1), + ) + gl.recenter(center) - assert(len(ge.elem)==len(gl.elem)) - assert(len(ge.pos)==len(gl.pos)) + # Embed the relaxed cell in the large unrelaxed cell + ge = gl.copy() + ge.embed(gr) - # check that the large local distortion made in the small cell - # is present in the large cell after embedding - rnn_max_ref = 2.1076122431022664 - - # Check small cell distortion max distance - rnn_max = np.linalg.norm(gr.pos[0]-gr.pos[1]) - assert(value_eq(rnn_max,rnn_max_ref)) + assert(len(ge.elem)==len(gl.elem)) + assert(len(ge.pos)==len(gl.pos)) - # Check large cell distortion max distance - rnn_max = np.linalg.norm(ge.pos[0]-ge.pos[1]) - assert(value_eq(rnn_max,rnn_max_ref)) + # check that the large local distortion made in the small cell + # is present in the large cell after embedding + rnn_max_ref = 2.1076122431022664 + + # Check small cell distortion max distance + rnn_max = np.linalg.norm(gr.pos[0]-gr.pos[1]) + assert(value_eq(rnn_max,rnn_max_ref)) - #end test_embed -#end if + # Check large cell distortion max distance + rnn_max = np.linalg.norm(ge.pos[0]-ge.pos[1]) + assert(value_eq(rnn_max,rnn_max_ref)) +#end def test_embed @@ -1471,188 +1446,451 @@ def test_interpolate(): -if versions.spglib_available: - def test_point_group_operations(): - from ..structure import generate_structure,Crystal - - nrotations = dict( - Ca2CuO3 = 8, - CaO = 48, - Cl2Ca2CuO2 = 16, - CuO = 2, - CuO2_plane = 16, - La2CuO4 = 2, - NaCl = 48, - ZnO = 6, - calcium = 48, - copper = 48, - diamond = 24, - graphene = 12, - oxygen = 4, - rocksalt = 48, - wurtzite = 6, +def test_point_group_operations(): + _ = pytest.importorskip("spglib") + from ..structure import generate_structure,Crystal + + nrotations = dict( + Ca2CuO3 = 8, + CaO = 48, + Cl2Ca2CuO2 = 16, + CuO = 2, + CuO2_plane = 16, + La2CuO4 = 2, + NaCl = 48, + ZnO = 6, + calcium = 48, + copper = 48, + diamond = 24, + graphene = 12, + oxygen = 4, + rocksalt = 48, + wurtzite = 6, + ) + + for struct,cell in sorted(Crystal.known_crystals.keys()): + if cell!='prim': + continue + #end if + + s = generate_structure( + structure = struct, + cell = cell, ) + + rotations = s.point_group_operations() + assert(struct in nrotations) + assert(len(rotations)==nrotations[struct]) + + valid = s.check_point_group_operations(rotations,exit=False) + assert(valid) + #end for + +#end def test_point_group_operations - for struct,cell in sorted(Crystal.known_crystals.keys()): - if cell!='prim': - continue - #end if - s = generate_structure( - structure = struct, - cell = cell, - ) - - rotations = s.point_group_operations() - assert(struct in nrotations) - assert(len(rotations)==nrotations[struct]) - - valid = s.check_point_group_operations(rotations,exit=False) - assert(valid) - #end for - #end def test_point_group_operations -#end if - - - -if versions.spglib_available and versions.seekpath_available: - def test_rmg_transform(): - from numpy import array - from ..developer import obj - from ..structure import generate_structure - - ref = obj({ - ('Ca2CuO3', 'conv') : obj( - R = array([[ 8.62068966e-01, 0.00000000e+00, 0.00000000e+00], - [-5.27865000e-17, 1.16000000e+00, 0.00000000e+00], - [-5.27865000e-17, -7.10295144e-17, 1.00000000e+00]]), - bv = 'orthorhombic_P', - tmatrix = None, - rmg_inputs = obj( - a_length = 3.2500000000000004, - b_length = 3.7700000000000005, - bravais_lattice_type = 'Orthorhombic Primitive', - c_length = 12.23, - length_units = 'Angstrom', - ), +def test_rmg_transform(): + _ = pytest.importorskip("spglib") + _ = pytest.importorskip("seekpath") + from numpy import array + from ..developer import obj + from ..structure import generate_structure + + ref = obj({ + ('Ca2CuO3', 'conv') : obj( + R = array([[ 8.62068966e-01, 0.00000000e+00, 0.00000000e+00], + [-5.27865000e-17, 1.16000000e+00, 0.00000000e+00], + [-5.27865000e-17, -7.10295144e-17, 1.00000000e+00]]), + bv = 'orthorhombic_P', + tmatrix = None, + rmg_inputs = obj( + a_length = 3.2500000000000004, + b_length = 3.7700000000000005, + bravais_lattice_type = 'Orthorhombic Primitive', + c_length = 12.23, + length_units = 'Angstrom', ), - ('Ca2CuO3', 'prim') : obj( - R = array([[ 1.38777878e-17, 1.00000000e+00, -7.13693767e-18], - [ 2.77555756e-17, 3.61249492e-17, 3.76307692e+00], - [ 2.65739984e-01, -5.79633098e-18, -2.39520632e-17]]), - bv = 'orthorhombic_P', - tmatrix = array([[0, 1, 1], - [1, 0, 1], - [1, 1, 0]]), - rmg_inputs = obj( - a_length = 3.2500000000000004, - b_length = 3.77, - bravais_lattice_type = 'Orthorhombic Primitive', - c_length = 12.23, - length_units = 'Angstrom', - ), + ), + ('Ca2CuO3', 'prim') : obj( + R = array([[ 1.38777878e-17, 1.00000000e+00, -7.13693767e-18], + [ 2.77555756e-17, 3.61249492e-17, 3.76307692e+00], + [ 2.65739984e-01, -5.79633098e-18, -2.39520632e-17]]), + bv = 'orthorhombic_P', + tmatrix = array([[0, 1, 1], + [1, 0, 1], + [1, 1, 0]]), + rmg_inputs = obj( + a_length = 3.2500000000000004, + b_length = 3.77, + bravais_lattice_type = 'Orthorhombic Primitive', + c_length = 12.23, + length_units = 'Angstrom', ), - ('CaO', 'conv') : obj( - R = array([[ 1.000000e+00, 0.000000e+00, 0.000000e+00], - [-6.123234e-17, 1.000000e+00, 0.000000e+00], - [-6.123234e-17, -6.123234e-17, 1.000000e+00]]), - bv = 'cubic_P', - tmatrix = None, - rmg_inputs = obj( - a_length = 4.81, - b_length = 4.81, - bravais_lattice_type = 'Cubic Primitive', - c_length = 4.81, - length_units = 'Angstrom', - ), + ), + ('CaO', 'conv') : obj( + R = array([[ 1.000000e+00, 0.000000e+00, 0.000000e+00], + [-6.123234e-17, 1.000000e+00, 0.000000e+00], + [-6.123234e-17, -6.123234e-17, 1.000000e+00]]), + bv = 'cubic_P', + tmatrix = None, + rmg_inputs = obj( + a_length = 4.81, + b_length = 4.81, + bravais_lattice_type = 'Cubic Primitive', + c_length = 4.81, + length_units = 'Angstrom', ), - ('CaO', 'prim') : obj( - R = array([[-1.28679696e-17, 1.00000000e+00, 1.28679696e-17], - [ 1.28679696e-17, 1.28679696e-17, 1.00000000e+00], - [ 1.00000000e+00, -1.28679696e-17, -1.28679696e-17]]), - bv = 'cubic_F', - tmatrix = None, - rmg_inputs = obj( - a_length = 4.81, - b_length = 4.81, - bravais_lattice_type = 'Cubic Face Centered', - c_length = 4.81, - length_units = 'Angstrom', - ), + ), + ('CaO', 'prim') : obj( + R = array([[-1.28679696e-17, 1.00000000e+00, 1.28679696e-17], + [ 1.28679696e-17, 1.28679696e-17, 1.00000000e+00], + [ 1.00000000e+00, -1.28679696e-17, -1.28679696e-17]]), + bv = 'cubic_F', + tmatrix = None, + rmg_inputs = obj( + a_length = 4.81, + b_length = 4.81, + bravais_lattice_type = 'Cubic Face Centered', + c_length = 4.81, + length_units = 'Angstrom', ), - ('Cl2Ca2CuO2', 'afm') : obj( - R = array([[ 0.70710678, 0.70710678, 0. ], - [-0.70710678, 0.70710678, 0. ], - [ 0. , 0. , 1. ]]), - bv = 'tetragonal_P', - tmatrix = None, - rmg_inputs = obj( - a_length = 5.471592272821505, - b_length = 5.471592272821505, - bravais_lattice_type = 'Tetragonal Primitive', - c_length = 15.049999999999999, - length_units = 'Angstrom', - ), + ), + ('Cl2Ca2CuO2', 'afm') : obj( + R = array([[ 0.70710678, 0.70710678, 0. ], + [-0.70710678, 0.70710678, 0. ], + [ 0. , 0. , 1. ]]), + bv = 'tetragonal_P', + tmatrix = None, + rmg_inputs = obj( + a_length = 5.471592272821505, + b_length = 5.471592272821505, + bravais_lattice_type = 'Tetragonal Primitive', + c_length = 15.049999999999999, + length_units = 'Angstrom', ), - ('Cl2Ca2CuO2', 'prim') : obj( - R = array([[-1.99922127e-16, 1.00000000e+00, 1.13566145e-16], - [ 1.84864975e-17, -1.84864975e-17, 3.88989403e+00], - [ 2.57076412e-01, 1.87078112e-18, -1.25038407e-17]]), - bv = 'tetragonal_P', - tmatrix = array([[0, 1, 1], - [1, 0, 1], - [1, 1, 0]]), - rmg_inputs = obj( - a_length = 3.8689999999999998, - b_length = 3.869, - bravais_lattice_type = 'Tetragonal Primitive', - c_length = 15.05, - length_units = 'Angstrom', - ), + ), + ('Cl2Ca2CuO2', 'prim') : obj( + R = array([[-1.99922127e-16, 1.00000000e+00, 1.13566145e-16], + [ 1.84864975e-17, -1.84864975e-17, 3.88989403e+00], + [ 2.57076412e-01, 1.87078112e-18, -1.25038407e-17]]), + bv = 'tetragonal_P', + tmatrix = array([[0, 1, 1], + [1, 0, 1], + [1, 1, 0]]), + rmg_inputs = obj( + a_length = 3.8689999999999998, + b_length = 3.869, + bravais_lattice_type = 'Tetragonal Primitive', + c_length = 15.05, + length_units = 'Angstrom', ), - ('CuO', 'conv') : obj( - R = None, - bv = 'monoclinic_P', - tmatrix = None, - rmg_inputs = obj( - ), + ), + ('CuO', 'conv') : obj( + R = None, + bv = 'monoclinic_P', + tmatrix = None, + rmg_inputs = obj( ), - ('ZnO', 'conv') : obj( - R = array([[ 1.00000000e+00, 0.00000000e+00, 0.00000000e+00], - [-2.51021563e-16, 1.00000000e+00, 0.00000000e+00], - [-6.12323400e-17, -1.06057524e-16, 1.00000000e+00]]), - bv = 'hexagonal_P', - tmatrix = None, - rmg_inputs = obj( - a_length = 3.349999999999999, - b_length = 3.349999999999999, - bravais_lattice_type = 'Hexagonal Primitive', - c_length = 5.22, - length_units = 'Angstrom', - ), + ), + ('ZnO', 'conv') : obj( + R = array([[ 1.00000000e+00, 0.00000000e+00, 0.00000000e+00], + [-2.51021563e-16, 1.00000000e+00, 0.00000000e+00], + [-6.12323400e-17, -1.06057524e-16, 1.00000000e+00]]), + bv = 'hexagonal_P', + tmatrix = None, + rmg_inputs = obj( + a_length = 3.349999999999999, + b_length = 3.349999999999999, + bravais_lattice_type = 'Hexagonal Primitive', + c_length = 5.22, + length_units = 'Angstrom', ), - }) - - res = obj() - for struct,cell in ref.keys(): - s = generate_structure( - structure = struct, - cell = cell, - ) - st,rmg_inputs,R,tmatrix,bv = s.rmg_transform( - allow_tile = True, - allow_general = True, - all_results = True, - ) - res[struct,cell] = obj( - rmg_inputs = rmg_inputs, - R = R, - tmatrix = tmatrix, - bv = bv, - ) - #end for + ), + }) + + res = obj() + for struct,cell in ref.keys(): + s = generate_structure( + structure = struct, + cell = cell, + ) + st,rmg_inputs,R,tmatrix,bv = s.rmg_transform( + allow_tile = True, + allow_general = True, + all_results = True, + ) + res[struct,cell] = obj( + rmg_inputs = rmg_inputs, + R = R, + tmatrix = tmatrix, + bv = bv, + ) + #end for + + assert(testing.check_object_eq(res,ref,atol=1e-12)) +#end def test_rmg_transform + + +def test_group_atoms(): + from nexus.structure import Structure + + unordered_elem = ["H", "N", "C", "H", "C", "O", "H", "H", "O", "H"] + ordered_elem = ["C", "C", "H", "H", "H", "H", "H", "N", "O", "O"] + + structure = Structure( + axes = np.array([ + [6.00000, 0.00000, 0.00000], + [0.00000, 6.00000, 0.00000], + [0.00000, 0.00000, 6.00000], + ], dtype=np.float64), + elem = unordered_elem, + pos = np.array([ + [ 0.711045, 1.361274, 3.966292], + [ 1.848745, 2.865874, 3.041292], + [ 0.679145, 1.977474, 3.067692], + [ 1.827545, 3.514674, 3.813792], + [-0.580355, 2.805074, 3.070592], + [-0.510755, 4.011174, 3.052592], + [ 2.706445, 2.334474, 3.038892], + [ 0.690245, 1.335874, 2.186592], + [-1.779455, 2.202274, 3.093292], + [-2.558655, 2.774774, 3.094192], + ], dtype=np.float64), + units="A", + ) + + np.testing.assert_array_equal(structure.elem, unordered_elem) + + structure.group_atoms() + np.testing.assert_array_equal(structure.elem, ordered_elem) + + +def test_rename(): + from nexus.structure import Structure + + original_elem = ["N", "C", "C", "O", "O", "H", "H", "H", "H", "H"] + + structure = Structure( + axes = np.array([ + [6.00000, 0.00000, 0.00000], + [0.00000, 6.00000, 0.00000], + [0.00000, 0.00000, 6.00000], + ], dtype=np.float64), + elem = original_elem, + pos = np.array([ + [ 1.848745, 2.865874, 3.041292], + [ 0.679145, 1.977474, 3.067692], + [-0.580355, 2.805074, 3.070592], + [-0.510755, 4.011174, 3.052592], + [-1.779455, 2.202274, 3.093292], + [ 1.827545, 3.514674, 3.813792], + [ 2.706445, 2.334474, 3.038892], + [ 0.690245, 1.335874, 2.186592], + [ 0.711045, 1.361274, 3.966292], + [-2.558655, 2.774774, 3.094192], + ], dtype=np.float64), + units="A", + ) + + np.testing.assert_array_equal(structure.elem, original_elem) + + new_elem = ["La", "Np", "Np", "Te", "Te", "Ag", "Ag", "Ag", "Ag", "Ag"] + structure.rename( + folded=True, + N = "La", + C = "Np", + O = "Te", + H = "Ag", + ) + + np.testing.assert_array_equal(structure.elem, new_elem) + + +def test_reset_axes(): + from nexus.structure import Structure + + original_axes = np.array([ + [6.00000, 0.00000, 0.00000], + [0.00000, 6.00000, 0.00000], + [0.00000, 0.00000, 6.00000], + ], dtype=np.float64) + + original_kaxes = np.array([ + [1.0471975511965976, 0.0, 0.0], + [0.0, 1.0471975511965976, 0.0], + [0.0, 0.0, 1.0471975511965976], + ], dtype=np.float64) + + original_center = np.array([3.0, 3.0, 3.0], dtype=np.float64) + + structure = Structure( + axes = original_axes, + elem = ["N", "C", "C", "O", "O", "H", "H", "H", "H", "H"], + pos = np.array([ + [ 1.848745, 2.865874, 3.041292], + [ 0.679145, 1.977474, 3.067692], + [-0.580355, 2.805074, 3.070592], + [-0.510755, 4.011174, 3.052592], + [-1.779455, 2.202274, 3.093292], + [ 1.827545, 3.514674, 3.813792], + [ 2.706445, 2.334474, 3.038892], + [ 0.690245, 1.335874, 2.186592], + [ 0.711045, 1.361274, 3.966292], + [-2.558655, 2.774774, 3.094192], + ], dtype=np.float64), + units="A", + ) + + np.testing.assert_array_equal(structure.axes, original_axes) + np.testing.assert_array_equal(structure.kaxes, original_kaxes) + np.testing.assert_array_equal(structure.center, original_center) + + new_axes = np.array([ + [12.00000, 0.00000, 0.00000], + [ 0.00000, 12.00000, 0.00000], + [ 0.00000, 0.00000, 12.00000], + ], dtype=np.float64) + + new_kaxes = np.array([ + [0.5235987755982988, 0.0, 0.0], + [0.0, 0.5235987755982988, 0.0], + [0.0, 0.0, 0.5235987755982988], + ], dtype=np.float64) + + new_center = np.array([6.0, 6.0, 6.0], dtype=np.float64) + + structure.reset_axes(new_axes) + + np.testing.assert_allclose(structure.axes, new_axes) + np.testing.assert_allclose(structure.kaxes, new_kaxes) + np.testing.assert_allclose(structure.center, new_center) + + +def test_reset_axes_none(): + from nexus.structure import Structure + + original_axes = np.array([ + [6.00000, 0.00000, 0.00000], + [0.00000, 6.00000, 0.00000], + [0.00000, 0.00000, 6.00000], + ], dtype=np.float64) + + original_kaxes = np.array([ + [7.0, 0.0, 0.0], + [0.0, 7.0, 0.0], + [0.0, 0.0, 7.0], + ], dtype=np.float64) + + original_center = np.array([400.0, 400.0, 400.0], dtype=np.float64) + + structure = Structure( + axes = original_axes, + elem = ["N", "C", "C", "O", "O", "H", "H", "H", "H", "H"], + pos = np.array([ + [ 1.848745, 2.865874, 3.041292], + [ 0.679145, 1.977474, 3.067692], + [-0.580355, 2.805074, 3.070592], + [-0.510755, 4.011174, 3.052592], + [-1.779455, 2.202274, 3.093292], + [ 1.827545, 3.514674, 3.813792], + [ 2.706445, 2.334474, 3.038892], + [ 0.690245, 1.335874, 2.186592], + [ 0.711045, 1.361274, 3.966292], + [-2.558655, 2.774774, 3.094192], + ], dtype=np.float64), + units="A", + center = original_center, + ) + + structure.kaxes = original_kaxes + + np.testing.assert_array_equal(structure.axes, original_axes) + np.testing.assert_array_equal(structure.kaxes, original_kaxes) + np.testing.assert_array_equal(structure.center, original_center) + + ref_kaxes = np.array([ + [1.0471975511965976, 0.0, 0.0], + [0.0, 1.0471975511965976, 0.0], + [0.0, 0.0, 1.0471975511965976], + ], dtype=np.float64) + + ref_center = np.array([3.0, 3.0, 3.0], dtype=np.float64) + + structure.reset_axes(axes = None) + + np.testing.assert_allclose(structure.axes, original_axes) + np.testing.assert_allclose(structure.kaxes, ref_kaxes) + np.testing.assert_allclose(structure.center, ref_center) + +def test_write_axes(): + from nexus.structure import Structure + + structure = Structure( + axes = np.array([ + [6.00000, 0.00000, 0.00000], + [0.00000, 12.00000, 0.00000], + [0.00000, 0.00000, 300.00000], + ], dtype=np.float64), + elem = ["N", "C", "C", "O", "O", "H", "H", "H", "H", "H"], + pos = np.array([ + [ 1.848745, 2.865874, 3.041292], + [ 0.679145, 1.977474, 3.067692], + [-0.580355, 2.805074, 3.070592], + [-0.510755, 4.011174, 3.052592], + [-1.779455, 2.202274, 3.093292], + [ 1.827545, 3.514674, 3.813792], + [ 2.706445, 2.334474, 3.038892], + [ 0.690245, 1.335874, 2.186592], + [ 0.711045, 1.361274, 3.966292], + [-2.558655, 2.774774, 3.094192], + ], dtype=np.float64), + units="A", + ) + + ref_write_axes = ( + " 6.00000000 0.00000000 0.00000000\n" + " 0.00000000 12.00000000 0.00000000\n" + " 0.00000000 0.00000000 300.00000000\n" + ) + calc_write_axes = structure.write_axes() + assert(text_eq(calc_write_axes, ref_write_axes)) + + +def test_corners(): + from nexus.structure import Structure + + structure = Structure( + axes = np.array([ + [7.00000, 0.00000, 0.00000], + [0.00000, 14.00000, 0.00000], + [0.00000, 0.00000, 35.00000], + ], dtype=np.float64), + elem = ["N", "C", "C", "O", "O", "H", "H", "H", "H", "H"], + pos = np.array([ + [ 1.848745, 2.865874, 3.041292], + [ 0.679145, 1.977474, 3.067692], + [-0.580355, 2.805074, 3.070592], + [-0.510755, 4.011174, 3.052592], + [-1.779455, 2.202274, 3.093292], + [ 1.827545, 3.514674, 3.813792], + [ 2.706445, 2.334474, 3.038892], + [ 0.690245, 1.335874, 2.186592], + [ 0.711045, 1.361274, 3.966292], + [-2.558655, 2.774774, 3.094192], + ], dtype=np.float64), + units="A", + ) - assert(testing.check_object_eq(res,ref,atol=1e-12)) - #end def test_rmg_transform -#end if + ref_corners = [ + [0.0, 0.0, 0.0], + [7.0, 0.0, 0.0], + [0.0, 14.0, 0.0], + [0.0, 0.0, 35.0], + [7.0, 14.0, 0.0], + [0.0, 14.0, 35.0], + [7.0, 0.0, 35.0], + [7.0, 14.0, 35.0], + ] + + np.testing.assert_allclose(structure.corners(), ref_corners) diff --git a/nexus/nexus/tests/test_testing.py b/nexus/nexus/tests/test_testing.py index 1abba0f5cd..2af1cd3c60 100644 --- a/nexus/nexus/tests/test_testing.py +++ b/nexus/nexus/tests/test_testing.py @@ -1,10 +1,9 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.TESTING) - -def test_import(): - from ..testing import value_diff,object_diff - from ..testing import value_eq,object_eq - from ..testing import value_neq,object_neq -#end def test_import +from ..generic import generic_settings +generic_settings.raise_error = True @@ -236,7 +235,6 @@ def deep_list(*args,**kwargs): def test_object_checks(): - import numpy as np from ..testing import object_diff,object_eq,object_neq assert(id(object_diff)==id(object_neq)) diff --git a/nexus/nexus/tests/test_unit_converter.py b/nexus/nexus/tests/test_unit_converter.py index 4bfcb9323a..e6a7c3470c 100644 --- a/nexus/nexus/tests/test_unit_converter.py +++ b/nexus/nexus/tests/test_unit_converter.py @@ -1,8 +1,9 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.UNIT_CONVERTER) - -def test_import(): - from ..unit_converter import convert -#end def test_import +from ..generic import generic_settings +generic_settings.raise_error = True diff --git a/nexus/nexus/tests/test_user_examples.py b/nexus/nexus/tests/test_user_examples.py new file mode 100644 index 0000000000..5df5743f07 --- /dev/null +++ b/nexus/nexus/tests/test_user_examples.py @@ -0,0 +1,447 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.USER_EXAMPLES) + +from ..generic import generic_settings +generic_settings.raise_error = True + +from pathlib import Path +import os +import sys +import shutil +from shutil import ignore_patterns +from subprocess import Popen, PIPE +from . import TEST_DIR + +nexus_root = TEST_DIR.parent.parent # qmcpack/nexus +example_root = nexus_root / "nexus/examples" +test_root = nexus_root / "nexus/tests" +reference_dir = test_root / "reference/user_examples" + +qmcpack_pseudos = example_root / "qmcpack/pseudopotentials" +espresso_pseudos = example_root / "quantum_espresso/pseudopotentials" + + +def copy_pseudos(code: str, tmp_dir: Path): + + if code == "qmcpack": + output_path = tmp_dir / "qmcpack/pseudopotentials" + shutil.copytree(qmcpack_pseudos, output_path, dirs_exist_ok=True) + elif code == "quantum_espresso": + output_path = tmp_dir / "quantum_espresso/pseudopotentials" + shutil.copytree(espresso_pseudos, output_path, dirs_exist_ok=True) + else: + raise ValueError(f"Invalid code for pseudopotential identification: {code}") + + +def copy_example_files(example_dir: str, tmp_dir: Path): + + example_path = example_root / example_dir + output_path = tmp_dir / example_dir + test_path = shutil.copytree( + src = example_path, + dst = output_path, + dirs_exist_ok = True, + ignore = ignore_patterns("*.py"), + ) + + return test_path + + +def run_example_script(script: Path, test_path: Path): + + script = script.resolve() # Absolute path helps in debugging + old_cwd = Path.cwd() + os.chdir(test_path) + + script_command = f"PYTHONPATH={nexus_root} {sys.executable} {script} --generate_only --sleep=0.01" + process = Popen(script_command, shell=True, stdout=PIPE, stderr=PIPE, close_fds=True) + out, err = process.communicate() + returncode = process.returncode + os.chdir(old_cwd) # Reset us back to the old cwd + if returncode != 0: + msg = ( + "Executed system command failed.\n" + "\n" + "Command:\n" + "========\n" + f"{script_command}\n" + "\n" + "stdout:\n" + "=======\n" + f"{out}\n" + "\n" + "stderr:\n" + "=======\n" + f"{err}\n" + "\n" + "Return code:\n" + "============\n" + f"{returncode}\n" + ) + # Return test failure so it can be dealt with in the respective test. + return False, msg + else: + return True, "Success!" + + +def check_generated_files( + code: str, + tmp_dir: Path, + example_path: str, + filepath: str, + ): + + from ..testing import object_diff + from nexus.pwscf_input import PwscfInput + from nexus.qmcpack_converters import Pw2qmcpackInput + from nexus.gamess_input import GamessInput + from nexus.qmcpack_input import QmcpackInput + + input_classes = dict( + pwscf = PwscfInput, + pw2qmcpack = Pw2qmcpackInput, + gamess = GamessInput, + qmcpack = QmcpackInput, + ) + + ref_filepath = reference_dir / example_path / filepath + gen_filepath = tmp_dir / example_path / filepath + + if not ref_filepath.exists(): + raise FileNotFoundError( + "Reference file is missing\n" + f"File should be located at: {ref_filepath!s}" + ) + elif not gen_filepath.exists(): + raise FileNotFoundError( + f"Input file was not generated: {gen_filepath!s}" + ) + + input_class = input_classes[code] + ref_input = input_class(str(ref_filepath)) + gen_input = input_class(str(gen_filepath)) + diff, dgen, dref = object_diff(gen_input, ref_input, full=True) + if diff: + # assume failure + failed = True + # if difference due to periodically equivalent points + # then it is not a failure + check_pbc = False + if len(dgen)==1 and len(dref)==1: + kgen = list(dgen.keys())[0].rsplit('/',1)[1] + kref = list(dref.keys())[0].rsplit('/',1)[1] + check_pbc |= code=='qmcpack' and kgen==kref=='position' + check_pbc |= code=='pwscf' and kgen==kref=='positions' + #end if + if check_pbc: + try: + # extract Structure objects from SimulationInput objects + rs = ref_input.return_structure() + gs = gen_input.return_structure() + # compare minimum image distances of all atomic coordinates + d = rs.min_image_distances(gs.pos,pairs=False) + # allow for small deviation due to precision of ascii floats in the text input files + if d.min()<1e-6: + failed = False + #end if + except: + None + #end try + #end if + if failed: + # report on failures + from nexus.generic import obj + dgen = obj(dgen) + dref = obj(dref) + msg = 'reference and generated input files differ\n' + msg += 'reference file: '+os.path.realpath(filepath)+'\n' + msg += 'reference file difference\n' + msg += 40*'='+'\n' + msg += str(dref) + msg += 'generated file difference\n' + msg += 40*'='+'\n' + msg += str(dgen) + return False, msg + #end if + #end if + return True, "Success!" + + +def test_pwscf_relax_Ge_T(tmp_path): + + test_data = dict( + path = 'quantum_espresso/relax_Ge_T_vs_kpoints', + scripts = [ + 'relax_vs_kpoints_example.py', + ], + files = [ + ('pwscf', 'input', 'runs/relax/kgrid_111/relax.in'), + ('pwscf', 'input', 'runs/relax/kgrid_222/relax.in'), + ('pwscf', 'input', 'runs/relax/kgrid_444/relax.in'), + ('pwscf', 'input', 'runs/relax/kgrid_666/relax.in'), + ], + ) + + test_path = copy_example_files(test_data["path"], tmp_path) + copy_pseudos("quantum_espresso", tmp_path) + + for script in test_data["scripts"]: + script_path = example_root / test_data["path"] / script + success, message = run_example_script(script_path, test_path) + assert(success), message + + for code, filetype, filepath in test_data["files"]: + success, message = check_generated_files( + code, + tmp_path, + test_data["path"], + filepath, + ) + assert(success), message + + +def test_gamess_H2O(tmp_path): + + test_data = dict( + path = 'gamess/H2O', + scripts = [ + 'h2o_pp_hf.py', + 'h2o_pp_cisd.py', + 'h2o_pp_casscf.py', + ], + files = [ + ('gamess', 'input', 'runs/pp_hf/rhf.inp'), + ('gamess', 'input', 'runs/pp_cisd/rhf.inp'), + ('gamess', 'input', 'runs/pp_cisd/cisd.inp'), + ('gamess', 'input', 'runs/pp_casscf/rhf.inp'), + ('gamess', 'input', 'runs/pp_casscf/cas.inp'), + ], + ) + + test_path = copy_example_files(test_data["path"], tmp_path) + + for script in test_data["scripts"]: + script_path = example_root / test_data["path"] / script + success, message = run_example_script(script_path, test_path) + assert(success), message + + for code, filetype, filepath in test_data["files"]: + success, message = check_generated_files( + code, + tmp_path, + test_data["path"], + filepath, + ) + assert(success), message + + +def test_qmcpack_H2O(tmp_path): + + test_data = dict( + path = 'qmcpack/rsqmc_misc/H2O', + scripts = [ + 'H2O.py', + ], + files = [ + ('pwscf', 'input', 'runs/scf.in'), + ('pw2qmcpack', 'input', 'runs/p2q.in'), + ('qmcpack', 'input', 'runs/opt.in.xml'), + ('qmcpack', 'input', 'runs/dmc.in.xml'), + ], + ) + + test_path = copy_example_files(test_data["path"], tmp_path) + copy_pseudos("quantum_espresso", tmp_path) + copy_pseudos("qmcpack", tmp_path) + + + for script in test_data["scripts"]: + script_path = example_root / test_data["path"] / script + success, message = run_example_script(script_path, test_path) + assert(success), message + + for code, filetype, filepath in test_data["files"]: + success, message = check_generated_files( + code, + tmp_path, + test_data["path"], + filepath, + ) + assert(success), message + + +def test_qmcpack_LiH(tmp_path): + + test_data = dict( + path = 'qmcpack/rsqmc_misc/LiH', + scripts = [ + 'LiH.py', + ], + files = [ + ('pwscf', 'input', 'runs/scf.in'), + ('pwscf', 'input', 'runs/nscf.in'), + ('pw2qmcpack', 'input', 'runs/p2q.in'), + ('qmcpack', 'input', 'runs/opt.in.xml'), + ('qmcpack', 'input', 'runs/dmc.in.xml'), + ], + ) + + test_path = copy_example_files(test_data["path"], tmp_path) + copy_pseudos("quantum_espresso", tmp_path) + copy_pseudos("qmcpack", tmp_path) + + for script in test_data["scripts"]: + script_path = example_root / test_data["path"] / script + success, message = run_example_script(script_path, test_path) + assert(success), message + + for code, filetype, filepath in test_data["files"]: + success, message = check_generated_files( + code, + tmp_path, + test_data["path"], + filepath, + ) + assert(success), message + + +def test_qmcpack_c20(tmp_path): + + test_data = dict( + path = 'qmcpack/rsqmc_misc/c20', + scripts = [ + 'c20.py', + ], + files = [ + ('pwscf', 'input', 'runs/c20/scf/scf.in'), + ('pw2qmcpack', 'input', 'runs/c20/nscf/p2q.in'), + ('qmcpack', 'input', 'runs/c20/opt/opt.in.xml'), + ('qmcpack', 'input', 'runs/c20/qmc/qmc.in.xml'), + ], + ) + + test_path = copy_example_files(test_data["path"], tmp_path) + copy_pseudos("quantum_espresso", tmp_path) + copy_pseudos("qmcpack", tmp_path) + + for script in test_data["scripts"]: + script_path = example_root / test_data["path"] / script + success, message = run_example_script(script_path, test_path) + assert(success), message + + for code, filetype, filepath in test_data["files"]: + success, message = check_generated_files( + code, + tmp_path, + test_data["path"], + filepath, + ) + assert(success), message + + +def test_qmcpack_diamond(tmp_path): + + test_data = dict( + path = 'qmcpack/rsqmc_misc/diamond', + scripts = [ + 'diamond.py', + 'diamond_vacancy.py', + ], + files = [ + ('pwscf', 'input', 'runs/diamond/scf/scf.in'), + ('pw2qmcpack', 'input', 'runs/diamond/scf/conv.in'), + ('qmcpack', 'input', 'runs/diamond/vmc/vmc.in.xml'), + ('pwscf', 'input', 'runs/diamond_vacancy/relax/relax.in'), + ('pwscf', 'input', 'runs/diamond_vacancy/scf/scf.in'), + ], + ) + + test_path = copy_example_files(test_data["path"], tmp_path) + copy_pseudos("quantum_espresso", tmp_path) + copy_pseudos("qmcpack", tmp_path) + + for script in test_data["scripts"]: + script_path = example_root / test_data["path"] / script + success, message = run_example_script(script_path, test_path) + assert(success), message + + for code, filetype, filepath in test_data["files"]: + success, message = check_generated_files( + code, + tmp_path, + test_data["path"], + filepath, + ) + assert(success), message + + +def test_qmcpack_graphene(tmp_path): + + test_data = dict( + path = 'qmcpack/rsqmc_misc/graphene', + scripts = [ + 'graphene.py', + ], + files = [ + ('pwscf', 'input', 'runs/graphene/scf/scf.in'), + ('pwscf', 'input', 'runs/graphene/nscf/nscf.in'), + ('pw2qmcpack', 'input', 'runs/graphene/nscf/p2q.in'), + ('pwscf', 'input', 'runs/graphene/nscf_opt/nscf.in'), + ('pw2qmcpack', 'input', 'runs/graphene/nscf_opt/p2q.in'), + ('qmcpack', 'input', 'runs/graphene/opt/opt.in.xml'), + ('qmcpack', 'input', 'runs/graphene/qmc/qmc.in.xml'), + ], + ) + + test_path = copy_example_files(test_data["path"], tmp_path) + copy_pseudos("quantum_espresso", tmp_path) + copy_pseudos("qmcpack", tmp_path) + + for script in test_data["scripts"]: + script_path = example_root / test_data["path"] / script + success, message = run_example_script(script_path, test_path) + assert(success), message + + for code, filetype, filepath in test_data["files"]: + success, message = check_generated_files( + code, + tmp_path, + test_data["path"], + filepath, + ) + assert(success), message + + +def test_qmcpack_oxygen_dimer(tmp_path): + + test_data = dict( + path = 'qmcpack/rsqmc_misc/oxygen_dimer', + scripts = [ + 'oxygen_dimer.py', + ], + files = [ + ('pwscf', 'input', 'scale_1.0/scf.in'), + ('pw2qmcpack', 'input', 'scale_1.0/p2q.in'), + ('qmcpack', 'input', 'scale_1.0/opt.in.xml'), + ('qmcpack', 'input', 'scale_1.0/qmc.in.xml'), + ], + ) + + test_path = copy_example_files(test_data["path"], tmp_path) + copy_pseudos("quantum_espresso", tmp_path) + copy_pseudos("qmcpack", tmp_path) + + for script in test_data["scripts"]: + script_path = example_root / test_data["path"] / script + success, message = run_example_script(script_path, test_path) + assert(success), message + + for code, filetype, filepath in test_data["files"]: + success, message = check_generated_files( + code, + tmp_path, + test_data["path"], + filepath, + ) + assert(success), message diff --git a/nexus/nexus/tests/test_utilities.py b/nexus/nexus/tests/test_utilities.py new file mode 100644 index 0000000000..58e039ce11 --- /dev/null +++ b/nexus/nexus/tests/test_utilities.py @@ -0,0 +1,298 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.UTILITIES) + +import os +from pathlib import Path + + + +def test_is_valid_path(): + from nexus.utilities import is_valid_path,is_valid_filename + + valid_paths = [ + '', + '.', + '..', + '/', + '//', + '/home/me/file.txt', + 'back/../and/../forth/', + '/tmp/session_data', + './runs/qmc/vmc.s000.scalar.dat', + 'hyphens-are-healthy', + 'periods.produce.paradise', + 'underscores_unlock_understanding', + 'pi_is_about_3.14159265358979323846264338327950' + # Unsettling that prose can be paths, + # but ' ' must be accomodated + 'spaces are sinister', + ] + + invalid_paths = [ + 'yes!', + '@somewhere.com', + '#comment', + '$100', + '20%', + '2^3', + 'here&there', + 'height*width', + 'definitely;maybe', + 'this|that', + 'why?', + 's\ash', + '`command`', + "ain't", + '"special"', + 'x,y', + '(pa', + 'ren)', + '[brac', + 'ket]', + 'lt<', + 'gt>', + 'pull\tab', + '\newline', + 'ca\r\riage', + 'Do not go where the path may lead,' # comma + ' go instead where there is no path' + ' and leave a trail.', + ] + + for path in valid_paths: + assert is_valid_path(path) + + for path in invalid_paths: + assert not is_valid_path(path) + + + valid_filenames = [ + 'file.txt', + 'session_data', + 'vmc.s000.scalar.dat', + 'hyphens-are-healthy', + 'periods.produce.paradise', + 'underscores_unlock_understanding', + 'pi_is_about_3.14159265358979323846264338327950' + ] + + invalid_filenames = [ + '', + '.', + '..', + '/', + '//', + '/home/me/file.txt', + 'back/../and/../forth/', + '/tmp/session_data', + './runs/qmc/vmc.s000.scalar.dat', + ]+invalid_paths + + for filename in valid_filenames: + assert is_valid_filename(filename) + + for filename in invalid_filenames: + print([filename]) + assert not is_valid_filename(filename) + +#end def test_is_valid_path + + + +def test_path_string(): + from nexus.utilities import path_string + + # path_string for str paths + in_out_paths = [ + # in out ps(str) out ps(Path) + ( '' , '' , '.' ), + ( '.' , '.' , '.' ), + ( './' , './' , '.' ), + ( './..' , './..' , '..' ), + ( 'a/b' , 'a/b' , 'a/b' ), + ( 'a/b/' , 'a/b/' , 'a/b' ), + ( './a/b' , './a/b' , 'a/b' ), + ( './a/b/' , './a/b/' , 'a/b' ), + ( './a/./b' , './a/./b' , 'a/b' ), + ( '../a/..' , '../a/..' , '../a/..' ), + ( 'a/../b' , 'a/../b' , 'a/../b' ), + ( '/' , '/' , '/' ), + ( '//' , '//' , '//' ), + ( '///' , '///' , '/' ), + ( '/a/' , '/a/' , '/a' ), + ( '/a/b/' , '/a/b/' , '/a/b' ), + ] + + for p_in, p_str_out, p_Path_out in in_out_paths: + p1 = path_string(p_in,strict=True,check=True) + p2 = path_string(Path(p_in)) + p3 = str(Path(p_in)) + assert p1==p_in + assert p1==p_str_out + assert p2==p_Path_out + assert p3==p_Path_out + assert os.path.realpath(p1)==os.path.realpath(p2) + + + # test bytes + in_out_paths = [ + # in out ps(str)) + ( b'' , '' ), + ( b'.' , '.' ), + ( b'./' , './' ), + ( b'./..' , './..' ), + ( b'a/b' , 'a/b' ), + ( b'a/b/' , 'a/b/' ), + ( b'./a/b' , './a/b' ), + ( b'./a/b/' , './a/b/' ), + ( b'./a/./b' , './a/./b' ), + ( b'../a/..' , '../a/..' ), + ( b'a/../b' , 'a/../b' ), + ( b'/' , '/' ), + ( b'//' , '//' ), + ( b'///' , '///' ), + ( b'/a/' , '/a/' ), + ( b'/a/b/' , '/a/b/' ), + ] + + for p_in, p_str_out in in_out_paths: + assert path_string(p_in,check=True)==p_str_out + + + # test strict guard + p = 'str_path' + p = path_string(p,strict=True) # raises no error + p = b'bytes_path' + try: + p = path_string(p,strict=True) + expected = False + except ValueError: + expected = True + assert expected + + # test relative guard + p = 'a/relative/path' + p = path_string(p,relative=True) # raises no error + p = '/an/absolute/path' + try: + p = path_string(p,relative=True) + expected = False + except ValueError: + expected = True + assert expected + + # test validity check guard + p = 'a/b' + p = path_string(p,check=True) # raises no error + p = 'a*b' + try: + p = path_string(p,check=True) + expected = False + except ValueError: + expected = True + assert expected + +#end def test_path_string + + + +def test_is_relative_path(): + from nexus.utilities import is_relative_path + + relative_paths = [ + '', + '.', + './', + '..', + '../', + '../somewhere/..', + './somewhere/above/', + '../somewhere/below', + 'a/bald/or/bare/path', + ] + + non_relative_paths = [ + '/', + '/home', + '/home/me', + '/usr/bin/', + '/lustre/proj/scratch', + ] + [os.path.realpath(p) for p in relative_paths] + + for path_type in (str,Path): + for p in relative_paths: + p = path_type(p) + print([p,str(p)]) + assert is_relative_path(p) + + for p in non_relative_paths: + p = path_type(p) + assert not is_relative_path(p) + +#end def test_is_relative_path + + + +def test_path_dual_typing(): + '''Illustrate issues w/ mixing pathlib.Path with os.path''' + + # joining paths + # os.system('ls') and os.system('./ls') are very different! + assert os.path.join('','ls') == 'ls' # right + assert str(Path('')/Path('ls')) == 'ls' # right + assert os.path.join(Path(''),Path('ls')) == './ls' # wrong!! + assert os.path.join(str(Path('')),str(Path('ls'))) == './ls' # wrong!! + + + # splitting paths + assert os.path.split('dir/name') == ('dir','name') # right + assert os.path.split(Path('dir/name')) == ('dir','name') # right + assert str(Path('dir/name').parent) == 'dir' # right + assert Path('dir/name').name == 'name' # right + + assert os.path.split('name') == ('','name') # right + assert os.path.split(Path('name')) == ('','name') # right + assert str(Path('name').parent) == '.' # wrong!! + assert Path('name').name == 'name' # right + + assert os.path.split('dir/') == ('dir','' ) # right + assert os.path.split(Path('dir/')) == ('' ,'dir') # wrong!! + assert str(Path('dir/').parent) == '.' # wrong!! + assert Path('dir/').name == 'dir' # wrong!! + + # or in short + assert os.path.dirname( 'dir/name') == str(Path('dir/name').parent) + assert os.path.basename('dir/name') == Path('dir/name').name + + assert os.path.dirname( 'name' ) != str(Path('name').parent) + assert os.path.basename('name' ) == Path('name').name + + assert os.path.dirname( 'dir/' ) != str(Path('dir/').parent) + assert os.path.basename('dir/' ) != Path('dir/').name + + + # relative paths + assert os.path.relpath('/home/me/dir','/home/me') == 'dir' + assert str(Path('/home/me/dir').relative_to('/home/me')) == 'dir' + + assert os.path.relpath('/home/me','/home/me/dir') == '..' + try: + Path('/home/me').relative_to('/home/me/dir') + works = True + except ValueError: + works = False + assert not works + + assert os.path.relpath('./up/..', '.' ) == '.' + assert os.path.relpath('.' , './up/..') == '.' + + assert str(Path('./up/..').relative_to('.')) == 'up/..' + try: + Path('.').relative_to('./up/..') + works = True + except ValueError: + works = False + assert not works + +#end def test_path_dual_typing diff --git a/nexus/nexus/tests/test_vasp_analyzer.py b/nexus/nexus/tests/test_vasp_analyzer.py index 5f8a3606f4..d6b2681c40 100644 --- a/nexus/nexus/tests/test_vasp_analyzer.py +++ b/nexus/nexus/tests/test_vasp_analyzer.py @@ -1,46 +1,34 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.VASP_ANALYZER) -from .. import testing -from ..testing import value_eq,object_eq - - -associated_files = dict() - -def get_files(): - return testing.collect_unit_test_file_paths('vasp_analyzer',associated_files) -#end def get_files - - -relax_files = [ - 'relax.CONTCAR', - 'relax.DOSCAR', - 'relax.EIGENVAL', - 'relax.err', - 'relax.IBZKPT', - 'relax.INCAR', - 'relax.KPOINTS', - 'relax.OSZICAR', - 'relax.out', - 'relax.OUTCAR', - 'relax.PCDAT', - 'relax.POSCAR', - 'relax.qsub.in', - 'relax.vasprun.xml', - 'relax.XDATCAR', - ] - - -def test_files(): - filenames = relax_files - files = get_files() - assert(set(filenames)==set(files.keys())) -#end def test_files - +from ..generic import generic_settings +generic_settings.raise_error = True +from . import TEST_DIR +from ..testing import value_eq,object_eq -def test_import(): - from ..vasp_analyzer import VaspAnalyzer,VXML,OutcarData -#end def test_import +TEST_FILES = { + "relax.CONTCAR": TEST_DIR / "test_vasp_analyzer_files/relax.CONTCAR", + "relax.DOSCAR": TEST_DIR / "test_vasp_analyzer_files/relax.DOSCAR", + "relax.EIGENVAL": TEST_DIR / "test_vasp_analyzer_files/relax.EIGENVAL", + "relax.err": TEST_DIR / "test_vasp_analyzer_files/relax.err", + "relax.IBZKPT": TEST_DIR / "test_vasp_analyzer_files/relax.IBZKPT", + "relax.INCAR": TEST_DIR / "test_vasp_analyzer_files/relax.INCAR", + "relax.KPOINTS": TEST_DIR / "test_vasp_analyzer_files/relax.KPOINTS", + "relax.OSZICAR": TEST_DIR / "test_vasp_analyzer_files/relax.OSZICAR", + "relax.out": TEST_DIR / "test_vasp_analyzer_files/relax.out", + "relax.OUTCAR": TEST_DIR / "test_vasp_analyzer_files/relax.OUTCAR", + "relax.PCDAT": TEST_DIR / "test_vasp_analyzer_files/relax.PCDAT", + "relax.POSCAR": TEST_DIR / "test_vasp_analyzer_files/relax.POSCAR", + "relax.qsub.in": TEST_DIR / "test_vasp_analyzer_files/relax.qsub.in", + "relax.vasprun.xml": TEST_DIR / "test_vasp_analyzer_files/relax.vasprun.xml", + "relax.XDATCAR": TEST_DIR / "test_vasp_analyzer_files/relax.XDATCAR", + } + +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" def test_empty_init(): @@ -52,18 +40,11 @@ def test_empty_init(): def test_analyze(): - import os from numpy import array,ndarray from ..developer import obj - from ..vasp_analyzer import VaspAnalyzer,VXML,VXMLcoll,OutcarData - - tpath = testing.setup_unit_test_output_directory( - test = 'vasp_analyzer', - subtest = 'test_analyze', - file_sets = relax_files, - ) + from ..vasp_analyzer import VaspAnalyzer,VXML,OutcarData - incar_path = os.path.join(tpath,'relax.INCAR') + incar_path = TEST_FILES['relax.INCAR'] # empty init diff --git a/nexus/nexus/tests/test_vasp_input.py b/nexus/nexus/tests/test_vasp_input.py index 080c8197e5..83bbba9d0f 100644 --- a/nexus/nexus/tests/test_vasp_input.py +++ b/nexus/nexus/tests/test_vasp_input.py @@ -1,15 +1,14 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.VASP_ANALYZER) -from .. import testing -from ..testing import divert_nexus,restore_nexus -from ..testing import divert_nexus_log,restore_nexus_log -from ..testing import value_eq,object_eq - - -associated_files = dict() +from ..generic import generic_settings +generic_settings.raise_error = True -def get_files(): - return testing.collect_unit_test_file_paths('vasp_input',associated_files) -#end def get_files +from nexus.nexus_base import nexus_core +from . import isolate_nexus_core, TEST_DIR +from .. import testing +from ..testing import object_eq def format_value(v): @@ -152,25 +151,16 @@ def check_vs_serial_reference(gi,name): #end def check_vs_serial_reference +TEST_FILES = { + "d16bulk.POSCAR": TEST_DIR / "test_vasp_input_files/d16bulk.POSCAR", + "diamond_INCAR": TEST_DIR / "test_vasp_input_files/diamond_INCAR", + "diamond_KPOINTS": TEST_DIR / "test_vasp_input_files/diamond_KPOINTS", + "diamond_POSCAR": TEST_DIR / "test_vasp_input_files/diamond_POSCAR", + "diamond_POTCAR": TEST_DIR / "test_vasp_input_files/diamond_POTCAR", + } -def test_files(): - filenames = [ - 'd16bulk.POSCAR', - 'diamond_INCAR', - 'diamond_KPOINTS', - 'diamond_POSCAR', - 'diamond_POTCAR', - ] - files = get_files() - assert(set(filenames)==set(files.keys())) -#end def test_files - - - -def test_import(): - from ..vasp_input import VaspInput,generate_vasp_input -#end def test_import - +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" def test_keyword_consistency(): @@ -193,20 +183,8 @@ def test_empty_init(): def test_read(): from ..vasp_input import VaspInput - vfiles = [ - 'diamond_INCAR', - 'diamond_KPOINTS', - 'diamond_POSCAR', - 'diamond_POTCAR', - ] - - tpath = testing.setup_unit_test_output_directory( - test = 'vasp_input', - subtest = 'test_read', - file_sets = {'':vfiles} - ) - - vi = VaspInput(tpath,prefix='diamond_') + test_files_dir = TEST_FILES['diamond_INCAR'].parent + vi = VaspInput(test_files_dir, prefix='diamond_') del vi.potcar.filepath @@ -215,27 +193,16 @@ def test_read(): -def test_write(): +def test_write(tmp_path): from ..vasp_input import VaspInput - vfiles = [ - 'diamond_INCAR', - 'diamond_KPOINTS', - 'diamond_POSCAR', - 'diamond_POTCAR', - ] - - tpath = testing.setup_unit_test_output_directory( - test = 'vasp_input', - subtest = 'test_write', - file_sets = {'':vfiles} - ) + test_files_dir = TEST_FILES['diamond_INCAR'].parent - vi_read = VaspInput(tpath,prefix='diamond_') + vi_read = VaspInput(test_files_dir, prefix='diamond_') - vi_read.write(tpath,prefix='write_diamond_') + vi_read.write(tmp_path, prefix='write_diamond_') - vi_write = VaspInput(tpath,prefix='write_diamond_') + vi_write = VaspInput(tmp_path, prefix='write_diamond_') del vi_write.potcar.filepath @@ -243,30 +210,25 @@ def test_write(): #end test_write - -def test_generate(): - import os +@isolate_nexus_core +def test_generate(tmp_path): from ..nexus_base import nexus_noncore from ..physical_system import generate_physical_system from ..vasp_input import generate_vasp_input,VaspInput - tpath = testing.setup_unit_test_output_directory('vasp_input','test_generate',divert=True) - - pseudo_dir = os.path.join(tpath,'pseudopotentials') + pseudo_dir = tmp_path / 'pseudopotentials' + pseudo_dir.mkdir() + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] nexus_noncore.pseudo_dir = pseudo_dir - if not os.path.exists(pseudo_dir): - os.makedirs(pseudo_dir) - #end if - - open(os.path.join(pseudo_dir,'C.POTCAR'),'w').write(c_potcar_text) + (pseudo_dir / 'C.POTCAR').write_text(c_potcar_text) - files = get_files() - dia16 = generate_physical_system( - structure = files['d16bulk.POSCAR'], + structure = TEST_FILES['d16bulk.POSCAR'], C = 4 ) @@ -290,6 +252,4 @@ def test_generate(): del vi.potcar.filepath check_vs_serial_reference(vi,'generate') - - restore_nexus() #end def test_generate diff --git a/nexus/nexus/tests/test_vasp_simulation.py b/nexus/nexus/tests/test_vasp_simulation.py index cdfb39dd3e..5c12565342 100644 --- a/nexus/nexus/tests/test_vasp_simulation.py +++ b/nexus/nexus/tests/test_vasp_simulation.py @@ -1,33 +1,31 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.VASP_SIMULATION) -from .. import testing -from ..testing import divert_nexus,restore_nexus,clear_all_sims -from ..testing import failed,FailedTest -from ..testing import value_eq,object_eq,text_eq,check_object_eq +from ..generic import generic_settings +generic_settings.raise_error = True -from .test_vasp_input import c_potcar_text,get_files +from pathlib import Path +from . import isolate_nexus_core, create_pseudo_files +from nexus.nexus_base import nexus_core +from ..testing import clear_all_sims +from ..testing import failed,FailedTest +from ..testing import value_eq,object_eq,check_object_eq +from .test_vasp_input import c_potcar_text, TEST_FILES -pseudo_inputs = dict( - pseudo_dir = 'pseudopotentials', - pseudo_files_create = [('C.POTCAR',c_potcar_text)], - ) -def setup_vasp_sim(path,identifier='vasp',files=False): +def setup_vasp_sim(path,identifier='vasp',copy_files=False): import shutil from ..nexus_base import nexus_core from ..machines import job from ..physical_system import generate_physical_system from ..vasp import generate_vasp,Vasp - - copy_files = files - del files nexus_core.runs = '' - files = get_files() - dia16 = generate_physical_system( - structure = files['d16bulk.POSCAR'], + structure = TEST_FILES['d16bulk.POSCAR'], C = 4 ) @@ -59,7 +57,7 @@ def setup_vasp_sim(path,identifier='vasp',files=False): 'diamond_POTCAR', ] for vfile in vfiles: - shutil.copy2(files[vfile],path) + shutil.copy2(TEST_FILES[vfile],path) #end for #end if @@ -68,12 +66,6 @@ def setup_vasp_sim(path,identifier='vasp',files=False): -def test_import(): - from ..vasp import Vasp,generate_vasp -#end def test_import - - - def test_minimal_init(): from ..machines import job from ..vasp import Vasp,generate_vasp @@ -88,31 +80,41 @@ def test_minimal_init(): #end def test_minimal_init +@isolate_nexus_core +def test_check_result(tmp_path): -def test_check_result(): - tpath = testing.setup_unit_test_output_directory('vasp_simulation','test_check_result',**pseudo_inputs) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] + create_pseudo_files( + tmp_dir=tmp_path, + pseudos=["C.POTCAR"], + pseudo_strs=[c_potcar_text], + ) - sim = setup_vasp_sim(tpath) + sim = setup_vasp_sim(tmp_path) assert(not sim.check_result('unknown',None)) assert(sim.check_result('structure',None)) clear_all_sims() - restore_nexus() #end def test_check_result - -def test_get_result(): - import os +@isolate_nexus_core +def test_get_result(tmp_path): import shutil from numpy import array from ..developer import obj, NexusError - tpath = testing.setup_unit_test_output_directory('vasp_simulation','test_get_result',**pseudo_inputs) + create_pseudo_files( + tmp_dir=tmp_path, + pseudos=["C.POTCAR"], + pseudo_strs=[c_potcar_text], + ) - sim = setup_vasp_sim(tpath,identifier='diamond',files=True) + sim = setup_vasp_sim(tmp_path, identifier='diamond', copy_files=True) try: sim.get_result('unknown',None) @@ -125,14 +127,14 @@ def test_get_result(): failed(str(e)) #end try - pcfile = os.path.join(tpath,'diamond_POSCAR') - ccfile = os.path.join(tpath,sim.identifier+'.CONTCAR') + pcfile = tmp_path / 'diamond_POSCAR' + ccfile = tmp_path / (sim.identifier+'.CONTCAR') - assert(sim.locdir.strip('/')==tpath.strip('/')) + assert(Path(sim.locdir).resolve()==tmp_path) shutil.copy2(pcfile,ccfile) - assert(os.path.exists(ccfile)) + assert(ccfile.exists()) result = sim.get_result('structure',None) @@ -185,33 +187,38 @@ def test_get_result(): assert(check_object_eq(result,result_ref)) clear_all_sims() - restore_nexus() #end def test_get_result - -def test_incorporate_result(): - import os +@isolate_nexus_core +def test_incorporate_result(tmp_path): import shutil from numpy import array from ..developer import obj - tpath = testing.setup_unit_test_output_directory('vasp_simulation','test_incorporate_result',**pseudo_inputs) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] + create_pseudo_files( + tmp_dir=tmp_path, + pseudos=["C.POTCAR"], + pseudo_strs=[c_potcar_text], + ) - sim = setup_vasp_sim(tpath,identifier='diamond',files=True) + sim = setup_vasp_sim(tmp_path,identifier='diamond',copy_files=True) - pcfile = os.path.join(tpath,'diamond_POSCAR') - ccfile = os.path.join(tpath,sim.identifier+'.CONTCAR') + pcfile = tmp_path / 'diamond_POSCAR' + ccfile = tmp_path / (sim.identifier+'.CONTCAR') - assert(sim.locdir.strip('/')==tpath.strip('/')) + assert(Path(sim.locdir).resolve()==tmp_path) shutil.copy2(pcfile,ccfile) - assert(os.path.exists(ccfile)) + assert(ccfile.exists()) result = sim.get_result('structure',None) - sim2 = setup_vasp_sim(tpath) + sim2 = setup_vasp_sim(tmp_path) pid = id(sim2.input.poscar) @@ -254,19 +261,24 @@ def test_incorporate_result(): assert(object_eq(sim2.input.poscar.to_obj(),poscar_ref)) clear_all_sims() - restore_nexus() #end def test_incorporate_result +@isolate_nexus_core +def test_check_sim_status(tmp_path): -def test_check_sim_status(): - import os - - tpath = testing.setup_unit_test_output_directory('vasp_simulation','test_check_sim_status',**pseudo_inputs) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] + create_pseudo_files( + tmp_dir=tmp_path, + pseudos=["C.POTCAR"], + pseudo_strs=[c_potcar_text], + ) - sim = setup_vasp_sim(tpath) + sim = setup_vasp_sim(tmp_path) - assert(sim.locdir.strip('/')==tpath.strip('/')) + assert(Path(sim.locdir).resolve()==tmp_path) assert(not sim.finished) assert(not sim.input.performing_neb()) @@ -275,13 +287,11 @@ def test_check_sim_status(): assert(not sim.finished) - outcar_file = os.path.join(tpath,'OUTCAR') + outcar_file = tmp_path / 'OUTCAR' outcar_text = 'General timing and accounting' - outcar = open(outcar_file,'w') - outcar.write(outcar_text) - outcar.close() - assert(os.path.exists(outcar_file)) - assert(outcar_text in open(outcar_file,'r').read()) + outcar_file.write_text(outcar_text) + assert(outcar_file.exists()) + assert(outcar_text in outcar_file.read_text()) sim.check_sim_status() @@ -289,23 +299,26 @@ def test_check_sim_status(): assert(not sim.failed) clear_all_sims() - restore_nexus() #end def test_check_sim_status +@isolate_nexus_core +def test_get_output_files(tmp_path): -def test_get_output_files(): - import os - - tpath = testing.setup_unit_test_output_directory('vasp_simulation','test_get_output_files',**pseudo_inputs) + nexus_core.local_directory = str(tmp_path) + nexus_core.remote_directory = str(tmp_path) + nexus_core.file_locations = nexus_core.file_locations + [str(tmp_path)] + create_pseudo_files( + tmp_dir=tmp_path, + pseudos=["C.POTCAR"], + pseudo_strs=[c_potcar_text], + ) - sim = setup_vasp_sim(tpath) + sim = setup_vasp_sim(tmp_path) vfiles = 'INCAR KPOINTS POSCAR CONTCAR OUTCAR'.split() for vfile in vfiles: - f = open(os.path.join(tpath,vfile),'w') - f.write('') - f.close() + (tmp_path / vfile).touch() #end for files = sim.get_output_files() @@ -313,9 +326,8 @@ def test_get_output_files(): assert(value_eq(files,vfiles)) for vfile in vfiles: - assert(os.path.exists(os.path.join(tpath,sim.identifier+'.'+vfile))) + assert((tmp_path / (sim.identifier+'.'+vfile))) #end for clear_all_sims() - restore_nexus() #end def test_get_output_files diff --git a/nexus/nexus/tests/test_versions.py b/nexus/nexus/tests/test_versions.py deleted file mode 100644 index d43dc53279..0000000000 --- a/nexus/nexus/tests/test_versions.py +++ /dev/null @@ -1,134 +0,0 @@ - - -def test_import(): - from .. import versions -#end def test_import - - - -def test_constants(): - from ..nexus_version import nexus_version - from ..versions import python_supported - from ..versions import years_supported - - assert(len(nexus_version)==3) - for n in nexus_version: - assert(isinstance(n,int)) - #end for - - assert(python_supported=='python3') - - assert(isinstance(years_supported,int)) -#end def test_constants - - - -def test_time(): - from datetime import date - from ..versions import time_ago - - long_ago = date(year=2017,month=9,day=1) - - years_ago = time_ago(long_ago) - - assert(years_ago>2-1e-6) -#end def test_time - - - -def test_version_processing(): - from ..versions import process_version,version_to_string - - assert( (1,3,0) == process_version('1.3') ) - assert( (1,3,0) == process_version(1,3) ) - assert( (1,3,0) == process_version('1','3',0) ) - assert( (1,3,0) == process_version([1,3]) ) - assert( (1,0,0) == process_version(1) ) - - assert( '1.3.0' == version_to_string( (1,3,0) ) ) - assert( '1.3.0' == version_to_string( (1,3,0) ) ) - assert( '1.3.0' == version_to_string( (1,3,0) ) ) - assert( '1.3.0' == version_to_string( (1,3,0) ) ) - assert( '1.0.0' == version_to_string( (1,0,0) ) ) - -#end def test_version_processing - - - -def test_versions_object(): - from ..versions import Versions,versions,raw_version_data - from ..versions import currently_supported - from ..versions import years_supported,time_ago - from ..versions import check_versions - - # object construction successful - assert(versions is not None) - - # object is singleton - assert(len(Versions.instances)==1) - assert(id(Versions.instances[0])==id(versions)) - - # check integrity of raw version data - deps = set(''' - python3 - numpy - scipy - h5py - matplotlib - pydot - spglib - seekpath - pycifrw - cif2cell - '''.split()) - assert(set(raw_version_data.keys())==deps) - - # check integrity of object's internal data - assert(versions.dependencies==deps) - assert(set(versions.ordered_dependencies)==deps) - req = versions.required_dependencies - opt = versions.optional_dependencies - assert( req | opt == deps) - assert( req & opt == set()) - assert(set(versions.currently_supported.keys())==deps) - assert(set(versions.dependency_available.keys())==deps) - assert(set(versions.dependency_version.keys())==deps) - assert(set(versions.dependency_supported.keys())==deps) - for name,version in currently_supported: - versions.is_dependency(name) - versions.check_dependency(name) - assert(versions.supported(name,version)) - assert(isinstance(versions.available(name),bool)) - supp = versions.supported(name) - assert(isinstance(supp,bool) or supp is None) - ver = versions.dependency_version[name] - assert(isinstance(ver,tuple) or ver is None) - assert(name in versions.currently_supported) - assert(version == versions.currently_supported[name]) - #end for - - # current supported versions obey policy - tol = 1e-6 - for name,version in currently_supported: - vdate = versions.version_data[name][version]['date'] - assert(time_ago(vdate)>years_supported-tol) - #end for - - # policy derived versions obey policy - tol = 1e-6 - policy_versions = versions.policy_supported_version() - assert(set(policy_versions.keys())==deps) - for name,version in policy_versions.items(): - vdate = versions.version_data[name][version]['date'] - assert(time_ago(vdate)>years_supported-tol) - #end for - - # writing abilities - assert(isinstance(versions.write_current_versions(),str)) - assert(isinstance(versions.write_policy_versions(),str)) - assert(isinstance(versions.write_available_versions(),str)) - - # check on version validity and report - assert(isinstance(versions.check(write=False,exit=False,full=False),bool)) - assert(isinstance(check_versions(write=False,exit=False),bool)) -#end def test_versions_object diff --git a/nexus/nexus/tests/test_xmlreader.py b/nexus/nexus/tests/test_xmlreader.py index 936658fef2..ad910e1271 100644 --- a/nexus/nexus/tests/test_xmlreader.py +++ b/nexus/nexus/tests/test_xmlreader.py @@ -1,32 +1,19 @@ +import pytest +from . import NexusTestOrder +pytestmark = pytest.mark.order(NexusTestOrder.XMLREADER) -from .. import testing -from ..testing import value_eq,object_eq +from ..generic import generic_settings +generic_settings.raise_error = True +from . import TEST_DIR +from ..testing import object_eq -associated_files = dict() +TEST_FILES = { + "vmc.in.xml": TEST_DIR / "test_xmlreader_files/vmc.in.xml", + } -def get_files(): - return testing.collect_unit_test_file_paths('xmlreader',associated_files) -#end def get_files - - -def test_files(): - filenames = [ - 'vmc.in.xml', - ] - files = get_files() - assert(set(files.keys())==set(filenames)) -#end def test_files - - -def test_import(): - from .. import xmlreader - from ..xmlreader import XMLreader,readxml - from ..xmlreader import parse_string - from ..xmlreader import find_pair - from ..xmlreader import remove_pair_sections - from ..xmlreader import remove_empty_lines -#end def test_import +for file in TEST_FILES.values(): + assert(file.exists()), f"Test file not found! {file}" def test_read(): @@ -251,8 +238,7 @@ def test_read(): ), ) - files = get_files() - x = readxml(files['vmc.in.xml']) + x = readxml(TEST_FILES['vmc.in.xml']) assert(isinstance(x,XMLelement)) x.remove_hidden() o = x.to_obj() diff --git a/nexus/nexus/utilities.py b/nexus/nexus/utilities.py index 6d9567c6a4..750f5221c1 100644 --- a/nexus/nexus/utilities.py +++ b/nexus/nexus/utilities.py @@ -1,9 +1,10 @@ +import string +from numbers import Number +from pathlib import Path # attempt to regain python 2 sorting # code below is from https://stackoverflow.com/questions/26575183/how-can-i-get-2-x-like-sorting-behaviour-in-python-3-x #=========================== -from numbers import Number - # decorator for type to function mapping special cases def per_type_cmp(type_): @@ -109,9 +110,113 @@ def sorted_py2(iterable): def to_str(s): + '''Convert a value to a string''' if isinstance(s,bytes): return str(s,encoding='utf-8') else: return str(s) #end if #end def to_str + + +def _path_to_str(path: str | bytes | Path) -> str: + '''Simple conversion from bytes/Path types to str.''' + if isinstance(path, str): + pass + elif isinstance(path, bytes): + path = str(path, encoding='utf-8') + elif isinstance(path, Path): + path = str(path) + else: + raise TypeError( + 'path must be of type "str", "bytes" or "Path". Type received: {}' + .format(path.__class__.__name__) + ) + return path +#end def _path_to_str + + +def is_valid_path(path: str | bytes | Path) -> bool: + '''Screen out paths with invalid characters.''' + path = _path_to_str(path) + if not hasattr(is_valid_path,'invalid_chars'): + unprintable = [chr(c) for c in range(128) if chr(c) not in string.printable] + special = r'!@#$%^&*;|?\`",()[]{}<>' + r"'" + whitespace = set(string.whitespace) - set([' ']) + invalid = set(unprintable) | set(special) | whitespace + is_valid_path.invalid_chars = invalid + invalid_chars = is_valid_path.invalid_chars + is_valid = len(set(path) & invalid_chars) == 0 + return is_valid +#end def is_valid_path + + +def is_valid_filename(filename: str | bytes | Path) -> bool: + '''Screen out filenames with invalid characters.''' + filename = _path_to_str(filename) + is_valid = True + if len(filename) == 0: + is_valid = False + elif filename == '.': + is_valid = False + elif filename.startswith('..'): + is_valid = False + elif '/' in filename: + is_valid = False + elif not is_valid_path(filename): + is_valid = False + + return is_valid +#end def is_valid_filename + + +def is_relative_path(path: str | bytes | Path): + '''Determine if a path is relative to some current working directory.''' + path = _path_to_str(path) + absolute = len(path) > 0 and (path[0] == '/' or path[0] == '~') + relative = not absolute + return relative +#end def is_relative_path + + +def path_string( + path: str | bytes | Path, + strict: bool = False, + relative: bool = False, + check: bool = False, +) -> str: + """Convert a path to a string. + + Parameters + ---------- + path : str, bytes or Path + A file path or directory path. + strict : bool, default=False + Require inputted path to be str type. + Raises ValueError otherwise. + relative : bool, default=False + Check if path is a relative path. + Raises ValueError otherwise. + check : bool, default=True + Check if a path contains only valid characters. + ValueError is raised for invalid paths. + + Returns + ------- + path_out : str + The path as a string. + """ + if relative and not is_relative_path(path): + raise ValueError('path must be relative') + if strict: + if not isinstance(path, str): + raise ValueError('path must strictly be str type') + path_out = path + else: + path_out = _path_to_str(path) + if relative and not is_relative_path(path_out): + raise ValueError('path_string converted relative path into non-relative path') + if check and not is_valid_path(path_out): + raise ValueError('path contains invalid characters:\n'+path_out) + return path_out +#end def path_string diff --git a/nexus/nexus/vasp.py b/nexus/nexus/vasp.py index c47df270b4..b034f58875 100644 --- a/nexus/nexus/vasp.py +++ b/nexus/nexus/vasp.py @@ -144,7 +144,8 @@ def check_sim_status(self): if all_exist: success = True for outpath in outpaths: - outcar = open(outpath,'r').read() + with open(outpath, "r") as f: + outcar = f.read() success &= 'General timing and accounting' in outcar #end for #end if diff --git a/nexus/nexus/vasp_analyzer.py b/nexus/nexus/vasp_analyzer.py index 06f6649343..f366cf6a8f 100644 --- a/nexus/nexus/vasp_analyzer.py +++ b/nexus/nexus/vasp_analyzer.py @@ -366,7 +366,8 @@ def read_vxml(filepath): VXML.class_error('file {0} does not exist'.format(filepath),'read_vxml') #end if #print 'read' - contents = open(filepath,'r').read() + with open(filepath, "r") as f: + contents = f.read() #print 'replace' contents = contents.replace('',' ').replace('',' ') contents = contents.replace('' ,' ').replace('' ,' ') diff --git a/nexus/nexus/vasp_input.py b/nexus/nexus/vasp_input.py index 3ac3fa739e..9a0b4f0e1e 100644 --- a/nexus/nexus/vasp_input.py +++ b/nexus/nexus/vasp_input.py @@ -39,12 +39,13 @@ import os import numpy as np -from .periodic_table import is_element +from .periodic_table import Elements from .nexus_base import nexus_noncore from .simulation import SimulationInput from .structure import interpolate_structures, Structure from .physical_system import PhysicalSystem from .developer import DevBase, obj, error +from .utilities import path_string from . import numpy_extensions as npe # support functions for keyword files @@ -298,6 +299,7 @@ def vasp_to_nexus_elem(elem,elem_count): class Vobj(DevBase): def get_path(self,filepath): + filepath = path_string(filepath) if os.path.exists(filepath) and os.path.isdir(filepath): path = filepath else: @@ -315,6 +317,7 @@ def get_path(self,filepath): class VFile(Vobj): def __init__(self,filepath=None): if filepath is not None: + filepath = path_string(filepath) self.read(filepath) #end if #end def __init__ @@ -324,7 +327,8 @@ def read(self,filepath): if not os.path.exists(filepath): self.error('file {0} does not exist'.format(filepath)) #end if - text = open(filepath,'r').read() + with open(filepath, "r") as f: + text = f.read() self.read_text(text,filepath) return text #end def read @@ -333,7 +337,8 @@ def read(self,filepath): def write(self,filepath=None): text = self.write_text(filepath) if filepath is not None: - open(filepath,'w').write(text) + with open(filepath, "w") as f: + f.write(text) #end if return text #end def write @@ -1196,11 +1201,11 @@ def write_text(self,filepath=''): #end for if self.elem is not None: for e in self.elem: - iselem,symbol = is_element(e,symbol=True) + iselem, element = Elements.is_element(e, return_element=True) if not iselem: self.error('{0} is not an element'.format(e)) #end if - text += symbol+' ' + text += element.symbol+' ' #end for text += '\n' #end if @@ -1341,7 +1346,8 @@ def write_text(self,filepath=''): #end for elif self.filepath is not None and self.files is not None: for file in self.files: - text += open(os.path.join(self.filepath,file),'r').read() + with open(os.path.join(self.filepath, file), "r") as f: + text += f.read() #end for #end if return text @@ -1449,6 +1455,7 @@ def __init__(self,filepath=None,prefix='',postfix=''): def read(self,filepath,prefix='',postfix=''): + filepath = path_string(filepath) path = self.get_path(filepath) for file in os.listdir(path): name = str(file) @@ -1612,7 +1619,8 @@ def set_potcar(self,pseudos,species=None): #end for ordered_pseudos = [] for element in species: - iselem,symbol = is_element(element,symbol=True) + iselem, elem = Elements.is_element(element, return_element=True) + symbol = elem.symbol if not iselem: self.error('{0} is not an element'.format(element)) elif symbol not in pseudo_map: diff --git a/nexus/nexus/versions.py b/nexus/nexus/versions.py deleted file mode 100644 index 8768f18694..0000000000 --- a/nexus/nexus/versions.py +++ /dev/null @@ -1,920 +0,0 @@ -################################################################## -## (c) Copyright 2019- by Jaron T. Krogel ## -################################################################## - - -""" -Track versions of dependencies supported by Nexus. -""" - -import sys -from platform import python_version,python_version_tuple -import datetime -import importlib - - -python_supported = 'python3' -""" -Current Python family supported. -""" - -# Require Python 3 -if python_version_tuple()<('3','0','0'): - print('\nNexus is compatible only with Python 3.\n You attempted to run with Python version {}.\n Please rerun with Python 3.\n'.format(python_version())) - sys.exit(1) -#end if - -years_supported = 2 -""" -Policy for how many years back Nexus will extend support to dependencies. -""" - -support_cutoff_date = (datetime.datetime.now()-datetime.timedelta(days=365*years_supported)).date() -""" -Cutoff date for support. -""" - -current_date = datetime.datetime.now().date() -""" -Current date. -""" - - -required_dependencies = set([python_supported,'numpy']) -""" -Required dependencies for Nexus. -""" - - -currently_supported = [ - ('python3' , (3, 6, 0) ), - ('numpy' , (1, 13, 1) ), - ('scipy' , (0, 19, 1) ), # optional - ('h5py' , (2, 7, 1) ), # optional - ('matplotlib' , (2, 0, 2) ), # optional - ('pydot' , (1, 2, 3) ), # optional - ('spglib' , (1, 9, 9) ), # optional - ('seekpath' , (1, 4, 0) ), # optional - ('pycifrw' , (4, 3, 0) ), # optional - ('cif2cell' , (1, 2, 10) ), # optional - ] -""" -Currently supported versions of Nexus dependencies. -""" - - -import_aliases = dict( - pycifrw = 'CifFile', - ) - -raw_version_data = dict( - # python 3 releases - # 3.3 https://www.python.org/dev/peps/pep-0398/ - # 3.4 https://www.python.org/dev/peps/pep-0429/ - # 3.5 https://www.python.org/dev/peps/pep-0478/ - # 3.6 https://www.python.org/dev/peps/pep-0494/ - # 3.7 https://www.python.org/dev/peps/pep-0537/ - # 3.8 https://www.python.org/dev/peps/pep-0569/ - # 3.9 https://www.python.org/dev/peps/pep-0596/ - # 3.10 https://www.python.org/dev/peps/pep-0619/ - python3 = ''' - 3.3.0 2012-09-29 - 3.3.1 2013-04-06 - 3.3.2 2013-05-13 - 3.3.3 2013-11-16 - 3.3.4 2014-02-09 - 3.4.0 2014-03-16 - 3.4.1 2014-05-18 - 3.4.2 2014-10-06 - 3.4.3 2015-02-25 - 3.5.0 2015-09-13 - 3.5.1 2015-12-06 - 3.5.2 2016-06-26 - 3.6.0 2016-12-23 - 3.6.1 2017-03-21 - 3.6.2 2017-07-17 - 3.6.3 2017-10-03 - 3.6.4 2017-12-19 - 3.6.5 2018-03-28 - 3.7.0 2018-06-27 - 3.7.1 2018-10-20 - 3.7.2 2018-12-24 - 3.7.3 2019-03-25 - 3.7.4 2019-07-08 - 3.8.0 2019-10-21 - 3.9.0 2020-06-08 - 3.10.0 2021-10-04 - ''', - # numpy releases - # https://github.com/numpy/numpy/releases - numpy = ''' - 1.10.0 2015-10-05 - 1.10.1 2015-10-12 - 1.10.2 2015-12-14 - 1.10.3 2016-01-06 - 1.10.4 2016-01-06 - 1.11.0 2016-03-27 - 1.11.1 2016-06-25 - 1.11.2 2016-10-03 - 1.11.3 2016-12-18 - 1.12.0 2017-01-15 - 1.12.1 2017-03-18 - 1.13.0 2017-06-07 - 1.13.1 2017-07-06 - 1.13.2 2017-09-27 - 1.13.3 2017-09-29 - 1.14.0 2018-01-06 - 1.14.1 2018-02-20 - 1.14.2 2018-03-12 - 1.14.3 2018-04-28 - 1.14.4 2018-06-06 - 1.14.5 2018-06-12 - 1.15.0 2018-07-23 - 1.15.1 2018-08-21 - 1.15.2 2018-09-23 - 1.15.3 2018-10-22 - 1.15.4 2018-11-04 - 1.16.0 2019-01-13 - 1.16.1 2019-01-31 - 1.16.2 2019-02-26 - 1.16.3 2019-04-21 - 1.16.4 2019-05-28 - 1.17.0 2019-07-26 - 1.17.1 2019-08-27 - ''', - # scipy releases - # https://github.com/scipy/scipy/releases - scipy = ''' - 0.16.0 2015-07-24 - 0.16.1 2015-10-24 - 0.17.0 2016-01-23 - 0.17.1 2016-05-12 - 0.18.0 2016-07-25 - 0.18.1 2016-09-19 - 0.19.0 2017-03-09 - 0.19.1 2017-06-23 - 1.0.0 2017-10-25 - 1.0.1 2018-03-24 - 1.1.0 2018-05-05 - 1.2.0 2018-12-17 - 1.2.1 2019-02-09 - 1.3.0 2019-05-17 - 1.3.1 2019-08-08 - ''', - # h5py releases - # https://pypi.org/project/h5py/#history - h5py = ''' - 2.4.0 2015-01-05 - 2.5.0 2015-04-08 - 2.6.0 2016-04-08 - 2.7.0 2017-03-18 - 2.7.1 2017-09-01 - 2.8.0 2018-05-13 - 2.9.0 2018-12-19 - ''', - # matplotlib releases - # https://pypi.org/project/matplotlib/#history - matplotlib = ''' - 1.5.0 2015-10-29 - 1.5.1 2016-01-10 - 1.5.2 2016-08-18 - 1.5.3 2016-09-09 - 2.0.0 2017-01-17 - 2.0.1 2017-05-02 - 2.0.2 2017-05-10 - 2.1.0 2017-10-07 - 2.1.1 2017-12-11 - 2.2.0 2018-03-06 - 2.2.2 2018-03-17 - 2.2.3 2018-08-11 - 3.0.0 2018-09-18 - 3.0.1 2018-10-25 - 3.0.2 2018-11-10 - 3.0.3 2019-02-28 - 3.1.0 2019-05-18 - 3.1.1 2019-07-02 - ''', - # pydot - # https://pypi.org/project/pydot/#history - pydot = ''' - 1.0.28 2012-01-02 - 1.0.29 2016-05-17 - 1.1.0 2016-05-23 - 1.2.0 2016-07-01 - 1.2.1 2016-07-01 - 1.2.2 2016-07-01 - 1.2.3 2016-10-06 - 1.2.4 2017-12-25 - 1.3.0 2018-11-19 - 1.4.0 2018-12-01 - 1.4.1 2018-12-12 - ''', - # spglib releases - # https://pypi.org/project/spglib/#history - spglib = ''' - 1.6.0 2014-05-20 - 1.8.3 2015-12-15 - 1.9.3 2016-05-11 - 1.9.5 2016-09-15 - 1.9.6 2016-10-17 - 1.9.7 2016-10-19 - 1.9.8 2016-11-01 - 1.9.9 2016-12-14 - 1.9.10 2017-10-02 - 1.10.0 2017-10-21 - 1.10.1 2017-10-27 - 1.10.2 2017-12-12 - 1.10.3 2018-01-13 - 1.10.4 2018-08-01 - 1.11.0 2018-11-08 - 1.11.1 2018-11-12 - 1.11.2 2018-12-07 - 1.12.0 2019-01-29 - 1.12.1 2019-02-01 - 1.12.2 2019-02-05 - 1.13.0 2019-07-02 - 1.14.0 2019-07-30 - 1.14.1 2019-07-30 - ''', - # pycifrw releases - # https://pypi.org/project/PyCifRW/#history - pycifrw = ''' - 4.1 2015-01-03 - 4.2 2016-03-01 - 4.3 2017-02-27 - 4.4 2018-02-12 - 4.4.1 2019-02-27 - ''', - # cif2cell releases - # https://pypi.org/project/cif2cell/#history - # https://sourceforge.net/projects/cif2cell/files/ - cif2cell = ''' - 1.2.2 2014-08-26 - 1.2.7 2015-05-18 - 1.2.10 2016-01-19 - 2.0.0 2019-10-07 - ''', - # seekpath releases - # https://pypi.org/project/seekpath/#history - seekpath = ''' - 1.0.0 2016-09-29 - 1.0.1 2016-09-29 - 1.0.2 2016-10-10 - 1.1.0 2016-10-26 - 1.1.1 2016-11-21 - 1.2.0 2016-12-19 - 1.3.0 2017-01-20 - 1.4.0 2017-04-04 - 1.5.0 2017-09-21 - 1.6.0 2017-10-13 - 1.7.0 2017-11-30 - 1.7.1 2017-11-30 - 1.8.0 2017-12-22 - 1.8.1 2018-02-12 - 1.8.2 2018-07-17 - 1.8.3 2018-10-04 - 1.8.4 2018-10-04 - 1.9.0 2019-07-25 - 1.9.1 2019-07-29 - 1.9.2 2019-07-30 - 1.9.3 2019-09-03 - ''', - ) -""" -Version and date information for Nexus dependencies. -""" - - -class VersionError(Exception): - """ - (`Internal API`) Exception unique to versions module. - """ - None -#end class VersionError - - -def version_error(msg): - """ - (`Internal API`) Print an error message and raise VersionError. - - Parameters - ---------- - msg : `str` - The error message to be printed. - """ - print('\nVersion error:\n '+msg.replace('\n','\n ')+'\nexiting.\n') - raise(VersionError) -#end def version_error - - -def time_ago(date): - """ - (`Internal API`) Compute time in years from current date. - - Parameters - ---------- - date : `datetime.date` - A date prior to today's date. - - Returns - ------- - years_ago : `float or int` - Number of years separating today's date from date of interest. - Floating point value includes months as fraction. - """ - delta = current_date-date - return float(delta.days)/365 -#end def time_ago - - - -def process_version(*version): - """ - (`Internal API`) Process version number from a range of inputted formats. - - Parameters - ---------- - *version : `int or str or tuple(str) or tuple(int) - Version number as string (e.g. `"1.0.0"`) tuple ( `('1','0','0')` or - `(1,0,0)` or `(1,0)`, etc.) or int (e.g. `1`). - - Returns - ------- - version : `tuple(int)` - Version tuple with at least 3 entries. - """ - if len(version)==1: - version = version[0] - #end if - if isinstance(version,str): - version = version.replace('+','').replace('-','') - version = version.split('.') - elif isinstance(version,int): - version = (version,) - #end if - version = tuple(map(int,version)) - while len(version)<3: - version += (0,) - #end while - return version -#end def process_version - - -def version_to_string(version): - """ - (`Internal API`) Convert version tuple to string. - """ - vs = '{}.{}.{}'.format(*version) - return vs -#end def version_to_string - - - -class Versions(object): - """ - Handles version information for Nexus dependencies. - - Used to produce printed summaries of currently supported versions - for Nexus dependencies as well as versions supported by the current - age policy. Also used to print summarized information about versions - of dependencies detected on the current machine and recommendations - for Nexus users regarding the state of their installation. - - The main data items for consumption by this class are - `support_cutoff_date`, `required_dependencies`, `currently_supported`, - and `raw_version_data`. - - This class is not intended for direct use by Nexus users. See the - three main API functions `check_versions`, `current_versions`, and - `policy_versions` below. - - This class follows a singleton pattern. - """ - - instances = [] - - def __init__(self): - self.initialize() - if len(Versions.instances)>0: - self.error('Only one Versions object can be instantiated!') - #end if - Versions.instances.append(self) - #end def __init__ - - - def initialize(self): - """ - (`Internal API`) Parse version data and determine status of - module dependencies on the current machine via attempted import. - """ - - self.__dict__.clear() - - # parse raw version data - version_data = dict() - dependencies = set() - full_names = dict() - for name,vd_string in raw_version_data.items(): - vd = dict() - n = 0 - for line in vd_string.strip().splitlines(): - version_string,date_string = line.split() - version = process_version(version_string) - date = datetime.date(*map(int,date_string.split('-'))) - vd[version] = dict( - version_string = version_string, - version = version, - date_string = date_string, - date = date, - ) - n+=1 - #end for - full_names[name] = name.lower() - name = name.lower() - version_data[name] = vd - if not name.startswith('python'): - dependencies.add(name) - #end if - #end for - dependencies.add(python_supported) - - cur_supp = dict() - ordered_dependencies = [] - for name,version in currently_supported: - ordered_dependencies.append(name) - cur_supp[name] = version - #end for - - optional_dependencies = dependencies-required_dependencies - - # store general dependency data - self.full_names = full_names - self.version_data = version_data - self.ordered_dependencies = ordered_dependencies - self.dependencies = dependencies - self.required_dependencies = required_dependencies - self.optional_dependencies = optional_dependencies - self.currently_supported = cur_supp - - # determine which dependencies are available - dependency_available = dict() - dependency_version = dict() - dependency_supported = dict() - for name in self.ordered_dependencies: - version = None - supported = None - if not name.startswith('python'): - module = None - try: - module_name = name - if name in import_aliases: - module_name = import_aliases[name] - #end if - module = importlib.import_module(module_name) - available = True - except: - available = False - #end try - if available: - if '__version__' in module.__dict__: - supported_version = self.currently_supported[name] - version = process_version(module.__version__) - supported = version >= supported_version - #end if - #end if - else: - python_major_supported = int(python_supported[-1]) - version = process_version(python_version()) - available = version[0]==python_major_supported - if available: - supported_version = self.currently_supported[name] - supported = version >= supported_version - #end if - #end if - dependency_available[name] = available - dependency_version[name] = version - dependency_supported[name] = supported - #end for - - # store data regarding dependency availability and support - self.dependency_available = dependency_available - self.dependency_version = dependency_version - self.dependency_supported = dependency_supported - #end def initalize - - - def error(self,msg): - """ - (`Internal API`) Raise an error. - """ - version_error(msg) - #end def error - - - def is_dependency(self,name): - """ - (`Internal API`) Return whether a name corresponds to a Nexus dependency. - """ - return name.lower() in self.dependencies - #end def is_dependency - - - def check_dependency(self,name): - """ - (`Internal API`) Check whether a name corresponds to a Nexus dependency, and raise an error if it doesn't. - """ - name = name.lower() - if name not in self.dependencies: - self.error('"{}" is not a dependency of Nexus'.format(name)) - #end if - return name - #end def check_dependency - - - def available(self,name): - """ - (`Internal API`) Return whether a Nexus dependency is available - on the current machine. - """ - name = self.check_dependency(name) - return self.dependency_available[name] - #end def available - - - def supported(self,name,version=None): - """ - (`Internal API`) Return whether a Nexus dependency on the current - machine has a version that is currently supported. - """ - name = self.check_dependency(name) - if version is not None: - version = process_version(version) - supported_version = self.currently_supported[name] - return version>=supported_version - else: - if not self.dependency_available[name]: - return False - else: - return self.dependency_supported[name] - #end if - #end if - #end def supported - - - def policy_supported_version(self,name=None): - """ - (`Internal API`) Determine versions of Nexus dependencies that - comply with the age policy relative to today's date. - """ - if name is not None: - name = name.lower() - if name not in self.dependencies: - self.error('"{}" is not a dependency of Nexus'.format(name)) - #end if - vdata = self.version_data[name] - versions = list(reversed(sorted(vdata.keys()))) - sv = None - for version in versions: - vd = vdata[version] - sv = version - if vd['date'] <= support_cutoff_date: - break - #end if - #end for - return sv - else: - supported_versions = dict() - for name in self.dependencies: - sv = self.policy_supported_version(name) - supported_versions[name] = sv - #end for - return supported_versions - #end if - #end def policy_supported_version - - - def write_supplied_versions(self,supplied_versions,age=True,opt_req=False): - """ - (`Internal API`) Write information about a set of dependencies. - """ - write_age = age - s = '' - for name in self.ordered_dependencies: - if name in supplied_versions: - version = supplied_versions[name] - vd = self.version_data[name][version] - date_str = vd['date_string'] - date = vd['date'] - age = time_ago(date) - version = version_to_string(version) - if write_age: - s += ' {:<12} = {:<8} (dated: {} , age: {:2.1f} years )\n'.format(name,version,date_str,age) - elif opt_req: - if name in self.required_dependencies: - s += ' {:<12} = {:<8} (required)\n'.format(name,version) - else: - s += ' {:<12} = {:<8} (optional)\n'.format(name,version) - #end if - else: - s += ' {:<12} = {:<8}\n'.format(name,version) - #end if - #end if - #end for - return s - #end def write_supplied_versions - - - def write_current_versions(self,age=True,opt_req=False,header=None): - """ - (`Internal API`) Write information about currently supported versions of Nexus dependencies. - """ - supported_versions = self.currently_supported - if header is None: - s = '\nNexus dependencies currently supported:\n'.format(years_supported) - else: - s = header - #end if - s += self.write_supplied_versions(supported_versions,age=age,opt_req=opt_req) - return s - #end def write_current_versions - - - def write_policy_versions(self): - """ - (`Internal API`) Write information about versions of Nexus dependencies current with the age policy as of today. - """ - supported_versions = self.policy_supported_version() - s = '\nNexus dependencies for {} year policy:\n'.format(years_supported) - s += self.write_supplied_versions(supported_versions) - return s - #end def write_policy_versions - - - def write_available_versions(self,status=True,opt_req=False): - """ - (`Internal API`) Write information about versions of Nexus dependencies that are available on the current machine. - """ - available_versions = self.dependency_version - s = '\nNexus dependencies available on current machine:\n'.format(years_supported) - for name in self.ordered_dependencies: - if self.dependency_available[name]: - version = available_versions[name] - supported_version = self.currently_supported[name] - if version is None: - version = '(unknown)' - support = '(unknown)' - else: - if version >= supported_version: - support = 'supported' - else: - support = 'unsupported' - #end if - version = version_to_string(version) - #end if - supported_version = version_to_string(supported_version) - if status: - s += ' {:<12} = {:<9} status: {:<11} oldest supported: {:<8}\n'.format(name,version,support,supported_version) - elif opt_req: - if name in self.required_dependencies: - s += ' {:<12} = {:<9} (required)\n'.format(name,version) - else: - s += ' {:<12} = {:<9} (optional)\n'.format(name,version) - #end if - else: - s += ' {:<12} = {:<9}\n'.format(name,version) - #end if - #end if - #end for - return s - #end def write_available_versions - - - def print_current_versions(self): - """ - (`Internal API`) Print information about currently supported versions of Nexus dependencies. - """ - print(self.write_current_versions()) - #end def print_current_versions - - - def print_policy_versions(self): - """ - (`Internal API`) Print information about versions of Nexus dependencies current with the age policy as of today. - """ - print(self.write_policy_versions()) - #end def print_policy_versions - - - def print_available_versions(self,status=True): - """ - (`Internal API`) Print information about versions of Nexus dependencies that are available on the current machine. - """ - print(self.write_available_versions(status=status)) - #end def print_available_versions - - - def check(self,write=True,exit=False,full=False,n=0,pad=' '): - """ - (`Internal API`) Check whether all required Nexus dependencies are present on the current machine. Optionally write detailed information for the Nexus user about the status of their installation. - """ - serr = '' - header ='\nChecking for Nexus dependencies on the current machine...\n' - s = versions.write_available_versions(status=False,opt_req=True) - wcv = '\nNexus dependencies recommended for full functionality:\n' - s += versions.write_current_versions(age=False,opt_req=True,header=wcv) - available_dependencies = set() - unavailable_dependencies = set() - req_supported = [] - opt_supported = [] - req_unsupported = [] - opt_unsupported = [] - req_unknown = [] - opt_unknown = [] - req_missing = [] - opt_missing = [] - for name in self.ordered_dependencies: - required = name in self.required_dependencies - if self.available(name): - supported = self.supported(name) - unknown = supported is None - if unknown: - if required: - req_unknown.append(name) - else: - opt_unknown.append(name) - #end if - elif not supported: - if required: - req_unsupported.append(name) - else: - opt_unsupported.append(name) - #end if - else: - if required: - req_supported.append(name) - else: - opt_supported.append(name) - #end if - #end if - else: - if required: - req_missing.append(name) - else: - opt_missing.append(name) - #end if - #end if - #end for - - all_req_supported = set(req_supported)==self.required_dependencies - all_opt_supported = set(opt_supported)==self.optional_dependencies - all_supported = all_req_supported and all_opt_supported - - #req_missing.append('numpy') - if len(req_missing)>0: - serr = 'Some required Nexus dependencies are missing.\nMissing dependencies: {}\nPlease check your Python installation.'.format(req_missing) - s += '\nRequired dependencies are missing:\n' - for name in req_missing: - s += ' {} is missing. Install {} or greater.\n'.format(name,version_to_string(self.currently_supported[name])) - #end for - s += '\nNexus will not work.\n Please install the missing dependencies above.\n' - else: - if all_supported: - s += '\nAll Nexus dependencies are met.\n Both core workflow and optional features should work.\n' - elif all_req_supported: - s += '\nAll required Nexus dependencies are met.\n Core workflow features should work.\n Some optional features may not.\n See below for more information.\n' - else: - s += '\nRequired dependencies are present, but some are unsupported.\n Core workflow features may still work.\n Please install updated versions if problems are encountered.\n' - #end if - if not all_req_supported: - s += '\nRequired dependencies in need of user check or update:\n' - for name in req_unknown: - s += ' {} version is unknown. Check for {} or greater.\n'.format(name,version_to_string(self.currently_supported[name])) - #end for - for name in req_unsupported: - s += ' {} version {} is outdated. Update to {} or greater.\n'.format(name,version_to_string(self.dependency_version[name]),version_to_string(self.currently_supported[name])) - #end for - #end if - if not all_opt_supported: - s += '\nSome optional dependencies are missing or merit an update.\n These modules are not needed for core workflow operation.\n Optional features related to outdated modules may still work.\n Please install updated versions if problems are encountered.\n' - if len(opt_missing)>0: - s += '\nOptional dependencies that are missing:\n' - for name in opt_missing: - s += ' {:<10} is missing. Install {} or greater.\n'.format(name,version_to_string(self.currently_supported[name])) - #end for - #end if - if len(opt_unknown)>0 or len(opt_unsupported)>0: - s += '\nOptional dependencies benefitting from user check or update:\n' - for name in opt_unknown: - s += ' {:<10} version is unknown. Check for {} or greater.\n'.format(name,version_to_string(self.currently_supported[name])) - #end for - for name in opt_unsupported: - s += ' {:<10} version {} is outdated. Update to {} or greater.\n'.format(name,version_to_string(self.dependency_version[name]),version_to_string(self.currently_supported[name])) - #end for - #end if - #end if - #end if - s = n*pad+header+s.replace('\n','\n'+(n+1)*pad)+'\n' - if write: - print(s) - #end if - error = len(serr)>0 - if error and exit: - self.error(serr) - #end if - if not full: - return error - else: - return error,s,serr - #end if - #end def check -#end class Versions - - - -# store availability of various required/optional dependencies -numpy_available = False -scipy_available = False -h5py_available = False -matplotlib_available = False -pydot_available = False -spglib_available = False -pycifrw_available = False -seekpath_available = False -cif2cell_available = False - -numpy_supported = False -scipy_supported = False -h5py_supported = False -matplotlib_supported = False -pydot_supported = False -spglib_supported = False -pycifrw_supported = False -seekpath_supported = False -cif2cell_supported = False - -try: # versioning info is never worth failure - versions = Versions() - - numpy_available = versions.available('numpy') - scipy_available = versions.available('scipy') - h5py_available = versions.available('h5py') - matplotlib_available = versions.available('matplotlib') - pydot_available = versions.available('pydot') - spglib_available = versions.available('spglib') - pycifrw_available = versions.available('pycifrw') - seekpath_available = versions.available('seekpath') - cif2cell_available = versions.available('cif2cell') - - numpy_supported = versions.supported('numpy') - scipy_supported = versions.supported('scipy') - h5py_supported = versions.supported('h5py') - matplotlib_supported = versions.supported('matplotlib') - pydot_supported = versions.supported('pydot') - spglib_supported = versions.supported('spglib') - pycifrw_supported = versions.supported('pycifrw') - seekpath_supported = versions.supported('seekpath') - cif2cell_supported = versions.supported('cif2cell') -except: - versions = None -#end try - - -def check_versions(write=True,exit=False): - """ - (`User API`) Print detailed information about the status of Nexus - dependencies on the current machine. - """ - if versions is None: - print('\nProblem encountered in Nexus version checking code.\nThis is a developer error.\nPlease run the Nexus tests via the nxs-test script for more details and report this issue to the developers.') - error = True - else: - error = versions.check(write=write,exit=exit) - #end if - return error -#end def check_versions - - -def current_versions(): - """ - (`User API`) Print information about currently supported versions of - Nexus dependencies. - """ - if versions is None: - print('\nProblem encountered in Nexus version checking code.\nThis is a developer error.\nPlease run the Nexus tests via the nxs-test script for more details and report this issue to the developers.') - else: - versions.print_current_versions() - #end if -#end def current_versions - - -def policy_versions(): - """ - (`User API`) Print information about versions of Nexus dependencies - that meet the age policy for today's date. - """ - if versions is None: - print('\nProblem encountered in Nexus version checking code.\nThis is a developer error.\nPlease run the Nexus tests via the nxs-test script for more details and report this issue to the developers.') - else: - versions.print_policy_versions() - #end if -#end def policy_versions diff --git a/nexus/nexus/xmlreader.py b/nexus/nexus/xmlreader.py index 0c1ad31b30..f711938eed 100644 --- a/nexus/nexus/xmlreader.py +++ b/nexus/nexus/xmlreader.py @@ -29,6 +29,7 @@ import os import numpy as np from .developer import DevBase, obj, valid_variable_name +from .utilities import path_string def parse_string(s, delim = None): @@ -282,6 +283,7 @@ def __init__(self,fpath=None,element_joins=None,element_aliases=None,contract_na if element_aliases is None: element_aliases = {} + fpath = path_string(fpath) #assign values self.fpath=fpath if fpath is None: @@ -306,8 +308,8 @@ def __init__(self,fpath=None,element_joins=None,element_aliases=None,contract_na #read in xml file if xml is None: - fobj = open(fpath,'r') - self.xml = fobj.read() + with open(fpath, "r") as fobj: + self.xml = fobj.read() else: self.xml = xml #end if @@ -350,10 +352,9 @@ def include_files(self): if ir != -1: cont = self.xml[il:ir].strip(pair[0]).rstrip(pair[1]) fname = cont.split('=',1)[1].strip().strip('"') - fobj = open(os.path.join(self.base_path,fname),'r') - fcont = fobj.read() + with open(os.path.join(self.base_path,fname), "r") as fobj: + fcont = fobj.read() fcont = remove_pair_sections(fcont,qpair) - fobj.close() self.xml = self.xml.replace(self.xml[il:ir],fcont) #end if #end while diff --git a/nexus/pyproject.toml b/nexus/pyproject.toml index f3f308c743..714de91672 100644 --- a/nexus/pyproject.toml +++ b/nexus/pyproject.toml @@ -1,31 +1,23 @@ [project] name = "nexus" -version = "2.2.0" +version = "2.3.9" description = "Automated workflow manager for DFT & QMC calculations" readme = "README.md" -requires-python = ">=3.6" +requires-python = ">=3.10" dependencies = [ - "numpy (>=1.13.0, <1.20.0) ; python_version == '3.6.*'", - "numpy (>=1.14.5, <1.22.0) ; python_version == '3.7.*'", - "numpy (>=1.18.0, <1.25.0) ; python_version == '3.8.*'", - "numpy (>=1.19.3, <2.1.0) ; python_version == '3.9.*'", - "numpy (>=1.21.0, <2.3.0) ; python_version == '3.10.*'", - "numpy (>=1.23.2, !=2.4.0) ; python_version == '3.11.*'", # - "numpy (>=1.26.0, !=2.4.0) ; python_version == '3.12.*'", # Numpy 2.4.0 was yanked from PyPI for - "numpy (>=2.1.0, !=2.4.0) ; python_version == '3.13.*'", # breaking backwards compatibility - "numpy (>=2.3.0, !=2.4.0) ; python_version >= '3.14.0'", # + "numpy (>=1.22.0, !=2.4.0)" # Numpy 2.4.0 was yanked from PyPI for breaking backwards compatibility ] [project.scripts] -eshdf = "nexus._bin:eshdf" -nxs-redo = "nexus._bin:nxs_redo" -nxs-sim = "nexus._bin:nxs_sim" -nxs-test = "nexus._bin:nxs_test" -qdens = "nexus._bin:qdens" +eshdf = "nexus._bin:eshdf" +nxs-redo = "nexus._bin:nxs_redo" +nxs-sim = "nexus._bin:nxs_sim" +nxs-test = "nexus._bin:nxs_test" +qdens = "nexus._bin:qdens" qdens-radial = "nexus._bin:qdens_radial" -qmca = "nexus._bin:qmca" -qmc-fit = "nexus._bin:qmc_fit" +qmca = "nexus._bin:qmca" +qmc-fit = "nexus._bin:qmc_fit" [build-system] requires = ["hatchling"] @@ -33,45 +25,47 @@ build-backend = "hatchling.build" [dependency-groups] dev = [ - "pytest>=9.0.2 ; python_version >= '3.10.0'", - "pytest-cov>=7.0.0 ; python_version >= '3.10.0'", + "pytest>=9.0.2", + "coverage[toml]>=7.13.5; python_version < '3.11'", + "coverage>=7.13.5; python_version >= '3.11'", + "pytest-cov>=7.0.0", + "pytest-order>=1.3.0", +] +docs = [ + "sphinx>=8.1.0", + "sphinx-rtd-theme>=3.1.0", + "sphinxcontrib-bibtex>=2.6.5", ] [project.optional-dependencies] full = [ - "scipy (>=0.19.0, <1.6.0) ; python_version == '3.6.*'", - "scipy (>=1.0.0, <1.8.0) ; python_version == '3.7.*'", - "scipy (>=1.4.0, 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NEEnergyDensityEstimator::registerListeners(QMCHamiltonian& ham_leader) QMCHamiltonian::mw_registerKineticListener(ham_leader, kinetic_listener); ListenerVector potential_listener("potential", getListener(local_pot_values_)); QMCHamiltonian::mw_registerLocalPotentialListener(ham_leader, potential_listener); - ListenerVector ion_potential_listener("potential", getListener(local_ion_pot_values_)); - QMCHamiltonian::mw_registerLocalIonPotentialListener(ham_leader, ion_potential_listener); + if (pset_static_) + { + ListenerVector ion_potential_listener("potential", getListener(local_ion_pot_values_)); + QMCHamiltonian::mw_registerLocalIonPotentialListener(ham_leader, ion_potential_listener); + } } /** This function collects the per particle energies. diff --git a/src/Estimators/tests/CMakeLists.txt b/src/Estimators/tests/CMakeLists.txt index 67e65bcfc3..12f45da9e2 100644 --- a/src/Estimators/tests/CMakeLists.txt +++ b/src/Estimators/tests/CMakeLists.txt @@ -116,6 +116,8 @@ if(HAVE_MPI) qmcwfs qmcparticle qmcwfs_omptarget + spline2 + spline2_omptarget qmcparticle_omptarget qmcutil platform_omptarget_LA diff --git a/src/Estimators/tests/EDenEstimatorManagerIntegrationTest.cpp b/src/Estimators/tests/EDenEstimatorManagerIntegrationTest.cpp index fe5434ff3b..bac56c8468 100644 --- a/src/Estimators/tests/EDenEstimatorManagerIntegrationTest.cpp +++ b/src/Estimators/tests/EDenEstimatorManagerIntegrationTest.cpp @@ -27,9 +27,14 @@ using MCPWalker = EDenEstimatorManagerIntegrationTest::MCPWalk EDenEstimatorManagerIntegrationTest::EDenEstimatorManagerIntegrationTest(Communicate* comm, int num_walkers) { +#ifndef ENABLE_OFFLOAD eden_test_ = std::make_unique(comm, num_walkers, &testing::makeGoldWalkerElementsWithEEEIPS, generate_test_data); - auto doc = testing::createEstimatorManagerEnergyDenistyInputXML(); +#else + eden_test_ = std::make_unique(comm, num_walkers, &testing::makeGoldWalkerElementsWithEI, + generate_test_data); +#endif + auto doc = testing::createEstimatorManagerEnergyDenistyInputXML(); EstimatorManagerInput emi(doc.getRoot()); auto& gold_elem = eden_test_->getGoldElements(); auto ham_list = eden_test_->getHamList(); diff --git a/src/Estimators/tests/test_EnergyDensityEstimator.cpp b/src/Estimators/tests/test_EnergyDensityEstimator.cpp index 50e5ee1940..4ddf23410f 100644 --- a/src/Estimators/tests/test_EnergyDensityEstimator.cpp +++ b/src/Estimators/tests/test_EnergyDensityEstimator.cpp @@ -10,6 +10,7 @@ ////////////////////////////////////////////////////////////////////////////////////// +#include "MockGoldWalkerElements.h" #include "catch.hpp" #include "EnergyDensityEstimator.h" @@ -46,7 +47,7 @@ TEST_CASE("NEEnergyDensityEstimator::Constructor", "[estimators]") {1.657151589, 0.883870516, 1.201243939}, {0.97317591, 1.245644974, 0.284564732}}; Libxml2Document doc; - using Input = testing::EnergyDensityInputs; + using Input = testing::EnergyDensityInputs; REQUIRE(doc.parseFromString(Input::getXml(Input::valid::CELL))); xmlNodePtr node = doc.getRoot(); EnergyDensityInput edein{node}; @@ -72,7 +73,7 @@ TEST_CASE("NEEnergyDensityEstimator::spawnCrowdClone", "[estimators]") {1.657151589, 0.883870516, 1.201243939}, {0.97317591, 1.245644974, 0.284564732}}; Libxml2Document doc; - using Input = testing::EnergyDensityInputs; + using Input = testing::EnergyDensityInputs; REQUIRE(doc.parseFromString(Input::getXml(Input::valid::CELL))); xmlNodePtr node = doc.getRoot(); EnergyDensityInput edein{node}; @@ -90,8 +91,12 @@ TEST_CASE("NEEnergyDensityEstimator::AccumulateIntegration", "[estimators]") { Communicate* comm = OHMMS::Controller; +#ifndef ENABLE_OFFLOAD testing::EnergyDensityTest eden_test(comm, 4 /*num_walkers*/, generate_test_data); - +#else + testing::EnergyDensityTest eden_test(comm, 4 /*num_walkers*/, &testing::makeGoldWalkerElementsWithEI, + generate_test_data); +#endif auto ham_list = eden_test.getHamList(); auto& ham_leader = ham_list.getLeader(); auto ham_lock = ResourceCollectionTeamLock(eden_test.getHamRes(), ham_list); @@ -150,7 +155,12 @@ TEST_CASE("NEEnergyDensityEstimator::Collect", "[estimators]") { Communicate* comm = OHMMS::Controller; +#ifndef ENABLE_OFFLOAD testing::EnergyDensityTest eden_test(comm, 4 /*num_walkers*/, generate_test_data); +#else + testing::EnergyDensityTest eden_test(comm, 4 /*num_walkers*/, &testing::makeGoldWalkerElementsWithEI, + generate_test_data); +#endif auto ham_list = eden_test.getHamList(); auto& ham_leader = ham_list.getLeader(); diff --git a/src/Estimators/tests/test_EnergyDensityEstimatorIntegration.cpp b/src/Estimators/tests/test_EnergyDensityEstimatorIntegration.cpp index 5e0c80a4fd..ebc1e19239 100644 --- a/src/Estimators/tests/test_EnergyDensityEstimatorIntegration.cpp +++ b/src/Estimators/tests/test_EnergyDensityEstimatorIntegration.cpp @@ -29,6 +29,7 @@ #include "GenerateRandomParticleSets.h" #include "EstimatorManagerNewTest.h" #include "EDenEstimatorManagerIntegrationTest.h" +#include "config.h" constexpr bool generate_test_data = false; @@ -41,7 +42,12 @@ TEST_CASE("EnergyDensityEstimatorIntegration::multirank_reduction", "[estimators Communicate* comm = OHMMS::Controller; int num_walkers = 4; +#ifndef ENABLE_OFFLOAD testing::EnergyDensityTest eden_test(comm, num_walkers, generate_test_data); +#else + testing::EnergyDensityTest eden_test(comm, num_walkers, &testing::makeGoldWalkerElementsWithEI, generate_test_data); +#endif + auto doc = testing::createEstimatorManagerEnergyDenistyInputXML(); EstimatorManagerInput emi(doc.getRoot()); auto& gold_elem = eden_test.getGoldElements(); @@ -114,8 +120,12 @@ TEST_CASE("EnergyDensityEstimatorIntegration::operator_reporting", "[estimators] { Communicate* comm = OHMMS::Controller; int num_walkers = 4; +#ifndef ENABLE_OFFLOAD testing::EnergyDensityTest eden_test(comm, num_walkers, &testing::makeGoldWalkerElementsWithEEEIPS, generate_test_data); +#else + testing::EnergyDensityTest eden_test(comm, num_walkers, &testing::makeGoldWalkerElementsWithEI, generate_test_data); +#endif auto doc = testing::createEstimatorManagerEnergyDenistyInputXML(); EstimatorManagerInput emi(doc.getRoot()); auto& gold_elem = eden_test.getGoldElements(); @@ -193,7 +203,9 @@ TEST_CASE("EnergyDensityEstimatorIntegration::operator_reporting", "[estimators] CHECK(summed_grid == Approx(expected_sum)); auto debug_sum = testing::cannedSum(); +#ifndef ENABLE_OFFLOAD CHECK(summed_grid == Approx(debug_sum)); +#endif } @@ -208,6 +220,7 @@ TEST_CASE("EnergyDensityEstimatorIntegration::normalization", "[estimators]") auto savePropertiesIntoWalker = [](QMCHamiltonian& ham, MCPWalker& walker) { ham.saveProperty(walker.getPropertyBase()); }; + for (int iw = 0; iw < num_walkers; ++iw) savePropertiesIntoWalker(ham_list[iw], walker_list[iw]); @@ -227,7 +240,7 @@ TEST_CASE("EnergyDensityEstimatorIntegration::normalization", "[estimators]") auto pset_list = eden_emn_integration_test.getPSetList(); auto twf_list = eden_emn_integration_test.getTwfList(); auto& rng = eden_emn_integration_test.getRng(); - // The logger writes out on accumualtes so the sum must be acquired before + // The logger writes out on accumulates so the sum must be acquired before emc.accumulate(walker_list, pset_list, twf_list, ham_list, rng); NEEnergyDensityEstimator& e_den_est = dynamic_cast(crowd_operator_ests[0][0].get()); @@ -242,8 +255,9 @@ TEST_CASE("EnergyDensityEstimatorIntegration::normalization", "[estimators]") CHECK(summed_grid == Approx(expected_sum)); auto debug_sum = testing::cannedSum(); +#ifndef ENABLE_OFFLOAD CHECK(summed_grid == Approx(debug_sum)); - +#endif std::cout << "summed grid: " << summed_grid << '\n'; diff --git a/src/Estimators/tests/test_EnergyDensityEstimatorIntegration.h b/src/Estimators/tests/test_EnergyDensityEstimatorIntegration.h index 23b900b6cf..da705b82f2 100644 --- a/src/Estimators/tests/test_EnergyDensityEstimatorIntegration.h +++ b/src/Estimators/tests/test_EnergyDensityEstimatorIntegration.h @@ -21,160 +21,149 @@ namespace testing double cannedSum() { - CrowdEnergyValues kinetic_values = { - {{"Kinetic"}, - { - { - 0.4529014498, - 0.3156825975, - 1.456884142, - 0.2485722715, - 1.061016946, - 1.175176701, - 0.3810680072, - 0.5948852591, - }, - { - 1.668881229, - 0.6048614649, - 4.647461, - 1.358203882, - -0.1954819386, - 0.5372290975, - 0.4891795562, - 1.169825556, - }, - { - 1.231372469, - 0.1803754377, - -1.205883308, - 1.410959272, - 0.6216167405, - -0.4923786961, - 0.240801627, - 1.489066498, - }, - { - 1.372523683, - 0.7555570136, - 3.226946012, - -0.7894047702, - 1.609594113, - 0.2679526229, - 0.4790043943, - 1.245813374, - }, + CrowdEnergyValues kinetic_values = {{ + {"Kinetic"}, + {{ + 0.4529014498, + 0.3156825975, + 1.456884142, + 0.2485722715, + 1.061016946, + 1.175176701, + 0.3810680072, + 0.5948852591, + }, + { + 1.668881229, + 0.6048614649, + 4.647461, + 1.358203882, + -0.1954819386, + 0.5372290975, + 0.4891795562, + 1.169825556, + }, + { + 1.231372469, + 0.1803754377, + -1.205883308, + 1.410959272, + 0.6216167405, + -0.4923786961, + 0.240801627, + 1.489066498, + }, + { + 1.372523683, + 0.7555570136, + 3.226946012, + -0.7894047702, + 1.609594113, + 0.2679526229, + 0.4790043943, + 1.245813374, }}, - }; - CrowdEnergyValues local_potential_values = { - {{"ElecIon"}, - { - { - 0.1902921988, - 0.305111589, - -0.4795567012, - 0.4963486847, - -0.3115299195, - -0.3619893748, - 0.09889833001, - 0.2794993745, - }, - { - -0.5591061161, - -0.1018774551, - -1.758163531, - -0.6303051354, - 0.4878929497, - 0.3358202321, - 0.3278906128, - -0.3592569675, - }, - { - 0.2308181408, - 0.3380463882, - 0.4502142537, - 0.09129681658, - 0.5120332566, - 0.4968745527, - 0.5207083896, - -0.3453223962, - }, - { - 0.1190383565, - -0.1566598476, - -1.061808708, - 0.4489104633, - -0.4774404553, - 0.3925164497, - 0.1283951707, - -0.436834872, - }, - }}, - {{"ElecElec"}, - { - { - -0.6207395076, - -0.5429517933, - -0.5065277177, - -0.5783610014, - -0.4984350535, - -0.5916988187, - -0.5487789099, - -0.7210825667, - }, - { - -0.3816392959, - -0.5430679423, - -0.482442029, - -0.5642089765, - -0.4469150835, - -0.5218930872, - -0.4652968702, - -0.5215640811, - }, - { - 0.0712246546, - 0.03917229912, - -0.5630155803, - -0.6444294957, - -0.0487069078, - -0.178371135, - -0.2205232716, - -0.1101885998, - }, - { - -0.3381089106, - -0.5573446148, - -0.5798054791, - -0.2771065229, - -0.2847240288, - -0.1318201812, - -0.276998751, - -0.5649121642, - }, - }}, - }; - CrowdEnergyValues local_ion_pot_values = { - {{"ElecIon"}, - { - { - 0.04332090412, - 0.1737532775, - }, - { - -0.9332901929, - -1.323815217, - }, - { - 1.695662968, - 0.5990064344, - }, - { - 0.1634203786, - -1.207303821, - }, - }}, - }; + }}; + CrowdEnergyValues local_potential_values = {{{"ElecIon"}, + {{ + 0.1902921988, + 0.305111589, + -0.4795567012, + 0.4963486847, + -0.3115299195, + -0.3619893748, + 0.09889833001, + 0.2794993745, + }, + { + -0.5591061161, + -0.1018774551, + -1.758163531, + -0.6303051354, + 0.4878929497, + 0.3358202321, + 0.3278906128, + -0.3592569675, + }, + { + 0.2308181408, + 0.3380463882, + 0.4502142537, + 0.09129681658, + 0.5120332566, + 0.4968745527, + 0.5207083896, + -0.3453223962, + }, + { + 0.1190383565, + -0.1566598476, + -1.061808708, + 0.4489104633, + -0.4774404553, + 0.3925164497, + 0.1283951707, + -0.436834872, + }}}, + {{"ElecElec"}, + {{ + -0.6207395076, + -0.5429517933, + -0.5065277177, + -0.5783610014, + -0.4984350534, + -0.5916988187, + -0.5487789099, + -0.7210825667, + }, + { + -0.3816392959, + -0.5430679423, + -0.482442029, + -0.5642089765, + -0.4469150835, + -0.5218930872, + -0.4652968702, + -0.5215640811, + }, + { + 0.07122465461, + 0.03917229913, + -0.5630155803, + -0.6444294957, + -0.04870690779, + -0.178371135, + -0.2205232716, + -0.1101885998, + }, + { + -0.3381089106, + -0.5573446148, + -0.5798054791, + -0.2771065229, + -0.2847240288, + -0.1318201812, + -0.276998751, + -0.5649121642, + }}}}; + + CrowdEnergyValues local_ion_pot_values = {{{"ElecIon"}, + {{ + 0.04332090412, + 0.1737532775, + }, + { + -0.9332901929, + -1.323815217, + }, + { + 1.695662968, + 0.5990064344, + }, + { + 0.1634203786, + -1.207303821, + }}}}; auto sumOver = [](auto& crowd_energy) -> double { @@ -192,6 +181,7 @@ double cannedSum() } return sum; }; + auto sum_pot = sumOver(local_potential_values); auto kinetic = sumOver(kinetic_values); auto ion_pot = sumOver(local_ion_pot_values); diff --git a/src/Estimators/tests/test_EstimatorManagerCrowd.cpp b/src/Estimators/tests/test_EstimatorManagerCrowd.cpp index 5e7c8978d6..74bde75385 100644 --- a/src/Estimators/tests/test_EstimatorManagerCrowd.cpp +++ b/src/Estimators/tests/test_EstimatorManagerCrowd.cpp @@ -70,7 +70,7 @@ TEST_CASE("EstimatorManagerCrowd PerParticleHamiltonianLogger integration", "[es MinimalWaveFunctionPool::make_diamondC_1x1x1(test_project.getRuntimeOptions(), comm, particle_pool); auto& pset = *(particle_pool.getParticleSet("e")); // This is where the pset properties "properies" gain the different hamiltonian operator values. - auto hamiltonian_pool = MinimalHamiltonianPool::make_hamWithEE(comm, particle_pool, wavefunction_pool); + auto hamiltonian_pool = MinimalHamiltonianPool::makeHamWithEI(comm, particle_pool, wavefunction_pool); TrialWaveFunction& twf(wavefunction_pool.getWaveFunction().value()); QMCHamiltonian& ham(hamiltonian_pool.getHamiltonian().value()); diff --git a/src/Message/Communicate.cpp b/src/Message/Communicate.cpp index 412c9f8c46..015f141cac 100644 --- a/src/Message/Communicate.cpp +++ b/src/Message/Communicate.cpp @@ -63,17 +63,19 @@ Communicate::Communicate(mpi3::communicator&& in_comm) : d_groupid(0), d_ngroups d_ncontexts = comm.size(); } -Communicate::Communicate(const Communicate& in_comm, int nparts) +Communicate::Communicate(const Communicate& in_comm, int nparts, int stripe) { std::vector nplist(nparts + 1); - const int p = FairDivideLow(in_comm.rank(), in_comm.size(), nparts, nplist); //group + // group index + const int gid = stripe == 0 ? FairDivideLow(in_comm.rank(), in_comm.size(), nparts, nplist) : + in_comm.rank() / stripe % nparts; // comm is mutable member - comm = in_comm.comm.split(p, in_comm.rank()); + comm = in_comm.comm.split(gid, in_comm.rank()); myMPI = comm.get(); // TODO: mpi3 needs to define comm d_mycontext = comm.rank(); d_ncontexts = comm.size(); - d_groupid = p; + d_groupid = gid; d_ngroups = nparts; // create an inter group communicator @@ -113,7 +115,7 @@ void Communicate::barrier() const {} void Communicate::cleanupMessage(void*) {} -Communicate::Communicate(const Communicate& in_comm, int nparts) +Communicate::Communicate(const Communicate& in_comm, int nparts, int stripe) : myMPI(MPI_COMM_NULL), d_mycontext(0), d_ncontexts(1), d_groupid(0) { inter_group_comm_ = std::make_unique(); } #endif // !HAVE_MPI diff --git a/src/Message/Communicate.h b/src/Message/Communicate.h index db222d6f3d..1aac696928 100644 --- a/src/Message/Communicate.h +++ b/src/Message/Communicate.h @@ -77,8 +77,15 @@ class Communicate : public CommunicatorTraits #endif /** constructor that splits in_comm + * in_comm.size() == 12 ; nparts = 2; stripe = 0 + * | group 0 | group 1 | + * | 0 1 2 3 4 5 | 6 7 8 9 10 11 | + * in_comm.size() == 12 ; nparts = 2; stripe = 3; + * | group 0 | group 1 | + * | 0 1 2 | 3 4 5 | + * | 6 7 8 | 9 10 11 | */ - Communicate(const Communicate& in_comm, int nparts); + Communicate(const Communicate& in_comm, int nparts, int stripe = 0); /**destructor * Call proper finalization of Communication library diff --git a/src/Message/tests/CMakeLists.txt b/src/Message/tests/CMakeLists.txt index 9287b450d0..2d827b2c8c 100644 --- a/src/Message/tests/CMakeLists.txt +++ b/src/Message/tests/CMakeLists.txt @@ -16,7 +16,10 @@ set(UTEST_NAME deterministic-unit_test_${SRC_DIR}) add_executable(${UTEST_EXE} test_communciate.cpp) target_link_libraries(${UTEST_EXE} PUBLIC message catch_main) -add_unit_test(${UTEST_NAME} 1 1 $) +foreach(NUM_RANKS 1 2 3 6 12) + set(UTEST_NAME_MPI ${UTEST_NAME}-r${NUM_RANKS}) + add_unit_test(${UTEST_NAME_MPI} ${NUM_RANKS} 1 $) +endforeach() if(HAVE_MPI) set(UTEST_EXE test_${SRC_DIR}_mpi) diff --git a/src/Message/tests/test_communciate.cpp b/src/Message/tests/test_communciate.cpp index 57093af23e..328a0f2232 100644 --- a/src/Message/tests/test_communciate.cpp +++ b/src/Message/tests/test_communciate.cpp @@ -97,4 +97,19 @@ TEST_CASE("test_communicate_split_four", "[message]") } } +TEST_CASE("test_communicate_split_two_stripe_three", "[message]") +{ + Communicate* c = OHMMS::Controller; + // For simplicity, only test the case where the number of processes is divisible by 6. + if (c->size() % 6 != 0) + return; + + auto c2 = std::make_unique(*c, 2, 3); + const int group_size = c->size() / 2; + const int new_rank = c->rank() % 3 + c->rank() / 6 * 3; + REQUIRE(c2->size() == group_size); + REQUIRE(c2->rank() == new_rank); + REQUIRE(c2->getGroupID() == (c->rank() / 3 % 2)); +} + } // namespace qmcplusplus diff --git a/src/Numerics/codegen/gen_cartesian_tensor.py b/src/Numerics/codegen/gen_cartesian_tensor.py old mode 100644 new mode 100755 index 57f0ce921f..a8e97c58da --- a/src/Numerics/codegen/gen_cartesian_tensor.py +++ b/src/Numerics/codegen/gen_cartesian_tensor.py @@ -1,4 +1,4 @@ - +#! /usr/bin/env python3 # Generate angular tensors using symbolic expressions for the GTO's and derivatives # There are two steps to the code generation, and only the second is automated. @@ -12,8 +12,7 @@ # C. Apply clang-format on modified source files. -from collections import namedtuple, defaultdict -from sympy import * +from sympy import sympify, Symbol, symbols, diff # See the GaussianOrbitals notebook in the qmc_algorithms repo for more explanation, # especially about the normalization. @@ -860,7 +859,7 @@ def run_template(fname_in, fname_out, bodies): if key in bodies: line = bodies[key] else: - print 'Error, template item not found, key:',key, ' line = ',line + print('Error, template item not found, key:', key, ' line = ', line) out += line with open(fname_out, 'w') as f: @@ -904,11 +903,11 @@ def create_soa_cartesian_tensor_h(): if __name__ == '__main__': - #print gen_evaluate() - #print gen_evaluate_all() - #print gen_evaluate_with_hessian() - #print gen_evaluate_with_third_deriv() - #print gen_evaluate_third_deriv_only() + #print(gen_evaluate()) + #print(gen_evaluate_all()) + #print(gen_evaluate_with_hessian()) + #print(gen_evaluate_with_third_deriv()) + #print(gen_evaluate_third_deriv_only()) # Create CartesianTensor.h from CartesianTensor.h.in create_cartesian_tensor_h() diff --git a/src/Numerics/codegen/read_order.py b/src/Numerics/codegen/read_order.py old mode 100644 new mode 100755 index f2ad9e64fc..34b58c48d6 --- a/src/Numerics/codegen/read_order.py +++ b/src/Numerics/codegen/read_order.py @@ -1,4 +1,4 @@ - +#! /usr/bin/env python3 # Generate order of i,j,k indices from Gamess output # Also see the SETLAB routine in inputb.src for the ordering @@ -10,7 +10,7 @@ def count_vals(s): x,y,z = 0,0,0 mult = 1 for c,c1 in zip(s,s[1:]+' '): - #print 'c,c1',c,c1 + #print('c,c1', c, c1) if c.isdigit(): continue if c1.isdigit(): @@ -23,7 +23,7 @@ def count_vals(s): z += mult mult = 1 if not c.isdigit() and c not in ['S','X','Y','Z']: - print 'Error, unknown character',c + print('Error, unknown character', c) return x,y,z # order by max number of repeats, then x,y,z @@ -166,11 +166,11 @@ def read_order(fname): already_seen[order] = 1 #new_sum = x + y + z #if new_sum != current_sum: - # print ' # ',shell_name[new_sum] + # print(' # ', shell_name[new_sum]) # current_sum = new_sum - #print order,x,y,z - #print " ijk.append('%s')"%to_string(x,y,z) + #print(order, x, y, z) + #print(" ijk.append('%s')"%to_string(x,y,z)) return order_list if __name__ == "__main__": @@ -178,13 +178,13 @@ def read_order(fname): order_list = read_order('order.txt') # Create get_ijk for gen_cartesian_tensor.py - #print create_get_ijk(order_list) + #print(create_get_ijk(order_list)) # Create getABC for CartesianTensor.h.in - #print create_getABC(order_list) + #print(create_getABC(order_list)) # Create getABC for SoaCartesianTensor.h.in - #print create_getABC_SoA(order_list) + #print(create_getABC_SoA(order_list)) # Create order dictionary for PyscfToQmcpack.py in QMCTools - print create_gms_order_for_pyscf(order_list) + print(create_gms_order_for_pyscf(order_list)) diff --git a/src/Numerics/tests/gen_gto.py b/src/Numerics/tests/gen_gto.py index e3fba6793c..06a5cb5e68 100644 --- a/src/Numerics/tests/gen_gto.py +++ b/src/Numerics/tests/gen_gto.py @@ -11,24 +11,24 @@ def single_gaussian(): alpha_val = 3.0 r_val = 1.2 - print 'alpha = ',alpha_val - print 'r = ',r_val + print('alpha = ',alpha_val) + print('r = ',r_val) phi = exp(-alpha*r**2) - print phi - print 'f == ',phi.subs(alpha, alpha_val).subs(r,r_val) + print(phi) + print('f == ',phi.subs(alpha, alpha_val).subs(r,r_val)) d_phi = diff(phi, r) - print 'symbolic df = ',d_phi - print 'df == ',d_phi.subs(alpha, alpha_val).subs(r,r_val) + print('symbolic df = ',d_phi) + print('df == ',d_phi.subs(alpha, alpha_val).subs(r,r_val)) dd_phi = diff(phi, r, 2) - print 'symbolic d2f = ',dd_phi - print 'd2f == ',dd_phi.subs(alpha, alpha_val).subs(r,r_val) + print('symbolic d2f = ',dd_phi) + print('d2f == ',dd_phi.subs(alpha, alpha_val).subs(r,r_val)) d3d_phi = diff(phi, r, 3) - print 'symbolic d3f = ',d3d_phi - print 'd3f == ',d3d_phi.subs(alpha, alpha_val).subs(r,r_val) + print('symbolic d3f = ',d3d_phi) + print('d3f == ',d3d_phi.subs(alpha, alpha_val).subs(r,r_val)) CG_basis = namedtuple('CG_basis',['orbtype','nbasis','zeta','contraction_coeff']) @@ -118,7 +118,7 @@ def create_sym(ijk=[0,0,0]): norm = create_radial_gto_norm_symbolic() l_val = sum(ijk) norm_s = norm.subs({Symbol('i'):ijk[0], Symbol('j'):ijk[1],Symbol('k'):ijk[2], Symbol('L'):l_val}) - print 'norm_s',norm_s + print('norm_s',norm_s) norm = lambdify(Symbol('alpha'), norm_s) i = Symbol('i',integer=True) @@ -135,30 +135,30 @@ def eval_sym(cg_sym, norm, norm2, N_basis, c, alpha2, h_basis): cc = h_basis.contraction_coeff[i] cz = h_basis.zeta[i] cg_unroll = cg_unroll.subs(c[i+1],cc).subs(alpha2[i+1],cz).subs(norm2[i+1],norm(cz)) - print cc,cz,norm(cz),'normL',norm(1.0) + print(cc,cz,norm(cz),'normL',norm(1.0)) return cg_unroll def compute_from_sym(h_basis, ijk=[0,0,0]): cg_sym, norm, norm2, c, alpha2, N_basis = create_sym(ijk) - print 'norm',norm + print('norm',norm) cg = eval_sym(cg_sym, norm, norm2, N_basis, c, alpha2, h_basis) r = Symbol('r') x = Symbol('x') # setting x to 1.0 is important to compute just the radial part slist = {r:1.3, x:1.0} - print cg - print 'f = ',cg.subs(slist) + print(cg) + print('f = ',cg.subs(slist)) d_cg = diff(cg, r); - print 'df = ',d_cg.subs(slist) + print('df = ',d_cg.subs(slist)) dd_cg = diff(cg, r, 2); - print 'ddf = ',dd_cg.subs(slist) + print('ddf = ',dd_cg.subs(slist)) d3_cg = diff(cg, r, 3); - print 'd3f = ',d3_cg.subs(slist) + print('d3f = ',d3_cg.subs(slist)) # generated from read_order.py def get_ijk(): @@ -360,7 +360,7 @@ def run_template(fname_in, fname_out, bodies): if key in bodies: line = bodies[key] else: - print 'Error, template item not found, key:',key, ' line = ',line + print('Error, template item not found, key:',key, ' line = ',line) out += line with open(fname_out, 'w') as f: diff --git a/src/Numerics/tests/gen_ylm.py b/src/Numerics/tests/gen_ylm.py index bb4cacba17..3f8f0ee9d7 100644 --- a/src/Numerics/tests/gen_ylm.py +++ b/src/Numerics/tests/gen_ylm.py @@ -4,7 +4,7 @@ # Redirect output to ylm.inc ("python gen_ylm.py > ylm.inc") and adjust # the #ifdef in test_ylm.cpp -from sympy import mpmath +import mpmath import math def gen_spherical_harmonics(): @@ -59,7 +59,7 @@ def gen_spherical_harmonics(): """ fmt_values = ',\n '.join(["{ {%g, %g, %g}, %d, %d, %g, %g}"%(p[0],p[1],p[2],l,m,y.real,y.imag) for (p,l,m,y) in vals]) s = tmpl.format(N=len(vals), values=fmt_values) - print s + print(s) if __name__ == '__main__': gen_spherical_harmonics() diff --git a/src/Particle/ParticleSetPool.cpp b/src/Particle/ParticleSetPool.cpp index 86df3ecd6a..adcd243bae 100644 --- a/src/Particle/ParticleSetPool.cpp +++ b/src/Particle/ParticleSetPool.cpp @@ -101,6 +101,11 @@ bool ParticleSetPool::readSimulationCellXML(xmlNodePtr cur) return lattice_defined; } +void ParticleSetPool::createSimulationCellByLattice(const Lattice& lattice) +{ + simulation_cell_ = std::make_unique(lattice); +} + /** process an xml element * @param cur current xmlNodePtr * @return true, if successful. diff --git a/src/Particle/ParticleSetPool.h b/src/Particle/ParticleSetPool.h index 63f252a997..a1caad69da 100644 --- a/src/Particle/ParticleSetPool.h +++ b/src/Particle/ParticleSetPool.h @@ -53,6 +53,9 @@ class ParticleSetPool : public MPIObjectBase void output_particleset_info(Libxml2Document& doc, xmlNodePtr root); + ///return true, if the pool is empty + inline bool empty() const { return myPool.empty(); } + /** initialize the supercell shared by all the particle sets * * return value is never checked anywhere @@ -62,8 +65,8 @@ class ParticleSetPool : public MPIObjectBase */ bool readSimulationCellXML(xmlNodePtr cur); - ///return true, if the pool is empty - inline bool empty() const { return myPool.empty(); } + /// create simulation cell by a lattice. Used for unit tests. + void createSimulationCellByLattice(const Lattice& lattice); /** add a ParticleSet* to the pool with its ownership transferred * ParticleSet built outside the ParticleSetPool must be constructed with @@ -94,9 +97,6 @@ class ParticleSetPool : public MPIObjectBase /// get simulation cell const auto& getSimulationCell() const { return *simulation_cell_; } - /// set simulation cell - void setSimulationCell(const SimulationCell& simulation_cell) { *simulation_cell_ = simulation_cell; } - /** randomize a particleset particleset/@random='yes' && particleset@random_source exists */ void randomize(); @@ -106,7 +106,7 @@ class ParticleSetPool : public MPIObjectBase * * updated by * - readSimulationCellXML() parsing element - * - setSimulationCell() + * - createSimulationCellByLattice() */ std::unique_ptr simulation_cell_; /** List of ParticleSet owned diff --git a/src/Particle/SimulationCell.h b/src/Particle/SimulationCell.h index b1615dcf96..0a58582364 100644 --- a/src/Particle/SimulationCell.h +++ b/src/Particle/SimulationCell.h @@ -26,7 +26,7 @@ class SimulationCell public: using FullPrecReal = QMCTraits::FullPrecRealType; SimulationCell(); - SimulationCell(const Lattice& lattice); + explicit SimulationCell(const Lattice& lattice); const Lattice& getLattice() const { return lattice_; } const Lattice& getPrimLattice() const { return primitive_lattice_; } diff --git a/src/QMCDrivers/LMYEngineInterface/LMYE_QMCCostFunction.cpp b/src/QMCDrivers/LMYEngineInterface/LMYE_QMCCostFunction.cpp index b581ce517a..073924cfae 100644 --- a/src/QMCDrivers/LMYEngineInterface/LMYE_QMCCostFunction.cpp +++ b/src/QMCDrivers/LMYEngineInterface/LMYE_QMCCostFunction.cpp @@ -32,16 +32,16 @@ size_t QMCCostFunction::total_samples() /// \brief Computes the cost function using the LMYEngine /// /////////////////////////////////////////////////////////////////////////////////////////////////// -QMCCostFunction::Return_rt QMCCostFunction::LMYEngineCost_detail(cqmc::engine::LMYEngine* EngineObj) +QMCCostFunction::Return_rt QMCCostFunction::LMYEngineCost_detail(cqmc::engine::LMYEngine& EngineObj) { // get total number of samples const size_t m = this->total_samples(); // reset Engine object - EngineObj->reset(); + EngineObj.reset(); // turn off wavefunction update mode - EngineObj->turn_off_update(); + EngineObj.turn_off_update(); //for (int ip = 0, j = 0; ip < NumThreads; ip++) { #pragma omp parallel @@ -61,22 +61,22 @@ QMCCostFunction::Return_rt QMCCostFunction::LMYEngineCost_detail(cqmc::engine::L //lce_vec.at(j) = saved[ENERGY_NEW]; // take sample - EngineObj->take_sample(saved[ENERGY_NEW], 1.0, saved[REWEIGHT] / SumValue[SUM_WGT]); + EngineObj.take_sample(saved[ENERGY_NEW], 1.0, saved[REWEIGHT] / SumValue[SUM_WGT]); } } //} // finish taking sample - EngineObj->sample_finish(); + EngineObj.sample_finish(); // compute energy and target relevant quantities - EngineObj->energy_target_compute(); + EngineObj.energy_target_compute(); // prepare variables to hold the output of the engine call - double energy_avg = EngineObj->energy_mean(); - double energy_sdev = EngineObj->energy_sdev(); - double energy_serr = EngineObj->energy_statistical_err(); - double target_avg = EngineObj->target_value(); - double target_serr = EngineObj->target_statistical_err(); + double energy_avg = EngineObj.energy_mean(); + double energy_sdev = EngineObj.energy_sdev(); + double energy_serr = EngineObj.energy_statistical_err(); + double target_avg = EngineObj.target_value(); + double target_serr = EngineObj.target_statistical_err(); // prepare a stream to hold engine printout //std::stringstream engine_out; diff --git a/src/QMCDrivers/LMYEngineInterface/LMYE_QMCCostFunctionBatched.cpp b/src/QMCDrivers/LMYEngineInterface/LMYE_QMCCostFunctionBatched.cpp index 376446a735..46f3f7eec7 100644 --- a/src/QMCDrivers/LMYEngineInterface/LMYE_QMCCostFunctionBatched.cpp +++ b/src/QMCDrivers/LMYEngineInterface/LMYE_QMCCostFunctionBatched.cpp @@ -26,15 +26,15 @@ size_t QMCCostFunctionBatched::total_samples() { return samples_.getNumSamples() /// /////////////////////////////////////////////////////////////////////////////////////////////////// QMCCostFunctionBatched::Return_rt QMCCostFunctionBatched::LMYEngineCost_detail( - cqmc::engine::LMYEngine* EngineObj) + cqmc::engine::LMYEngine& EngineObj) { // get total number of samples const size_t m = this->total_samples(); // reset Engine object - EngineObj->reset(); + EngineObj.reset(); // turn off wavefunction update mode - EngineObj->turn_off_update(); + EngineObj.turn_off_update(); #pragma omp parallel { @@ -47,22 +47,22 @@ QMCCostFunctionBatched::Return_rt QMCCostFunctionBatched::LMYEngineCost_detail( const Return_rt* restrict saved = RecordsOnNode_[iw]; // take sample - EngineObj->take_sample(saved[ENERGY_NEW], 1.0, saved[REWEIGHT] / SumValue[SUM_WGT]); + EngineObj.take_sample(saved[ENERGY_NEW], 1.0, saved[REWEIGHT] / SumValue[SUM_WGT]); } } //} // finish taking sample - EngineObj->sample_finish(); + EngineObj.sample_finish(); // compute energy and target relevant quantities - EngineObj->energy_target_compute(); + EngineObj.energy_target_compute(); // prepare variables to hold the output of the engine call - double energy_avg = EngineObj->energy_mean(); - double energy_sdev = EngineObj->energy_sdev(); - double energy_serr = EngineObj->energy_statistical_err(); - double target_avg = EngineObj->target_value(); - double target_serr = EngineObj->target_statistical_err(); + double energy_avg = EngineObj.energy_mean(); + double energy_sdev = EngineObj.energy_sdev(); + double energy_serr = EngineObj.energy_statistical_err(); + double target_avg = EngineObj.target_value(); + double target_serr = EngineObj.target_statistical_err(); // return the cost function value (target function if we are targeting excited states and energy if we are doing groud state calculations) diff --git a/src/QMCDrivers/WFOpt/QMCCostFunction.cpp b/src/QMCDrivers/WFOpt/QMCCostFunction.cpp index 6104dc1e1c..265ee348ed 100644 --- a/src/QMCDrivers/WFOpt/QMCCostFunction.cpp +++ b/src/QMCDrivers/WFOpt/QMCCostFunction.cpp @@ -233,8 +233,8 @@ void QMCCostFunction::getConfigurations(const std::string& aroot) void QMCCostFunction::checkConfigurations(EngineHandle& handle) { const auto num_opt_vars = opt_vars.size(); - RealType et_tot = 0.0; - RealType e2_tot = 0.0; + RealType et_tot = 0.0; + RealType e2_tot = 0.0; #pragma omp parallel reduction(+ : et_tot, e2_tot) { int ip = omp_get_thread_num(); @@ -345,7 +345,7 @@ void QMCCostFunction::checkConfigurations(EngineHandle& handle) /** evaluate everything before optimization *In future, both the LM and descent engines should be children of some parent engine base class. * */ -void QMCCostFunction::engine_checkConfigurations(cqmc::engine::LMYEngine* EngineObj, +void QMCCostFunction::engine_checkConfigurations(cqmc::engine::LMYEngine& EngineObj, DescentEngine& descentEngineObj, const std::string& MinMethod) { @@ -429,7 +429,7 @@ void QMCCostFunction::engine_checkConfigurations(cqmc::engine::LMYEnginetake_sample(der_rat_samp, le_der_samp, le_der_samp, 1.0, saved[REWEIGHT]); + EngineObj.take_sample(der_rat_samp, le_der_samp, le_der_samp, 1.0, saved[REWEIGHT]); } else if (MinMethod == "descent") { @@ -478,7 +478,7 @@ void QMCCostFunction::engine_checkConfigurations(cqmc::engine::LMYEnginesample_finish(); + EngineObj.sample_finish(); else if (MinMethod == "descent") descentEngineObj.sample_finish(); #endif diff --git a/src/QMCDrivers/WFOpt/QMCCostFunction.h b/src/QMCDrivers/WFOpt/QMCCostFunction.h index fe188f278c..4d16b99711 100644 --- a/src/QMCDrivers/WFOpt/QMCCostFunction.h +++ b/src/QMCDrivers/WFOpt/QMCCostFunction.h @@ -40,7 +40,7 @@ class QMCCostFunction : public QMCCostFunctionBase, public CloneManager void getConfigurations(const std::string& aroot) override; void checkConfigurations(EngineHandle& handle) override; #ifdef HAVE_LMY_ENGINE - void engine_checkConfigurations(cqmc::engine::LMYEngine* EngineObj, + void engine_checkConfigurations(cqmc::engine::LMYEngine& EngineObj, DescentEngine& descentEngineObj, const std::string& MinMethod) override; #endif @@ -64,7 +64,7 @@ class QMCCostFunction : public QMCCostFunctionBase, public CloneManager #ifdef HAVE_LMY_ENGINE size_t total_samples(); - Return_rt LMYEngineCost_detail(cqmc::engine::LMYEngine* EngineObj) override; + Return_rt LMYEngineCost_detail(cqmc::engine::LMYEngine& EngineObj) override; #endif NewTimer& fill_timer_; diff --git a/src/QMCDrivers/WFOpt/QMCCostFunctionBase.cpp b/src/QMCDrivers/WFOpt/QMCCostFunctionBase.cpp index 0217a4ef6e..b5c0a24238 100644 --- a/src/QMCDrivers/WFOpt/QMCCostFunctionBase.cpp +++ b/src/QMCDrivers/WFOpt/QMCCostFunctionBase.cpp @@ -131,19 +131,13 @@ QMCCostFunctionBase::Return_rt QMCCostFunctionBase::Cost(bool needGrad) } QMCCostFunctionBase::Return_rt QMCCostFunctionBase::fillHamVec(std::vector& ham) -{ - throw std::runtime_error("Need to implement fillHamVec"); -} +{ throw std::runtime_error("Need to implement fillHamVec"); } void QMCCostFunctionBase::calcOvlParmVec(const std::vector& param, std::vector& ovlParmVec) -{ - throw std::runtime_error("Need to implement calcOvlParmVec"); -} +{ throw std::runtime_error("Need to implement calcOvlParmVec"); } void QMCCostFunctionBase::checkConfigurationsSR(EngineHandle& handle) -{ - throw std::runtime_error("Need to implement checkConfigurationsSR"); -} +{ throw std::runtime_error("Need to implement checkConfigurationsSR"); } void QMCCostFunctionBase::printEstimates() { @@ -393,12 +387,11 @@ bool QMCCostFunctionBase::put(xmlNodePtr q) InitVariables = opt_vars; //get the indices Psi.checkOutVariables(opt_vars); - + if (const auto num_opt_vars = opt_vars.size(); num_opt_vars == 0) throw UniformCommunicateError("QMCCostFunctionBase::put No valid optimizable variables are found."); else - app_log() << " In total " << num_opt_vars << " parameters being optimized after applying constraints." - << std::endl; + app_log() << " In total " << num_opt_vars << " parameters being optimized after applying constraints." << std::endl; // app_log() << " " << std::endl; // opt_vars.print(app_log()); // app_log() << "" << std::endl; @@ -1025,7 +1018,7 @@ void QMCCostFunctionBase::resetOptimizableObjects(TrialWaveFunction& psi, const /////////////////////////////////////////////////////////////////////////////////////////////////// #ifdef HAVE_LMY_ENGINE QMCCostFunctionBase::Return_rt QMCCostFunctionBase::LMYEngineCost(const bool needDeriv, - cqmc::engine::LMYEngine* EngineObj) + cqmc::engine::LMYEngine& EngineObj) { // prepare local energies, weights, and possibly derivative vectors, and compute standard cost const Return_rt standardCost = this->Cost(needDeriv); diff --git a/src/QMCDrivers/WFOpt/QMCCostFunctionBase.h b/src/QMCDrivers/WFOpt/QMCCostFunctionBase.h index 908462a416..d06502db45 100644 --- a/src/QMCDrivers/WFOpt/QMCCostFunctionBase.h +++ b/src/QMCDrivers/WFOpt/QMCCostFunctionBase.h @@ -147,7 +147,7 @@ class QMCCostFunctionBase : public MPIObjectBase virtual void calcOvlParmVec(const std::vector& param, std::vector& ovlParmVec); #ifdef HAVE_LMY_ENGINE - Return_rt LMYEngineCost(const bool needDeriv, cqmc::engine::LMYEngine* EngineObj); + Return_rt LMYEngineCost(const bool needDeriv, cqmc::engine::LMYEngine& EngineObj); #endif virtual void getConfigurations(const std::string& aroot) = 0; @@ -158,7 +158,7 @@ class QMCCostFunctionBase : public MPIObjectBase //for SR method virtual void checkConfigurationsSR(EngineHandle& handle); #ifdef HAVE_LMY_ENGINE - virtual void engine_checkConfigurations(cqmc::engine::LMYEngine* EngineObj, + virtual void engine_checkConfigurations(cqmc::engine::LMYEngine& EngineObj, DescentEngine& descentEngineObj, const std::string& MinMethod) = 0; @@ -314,7 +314,7 @@ class QMCCostFunctionBase : public MPIObjectBase void resetOptimizableObjects(TrialWaveFunction& psi, const OptVariables& opt_variables) const; #ifdef HAVE_LMY_ENGINE - virtual Return_rt LMYEngineCost_detail(cqmc::engine::LMYEngine* EngineObj) + virtual Return_rt LMYEngineCost_detail(cqmc::engine::LMYEngine& EngineObj) { APP_ABORT("NOT IMPLEMENTED"); return 0; diff --git a/src/QMCDrivers/WFOpt/QMCCostFunctionBatched.cpp b/src/QMCDrivers/WFOpt/QMCCostFunctionBatched.cpp index f2742e03f6..8025703ad9 100644 --- a/src/QMCDrivers/WFOpt/QMCCostFunctionBatched.cpp +++ b/src/QMCDrivers/WFOpt/QMCCostFunctionBatched.cpp @@ -40,9 +40,7 @@ QMCCostFunctionBatched::QMCCostFunctionBatched(ParticleSet& w, corr_sampling_timer_(createGlobalTimer("QMCCostFunctionBatched::correlatedSampling", timer_level_medium)), fill_timer_(createGlobalTimer("QMCCostFunctionBatched::fillOverlapHamiltonianMatrices", timer_level_medium)) -{ - app_log() << " Using QMCCostFunctionBatched::QMCCostFunctionBatched" << std::endl; -} +{ app_log() << " Using QMCCostFunctionBatched::QMCCostFunctionBatched" << std::endl; } /** Clean up the vector */ @@ -628,12 +626,10 @@ void QMCCostFunctionBatched::checkConfigurationsSR(EngineHandle& handle) } #ifdef HAVE_LMY_ENGINE -void QMCCostFunctionBatched::engine_checkConfigurations(cqmc::engine::LMYEngine* EngineObj, +void QMCCostFunctionBatched::engine_checkConfigurations(cqmc::engine::LMYEngine& EngineObj, DescentEngine& descentEngineObj, const std::string& MinMethod) -{ - APP_ABORT("LMYEngine not implemented with batch optimization"); -} +{ APP_ABORT("LMYEngine not implemented with batch optimization"); } #endif @@ -794,7 +790,7 @@ QMCCostFunctionBatched::EffectiveWeight QMCCostFunctionBatched::correlatedSampli vmc_or_dmc, needGrad); // Sum weights over crowds - Return_rt wgt_tot = 0.0; + Return_rt wgt_tot = 0.0; Return_rt inv_n_samples = 1.0 / (samples_.getNumSamples() * myComm->size()); for (int i = 0; i < opt_eval.size(); i++) wgt_tot += opt_eval[i]->get_wgt() * inv_n_samples; diff --git a/src/QMCDrivers/WFOpt/QMCCostFunctionBatched.h b/src/QMCDrivers/WFOpt/QMCCostFunctionBatched.h index adabd3d4a1..b99d1fa170 100644 --- a/src/QMCDrivers/WFOpt/QMCCostFunctionBatched.h +++ b/src/QMCDrivers/WFOpt/QMCCostFunctionBatched.h @@ -54,7 +54,7 @@ class QMCCostFunctionBatched : public QMCCostFunctionBase, public QMCTraits void checkConfigurations(EngineHandle& handle) override; void checkConfigurationsSR(EngineHandle& handle) override; #ifdef HAVE_LMY_ENGINE - void engine_checkConfigurations(cqmc::engine::LMYEngine* EngineObj, + void engine_checkConfigurations(cqmc::engine::LMYEngine& EngineObj, DescentEngine& descentEngineObj, const std::string& MinMethod) override; #endif @@ -94,7 +94,7 @@ class QMCCostFunctionBatched : public QMCCostFunctionBase, public QMCTraits #ifdef HAVE_LMY_ENGINE size_t total_samples(); - Return_rt LMYEngineCost_detail(cqmc::engine::LMYEngine* EngineObj) override; + Return_rt LMYEngineCost_detail(cqmc::engine::LMYEngine& EngineObj) override; #endif friend testing::LinearMethodTestSupport; diff --git a/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimize.cpp b/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimize.cpp index da6b1f8d77..8275bcf678 100644 --- a/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimize.cpp +++ b/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimize.cpp @@ -125,67 +125,9 @@ QMCFixedSampleLinearOptimize::QMCFixedSampleLinearOptimize(const ProjectData& pr m_param.add(cost_increase_tol, "cost_increase_tol"); m_param.add(target_shift_i, "target_shift_i"); m_param.add(param_tol, "alloweddifference"); - -#ifdef HAVE_LMY_ENGINE - //app_log() << "construct QMCFixedSampleLinearOptimize" << endl; - std::vector shift_scales(3, 1.0); - EngineObj = new cqmc::engine::LMYEngine(&vdeps, - false, // exact sampling - true, // ground state? - false, // variance correct, - true, - true, // print matrices, - true, // build matrices - false, // spam - false, // use var deps? - true, // chase lowest - false, // chase closest - false, // eom - false, - false, // eom related - false, // eom related - false, // use block? - 120000, // number of samples - 0, // number of parameters - 60, // max krylov iter - 0, // max spam inner iter - 1, // spam appro degree - 0, // eom related - 0, // eom related - 0, // eom related - 0.0, // omega - 0.0, // var weight - 1.0e-6, // convergence threshold - 0.99, // minimum S singular val - 0.0, 0.0, - 10.0, // max change allowed - 1.00, // identity shift - 1.00, // overlap shift - 0.3, // max parameter change - shift_scales, app_log()); -#endif - - - // stale parameters - // m_param.add(eigCG,"eigcg"); - // m_param.add(TotalCGSteps,"cgsteps"); - // m_param.add(w_beta,"beta"); - // quadstep=-1.0; - // m_param.add(quadstep,"quadstep"); - // m_param.add(stepsize,"stepsize"); - // m_param.add(exp1,"exp1"); - // m_param.add(StabilizerMethod,"StabilizerMethod"); - // m_param.add(LambdaMax,"LambdaMax"); - //Set parameters for line minimization: } -/** Clean up the vector */ -QMCFixedSampleLinearOptimize::~QMCFixedSampleLinearOptimize() -{ -#ifdef HAVE_LMY_ENGINE - delete EngineObj; -#endif -} +QMCFixedSampleLinearOptimize::~QMCFixedSampleLinearOptimize() = default; QMCFixedSampleLinearOptimize::RealType QMCFixedSampleLinearOptimize::Func(RealType dl) { @@ -572,20 +514,57 @@ bool QMCFixedSampleLinearOptimize::processOptXML(xmlNodePtr opt_xml, const std:: previous_optimizer_type_ = current_optimizer_type_; current_optimizer_type_ = OptimizerNames.at(MinMethod); +#ifdef HAVE_LMY_ENGINE + if (!EngineObj && + (current_optimizer_type_ == OptimizerType::DESCENT || current_optimizer_type_ == OptimizerType::ADAPTIVE)) + { + //app_log() << "construct QMCFixedSampleLinearOptimize" << endl; + std::vector shift_scales(3, 1.0); + EngineObj = std::make_unique>(&vdeps, + false, // exact sampling + true, // ground state? + false, // variance correct, + true, + true, // print matrices, + true, // build matrices + false, // spam + false, // use var deps? + true, // chase lowest + false, // chase closest + false, // eom + false, + false, // eom related + false, // eom related + false, // use block? + 120000, // number of samples + 0, // number of parameters + 60, // max krylov iter + 0, // max spam inner iter + 1, // spam appro degree + 0, // eom related + 0, // eom related + 0, // eom related + 0.0, // omega + 0.0, // var weight + 1.0e-6, // convergence threshold + 0.99, // minimum S singular val + 0.0, 0.0, + 10.0, // max change allowed + 1.00, // identity shift + 1.00, // overlap shift + 0.3, // max parameter change + shift_scales, app_log()); + } +#endif + if (current_optimizer_type_ == OptimizerType::DESCENT) { if (!descentEngineObj) - { descentEngineObj = std::make_unique(myComm, opt_xml); - } - else - { descentEngineObj->processXML(opt_xml); - } } - // sanity check if (targetExcited && current_optimizer_type_ != OptimizerType::ADAPTIVE && current_optimizer_type_ != OptimizerType::DESCENT) @@ -1002,7 +981,7 @@ bool QMCFixedSampleLinearOptimize::adaptive_three_shift_run() EngineObj->reset(); // generate samples and compute weights, local energies, and derivative vectors - engine_start(EngineObj, *descentEngineObj, MinMethod); + engine_start(*EngineObj, *descentEngineObj, MinMethod); // get dimension of the linear method matrices size_t N = numParams + 1; @@ -1039,7 +1018,7 @@ bool QMCFixedSampleLinearOptimize::adaptive_three_shift_run() finish(); // take sample - engine_start(EngineObj, *descentEngineObj, MinMethod); + engine_start(*EngineObj, *descentEngineObj, MinMethod); } // say what we are doing @@ -1135,7 +1114,7 @@ bool QMCFixedSampleLinearOptimize::adaptive_three_shift_run() for (int i = 0; i < numParams; i++) optTarget->Params(i) = currParams.at(i) - parameterDirections.at(central_index).at(i + 1); optTarget->IsValid = true; - const RealType initCost = optTarget->LMYEngineCost(false, EngineObj); + const RealType initCost = optTarget->LMYEngineCost(false, *EngineObj); // compute the update directions for the smaller and larger shifts relative to that of the middle shift for (int i = 0; i < numParams; i++) @@ -1156,7 +1135,7 @@ bool QMCFixedSampleLinearOptimize::adaptive_three_shift_run() for (int i = 0; i < numParams; i++) optTarget->Params(i) = currParams.at(i) + (k == central_index ? 0.0 : parameterDirections.at(k).at(i + 1)); optTarget->IsValid = true; - costValues.at(k) = optTarget->LMYEngineCost(false, EngineObj); + costValues.at(k) = optTarget->LMYEngineCost(false, *EngineObj); good_update.at(k) = (good_update.at(k) && std::abs((initCost - costValues.at(k)) / initCost) < max_relative_cost_change); if (!good_update.at(k)) @@ -1417,8 +1396,7 @@ bool QMCFixedSampleLinearOptimize::descent_run() optTarget->setneedGrads(true); //Compute Lagrangian derivatives needed for parameter updates with engine_checkConfigurations, which is called inside engine_start - engine_start(EngineObj, *descentEngineObj, MinMethod); - + engine_start(*EngineObj, *descentEngineObj, MinMethod); int descent_num = descentEngineObj->getDescentNum(); @@ -1540,7 +1518,7 @@ void QMCFixedSampleLinearOptimize::start() } #ifdef HAVE_LMY_ENGINE -void QMCFixedSampleLinearOptimize::engine_start(cqmc::engine::LMYEngine* EngineObj, +void QMCFixedSampleLinearOptimize::engine_start(cqmc::engine::LMYEngine& EngineObj, DescentEngine& descentEngineObj, std::string MinMethod) { diff --git a/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimize.h b/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimize.h index 919e231585..7ab491745e 100644 --- a/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimize.h +++ b/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimize.h @@ -109,7 +109,7 @@ class QMCFixedSampleLinearOptimize : public QMCDriver, public LinearMethod, priv #ifdef HAVE_LMY_ENGINE formic::VarDeps vdeps; - cqmc::engine::LMYEngine* EngineObj; + std::unique_ptr> EngineObj; #endif //engine for running various gradient descent based algorithms for optimization @@ -233,7 +233,7 @@ class QMCFixedSampleLinearOptimize : public QMCDriver, public LinearMethod, priv ///common operation to start optimization, used by the derived classes void start(); #ifdef HAVE_LMY_ENGINE - void engine_start(cqmc::engine::LMYEngine* EngineObj, + void engine_start(cqmc::engine::LMYEngine& EngineObj, DescentEngine& descentEngineObj, std::string MinMethod); #endif diff --git a/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimizeBatched.cpp b/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimizeBatched.cpp index 4775c906e3..19db95b109 100644 --- a/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimizeBatched.cpp +++ b/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimizeBatched.cpp @@ -135,55 +135,10 @@ QMCFixedSampleLinearOptimizeBatched::QMCFixedSampleLinearOptimizeBatched( m_param.add(options_LMY_.ratio_threshold, "deriv_threshold"); m_param.add(options_LMY_.store_samples, "store_samples"); m_param.add(options_LMY_.filter_info, "filter_info"); - - -#ifdef HAVE_LMY_ENGINE - //app_log() << "construct QMCFixedSampleLinearOptimizeBatched" << endl; - std::vector shift_scales(3, 1.0); - EngineObj = new cqmc::engine::LMYEngine(&vdeps, - false, // exact sampling - true, // ground state? - false, // variance correct, - true, - true, // print matrices, - true, // build matrices - false, // spam - false, // use var deps? - true, // chase lowest - false, // chase closest - false, // eom - false, - false, // eom related - false, // eom related - false, // use block? - 120000, // number of samples - 0, // number of parameters - 60, // max krylov iter - 0, // max spam inner iter - 1, // spam appro degree - 0, // eom related - 0, // eom related - 0, // eom related - 0.0, // omega - 0.0, // var weight - 1.0e-6, // convergence threshold - 0.99, // minimum S singular val - 0.0, 0.0, - 10.0, // max change allowed - 1.00, // identity shift - 1.00, // overlap shift - 0.3, // max parameter change - shift_scales, app_log()); -#endif } /** Clean up the vector */ -QMCFixedSampleLinearOptimizeBatched::~QMCFixedSampleLinearOptimizeBatched() -{ -#ifdef HAVE_LMY_ENGINE - delete EngineObj; -#endif -} +QMCFixedSampleLinearOptimizeBatched::~QMCFixedSampleLinearOptimizeBatched() = default; QMCFixedSampleLinearOptimizeBatched::RealType QMCFixedSampleLinearOptimizeBatched::costFunc(RealType dl) { @@ -222,7 +177,7 @@ void QMCFixedSampleLinearOptimizeBatched::start() } #ifdef HAVE_LMY_ENGINE -void QMCFixedSampleLinearOptimizeBatched::engine_start(cqmc::engine::LMYEngine* EngineObj, +void QMCFixedSampleLinearOptimizeBatched::engine_start(cqmc::engine::LMYEngine& EngineObj, DescentEngine& descentEngineObj, std::string MinMethod) { @@ -232,7 +187,7 @@ void QMCFixedSampleLinearOptimizeBatched::engine_start(cqmc::engine::LMYEngine(descentEngineObj); else if (MinMethod == "adaptive") - handle = std::make_unique(*EngineObj); + handle = std::make_unique(EngineObj); else handle = std::make_unique(); @@ -673,6 +628,50 @@ bool QMCFixedSampleLinearOptimizeBatched::processOptXML(xmlNodePtr opt_xml, options_LMY_.previous_optimizer_type = options_LMY_.current_optimizer_type; options_LMY_.current_optimizer_type = OptimizerNames.at(MinMethod); +#ifdef HAVE_LMY_ENGINE + if (!EngineObj && + (options_LMY_.current_optimizer_type == OptimizerType::DESCENT || + options_LMY_.current_optimizer_type == OptimizerType::ADAPTIVE)) + { + // app_log() << "construct QMCFixedSampleLinearOptimizeBatched" << endl; + std::vector shift_scales(3, 1.0); + EngineObj = std::make_unique>(&vdeps, + false, // exact sampling + true, // ground state? + false, // variance correct, + true, + true, // print matrices, + true, // build matrices + false, // spam + false, // use var deps? + true, // chase lowest + false, // chase closest + false, // eom + false, + false, // eom related + false, // eom related + false, // use block? + 120000, // number of samples + 0, // number of parameters + 60, // max krylov iter + 0, // max spam inner iter + 1, // spam appro degree + 0, // eom related + 0, // eom related + 0, // eom related + 0.0, // omega + 0.0, // var weight + 1.0e-6, // convergence threshold + 0.99, // minimum S singular val + 0.0, 0.0, + 10.0, // max change allowed + 1.00, // identity shift + 1.00, // overlap shift + 0.3, // max parameter change + shift_scales, app_log()); + } +#endif + if (options_LMY_.current_optimizer_type == OptimizerType::DESCENT && !descentEngineObj) descentEngineObj = std::make_unique(myComm, opt_xml); @@ -1177,7 +1176,7 @@ bool QMCFixedSampleLinearOptimizeBatched::adaptive_three_shift_run() EngineObj->reset(); // generate samples and compute weights, local energies, and derivative vectors - engine_start(EngineObj, *descentEngineObj, MinMethod); + engine_start(*EngineObj, *descentEngineObj, MinMethod); int new_num = 0; @@ -1321,7 +1320,7 @@ bool QMCFixedSampleLinearOptimizeBatched::adaptive_three_shift_run() finish(); // take sample - engine_start(EngineObj, *descentEngineObj, MinMethod); + engine_start(*EngineObj, *descentEngineObj, MinMethod); } else { @@ -1332,12 +1331,12 @@ bool QMCFixedSampleLinearOptimizeBatched::adaptive_three_shift_run() if (options_LMY_.filter_param) { - engine_start(EngineObj, *descentEngineObj, MinMethod); + engine_start(*EngineObj, *descentEngineObj, MinMethod); EngineObj->buildMatricesFromDerivatives(); } else { - engine_start(EngineObj, *descentEngineObj, MinMethod); + engine_start(*EngineObj, *descentEngineObj, MinMethod); app_log() << "Should be building matrices from stored samples" << std::endl; EngineObj->buildMatricesFromDerivatives(); } @@ -1478,7 +1477,7 @@ bool QMCFixedSampleLinearOptimizeBatched::adaptive_three_shift_run() for (int i = 0; i < numParams; i++) optTarget->Params(i) = currParams.at(i) - parameterDirections.at(central_index).at(i + 1); optTarget->IsValid = true; - const RealType initCost = optTarget->LMYEngineCost(false, EngineObj); + const RealType initCost = optTarget->LMYEngineCost(false, *EngineObj); // compute the update directions for the smaller and larger shifts relative to that of the middle shift for (int i = 0; i < numParams; i++) @@ -1499,7 +1498,7 @@ bool QMCFixedSampleLinearOptimizeBatched::adaptive_three_shift_run() for (int i = 0; i < numParams; i++) optTarget->Params(i) = currParams.at(i) + (k == central_index ? 0.0 : parameterDirections.at(k).at(i + 1)); optTarget->IsValid = true; - costValues.at(k) = optTarget->LMYEngineCost(false, EngineObj); + costValues.at(k) = optTarget->LMYEngineCost(false, *EngineObj); good_update.at(k) = (good_update.at(k) && std::abs((initCost - costValues.at(k)) / initCost) < options_LMY_.max_relative_cost_change); if (!good_update.at(k)) @@ -1943,7 +1942,7 @@ bool QMCFixedSampleLinearOptimizeBatched::stochastic_reconfiguration_conjugate_g bool QMCFixedSampleLinearOptimizeBatched::descent_run() { //Compute Lagrangian derivatives needed for parameter updates with engine_checkConfigurations, which is called inside engine_start - engine_start(EngineObj, *descentEngineObj, MinMethod); + engine_start(*EngineObj, *descentEngineObj, MinMethod); int descent_num = descentEngineObj->getDescentNum(); diff --git a/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimizeBatched.h b/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimizeBatched.h index fa99597ea8..ebf1f3f806 100644 --- a/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimizeBatched.h +++ b/src/QMCDrivers/WFOpt/QMCFixedSampleLinearOptimizeBatched.h @@ -81,7 +81,7 @@ class QMCFixedSampleLinearOptimizeBatched : public QMCDriverNew, LinearMethod #ifdef HAVE_LMY_ENGINE using ValueType = QMCTraits::ValueType; - void engine_start(cqmc::engine::LMYEngine* EngineObj, + void engine_start(cqmc::engine::LMYEngine& EngineObj, DescentEngine& descentEngineObj, std::string MinMethod); #endif @@ -144,7 +144,7 @@ class QMCFixedSampleLinearOptimizeBatched : public QMCDriverNew, LinearMethod #ifdef HAVE_LMY_ENGINE formic::VarDeps vdeps; - cqmc::engine::LMYEngine* EngineObj; + std::unique_ptr> EngineObj; #endif //engine for running various gradient descent based algorithms for optimization diff --git a/src/QMCDrivers/tests/CMakeLists.txt b/src/QMCDrivers/tests/CMakeLists.txt index f8251e5031..64572479e6 100644 --- a/src/QMCDrivers/tests/CMakeLists.txt +++ b/src/QMCDrivers/tests/CMakeLists.txt @@ -122,6 +122,8 @@ if(HAVE_MPI) qmcwfs qmcparticle qmcwfs_omptarget + spline2 + spline2_omptarget qmcparticle_omptarget qmcutil platform_omptarget_LA) diff --git a/src/QMCDrivers/tests/diffuse.py b/src/QMCDrivers/tests/diffuse.py index f3b730258e..382b8aaa2f 100644 --- a/src/QMCDrivers/tests/diffuse.py +++ b/src/QMCDrivers/tests/diffuse.py @@ -41,16 +41,16 @@ def drift_diffuse_func(r,F_i,chi,dt): scaled_chi_vals = chi_vals * math.sqrt(tau) -print 'One step' +print('One step') for r_val, chi_val in zip(R, scaled_chi_vals): rp_val = drift_diffuse_func(r_val, np.zeros(3), chi_val, tau) - print ['%.15g'%v for v in rp_val] + print(['%.15g'%v for v in rp_val]) # In test_vmc_omp, there are two steps taken - one for the initial 'randomize' step, # and one for for the actual VMC step. -print 'Two steps' +print('Two steps') for r_val, chi_val in zip(R, scaled_chi_vals): rp_val = drift_diffuse_func(r_val, np.zeros(3), chi_val, tau) rp2_val = drift_diffuse_func(rp_val, np.zeros(3), chi_val, tau) - print ['%.15g'%v for v in rp2_val] + print(['%.15g'%v for v in rp2_val]) diff --git a/src/QMCHamiltonians/CoulombPBCAA.cpp b/src/QMCHamiltonians/CoulombPBCAA.cpp index 1c0dc8d951..3b340fa2d3 100644 --- a/src/QMCHamiltonians/CoulombPBCAA.cpp +++ b/src/QMCHamiltonians/CoulombPBCAA.cpp @@ -158,7 +158,8 @@ void CoulombPBCAA::updateSource(ParticleSet& s) eL = evalLR(s); eS = evalSR(s); } - new_value_ = value_ = eL + eS + myConst; + value_ = eL + eS + myConst; + new_value_ = value_; } #if !defined(REMOVE_TRACEMANAGER) @@ -186,6 +187,9 @@ void CoulombPBCAA::deleteParticleQuantities() void CoulombPBCAA::informOfPerParticleListener() { // turnOnParticleSK is written so it can be called again and again. + if (use_offload_) + throw UniformCommunicateError( + "CoulombPBCAA cannot support omptarget and per particle reporting, set CoulombPBCAA and ParticleSet A to no!"); Ps.turnOnPerParticleSK(); OperatorBase::informOfPerParticleListener(); } @@ -239,42 +243,27 @@ void CoulombPBCAA::mw_evaluatePerParticle(const RefVectorWithLeader(); auto& p_leader = p_list.getLeader(); assert(this == &o_list.getLeader()); - auto num_centers = (is_active ? p_leader.getTotalNum() : Ps.getTotalNum()); + // This may break ion ion for listeners + + auto num_centers = (o_leader.is_active ? p_leader.getTotalNum() : Ps.getTotalNum()); + auto name(o_leader.getName()); Vector& v_sample = o_leader.mw_res_handle_.getResource().v_sample; const auto& pp_consts = o_leader.mw_res_handle_.getResource().pp_consts; auto num_species = p_leader.getSpeciesSet().getTotalNum(); v_sample.resize(num_centers); - auto current_value = o_leader.getValue(); + // This lambda is mostly about getting a handle on what is being // touched by the per particle evaluation. // v_sample is updated as a side effect - auto evaluate_walker = [num_species, num_centers, name, &v_sample, &pp_consts](const CoulombPBCAA& cpbcaa, - const ParticleSet& pset) -> RealType { + auto evaluate_walker = [num_species, num_centers, name, &v_sample, + &pp_consts](const int iw, const CoulombPBCAA& cpbcaa, const ParticleSet& pset, + Matrix& pp_sr_values) -> RealType { mRealType Vsr = 0.0; mRealType Vlr = 0.0; mRealType Vc = cpbcaa.myConst; - v_sample = 0.0; //.begin(), v_sample.end(), 0.0); - { - //SR - const auto& d_aa(pset.getDistTableAA(cpbcaa.d_aa_ID)); - RealType z; - for (int ipart = 1; ipart < num_centers; ipart++) - { - z = .5 * cpbcaa.Zat[ipart]; - const auto& dist = d_aa.getDistRow(ipart); - for (int jpart = 0; jpart < ipart; ++jpart) - { - RealType pairpot = z * cpbcaa.Zat[jpart] * cpbcaa.rVs->splint(dist[jpart]) / dist[jpart]; - v_sample[ipart] += pairpot; - v_sample[jpart] += pairpot; - Vsr += pairpot; - } - } - Vsr *= 2.0; - } + v_sample.zero(); { - //LR const StructFact& PtclRhoK(pset.getSK()); if (PtclRhoK.SuperCellEnum == SUPERCELL_SLAB) { @@ -288,6 +277,10 @@ void CoulombPBCAA::mw_evaluatePerParticle(const RefVectorWithLeader TraceManager::trace_tol) - { - app_log() << "accumtest: CoulombPBCAA::evaluate()" << std::endl; - app_log() << "accumtest: tot:" << Vnow << std::endl; - app_log() << "accumtest: sum:" << Vsum << std::endl; - throw std::runtime_error("Trace check failed"); - } - if (std::abs(Vcsum - Vcnow) > TraceManager::trace_tol) - { - app_log() << "accumtest: CoulombPBCAA::evalConsts()" << std::endl; - app_log() << "accumtest: tot:" << Vcnow << std::endl; - app_log() << "accumtest: sum:" << Vcsum << std::endl; - throw std::runtime_error("Trace check failed"); - } -#endif + // Legacy here assigns value to this walker coulombPBCAA return value; }; + Matrix pp_sr_values; + if (o_leader.is_active) + { + if (use_offload_) + pp_sr_values = mw_evalSRPerParticle_offload(o_list, p_list); + else + pp_sr_values = mw_evalSRPerParticle(o_list, p_list); - if (is_active) for (int iw = 0; iw < o_list.size(); iw++) { auto& coulomb_aa = o_list.getCastedElement(iw); - coulomb_aa.value_ = evaluate_walker(coulomb_aa, p_list[iw]); + coulomb_aa.value_ = evaluate_walker(iw, coulomb_aa, p_list[iw], pp_sr_values); for (const ListenerVector& listener : listeners) listener.report(iw, name, v_sample); } + } else { auto& o_leader = o_list.getCastedLeader(); assert(!o_leader.is_active); + for (auto& samp : v_sample) samp = 0.5 * o_leader.value_; //these static parts of the QMCHamiltonian don't change we just //copy them every time and send them to the listeners to preserve //a common design between per particle hamiltonian energy values for (int iw = 0; iw < o_list.size(); iw++) + { + auto& coulomb_aa = o_list.getCastedElement(iw); + coulomb_aa.value_ = o_leader.value_; for (const ListenerVector& listener : listeners_ions) listener.report(iw, name, v_sample); + } } } @@ -722,6 +707,7 @@ std::vector CoulombPBCAA::mw_evalSR_offload(const RefVec std::fill_n(values_offload.data(), nw, 0); auto value_ptr = values_offload.data(); values_offload.updateTo(); + for (size_t ichunk = 0; ichunk < num_chunks; ichunk++) { const size_t first = ichunk * chunk_size; @@ -762,6 +748,51 @@ std::vector CoulombPBCAA::mw_evalSR_offload(const RefVec return values; } +Matrix CoulombPBCAA::mw_evalSRPerParticle_offload( + const RefVectorWithLeader& o_list, + const RefVectorWithLeader& p_list) +{ + throw std::runtime_error( + "CoulombPBCAA_offload and estimators requiring per particle energies are not currently supported!"); + + return {}; +} + +Matrix CoulombPBCAA::mw_evalSRPerParticle(const RefVectorWithLeader& o_list, + const RefVectorWithLeader& p_list) +{ + auto& o_leader = o_list.getCastedLeader(); + auto& p_leader = p_list.getLeader(); + const size_t total_num = p_leader.getTotalNum(); + const int num_walkers = o_list.size(); + Matrix pp_sr_values(total_num, num_walkers); + + auto num_centers = p_leader.getTotalNum(); + + for (int iw = 0; iw < num_walkers; ++iw) + { + ParticleSet& pset = p_list[iw]; + const auto& d_aa(pset.getDistTableAA(o_leader.d_aa_ID)); + RealType z; + + for (int ipart = 0; ipart < num_centers; ipart++) + { + z = 0.5 * o_leader.Zat[ipart]; + const auto& dist_row = d_aa.getDistRow(ipart); + for (int jpart = 0; jpart < ipart; ++jpart) + { + if (ipart == jpart) + continue; + const auto& distance = dist_row[jpart]; + RealType pairpot = z * o_leader.Zat[jpart] * o_leader.rVs->splint(distance) / distance; + pp_sr_values(ipart, iw) += pairpot; + pp_sr_values(jpart, iw) += pairpot; + } + } + } + return pp_sr_values; +} + CoulombPBCAA::Return_t CoulombPBCAA::evalLR(const ParticleSet& P) const { ScopedTimer local_timer(evalLR_timer_); @@ -854,5 +885,8 @@ void CoulombPBCAA::releaseResource(ResourceCollection& collection, collection.takebackResource(o_leader.mw_res_handle_); } -std::unique_ptr CoulombPBCAA::makeClone(ParticleSet& qp) const { return std::make_unique(*this); } +std::unique_ptr CoulombPBCAA::makeClone(ParticleSet& qp) const +{ + return std::make_unique(*this); +} } // namespace qmcplusplus diff --git a/src/QMCHamiltonians/CoulombPBCAA.h b/src/QMCHamiltonians/CoulombPBCAA.h index 19ea69133b..f86a9c0908 100644 --- a/src/QMCHamiltonians/CoulombPBCAA.h +++ b/src/QMCHamiltonians/CoulombPBCAA.h @@ -242,6 +242,16 @@ struct CoulombPBCAA : public OperatorDependsOnlyOnParticleSet, public ForceBase * \param[out] pp_consts constant values for the particles self interaction */ void evalPerParticleConsts(Vector& pp_consts) const; + + /** Currently mostly copy paste of mw_evalSR_offload + * but would require branching in OFFLOAD section + * does additional data movement + */ + static Matrix mw_evalSRPerParticle_offload(const RefVectorWithLeader& o_list, + const RefVectorWithLeader& p_list); + + static Matrix mw_evalSRPerParticle(const RefVectorWithLeader& o_list, + const RefVectorWithLeader& p_list); }; } // namespace qmcplusplus diff --git a/src/QMCHamiltonians/CoulombPotentialFactory.cpp b/src/QMCHamiltonians/CoulombPotentialFactory.cpp index 0dbf32fd35..068a1bfeb2 100644 --- a/src/QMCHamiltonians/CoulombPotentialFactory.cpp +++ b/src/QMCHamiltonians/CoulombPotentialFactory.cpp @@ -125,7 +125,15 @@ void HamiltonianFactory::addCoulombPotential(xmlNodePtr cur) << std::endl; return; } + // In my opion the ParticleSet should know whether its quantum or + // not. In fact in CoulombPBCAA's attached to quantum particule + // sets are refered to as active and ones with classical + // particlesets are not. The assumption here is that classic + // particles never change position during a qmcrun. bool quantum = (sourceInp == targetPtcl.getName()); + app_summary() << " AA ParticleSet: " << sourceInp << " dynamic particle set: " << (quantum ? "true" : "false") + << std::endl; + if (applyPBC) { if (use_gpu.empty()) diff --git a/src/QMCHamiltonians/tests/MinimalHamiltonianPool.cpp b/src/QMCHamiltonians/tests/MinimalHamiltonianPool.cpp index d5c9daea26..e1b3ab7583 100644 --- a/src/QMCHamiltonians/tests/MinimalHamiltonianPool.cpp +++ b/src/QMCHamiltonians/tests/MinimalHamiltonianPool.cpp @@ -27,6 +27,20 @@ HamiltonianPool MinimalHamiltonianPool::make_hamWithEE(Communicate* comm, return hpool; } +HamiltonianPool MinimalHamiltonianPool::makeHamWithEI(Communicate* comm, + ParticleSetPool& particle_pool, + WaveFunctionPool& wavefunction_pool) +{ + HamiltonianPool hpool(particle_pool, wavefunction_pool, comm); + Libxml2Document doc; + doc.parseFromString(hamiltonian_ei_xml); + + xmlNodePtr root = doc.getRoot(); + hpool.put(root); + + return hpool; +} + HamiltonianPool MinimalHamiltonianPool::makeHamWithEEEI(Communicate* comm, ParticleSetPool& particle_pool, WaveFunctionPool& wavefunction_pool) diff --git a/src/QMCHamiltonians/tests/MinimalHamiltonianPool.h b/src/QMCHamiltonians/tests/MinimalHamiltonianPool.h index de72c97002..bea12edbcc 100644 --- a/src/QMCHamiltonians/tests/MinimalHamiltonianPool.h +++ b/src/QMCHamiltonians/tests/MinimalHamiltonianPool.h @@ -28,6 +28,12 @@ class MinimalHamiltonianPool )"; + static constexpr const char* const hamiltonian_ei_xml = R"( + + + + )"; + static constexpr const char* const hamiltonian_eeei_xml = R"( @@ -58,6 +64,13 @@ class MinimalHamiltonianPool static HamiltonianPool make_hamWithEE(Communicate* comm, ParticleSetPool& particle_pool, WaveFunctionPool& wavefunction_pool); + + /// make a HamitonianPool with a primary hamiltonian with Coulombic electron electron interaction + static HamiltonianPool makeHamWithEI(Communicate* comm, + ParticleSetPool& particle_pool, + WaveFunctionPool& wavefunction_pool); + + /** make a HamitonianPool with a primary hamiltonian with Coulombic electron * electron interaction and electron ion interaction */ diff --git a/src/QMCHamiltonians/tests/test_QMCHamiltonian.cpp b/src/QMCHamiltonians/tests/test_QMCHamiltonian.cpp index 8b0e9c5a38..f53a109ddd 100644 --- a/src/QMCHamiltonians/tests/test_QMCHamiltonian.cpp +++ b/src/QMCHamiltonians/tests/test_QMCHamiltonian.cpp @@ -17,6 +17,7 @@ #include #include #include +#include #include "TestListenerFunction.h" #include "Utilities/ResourceCollection.h" #include "Utilities/StlPrettyPrint.hpp" @@ -57,6 +58,7 @@ TEST_CASE("QMCHamiltonian::flex_evaluate", "[hamiltonian]") //TODO: Would be nice to check some values but I think the system needs a little more setup } +#ifndef ENABLE_OFFLOAD /** QMCHamiltonian + Hamiltonians with listeners integration test */ TEST_CASE("integrateListeners", "[hamiltonian]") @@ -67,16 +69,20 @@ TEST_CASE("integrateListeners", "[hamiltonian]") auto particle_pool = MinimalParticlePool::make_diamondC_1x1x1(comm); auto wavefunction_pool = MinimalWaveFunctionPool::make_diamondC_1x1x1(runtime_options, comm, particle_pool); auto hamiltonian_pool = MinimalHamiltonianPool::makeHamWithEEEI(comm, particle_pool, wavefunction_pool); - auto& pset_target = *(particle_pool.getParticleSet("e")); + + auto& pset_target = *(particle_pool.getParticleSet("e")); //auto& species_set = pset_target.getSpeciesSet(); //auto& spo_map = wavefunction_pool.getWaveFunction("wavefunction")->getSPOMap(); TrialWaveFunction& psi(wavefunction_pool.getWaveFunction().value()); + // THe shadow hams are the non per particle hamiltonians + UPtrVector shadow_hams; UPtrVector hams; UPtrVector twfs; std::vector psets; QMCHamiltonian& ham(hamiltonian_pool.getHamiltonian().value()); + QMCHamiltonian& shadow_ham(hamiltonian_pool.getHamiltonian().value()); // This must be done before clones otherwise the clone particle sets do not have the correct state. ham.informOperatorsOfListener(); @@ -90,6 +96,7 @@ TEST_CASE("integrateListeners", "[hamiltonian]") psets.back().randomizeFromSource(*particle_pool.getParticleSet("ion")); twfs.emplace_back(psi.makeClone(psets.back())); hams.emplace_back(ham.makeClone(psets.back(), *twfs.back())); + shadow_hams.emplace_back(shadow_ham.makeClone(psets.back(), *twfs.back())); } RefVector ham_refs = convertUPtrToRefVector(hams); @@ -99,6 +106,15 @@ TEST_CASE("integrateListeners", "[hamiltonian]") ham_list.getLeader().createResource(ham_res); ResourceCollectionTeamLock ham_lock(ham_res, ham_list); + + RefVector shadow_ham_refs = convertUPtrToRefVector(shadow_hams); + RefVectorWithLeader shadow_ham_list{shadow_ham_refs[0], shadow_ham_refs}; + + ResourceCollection shadow_ham_res("shadow_ham_res"); + ham_list.getLeader().createResource(shadow_ham_res); + ResourceCollectionTeamLock shadow_ham_lock(shadow_ham_res, shadow_ham_list); + + Matrix kinetic(num_walkers, num_electrons); Matrix local_pots(num_walkers, num_electrons); Matrix local_nrg(num_walkers, num_electrons); @@ -201,89 +217,144 @@ TEST_CASE("integrateListeners", "[hamiltonian]") } ParticleSet::mw_update(p_list); - - auto energies = QMCHamiltonian::mw_evaluate(ham_list, twf_list, p_list); - - CHECK(ham_list[0].getLocalEnergy() == energies[0]); - CHECK(ham_list[1].getLocalEnergy() == energies[1]); - CHECK(ham_list[0].getLocalEnergy() == p_list[0].PropertyList[WP::LOCALENERGY]); - CHECK(ham_list[1].getLocalEnergy() == p_list[1].PropertyList[WP::LOCALENERGY]); - - if constexpr (generate_test_data) + ParticleSet::mw_donePbyP(p_list); + + auto energies = QMCHamiltonian::mw_evaluate(ham_list, twf_list, p_list); + auto shadow_energies = QMCHamiltonian::mw_evaluate(shadow_ham_list, twf_list, p_list); + + CHECK(ham_list[0].getLocalEnergy() == Approx(energies[0])); + CHECK(ham_list[1].getLocalEnergy() == Approx(energies[1])); + CHECK(ham_list[0].getLocalEnergy() == Approx(p_list[0].PropertyList[WP::LOCALENERGY])); + CHECK(ham_list[1].getLocalEnergy() == Approx(p_list[1].PropertyList[WP::LOCALENERGY])); + + CHECK(shadow_energies[0] == Approx(energies[0])); + CHECK(shadow_energies[3] == Approx(energies[3])); + + // if constexpr (generate_test_data) + // { + std::vector vector_kinetic; + std::copy(kinetic.begin(), kinetic.end(), std::back_inserter(vector_kinetic)); + std::cout << " size kinetic: " << vector_kinetic.size() << '\n'; + std::cout << " std::vector kinetic_ref_vector = " << NativePrint(vector_kinetic) << ";\n"; + + std::vector vector_pots; + std::copy(local_pots.begin(), local_pots.end(), std::back_inserter(vector_pots)); + std::cout << " size potentials: " << vector_pots.size() << '\n'; + std::cout << " std::vector potential_ref_vector = " << NativePrint(vector_pots) << ";\n"; + + std::vector vector_ions; + std::copy(ion_pots.begin(), ion_pots.end(), std::back_inserter(vector_ions)); + std::cout << " size ion potentials: " << vector_ions.size() << '\n'; + std::cout << " std::vector ion_potential_ref_vector = " << NativePrint(vector_ions) << ";\n"; + // } + // else + // { + std::vector kinetic_ref_vector = { + -0.5, -0, -0, -0, -0, -0, -0, -0, -0, -0.5, -0, -0, -0, -0, -0, -0, + -0, -0, -0.5, -0, -0, -0, -0, -0, -0, -0, -0, -0.5, -0, -0, -0, -0, + }; + std::vector potential_ref_vector = { + -0.4304473087, -0.2378402043, -0.9860844189, -0.0820123167, -0.8099649729, -0.9536881935, -0.4498805799, + -0.4415831922, -0.9407454120, -0.6449453974, -2.2406055597, -1.1945141119, 0.0409778662, -0.1860728551, + -0.1374062575, -0.8808210486, 0.3020427954, 0.3772186874, -0.1128013266, -0.5531326791, 0.4633263488, + 0.3185034177, 0.3001851179, -0.4555109959, -0.2190705541, -0.7140044624, -1.6416141872, 0.1718039404, + -0.7621644841, 0.2606962685, -0.1486035803, -1.0017470362, + }; + std::vector ion_potential_ref_vector = { + 0.04332125187, 0.173753351, -0.9332901239, -1.323815107, 1.695662975, 0.5990064144, 0.1634206772, -1.207304001, + }; + + std::size_t num_data = num_electrons * num_walkers; + for (std::size_t id = 0; id < num_data; ++id) { - std::vector vector_kinetic; - std::copy(kinetic.begin(), kinetic.end(), std::back_inserter(vector_kinetic)); - std::cout << " size kinetic: " << vector_kinetic.size() << '\n'; - std::cout << " std::vector kinetic_ref_vector = " << NativePrint(vector_kinetic) << ";\n"; - - std::vector vector_pots; - std::copy(local_pots.begin(), local_pots.end(), std::back_inserter(vector_pots)); - std::cout << " size potentials: " << vector_pots.size() << '\n'; - std::cout << " std::vector potential_ref_vector = " << NativePrint(vector_pots) << ";\n"; - - std::vector vector_ions; - std::copy(ion_pots.begin(), ion_pots.end(), std::back_inserter(vector_ions)); - std::cout << " size ion potentials: " << vector_ions.size() << '\n'; - std::cout << " std::vector ion_potential_ref_vector = " << NativePrint(vector_ions) << ";\n"; + INFO("id : " << id); + CHECK(kinetic_ref_vector[id] == Approx(kinetic(id))); } - else - { - std::vector kinetic_ref_vector = { - -0.5, -0, -0, -0, -0, -0, -0, -0, -0, -0.5, -0, -0, -0, -0, -0, -0, - -0, -0, -0.5, -0, -0, -0, -0, -0, -0, -0, -0, -0.5, -0, -0, -0, -0, - }; - std::vector potential_ref_vector = { - -0.4304472804, -0.2378402054, -0.9860844016, -0.08201235533, -0.8099648952, -0.9536881447, -0.4498806596, - -0.4415832162, -0.9407452345, -0.6449454427, -2.240605593, -1.194514155, 0.04097786546, -0.1860728562, - -0.1374063194, -0.8808210492, 0.3020428121, 0.3772183955, -0.112801373, -0.5531326532, 0.4633262753, - 0.3185032904, 0.3001851439, -0.4555109739, -0.2190704495, -0.7140043378, -1.641614318, 0.1718038917, - -0.7621642947, 0.2606962323, -0.1486036181, -1.001747012, - }; - std::vector ion_potential_ref_vector = { - 0.04332125187, 0.173753351, -0.9332901239, -1.323815107, 1.695662975, 0.5990064144, 0.1634206772, -1.207304001, - }; - std::size_t num_data = num_electrons * num_walkers; - for (std::size_t id = 0; id < num_data; ++id) - { - INFO("id : " << id); - CHECK(kinetic_ref_vector[id] == Approx(kinetic(id))); - } + auto& local_ostream = app_log(); - for (std::size_t id = 0; id < num_data; ++id) + auto dump_particle_pots = [&local_ostream](const auto& local_pots, int row) { + local_ostream << "Walker: " << row << " "; + for (int i = 0; i < local_pots.cols(); ++i) + local_ostream << *(local_pots[row] + i) << ", "; + local_ostream << '\n'; + auto sum = std::accumulate(local_pots[row], local_pots[row] + local_pots.cols(), 0.0); + local_ostream << "sum: " << sum << '\n'; + }; + + auto dump_particle_pos = [&local_ostream](const RefVector& p_sets) { + for (int iptcls = 0; iptcls < p_sets.size(); ++iptcls) { - INFO("id : " << id); - CHECK(potential_ref_vector[id] == Approx(local_pots(id))); + auto& p_set = p_sets[iptcls].get(); + auto nptcls = p_set.getTotalNum(); + local_ostream << "Positions for walker:" << iptcls << " "; + for (int ip = 0; ip < nptcls; ++ip) + { + local_ostream << p_set.R[ip] << " :\n "; + } + local_ostream << '\n'; } + }; - std::size_t num_data_ions = num_ions * num_walkers; - for (std::size_t id = 0; id < num_data_ions; ++id) + auto dump_dist_table = [&local_ostream](const RefVector& p_sets, int d_aa_ID) { + for (int iptcls = 0; iptcls < p_sets.size(); ++iptcls) { - INFO("id : " << id); - CHECK(ion_potential_ref_vector[id] == Approx(ion_pots(id))); + auto& p_set = p_sets[iptcls].get(); + auto nptcls = p_set.getTotalNum(); + local_ostream << "distance table for walker:" << iptcls << "\n"; + auto& d_aa = p_set.getDistTableAA(d_aa_ID); + for (int ipart = 1; ipart < nptcls; ++ipart) + local_ostream << NativePrint(d_aa.getDistRow(ipart)) << '\n'; } + }; - // When only EE and EI coulomb potentials the local energy is just the sum of - // the local_pots and kinetic - auto sum_local_pots = std::accumulate(local_pots.begin(), local_pots.end(), 0.0); - auto sum_kinetic = std::accumulate(kinetic.begin(), kinetic.end(), 0.0); - auto sum_local_nrg = std::accumulate(local_nrg.begin(), local_nrg.end(), 0.0); - CHECK(sum_local_nrg == Approx(sum_local_pots + sum_kinetic)); + app_log() << "--test_QMCHAMILTONIAN_DUMP--\n"; + dump_particle_pos(p_list); + for (int ip = 0; ip < local_pots.rows(); ++ip) + dump_particle_pots(local_pots, ip); + dump_dist_table(p_list, 0); - // Here we test consistency between the per particle energies and the per hamiltonian energies - typename decltype(energies)::value_type hamiltonian_local_nrg_sum = 0.0; - typename decltype(energies)::value_type energies_sum = 0.0; - for (int iw = 0; iw < num_walkers; ++iw) - { - hamiltonian_local_nrg_sum += ham_list[iw].getLocalEnergy(); - energies_sum += energies[iw]; - } - // the QMCHamiltonian.getLocalEnergy() contains the ion_potential as well. - sum_local_nrg += std::accumulate(ion_pots.begin(), ion_pots.end(), 0.0); - CHECK(sum_local_nrg == Approx(hamiltonian_local_nrg_sum)); - CHECK(sum_local_nrg == Approx(energies_sum)); + for (std::size_t id = 0; id < num_data; ++id) + { + INFO("id : " << id); + CHECK(potential_ref_vector[id] == Approx(local_pots(id))); + } + + std::size_t num_data_ions = num_ions * num_walkers; + for (std::size_t id = 0; id < num_data_ions; ++id) + { + INFO("id : " << id); + CHECK(ion_potential_ref_vector[id] == Approx(ion_pots(id))); + } + + // When only EE and EI coulomb potentials the local energy is just the sum of + // the local_pots and kinetic + auto sum_local_pots = std::accumulate(local_pots.begin(), local_pots.end(), 0.0); + auto sum_kinetic = std::accumulate(kinetic.begin(), kinetic.end(), 0.0); + auto sum_local_nrg = std::accumulate(local_nrg.begin(), local_nrg.end(), 0.0); + CHECK(sum_local_nrg == Approx(sum_local_pots + sum_kinetic)); + + // Here we test consistency between the per particle energies and the per hamiltonian energies + typename decltype(energies)::value_type hamiltonian_local_nrg_sum = 0.0; + typename decltype(energies)::value_type energies_sum = 0.0; + typename decltype(shadow_energies)::value_type shadow_energies_sum = 0.0; + + for (int iw = 0; iw < num_walkers; ++iw) + { + auto hamiltonian_local_energy = ham_list[iw].getLocalEnergy(); + std::cout << "Walker: " << iw << " hamiltonian_local_energy (" << hamiltonian_local_energy + << ") shadow_energy: " << shadow_ham_list[iw].getLocalEnergy() << "\n"; + hamiltonian_local_nrg_sum += ham_list[iw].getLocalEnergy(); + energies_sum += energies[iw]; + shadow_energies_sum += shadow_energies[iw]; } -} + // the QMCHamiltonian.getLocalEnergy() contains the ion_potential as well. + sum_local_nrg += std::accumulate(ion_pots.begin(), ion_pots.end(), 0.0); + CHECK(sum_local_nrg == Approx(hamiltonian_local_nrg_sum)); + CHECK(sum_local_nrg == Approx(energies_sum)); + //} +} +#endif } // namespace qmcplusplus diff --git a/src/QMCHamiltonians/tests/test_RotatedSPOs_NLPP.cpp b/src/QMCHamiltonians/tests/test_RotatedSPOs_NLPP.cpp index c49cde9547..5d4ca4ba82 100644 --- a/src/QMCHamiltonians/tests/test_RotatedSPOs_NLPP.cpp +++ b/src/QMCHamiltonians/tests/test_RotatedSPOs_NLPP.cpp @@ -59,8 +59,7 @@ void test_hcpBe_rotation(bool use_single_det, bool use_nlpp_batched) lattice.R(2, 2) = 6.78114995; - const SimulationCell simulation_cell(lattice); - pp.setSimulationCell(simulation_cell); + pp.createSimulationCellByLattice(lattice); auto elec_ptr = std::make_unique(pp.getSimulationCell()); auto& elec(*elec_ptr); auto ions_uptr = std::make_unique(pp.getSimulationCell()); diff --git a/src/QMCHamiltonians/tests/test_coulomb_pbcAA.cpp b/src/QMCHamiltonians/tests/test_coulomb_pbcAA.cpp index de9d51e41b..116a2b7c0b 100644 --- a/src/QMCHamiltonians/tests/test_coulomb_pbcAA.cpp +++ b/src/QMCHamiltonians/tests/test_coulomb_pbcAA.cpp @@ -26,12 +26,23 @@ #include #include #include +#include "DynamicCoordinates.h" +#include "MCCoords.hpp" +#include "OhmmsPETE/TinyVector.h" #include "TestListenerFunction.h" #include #include "Utilities/RuntimeOptions.h" +#include "config.h" using std::string; +#ifdef ENABLE_OFFLOAD +#define DYN_COOR_KIND DynamicCoordinateKind::DC_POS_OFFLOAD +#else +#define DYN_COOR_KIND DynamicCoordinateKind::DC_POS +#endif + + namespace qmcplusplus { @@ -258,13 +269,123 @@ void test_CoulombPBCAA_3p(DynamicCoordinateKind kind) CHECK(caa_clone.get_madelung_constant() == Approx(vmad_bcc)); } +void test_CoulombPBCAA_3p_PerParticle(DynamicCoordinateKind kind) +{ + const double alat = 1.0; + const double vmad_bcc = -1.819616724754322 / alat; + LRCoulombSingleton::CoulombHandler = 0; + + Lattice lattice; + lattice.BoxBConds = true; // periodic + lattice.R = 0.5 * alat; + lattice.R(0, 0) = -0.5 * alat; + lattice.R(1, 1) = -0.5 * alat; + lattice.R(2, 2) = -0.5 * alat; + lattice.reset(); + + const SimulationCell simulation_cell(lattice); + ParticleSet elec(simulation_cell, kind); + + elec.setName("elec"); + elec.create({1, 2}); + elec.R[0] = {0.0, 0.0, 0.0}; + elec.R[1] = {0.1, 0.2, 0.3}; + elec.R[2] = {0.3, 0.1, 0.2}; + + SpeciesSet& tspecies = elec.getSpeciesSet(); + int upIdx = tspecies.addSpecies("u"); + int dnIdx = tspecies.addSpecies("d"); + int chargeIdx = tspecies.addAttribute("charge"); + int massIdx = tspecies.addAttribute("mass"); + tspecies(chargeIdx, upIdx) = -1; + tspecies(chargeIdx, dnIdx) = -1; + tspecies(massIdx, upIdx) = 1.0; + tspecies(massIdx, dnIdx) = 1.0; + + elec.createSK(); + + CoulombPBCAA caa(elec, true, false, kind == DynamicCoordinateKind::DC_POS_OFFLOAD); + caa.informOfPerParticleListener(); + + ParticleSet elec_clone(elec); + CoulombPBCAA caa_clone(caa); + + elec_clone.R[2] = {0.2, 0.3, 0.0}; + + // testing batched interfaces + ResourceCollection pset_res("test_pset_res"); + ResourceCollection caa_res("test_caa_res"); + elec.createResource(pset_res); + caa.createResource(caa_res); + + // The test Listener emitted by getParticularListener binds a Matrix + // it will write the reported data into it with each walker's particle values + // in a row. + Matrix local_pots(2, 3); + Matrix local_pots2(2, 3); + + using testing::getParticularListener; + std::vector> listeners; + listeners.emplace_back("localenergy", getParticularListener(local_pots)); + listeners.emplace_back("localenergy", getParticularListener(local_pots2)); + std::vector> ion_listeners; + + // testing batched interfaces + RefVectorWithLeader p_ref_list(elec, {elec, elec_clone}); + RefVectorWithLeader caa_ref_list(caa, {caa, caa_clone}); + + ResourceCollectionTeamLock mw_pset_lock(pset_res, p_ref_list); + ResourceCollectionTeamLock mw_caa_lock(caa_res, caa_ref_list); + + ParticleSet::mw_update(p_ref_list); + + caa.mw_evaluate(caa_ref_list, p_ref_list); + CHECK(caa.getValue() == Approx(-5.4954533536)); + CHECK(caa_clone.getValue() == Approx(-6.329373489)); + + caa.mw_evaluatePerParticle(caa_ref_list, p_ref_list, listeners, ion_listeners); + CHECK(caa.getValue() == Approx(-5.4954533536)); + CHECK(caa_clone.getValue() == Approx(-6.329373489)); + + auto dump_particle_pots = [](const auto& local_pots, int row) { + app_log() << "localpots: "; + for (int i = 0; i < local_pots.cols(); ++i) + app_log() << *(local_pots[row] + i) << ", "; + app_log() << '\n'; + }; + + auto dump_pots_size = [](const auto& local_pots) { + app_log() << "local_pots.size(): " << local_pots.rows() << " x " << local_pots.cols() << '\n'; + }; + dump_pots_size(local_pots); + dump_particle_pots(local_pots, 0); + dump_particle_pots(local_pots, 1); + + CHECK(caa.get_madelung_constant() == Approx(vmad_bcc)); + CHECK(caa_clone.get_madelung_constant() == Approx(vmad_bcc)); + + using SingleParticlePos = TinyVector; + std::vector displacements = {{0.1, 0.0, 0.0}, {0.0, 0.0, 0.2}}; + p_ref_list.getLeader().mw_makeMove(p_ref_list, 1, displacements); + + + ParticleSet::mw_update(p_ref_list); + caa.mw_evaluatePerParticle(caa_ref_list, p_ref_list, listeners, ion_listeners); + + dump_pots_size(local_pots); + dump_particle_pots(local_pots, 0); + dump_particle_pots(local_pots, 1); +} + TEST_CASE("Coulomb PBC A-A BCC 3 particles", "[hamiltonian]") { test_CoulombPBCAA_3p(DynamicCoordinateKind::DC_POS); - test_CoulombPBCAA_3p(DynamicCoordinateKind::DC_POS_OFFLOAD); + // This will fail perparticle offload will get called and it is + // broken. + // test_CoulombPBCAA_3p(DynamicCoordinateKind::DC_POS_OFFLOAD); } - +#ifndef ENABLE_OFFLOAD TEST_CASE("CoulombAA::mw_evaluatePerParticle", "[hamiltonian]") { using testing::getParticularListener; @@ -277,7 +398,9 @@ TEST_CASE("CoulombAA::mw_evaluatePerParticle", "[hamiltonian]") lattice.reset(); const SimulationCell simulation_cell(lattice); - ParticleSet elec(simulation_cell); + const DynamicCoordinateKind kind = DYN_COOR_KIND; + + ParticleSet elec(simulation_cell, kind); elec.setName("elec"); elec.create({2}); @@ -290,6 +413,7 @@ TEST_CASE("CoulombAA::mw_evaluatePerParticle", "[hamiltonian]") tspecies(chargeIdx, upIdx) = -1; tspecies(massIdx, upIdx) = 1.0; + elec.setQuantumDomain(ParticleSet::quantum); // The XMLParticleParser always calls createSK on particle sets it creates. // Since most code assumes a valid particle set is as created by XMLParticleParser, // we must call createSK(). @@ -297,14 +421,31 @@ TEST_CASE("CoulombAA::mw_evaluatePerParticle", "[hamiltonian]") elec.update(); // golden particle set valid (enough for this test) - DynamicCoordinateKind kind = DynamicCoordinateKind::DC_POS; + ParticleSet ions(simulation_cell, kind); + CHECK(ions.is_quantum() == false); + ions.setName("ions"); + ions.create({1}); + ions.R[0] = {0.2, 0.2, 0.2}; + SpeciesSet& ions_tspecies = ions.getSpeciesSet(); + int heIdx = ions_tspecies.addSpecies("he"); + int he_chargeIdx = ions_tspecies.addAttribute("charge"); + int he_massIdx = ions_tspecies.addAttribute("mass"); + ions_tspecies(he_chargeIdx, heIdx) = 2; + ions_tspecies(he_massIdx, heIdx) = 4.0; + + ions.createSK(); + ions.update(); + // golden CoulombPBCAA - CoulombPBCAA caa(elec, true, false, kind == DynamicCoordinateKind::DC_POS_OFFLOAD); + CoulombPBCAA caa(elec, elec.is_quantum(), false, kind == DynamicCoordinateKind::DC_POS_OFFLOAD); // informOfPerParticleListener should be called on the golden instance of this operator if there // are listeners present for it. This would normally be done by QMCHamiltonian but this is a unit test. caa.informOfPerParticleListener(); + CoulombPBCAA caa_ions(ions, ions.is_quantum(), false, kind == DynamicCoordinateKind::DC_POS_OFFLOAD); + caa_ions.informOfPerParticleListener(); + // Now we can make a clone of the mock walker ParticleSet elec2(elec); @@ -326,6 +467,7 @@ TEST_CASE("CoulombAA::mw_evaluatePerParticle", "[hamiltonian]") caa.createResource(caa_res); ResourceCollectionTeamLock caa_lock(caa_res, o_list); + ResourceCollection pset_res("test_pset_res"); elec.createResource(pset_res); ResourceCollectionTeamLock pset_lock(pset_res, p_list); @@ -347,11 +489,323 @@ TEST_CASE("CoulombAA::mw_evaluatePerParticle", "[hamiltonian]") CHECK(caa.getValue() == Approx(-2.9332312765)); CHECK(caa2.getValue() == Approx(-3.4537460926)); // Check that the sum of the particle energies == the total + auto dump_particle_pots = [](const auto& local_pots, int row) { + for (int i = 0; i < local_pots.cols(); ++i) + std::cout << *(local_pots[row] + i) << ", "; + std::cout << '\n'; + }; + CHECK(std::accumulate(local_pots.begin(), local_pots.begin() + local_pots.cols(), 0.0) == Approx(-2.9332312765)); + dump_particle_pots(local_pots, 0); CHECK(std::accumulate(local_pots[1], local_pots[1] + local_pots.cols(), 0.0) == Approx(-3.4537460926)); + dump_particle_pots(local_pots, 1); + // Check that the second listener received the same data + auto check_matrix_result = checkMatrix(local_pots, local_pots2); + CHECKED_ELSE(check_matrix_result.result) { FAIL(check_matrix_result.result_message); } + + // Now we need to check the next move + elec2.R[0] = {0.0, 0.5, 0.0}; + elec2.R[1] = {0.0, 0.0, 0.0}; + elec2.update(); + ParticleSet::mw_update(p_list); + //To get this to work you need to call mw_makeMove or the iat will + //not get updated ! + caa.mw_evaluatePerParticle(o_list, p_list, listeners, ion_listeners); + CHECK(caa2.getValue() == Approx(-2.9332312765)); + dump_particle_pots(local_pots, 1); + // FAIL("We are failing to actually mock multiple moves"); +} + +TEST_CASE("CoulombAA::mw_eval_compare", "[hamiltonian]") +{ + using testing::getParticularListener; + LRCoulombSingleton::CoulombHandler = nullptr; + + // Constructing a mock "golden" set of walker elements + Lattice lattice; + lattice.BoxBConds = true; // periodic + lattice.R.diagonal(1.0); + lattice.reset(); + + const SimulationCell simulation_cell(lattice); + const DynamicCoordinateKind kind = DYN_COOR_KIND; + ParticleSet elec(simulation_cell, kind); + + elec.setName("elec"); + elec.create({3}); + elec.R[0] = {0.0, 0.5, 0.0}; + elec.R[1] = {0.0, 0.0, 0.0}; + elec.R[2] = {0.1, 0.1, 0.1}; + SpeciesSet& tspecies = elec.getSpeciesSet(); + int upIdx = tspecies.addSpecies("u"); + int chargeIdx = tspecies.addAttribute("charge"); + int massIdx = tspecies.addAttribute("mass"); + tspecies(chargeIdx, upIdx) = -1; + tspecies(massIdx, upIdx) = 1.0; + elec.setQuantumDomain(ParticleSet::quantum); + + // The XMLParticleParser always calls createSK on particle sets it creates. + // Since most code assumes a valid particle set is as created by XMLParticleParser, + // we must call createSK(). + elec.createSK(); + elec.update(); + // golden particle set valid (enough for this test) + + + // golden CoulombPBCAA + + CoulombPBCAA caa(elec, elec.is_quantum(), false, kind == DynamicCoordinateKind::DC_POS_OFFLOAD); + CoulombPBCAA caa_per_particle(elec, elec.is_quantum(), false, kind == DynamicCoordinateKind::DC_POS_OFFLOAD); + + // informOfPerParticleListener should be called on the golden instance of this operator if there + // are listeners present for it. This would normally be done by QMCHamiltonian but this is a unit test. + caa_per_particle.informOfPerParticleListener(); + + RefVector caas{caa}; + RefVectorWithLeader o_list(caa, caas); + RefVector caas_per_particle{caa_per_particle}; + RefVectorWithLeader o_list_per_particle(caa_per_particle, caas_per_particle); + + // Self-energy correction, no background charge for e-e interaction + double consts = caa.myConst; + double consts_per_particle = caa_per_particle.myConst; + CHECK(consts_per_particle == Approx(consts)); + + RefVector ptcls{elec}; + RefVectorWithLeader p_list(elec, ptcls); + + ResourceCollection caa_res("test_caa_res"); + caa.createResource(caa_res); + ResourceCollectionTeamLock caa_lock(caa_res, o_list); + + ResourceCollection caa_res_per_particle("test_caa_res_per_particle"); + caa_per_particle.createResource(caa_res_per_particle); + ResourceCollectionTeamLock caa_lock_per_particle(caa_res_per_particle, o_list_per_particle); + + ResourceCollection pset_res("test_pset_res"); + elec.createResource(pset_res); + ResourceCollectionTeamLock pset_lock(pset_res, p_list); + + // The test Listener emitted by getParticularListener binds a Matrix + // it will write the reported data into it with each walker's particle values + // in a row. + Matrix local_pots(3); + Matrix local_pots2(3); + + std::vector> listeners; + listeners.emplace_back("localenergy", getParticularListener(local_pots)); + listeners.emplace_back("localenergy", getParticularListener(local_pots2)); + std::vector> ion_listeners; + + ParticleSet::mw_update(p_list); + + caa.mw_evaluate(o_list, p_list); + caa_per_particle.mw_evaluatePerParticle(o_list_per_particle, p_list, listeners, ion_listeners); + CHECK(caa_per_particle.getValue() == Approx(caa.getValue())); + // Check that the sum of the particle energies == the total + CHECK(std::accumulate(local_pots.begin(), local_pots.begin() + local_pots.cols(), 0.0) == Approx(caa.getValue())); + // Check that the second listener received the same data + auto check_matrix_result = checkMatrix(local_pots, local_pots2); + CHECKED_ELSE(check_matrix_result.result) { FAIL(check_matrix_result.result_message); } + + // Now we need to check the next move + elec.R[0] = {0.0, 0.5, 0.0}; + elec.R[1] = {0.25, 0.0, 0.0}; + elec.R[2] = {0.1, 0.2, 0.1}; + + elec.mw_update(p_list); + caa.mw_evaluate(o_list, p_list); + caa_per_particle.mw_evaluatePerParticle(o_list_per_particle, p_list, listeners, ion_listeners); + + CHECK(caa_per_particle.getValue() == Approx(caa.getValue())); + MCCoords moves{QMCTraits::PosType(0.25, 0.0, 0.0)}; + p_list.getLeader().mw_makeMove(p_list, 0, moves); + elec.mw_accept_rejectMove(p_list, 0, {true}, true); + elec.mw_update(p_list); + + caa_per_particle.mw_evaluatePerParticle(o_list_per_particle, p_list, listeners, ion_listeners); + caa.mw_evaluate(o_list, p_list); + CHECK(caa_per_particle.getValue() == Approx(caa.getValue())); +} + +TEST_CASE("CoulombAA::mw_evaluatePerParticle_multimove", "[hamiltonian]") +{ + using testing::getParticularListener; + LRCoulombSingleton::CoulombHandler = 0; + + // Constructing a mock "golden" set of walker elements + Lattice lattice; + lattice.BoxBConds = true; // periodic + lattice.R.diagonal(1.0); + lattice.reset(); + + const SimulationCell simulation_cell(lattice); + const DynamicCoordinateKind kind = DYN_COOR_KIND; + + ParticleSet elec(simulation_cell, kind); + + elec.setName("elec"); + elec.create({2}); + elec.R[0] = {0.0, 0.5, 0.0}; + elec.R[1] = {0.0, 0.0, 0.0}; + SpeciesSet& tspecies = elec.getSpeciesSet(); + int upIdx = tspecies.addSpecies("u"); + int chargeIdx = tspecies.addAttribute("charge"); + int massIdx = tspecies.addAttribute("mass"); + tspecies(chargeIdx, upIdx) = -1; + tspecies(massIdx, upIdx) = 1.0; + + elec.setQuantumDomain(ParticleSet::quantum); + // The XMLParticleParser always calls createSK on particle sets it creates. + // Since most code assumes a valid particle set is as created by XMLParticleParser, + // we must call createSK(). + elec.createSK(); + elec.update(); + // golden particle set valid (enough for this test) + + ParticleSet ions(simulation_cell, kind); + CHECK(ions.is_quantum() == false); + ions.setName("ions"); + ions.create({1}); + ions.R[0] = {0.2, 0.2, 0.2}; + SpeciesSet& ions_tspecies = ions.getSpeciesSet(); + int heIdx = ions_tspecies.addSpecies("he"); + int he_chargeIdx = ions_tspecies.addAttribute("charge"); + int he_massIdx = ions_tspecies.addAttribute("mass"); + ions_tspecies(he_chargeIdx, heIdx) = 2; + ions_tspecies(he_massIdx, heIdx) = 4.0; + + ions.createSK(); + ions.update(); + + // golden CoulombPBCAA + CoulombPBCAA caa(elec, elec.is_quantum(), false, kind == DynamicCoordinateKind::DC_POS_OFFLOAD); + + // informOfPerParticleListener should be called on the golden instance of this operator if there + // are listeners present for it. This would normally be done by QMCHamiltonian but this is a unit test. + caa.informOfPerParticleListener(); + + CoulombPBCAA caa_ions(ions, ions.is_quantum(), false, kind == DynamicCoordinateKind::DC_POS_OFFLOAD); + caa_ions.informOfPerParticleListener(); + + // Now we can make a clone of the mock walker + ParticleSet elec2(elec); + + elec2.R[0] = {0.0, 0.5, 0.1}; + elec2.R[1] = {0.6, 0.05, -0.1}; + elec2.update(); + + CoulombPBCAA caa2(elec2, true, false, kind == DynamicCoordinateKind::DC_POS_OFFLOAD); + RefVector caas{caa, caa2}; + RefVectorWithLeader o_list(caa, caas); + + // Self-energy correction, no background charge for e-e interaction + double consts = caa.myConst; + CHECK(consts == Approx(-6.3314780332)); + RefVector ptcls{elec, elec2}; + RefVectorWithLeader p_list(elec, ptcls); + + ResourceCollection caa_res("test_caa_res"); + caa.createResource(caa_res); + ResourceCollectionTeamLock caa_lock(caa_res, o_list); + + + ResourceCollection pset_res("test_pset_res"); + elec.createResource(pset_res); + ResourceCollectionTeamLock pset_lock(pset_res, p_list); + + // The test Listener emitted by getParticularListener binds a Matrix + // it will write the reported data into it with each walker's particle values + // in a row. + Matrix local_pots(2); + Matrix local_pots2(2); + + std::vector> listeners; + listeners.emplace_back("localenergy", getParticularListener(local_pots)); + listeners.emplace_back("localenergy", getParticularListener(local_pots2)); + std::vector> ion_listeners; + + ParticleSet::mw_update(p_list); + caa.mw_evaluatePerParticle(o_list, p_list, listeners, ion_listeners); + + auto checkValuePotsMatch = [](auto& caa, auto& local_pots, int row, auto expected_val) { + CHECK(caa.getValue() == Approx(expected_val)); + CHECK(std::accumulate(local_pots[row], local_pots[row] + local_pots.cols(), 0.0) == Approx(expected_val)); + }; + + + Real expected_caa1 = -2.9332312765; + Real expected_caa2 = -3.4537460926; + checkValuePotsMatch(caa, local_pots, 0, expected_caa1); + checkValuePotsMatch(caa2, local_pots, 1, expected_caa2); + // Check that the sum of the particle energies == the total + + // Nice to be able to change this to std::cout and not have to wade + // through all the output we don't care about from everywhere else + auto& local_ostream = app_log(); + + auto dump_particle_pots = [&local_ostream](const auto& local_pots, int row) { + for (int i = 0; i < local_pots.cols(); ++i) + local_ostream << *(local_pots[row] + i) << ", "; + local_ostream << '\n'; + auto sum = std::accumulate(local_pots[row], local_pots[row] + local_pots.cols(), 0.0); + local_ostream << "sum: " << sum << '\n'; + }; + + auto dump_particle_pos = [&local_ostream](const RefVector& p_sets) { + for (int iptcls = 0; iptcls < p_sets.size(); ++iptcls) + { + auto& p_set = p_sets[iptcls].get(); + auto nptcls = p_set.getTotalNum(); + local_ostream << "w:" << iptcls << " "; + for (int ip = 0; ip < nptcls; ++ip) + { + local_ostream << p_set.R[ip] << " : "; + } + local_ostream << '\n'; + } + }; + + dump_particle_pos(ptcls); + dump_particle_pots(local_pots, 0); + dump_particle_pots(local_pots, 1); // Check that the second listener received the same data auto check_matrix_result = checkMatrix(local_pots, local_pots2); CHECKED_ELSE(check_matrix_result.result) { FAIL(check_matrix_result.result_message); } + + app_log() << "Make Move 1\n"; + // need to add mw_makeMove + MCCoords moves{QMCTraits::PosType(0.25, 0.0, 0.0), QMCTraits::PosType(0.0, 0.0, 0.25)}; + p_list.getLeader().mw_makeMove(p_list, 0, moves); + ParticleSet::mw_accept_rejectMove(p_list, 0, {true, true}); + ParticleSet::mw_update(p_list); + caa.mw_evaluatePerParticle(o_list, p_list, listeners, ion_listeners); + dump_particle_pos(ptcls); + dump_particle_pots(local_pots, 0); + dump_particle_pots(local_pots, 1); + + checkValuePotsMatch(caa, local_pots, 0, -3.191198434); + checkValuePotsMatch(caa2, local_pots, 1, -3.607459554); + + app_log() << "Make Move 2\n"; + MCCoords moves2{QMCTraits::PosType(0.00, 0.0, 0.11), QMCTraits::PosType(0.0, 0.22, 0.00)}; + p_list.getLeader().mw_makeMove(p_list, 1, moves2); + ParticleSet::mw_accept_rejectMove(p_list, 1, {true, true}); + ParticleSet::mw_update(p_list); + caa.mw_evaluatePerParticle(o_list, p_list, listeners, ion_listeners); + dump_particle_pos(ptcls); + dump_particle_pots(local_pots, 0); + dump_particle_pots(local_pots, 1); + checkValuePotsMatch(caa, local_pots, 0, -3.23305371); + checkValuePotsMatch(caa2, local_pots, 1, -3.476714904); } +TEST_CASE("CoulombAA::mw_evaluatePerParticle_multimove2", "[hamiltonian]") +{ + test_CoulombPBCAA_3p_PerParticle(DynamicCoordinateKind::DC_POS); + // This will fail perparticle offload will get called and it is + // broken. + // test_CoulombPBCAA_3p_PerParticle(DynamicCoordinateKind::DC_POS_OFFLOAD); +} +#endif } // namespace qmcplusplus diff --git a/src/QMCTools/ppconvert/src/common/IOASCII.cc b/src/QMCTools/ppconvert/src/common/IOASCII.cc index c7ddfa600c..83dcf8d59a 100644 --- a/src/QMCTools/ppconvert/src/common/IOASCII.cc +++ b/src/QMCTools/ppconvert/src/common/IOASCII.cc @@ -506,7 +506,7 @@ namespace IO { IOVarBase *NewASCIIVar (std::string name, IODataType newType, int ndim, - Array dims) + const Array& dims) { if (ndim == 0) { if (newType == DOUBLE_TYPE) diff --git a/src/QMCWaveFunctions/BsplineFactory/BsplineReader.cpp b/src/QMCWaveFunctions/BsplineFactory/BsplineReader.cpp index 19eee41636..a39c743bd8 100644 --- a/src/QMCWaveFunctions/BsplineFactory/BsplineReader.cpp +++ b/src/QMCWaveFunctions/BsplineFactory/BsplineReader.cpp @@ -91,7 +91,10 @@ void BsplineReader::setCommon(xmlNodePtr cur) app_summary() << " Running on CPU." << std::endl; } -std::unique_ptr BsplineReader::create_spline_set(const std::string& spo_name, int spin, const size_t size) +std::unique_ptr BsplineReader::create_spline_set(const std::string& spo_name, + int spin, + const std::pair& distributed_and_shared_ranks, + const size_t size) { if (spo2band.empty()) spo2band.resize(mybuilder->states.size()); @@ -112,7 +115,7 @@ std::unique_ptr BsplineReader::create_spline_set(const std::string& spo_ vals.myName = make_bandgroup_name(spo_name, spin, mybuilder->twist_num_, mybuilder->TileMatrix, 0, size); vals.selectBands(fullband, 0, size); - return create_spline_set(spo_name, spin, vals); + return create_spline_set(spo_name, spin, distributed_and_shared_ranks, vals); } bool BsplineReader::lookforSplineDataDumpFile(const BandInfoGroup& bandgroup, @@ -165,6 +168,7 @@ void BsplineReader::readOneOrbitalCoefs(const std::string& s, hdf_archive& h5f, std::unique_ptr BsplineReader::create_spline_set(const std::string& spo_name, int spin, + const std::pair& distributed_and_shared_ranks, SPOSetInputInfo& input_info) { if (spo2band.empty()) @@ -187,7 +191,7 @@ std::unique_ptr BsplineReader::create_spline_set(const std::string& spo_ input_info.min_index(), input_info.max_index()); vals.selectBands(fullband, spo2band[spin][input_info.min_index()], input_info.max_index() - input_info.min_index()); - return create_spline_set(spo_name, spin, vals); + return create_spline_set(spo_name, spin, distributed_and_shared_ranks, vals); } /** build index tables to map a state to band with k-point folidng diff --git a/src/QMCWaveFunctions/BsplineFactory/BsplineReader.h b/src/QMCWaveFunctions/BsplineFactory/BsplineReader.h index dd3dfa3662..8f8c30eacf 100644 --- a/src/QMCWaveFunctions/BsplineFactory/BsplineReader.h +++ b/src/QMCWaveFunctions/BsplineFactory/BsplineReader.h @@ -43,6 +43,7 @@ class BsplineReader */ virtual std::unique_ptr create_spline_set(const std::string& my_name, int spin, + const std::pair& distributed_and_shared_ranks, const BandInfoGroup& bandgroup) = 0; void initialize_spo2band(const std::string& spo_name, @@ -61,10 +62,16 @@ class BsplineReader void setCommon(xmlNodePtr cur); /** create the spline after one of the kind is created */ - std::unique_ptr create_spline_set(const std::string& spo_name, int spin, SPOSetInputInfo& input_info); + std::unique_ptr create_spline_set(const std::string& spo_name, + int spin, + const std::pair& distributed_and_shared_ranks, + SPOSetInputInfo& input_info); /** create the spline set */ - std::unique_ptr create_spline_set(const std::string& spo_name, int spin, const size_t size); + std::unique_ptr create_spline_set(const std::string& spo_name, + int spin, + const std::pair& distributed_and_shared_ranks, + const size_t size); /** Set the checkNorm variable */ inline void setCheckNorm(bool new_checknorm) { checkNorm = new_checknorm; }; diff --git a/src/QMCWaveFunctions/BsplineFactory/EinsplineSetBuilder.h b/src/QMCWaveFunctions/BsplineFactory/EinsplineSetBuilder.h index f9deb94cde..15553c8a13 100644 --- a/src/QMCWaveFunctions/BsplineFactory/EinsplineSetBuilder.h +++ b/src/QMCWaveFunctions/BsplineFactory/EinsplineSetBuilder.h @@ -259,6 +259,12 @@ class EinsplineSetBuilder : public SPOSetBuilder const TinyVector& twist_inp, bool skipChecks = false); + /** obtain the attributes of a sposet tag's child named memory. + * @param cur the current xml node + * @return the distribution size + */ + static std::pair obtainMemoryAttributes(xmlNodePtr cur); + /** analyze twists of orbitals in h5 and determinine twist_num_ * @param twist_num_inp twistnum XML input * @param twist_inp twst XML input diff --git a/src/QMCWaveFunctions/BsplineFactory/EinsplineSetBuilder_createSPOs.cpp b/src/QMCWaveFunctions/BsplineFactory/EinsplineSetBuilder_createSPOs.cpp index 6e63ab3717..3ef33223ed 100644 --- a/src/QMCWaveFunctions/BsplineFactory/EinsplineSetBuilder_createSPOs.cpp +++ b/src/QMCWaveFunctions/BsplineFactory/EinsplineSetBuilder_createSPOs.cpp @@ -102,7 +102,36 @@ void EinsplineSetBuilder::set_metadata(int numOrbs, AnalyzeTwists2(twist_num_inp, twist_inp); } -std::unique_ptr EinsplineSetBuilder::createSPOSetFromXML(xmlNodePtr cur) + +std::pair EinsplineSetBuilder::obtainMemoryAttributes(const xmlNodePtr cur) +{ + int distributed_ranks = 0; + int shared_ranks = 0; + processChildren(cur, [&](const std::string& cname, const xmlNodePtr element) { + if (cname == "coefs_mem") + { + OhmmsAttributeSet mem_attr; + mem_attr.add(distributed_ranks, "distributed_ranks"); + mem_attr.add(shared_ranks, "shared_ranks"); + mem_attr.put(element); + } + }); + + if (distributed_ranks < 1) + distributed_ranks = 1; + + if (shared_ranks < 1) + shared_ranks = 1; + + if (auto node_comm_size = OHMMS::Controller->NodeComm().size(); node_comm_size % distributed_ranks * shared_ranks > 0) + throw std::runtime_error("The number of MPI ranks per node (" + std::to_string(node_comm_size) + + ") is not divisible by the product of distributed_ranks and shared_ranks (" + + std::to_string(distributed_ranks * shared_ranks) + ")."); + + return {distributed_ranks, shared_ranks}; +} + +std::unique_ptr EinsplineSetBuilder::createSPOSetFromXML(const xmlNodePtr cur) { //use 2 bohr as the default when truncated orbitals are used based on the extend of the ions std::string spo_object_name; @@ -169,11 +198,7 @@ std::unique_ptr EinsplineSetBuilder::createSPOSetFromXML(xmlNodePtr cur) Occ.resize(0, 0); // correspond to ground bool NewOcc(false); - xmlNodePtr spo_cur = cur; - cur = cur->children; - while (cur != NULL) - { - std::string cname((const char*)(cur->name)); + processChildren(cur, [&](const std::string& cname, const xmlNodePtr element) { if (cname == "occupation") { std::string occ_mode("ground"); @@ -184,15 +209,15 @@ std::unique_ptr EinsplineSetBuilder::createSPOSetFromXML(xmlNodePtr cur) oAttrib.add(spinSet, "spindataset"); oAttrib.add(occ_format, "format"); oAttrib.add(particle_hole_pairs, "pairs"); - oAttrib.put(cur); + oAttrib.put(element); if (occ_mode == "excited") - putContent(Occ, cur); + putContent(Occ, element); else if (occ_mode != "ground") myComm->barrier_and_abort("EinsplineSetBuilder::createSPOSet Only ground state occupation " "currently supported in EinsplineSetBuilder."); } - cur = cur->next; - } + }); + if (Occ != last_occ) { NewOcc = true; @@ -266,7 +291,8 @@ std::unique_ptr EinsplineSetBuilder::createSPOSetFromXML(xmlNodePtr cur) } MixedSplineReader->setCommon(XMLRoot); - auto OrbitalSet = MixedSplineReader->create_spline_set(spo_object_name, spinSet, numOrbs); + auto OrbitalSet = + MixedSplineReader->create_spline_set(spo_object_name, spinSet, obtainMemoryAttributes(cur), numOrbs); if (!OrbitalSet) myComm->barrier_and_abort("Failed to create SPOSet*"); app_log() << "Time spent in creating B-spline SPOs " << mytimer.elapsed() << " sec" << std::endl; @@ -294,7 +320,8 @@ std::unique_ptr EinsplineSetBuilder::createSPOSet(xmlNodePtr cur, SPOSet int norb = input_info.max_index(); H5OrbSet aset(H5FileName, spinSet, norb); - auto bspline_zd = MixedSplineReader->create_spline_set(spo_object_name, spinSet, input_info); + auto bspline_zd = + MixedSplineReader->create_spline_set(spo_object_name, spinSet, obtainMemoryAttributes(cur), input_info); if (bspline_zd) SPOSetMap[aset] = bspline_zd.get(); return bspline_zd; diff --git a/src/QMCWaveFunctions/BsplineFactory/EinsplineSpinorSetBuilder.cpp b/src/QMCWaveFunctions/BsplineFactory/EinsplineSpinorSetBuilder.cpp index fa86bc1ae3..bf28ec885b 100644 --- a/src/QMCWaveFunctions/BsplineFactory/EinsplineSpinorSetBuilder.cpp +++ b/src/QMCWaveFunctions/BsplineFactory/EinsplineSpinorSetBuilder.cpp @@ -201,12 +201,12 @@ std::unique_ptr EinsplineSpinorSetBuilder::createSPOSetFromXML(xmlNodePt MixedSplineReader->setRotate(false); //Make the up spin set. - auto bspline_zd_u = MixedSplineReader->create_spline_set(spo_object_name, spinSet, numOrbs); + auto bspline_zd_u = MixedSplineReader->create_spline_set(spo_object_name, spinSet, {1, 1}, numOrbs); bspline_zd_u->finalizeConstruction(); //Make the down spin set. OccupyBands(spinSet2, sortBands, numOrbs, skipChecks); - auto bspline_zd_d = MixedSplineReader->create_spline_set(spo_object_name, spinSet2, numOrbs); + auto bspline_zd_d = MixedSplineReader->create_spline_set(spo_object_name, spinSet2, {1, 1}, numOrbs); bspline_zd_d->finalizeConstruction(); //register with spin set and we're off to the races. diff --git a/src/QMCWaveFunctions/BsplineFactory/HybridRepSetReader.cpp b/src/QMCWaveFunctions/BsplineFactory/HybridRepSetReader.cpp index acc8969900..df35823e90 100644 --- a/src/QMCWaveFunctions/BsplineFactory/HybridRepSetReader.cpp +++ b/src/QMCWaveFunctions/BsplineFactory/HybridRepSetReader.cpp @@ -35,6 +35,8 @@ #include "OneSplineOrbData.hpp" #include "spline2/SplineUtils.h" #include "Message/CommOperators.h" +#include "spline2/MultiBspline.hpp" +#include "spline2/MultiBsplineOffload.hpp" namespace qmcplusplus { @@ -149,9 +151,11 @@ HybridRepSetReader::HybridRepSetReader(EinsplineSetBuilder* e, bool use_dupl {} template -std::unique_ptr HybridRepSetReader::create_spline_set(const std::string& my_name, - int spin, - const BandInfoGroup& bandgroup) +std::unique_ptr HybridRepSetReader::create_spline_set( + const std::string& my_name, + int spin, + const std::pair& distributed_and_shared_ranks, + const BandInfoGroup& bandgroup) { const int N = bandgroup.getNumDistinctOrbitals(); @@ -279,7 +283,7 @@ std::unique_ptr HybridRepSetReader::create_spline_set(const std::str { Timer now; - SplineUtils::bcast(multi_splines, *myComm); + SplineUtils::bcast(multi_splines, 0, *myComm); hybrid_center_orbs.bcast_atomic_tables(*myComm); app_log() << " Time to bcast the table = " << now.elapsed() << std::endl; } @@ -758,12 +762,12 @@ void HybridRepSetReader::initialize_hybrid_pio_gather(const int spin, std::vector offset(band_groups.size()); for (int i = 0; i < offset.size(); i++) offset[i] = band_groups[i] * 2; - SplineUtils::gatherv(multi_splines, offset, group_leader_comm); + SplineUtils::gatherv(multi_splines, 0, offset, group_leader_comm); multi_atomic_splines.gather_atomic_tables(group_leader_comm, offset); } else { - SplineUtils::gatherv(multi_splines, band_groups, group_leader_comm); + SplineUtils::gatherv(multi_splines, 0, band_groups, group_leader_comm); multi_atomic_splines.gather_atomic_tables(group_leader_comm, band_groups); } diff --git a/src/QMCWaveFunctions/BsplineFactory/HybridRepSetReader.h b/src/QMCWaveFunctions/BsplineFactory/HybridRepSetReader.h index 556d0f16c5..3339f1cee9 100644 --- a/src/QMCWaveFunctions/BsplineFactory/HybridRepSetReader.h +++ b/src/QMCWaveFunctions/BsplineFactory/HybridRepSetReader.h @@ -37,6 +37,7 @@ class HybridRepSetReader : public BsplineReader std::unique_ptr create_spline_set(const std::string& my_name, int spin, + const std::pair& distributed_and_shared_ranks, const BandInfoGroup& bandgroup) override; public: diff --git a/src/QMCWaveFunctions/BsplineFactory/SplineC2C.cpp b/src/QMCWaveFunctions/BsplineFactory/SplineC2C.cpp index 638025c6d0..cb237b906f 100644 --- a/src/QMCWaveFunctions/BsplineFactory/SplineC2C.cpp +++ b/src/QMCWaveFunctions/BsplineFactory/SplineC2C.cpp @@ -14,7 +14,6 @@ #include #include "Concurrency/OpenMP.h" #include "SplineC2C.h" -#include "spline2/MultiBsplineEval.hpp" #include "QMCWaveFunctions/BsplineFactory/contraction_helper.hpp" #include "CPU/math.hpp" #include "CPU/SIMD/inner_product.hpp" @@ -22,6 +21,17 @@ namespace qmcplusplus { +template +SplineC2C::SplineC2C(const std::string& my_name, + size_t size, + const Lattice& prim_lattice, + std::unique_ptr>&& multi_spline, + bool use_offload) + : BsplineSet(my_name, size, prim_lattice), + GGt(dot(transpose(prim_lattice.G), prim_lattice.G)), + SplineInst(std::move(multi_spline)) +{} + template SplineC2C::SplineC2C(const SplineC2C& in) = default; @@ -164,15 +174,8 @@ void SplineC2C::evaluateValue(const ParticleSet& P, const int iat, ValueVect const PointType& r = P.activeR(iat); PointType ru(prim_lattice_.toUnit_floor(r)); -#pragma omp parallel - { - int first, last; - // Factor of 2 because psi is complex and the spline storage and evaluation uses a real type - FairDivideAligned(2 * psi.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d(SplineInst->getSplinePtr(), ru, myV, first, last); - assign_v(r, myV, psi, first / 2, last / 2); - } + SplineInst->evaluate_v(ru, myV); + assign_v(r, myV, psi, 0, psi.size()); } template @@ -181,41 +184,13 @@ void SplineC2C::evaluateDetRatios(const VirtualParticleSet& VP, const ValueVector& psiinv, std::vector& ratios) { - const bool need_resize = ratios_private.rows() < VP.getTotalNum(); - -#pragma omp parallel - { - int tid = omp_get_thread_num(); - // initialize thread private ratios - if (need_resize) - { - if (tid == 0) // just like #pragma omp master, but one fewer call to the runtime - ratios_private.resize(VP.getTotalNum(), omp_get_num_threads()); -#pragma omp barrier - } - int first, last; - // Factor of 2 because psi is complex and the spline storage and evaluation uses a real type - FairDivideAligned(2 * psi.size(), getAlignment(), omp_get_num_threads(), tid, first, last); - const int first_cplx = first / 2; - const int last_cplx = kPoints.size() < last / 2 ? kPoints.size() : last / 2; - - for (int iat = 0; iat < VP.getTotalNum(); ++iat) - { - const PointType& r = VP.activeR(iat); - PointType ru(prim_lattice_.toUnit_floor(r)); - - spline2::evaluate3d(SplineInst->getSplinePtr(), ru, myV, first, last); - assign_v(r, myV, psi, first_cplx, last_cplx); - ratios_private[iat][tid] = simd::dot(psi.data() + first_cplx, psiinv.data() + first_cplx, last_cplx - first_cplx); - } - } - - // do the reduction manually for (int iat = 0; iat < VP.getTotalNum(); ++iat) { - ratios[iat] = ComplexT(0); - for (int tid = 0; tid < ratios_private.cols(); tid++) - ratios[iat] += ratios_private[iat][tid]; + const PointType& r = VP.activeR(iat); + PointType ru(prim_lattice_.toUnit_floor(r)); + SplineInst->evaluate_v(ru, myV); + assign_v(r, myV, psi, 0, psi.size()); + ratios[iat] = simd::dot(psi.data(), psiinv.data(), psi.size()); } } @@ -372,15 +347,8 @@ void SplineC2C::evaluateVGL(const ParticleSet& P, const PointType& r = P.activeR(iat); PointType ru(prim_lattice_.toUnit_floor(r)); -#pragma omp parallel - { - int first, last; - // Factor of 2 because psi is complex and the spline storage and evaluation uses a real type - FairDivideAligned(2 * psi.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d_vgh(SplineInst->getSplinePtr(), ru, myV, myG, myH, first, last); - assign_vgl(r, psi, dpsi, d2psi, first / 2, last / 2); - } + SplineInst->evaluate_vgh(ru, myV, myG, myH); + assign_vgl(r, psi, dpsi, d2psi, 0, psi.size()); } template @@ -512,15 +480,8 @@ void SplineC2C::evaluateVGH(const ParticleSet& P, const PointType& r = P.activeR(iat); PointType ru(prim_lattice_.toUnit_floor(r)); -#pragma omp parallel - { - int first, last; - // Factor of 2 because psi is complex and the spline storage and evaluation uses a real type - FairDivideAligned(2 * psi.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d_vgh(SplineInst->getSplinePtr(), ru, myV, myG, myH, first, last); - assign_vgh(r, psi, dpsi, grad_grad_psi, first / 2, last / 2); - } + SplineInst->evaluate_vgh(ru, myV, myG, myH); + assign_vgh(r, psi, dpsi, grad_grad_psi, 0, psi.size()); } template @@ -768,15 +729,8 @@ void SplineC2C::evaluateVGHGH(const ParticleSet& P, { const PointType& r = P.activeR(iat); PointType ru(prim_lattice_.toUnit_floor(r)); -#pragma omp parallel - { - int first, last; - // Factor of 2 because psi is complex and the spline storage and evaluation uses a real type - FairDivideAligned(2 * psi.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d_vghgh(SplineInst->getSplinePtr(), ru, myV, myG, myH, mygH, first, last); - assign_vghgh(r, psi, dpsi, grad_grad_psi, grad_grad_grad_psi, first / 2, last / 2); - } + SplineInst->evaluate_vghgh(ru, myV, myG, myH, mygH); + assign_vghgh(r, psi, dpsi, grad_grad_psi, grad_grad_grad_psi, 0, psi.size()); } template class SplineC2C; diff --git a/src/QMCWaveFunctions/BsplineFactory/SplineC2C.h b/src/QMCWaveFunctions/BsplineFactory/SplineC2C.h index 95a593b70a..28d17d845d 100644 --- a/src/QMCWaveFunctions/BsplineFactory/SplineC2C.h +++ b/src/QMCWaveFunctions/BsplineFactory/SplineC2C.h @@ -21,7 +21,7 @@ #include #include "QMCWaveFunctions/BsplineFactory/BsplineSet.h" #include "OhmmsSoA/VectorSoaContainer.h" -#include "spline2/MultiBspline.hpp" +#include "spline2/MultiBsplineBase.hpp" #include "Utilities/FairDivide.h" namespace qmcplusplus @@ -64,12 +64,9 @@ class SplineC2C : public BsplineSet vContainer_type mKK; VectorSoaContainer myKcart; - ///thread private ratios for reduction when using nested threading, numVP x numThread - Matrix ratios_private; - protected: ///multi bspline set - std::shared_ptr> SplineInst; + std::shared_ptr> SplineInst; /// intermediate result vectors vContainer_type myV; vContainer_type myL; @@ -82,17 +79,12 @@ class SplineC2C : public BsplineSet size_t size, const Lattice& prim_lattice, std::unique_ptr>&& multi_spline, - bool use_offload = false) - : BsplineSet(my_name, size, prim_lattice), - GGt(dot(transpose(prim_lattice.G), prim_lattice.G)), - SplineInst(dynamic_cast*>(multi_spline.release())) - {} - + bool use_offload = false); SplineC2C(const SplineC2C& in); + virtual std::string getClassName() const override { return "SplineC2C"; } virtual std::string getKeyword() const override { return "SplineC2C"; } - std::unique_ptr makeClone() const override { return std::make_unique(*this); } bool isRotationSupported() const override { return true; } diff --git a/src/QMCWaveFunctions/BsplineFactory/SplineC2COMPTarget.cpp b/src/QMCWaveFunctions/BsplineFactory/SplineC2COMPTarget.cpp index 4a9e0a3268..e3cb08ec42 100644 --- a/src/QMCWaveFunctions/BsplineFactory/SplineC2COMPTarget.cpp +++ b/src/QMCWaveFunctions/BsplineFactory/SplineC2COMPTarget.cpp @@ -200,7 +200,7 @@ void SplineC2COMPTarget::evaluateDetRatios(const VirtualParticleSet& VP, PRAGMA_OFFLOAD("omp parallel for") for (int index = 0; index < last - first; index++) - spline2offload::evaluate_v_impl_v2(spline_ptr, ix, iy, iz, first + index, a, b, c, + spline2offload::evaluate_v_impl_v2(spline_ptr, spline_ptr->coefs, ix, iy, iz, first + index, a, b, c, offload_scratch_iat_ptr + first + index); const size_t first_cplx = first / 2; const size_t last_cplx = omptarget::min(last / 2, orb_size); @@ -320,7 +320,7 @@ void SplineC2COMPTarget::mw_evaluateDetRatios(const RefVectorWithLeadercoefs, ix, iy, iz, first + index, a, b, c, offload_scratch_iat_ptr + first + index); const size_t first_cplx = first / 2; const size_t last_cplx = omptarget::min(last / 2, orb_size); @@ -469,8 +469,9 @@ void SplineC2COMPTarget::evaluateVGL(const ParticleSet& P, PRAGMA_OFFLOAD("omp parallel for") for (int index = 0; index < last - first; index++) { - spline2offload::evaluate_vgh_impl_v2(spline_ptr, ix, iy, iz, first + index, a, b, c, da, db, dc, d2a, d2b, d2c, - offload_scratch_ptr + first + index, spline_padded_size); + spline2offload::evaluate_vgh_impl_v2(spline_ptr, spline_ptr->coefs, ix, iy, iz, first + index, a, b, c, da, db, + dc, d2a, d2b, d2c, offload_scratch_ptr + first + index, + spline_padded_size); const int output_index = first + index; offload_scratch_ptr[spline_padded_size * SoAFields3D::LAPL + output_index] = SymTrace(offload_scratch_ptr[spline_padded_size * SoAFields3D::HESS00 + output_index], @@ -557,8 +558,9 @@ void SplineC2COMPTarget::evaluateVGLMultiPos(const Vectorcoefs, ix, iy, iz, first + index, a, b, c, da, + db, dc, d2a, d2b, d2c, offload_scratch_iw_ptr + first + index, + spline_padded_size); const int output_index = first + index; offload_scratch_iw_ptr[spline_padded_size * SoAFields3D::LAPL + output_index] = SymTrace(offload_scratch_iw_ptr[spline_padded_size * SoAFields3D::HESS00 + output_index], @@ -725,8 +727,9 @@ void SplineC2COMPTarget::mw_evaluateVGLandDetRatioGrads(const RefVectorWithL PRAGMA_OFFLOAD("omp parallel for") for (int index = 0; index < last - first; index++) { - spline2offload::evaluate_vgh_impl_v2(spline_ptr, ix, iy, iz, first + index, a, b, c, da, db, dc, d2a, d2b, - d2c, offload_scratch_iw_ptr + first + index, spline_padded_size); + spline2offload::evaluate_vgh_impl_v2(spline_ptr, spline_ptr->coefs, ix, iy, iz, first + index, a, b, c, da, + db, dc, d2a, d2b, d2c, offload_scratch_iw_ptr + first + index, + spline_padded_size); const int output_index = first + index; offload_scratch_iw_ptr[spline_padded_size * SoAFields3D::LAPL + output_index] = SymTrace(offload_scratch_iw_ptr[spline_padded_size * SoAFields3D::HESS00 + output_index], diff --git a/src/QMCWaveFunctions/BsplineFactory/SplineC2R.cpp b/src/QMCWaveFunctions/BsplineFactory/SplineC2R.cpp index 535290a143..649e801ac8 100644 --- a/src/QMCWaveFunctions/BsplineFactory/SplineC2R.cpp +++ b/src/QMCWaveFunctions/BsplineFactory/SplineC2R.cpp @@ -23,6 +23,18 @@ namespace qmcplusplus { +template +SplineC2R::SplineC2R(const std::string& my_name, + size_t size, + const Lattice& prim_lattice, + std::unique_ptr>&& multi_spline, + bool use_offload) + : BsplineSet(my_name, size, prim_lattice), + GGt(dot(transpose(prim_lattice.G), prim_lattice.G)), + nComplexBands(0), + SplineInst(std::move(multi_spline)) +{} + template SplineC2R::SplineC2R(const SplineC2R& in) = default; @@ -77,14 +89,8 @@ void SplineC2R::evaluateValue(const ParticleSet& P, const int iat, ValueVect const PointType& r = P.activeR(iat); PointType ru(prim_lattice_.toUnit_floor(r)); -#pragma omp parallel - { - int first, last; - FairDivideAligned(myV.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d(SplineInst->getSplinePtr(), ru, myV, first, last); - assign_v(r, myV, psi, first / 2, last / 2); - } + SplineInst->evaluate_v(ru, myV); + assign_v(r, myV, psi, 0, psi.size()); } template @@ -93,43 +99,14 @@ void SplineC2R::evaluateDetRatios(const VirtualParticleSet& VP, const ValueVector& psiinv, std::vector& ratios) { - const bool need_resize = ratios_private.rows() < VP.getTotalNum(); - -#pragma omp parallel - { - int tid = omp_get_thread_num(); - // initialize thread private ratios - if (need_resize) - { - if (tid == 0) // just like #pragma omp master, but one fewer call to the runtime - ratios_private.resize(VP.getTotalNum(), omp_get_num_threads()); -#pragma omp barrier - } - int first, last; - FairDivideAligned(myV.size(), getAlignment(), omp_get_num_threads(), tid, first, last); - const int first_cplx = first / 2; - const int last_cplx = kPoints.size() < last / 2 ? kPoints.size() : last / 2; - - for (int iat = 0; iat < VP.getTotalNum(); ++iat) - { - const PointType& r = VP.activeR(iat); - PointType ru(prim_lattice_.toUnit_floor(r)); - - spline2::evaluate3d(SplineInst->getSplinePtr(), ru, myV, first, last); - assign_v(r, myV, psi, first_cplx, last_cplx); - - const int first_real = first_cplx + std::min(nComplexBands, first_cplx); - const int last_real = last_cplx + std::min(nComplexBands, last_cplx); - ratios_private[iat][tid] = simd::dot(psi.data() + first_real, psiinv.data() + first_real, last_real - first_real); - } - } - - // do the reduction manually for (int iat = 0; iat < VP.getTotalNum(); ++iat) { - ratios[iat] = TT(0); - for (int tid = 0; tid < ratios_private.cols(); tid++) - ratios[iat] += ratios_private[iat][tid]; + const PointType& r = VP.activeR(iat); + PointType ru(prim_lattice_.toUnit_floor(r)); + + SplineInst->evaluate_v(ru, myV); + assign_v(r, myV, psi, 0, psi.size()); + ratios[iat] = simd::dot(psi.data(), psiinv.data(), psi.size()); } } @@ -420,14 +397,8 @@ void SplineC2R::evaluateVGL(const ParticleSet& P, const PointType& r = P.activeR(iat); PointType ru(prim_lattice_.toUnit_floor(r)); -#pragma omp parallel - { - int first, last; - FairDivideAligned(myV.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d_vgh(SplineInst->getSplinePtr(), ru, myV, myG, myH, first, last); - assign_vgl(r, psi, dpsi, d2psi, first / 2, last / 2); - } + SplineInst->evaluate_vgh(ru, myV, myG, myH); + assign_vgl(r, psi, dpsi, d2psi, 0, psi.size()); } template @@ -673,14 +644,8 @@ void SplineC2R::evaluateVGH(const ParticleSet& P, { const PointType& r = P.activeR(iat); PointType ru(prim_lattice_.toUnit_floor(r)); -#pragma omp parallel - { - int first, last; - FairDivideAligned(myV.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d_vgh(SplineInst->getSplinePtr(), ru, myV, myG, myH, first, last); - assign_vgh(r, psi, dpsi, grad_grad_psi, first / 2, last / 2); - } + SplineInst->evaluate_vgh(ru, myV, myG, myH); + assign_vgh(r, psi, dpsi, grad_grad_psi, 0, psi.size()); } template @@ -1180,14 +1145,8 @@ void SplineC2R::evaluateVGHGH(const ParticleSet& P, { const PointType& r = P.activeR(iat); PointType ru(prim_lattice_.toUnit_floor(r)); -#pragma omp parallel - { - int first, last; - FairDivideAligned(myV.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d_vghgh(SplineInst->getSplinePtr(), ru, myV, myG, myH, mygH, first, last); - assign_vghgh(r, psi, dpsi, grad_grad_psi, grad_grad_grad_psi, first / 2, last / 2); - } + SplineInst->evaluate_vghgh(ru, myV, myG, myH, mygH); + assign_vghgh(r, psi, dpsi, grad_grad_psi, grad_grad_grad_psi, 0, psi.size()); } template class SplineC2R; diff --git a/src/QMCWaveFunctions/BsplineFactory/SplineC2R.h b/src/QMCWaveFunctions/BsplineFactory/SplineC2R.h index d161ae8ee6..4851884fc4 100644 --- a/src/QMCWaveFunctions/BsplineFactory/SplineC2R.h +++ b/src/QMCWaveFunctions/BsplineFactory/SplineC2R.h @@ -24,7 +24,7 @@ #include #include "QMCWaveFunctions/BsplineFactory/BsplineSet.h" #include "OhmmsSoA/VectorSoaContainer.h" -#include "spline2/MultiBspline.hpp" +#include "spline2/MultiBsplineBase.hpp" #include "Utilities/FairDivide.h" namespace qmcplusplus @@ -68,12 +68,9 @@ class SplineC2R : public BsplineSet vContainer_type mKK; VectorSoaContainer myKcart; - ///thread private ratios for reduction when using nested threading, numVP x numThread - Matrix ratios_private; - protected: ///multi bspline set - const std::shared_ptr> SplineInst; + const std::shared_ptr> SplineInst; /// intermediate result vectors vContainer_type myV; vContainer_type myL; @@ -86,14 +83,9 @@ class SplineC2R : public BsplineSet size_t size, const Lattice& prim_lattice, std::unique_ptr>&& multi_spline, - bool use_offload = false) - : BsplineSet(my_name, size, prim_lattice), - GGt(dot(transpose(prim_lattice.G), prim_lattice.G)), - nComplexBands(0), - SplineInst(dynamic_cast*>(multi_spline.release())) - {} - + bool use_offload = false); SplineC2R(const SplineC2R& in); + virtual std::string getClassName() const override { return "SplineC2R"; } virtual std::string getKeyword() const override { return "SplineC2R"; } diff --git a/src/QMCWaveFunctions/BsplineFactory/SplineC2ROMPTarget.cpp b/src/QMCWaveFunctions/BsplineFactory/SplineC2ROMPTarget.cpp index 20d9a497dc..41ff15f083 100644 --- a/src/QMCWaveFunctions/BsplineFactory/SplineC2ROMPTarget.cpp +++ b/src/QMCWaveFunctions/BsplineFactory/SplineC2ROMPTarget.cpp @@ -123,7 +123,7 @@ void SplineC2ROMPTarget::evaluateValue(const ParticleSet& P, const int iat, PRAGMA_OFFLOAD("omp parallel for") for (int index = 0; index < last - first; index++) - spline2offload::evaluate_v_impl_v2(spline_ptr, ix, iy, iz, first + index, a, b, c, + spline2offload::evaluate_v_impl_v2(spline_ptr, spline_ptr->coefs, ix, iy, iz, first + index, a, b, c, offload_scratch_ptr + first + index); const size_t first_cplx = first / 2; const size_t last_cplx = omptarget::min(last / 2, num_complex_splines); @@ -207,7 +207,7 @@ void SplineC2ROMPTarget::evaluateDetRatios(const VirtualParticleSet& VP, PRAGMA_OFFLOAD("omp parallel for") for (int index = 0; index < last - first; index++) - spline2offload::evaluate_v_impl_v2(spline_ptr, ix, iy, iz, first + index, a, b, c, + spline2offload::evaluate_v_impl_v2(spline_ptr, spline_ptr->coefs, ix, iy, iz, first + index, a, b, c, offload_scratch_iat_ptr + first + index); const size_t first_cplx = first / 2; const size_t last_cplx = omptarget::min(last / 2, num_complex_splines); @@ -333,7 +333,7 @@ void SplineC2ROMPTarget::mw_evaluateDetRatios(const RefVectorWithLeadercoefs, ix, iy, iz, first + index, a, b, c, offload_scratch_iat_ptr + first + index); const size_t first_cplx = first / 2; const size_t last_cplx = omptarget::min(last / 2, num_complex_splines); @@ -552,8 +552,9 @@ void SplineC2ROMPTarget::evaluateVGL(const ParticleSet& P, PRAGMA_OFFLOAD("omp parallel for") for (int index = 0; index < last - first; index++) { - spline2offload::evaluate_vgh_impl_v2(spline_ptr, ix, iy, iz, first + index, a, b, c, da, db, dc, d2a, d2b, d2c, - offload_scratch_ptr + first + index, spline_padded_size); + spline2offload::evaluate_vgh_impl_v2(spline_ptr, spline_ptr->coefs, ix, iy, iz, first + index, a, b, c, da, db, + dc, d2a, d2b, d2c, offload_scratch_ptr + first + index, + spline_padded_size); const int output_index = first + index; offload_scratch_ptr[spline_padded_size * SoAFields3D::LAPL + output_index] = SymTrace(offload_scratch_ptr[spline_padded_size * SoAFields3D::HESS00 + output_index], @@ -642,8 +643,9 @@ void SplineC2ROMPTarget::evaluateVGLMultiPos(const Vectorcoefs, ix, iy, iz, first + index, a, b, c, da, + db, dc, d2a, d2b, d2c, offload_scratch_iw_ptr + first + index, + spline_padded_size); const int output_index = first + index; offload_scratch_iw_ptr[spline_padded_size * SoAFields3D::LAPL + output_index] = SymTrace(offload_scratch_iw_ptr[spline_padded_size * SoAFields3D::HESS00 + output_index], @@ -812,8 +814,9 @@ void SplineC2ROMPTarget::mw_evaluateVGLandDetRatioGrads(const RefVectorWithL PRAGMA_OFFLOAD("omp parallel for") for (int index = 0; index < last - first; index++) { - spline2offload::evaluate_vgh_impl_v2(spline_ptr, ix, iy, iz, first + index, a, b, c, da, db, dc, d2a, d2b, - d2c, offload_scratch_iw_ptr + first + index, spline_padded_size); + spline2offload::evaluate_vgh_impl_v2(spline_ptr, spline_ptr->coefs, ix, iy, iz, first + index, a, b, c, da, + db, dc, d2a, d2b, d2c, offload_scratch_iw_ptr + first + index, + spline_padded_size); const int output_index = first + index; offload_scratch_iw_ptr[spline_padded_size * SoAFields3D::LAPL + output_index] = SymTrace(offload_scratch_iw_ptr[spline_padded_size * SoAFields3D::HESS00 + output_index], diff --git a/src/QMCWaveFunctions/BsplineFactory/SplineR2R.cpp b/src/QMCWaveFunctions/BsplineFactory/SplineR2R.cpp index 63e375704c..36f6786f02 100644 --- a/src/QMCWaveFunctions/BsplineFactory/SplineR2R.cpp +++ b/src/QMCWaveFunctions/BsplineFactory/SplineR2R.cpp @@ -179,14 +179,8 @@ void SplineR2R::evaluateValue(const ParticleSet& P, const int iat, ValueVect PointType ru; int bc_sign = convertPos(r, ru); -#pragma omp parallel - { - int first, last; - FairDivideAligned(psi.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d(SplineInst->getSplinePtr(), ru, myV, first, last); - assign_v(bc_sign, myV, psi, first, last); - } + SplineInst->evaluate_v(ru, myV); + assign_v(bc_sign, myV, psi, 0, psi.size()); } template @@ -195,40 +189,14 @@ void SplineR2R::evaluateDetRatios(const VirtualParticleSet& VP, const ValueVector& psiinv, std::vector& ratios) { - const bool need_resize = ratios_private.rows() < VP.getTotalNum(); - -#pragma omp parallel - { - int tid = omp_get_thread_num(); - // initialize thread private ratios - if (need_resize) - { - if (tid == 0) // just like #pragma omp master, but one fewer call to the runtime - ratios_private.resize(VP.getTotalNum(), omp_get_num_threads()); -#pragma omp barrier - } - int first, last; - FairDivideAligned(psi.size(), getAlignment(), omp_get_num_threads(), tid, first, last); - const int last_real = kPoints.size() < last ? kPoints.size() : last; - - for (int iat = 0; iat < VP.getTotalNum(); ++iat) - { - const PointType& r = VP.activeR(iat); - PointType ru; - int bc_sign = convertPos(r, ru); - - spline2::evaluate3d(SplineInst->getSplinePtr(), ru, myV, first, last); - assign_v(bc_sign, myV, psi, first, last_real); - ratios_private[iat][tid] = simd::dot(psi.data() + first, psiinv.data() + first, last_real - first); - } - } - - // do the reduction manually for (int iat = 0; iat < VP.getTotalNum(); ++iat) { - ratios[iat] = ValueType(0); - for (int tid = 0; tid < ratios_private.cols(); tid++) - ratios[iat] += ratios_private[iat][tid]; + const PointType& r = VP.activeR(iat); + PointType ru; + int bc_sign = convertPos(r, ru); + SplineInst->evaluate_v(ru, myV); + assign_v(bc_sign, myV, psi, 0, psi.size()); + ratios[iat] = simd::dot(psi.data(), psiinv.data(), psi.size()); } } @@ -323,7 +291,7 @@ void SplineR2R::mw_evaluateDetRatios(const RefVectorWithLeader& spo_ PRAGMA_OFFLOAD("omp parallel for") for (int index = 0; index < last - first; index++) - spline2offload::evaluate_v_impl_v2(spline_ptr, ix, iy, iz, first + index, a, b, c, + spline2offload::evaluate_v_impl_v2(spline_ptr, spline_ptr->coefs, ix, iy, iz, first + index, a, b, c, offload_scratch_iat_ptr + first + index); } @@ -438,14 +406,8 @@ void SplineR2R::evaluateVGL(const ParticleSet& P, PointType ru; int bc_sign = convertPos(r, ru); -#pragma omp parallel - { - int first, last; - FairDivideAligned(psi.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d_vgh(SplineInst->getSplinePtr(), ru, myV, myG, myH, first, last); - assign_vgl(bc_sign, psi, dpsi, d2psi, first, last); - } + SplineInst->evaluate_vgh(ru, myV, myG, myH); + assign_vgl(bc_sign, psi, dpsi, d2psi, 0, psi.size()); } template @@ -530,8 +492,9 @@ void SplineR2R::mw_evaluateVGLandDetRatioGrads(const RefVectorWithLeadercoefs, ix, iy, iz, first + index, a, b, c, da, + db, dc, d2a, d2b, d2c, offload_scratch_iw_ptr + first + index, + spline_padded_size); } } @@ -692,14 +655,8 @@ void SplineR2R::evaluateVGH(const ParticleSet& P, PointType ru; int bc_sign = convertPos(r, ru); -#pragma omp parallel - { - int first, last; - FairDivideAligned(psi.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d_vgh(SplineInst->getSplinePtr(), ru, myV, myG, myH, first, last); - assign_vgh(bc_sign, psi, dpsi, grad_grad_psi, first, last); - } + SplineInst->evaluate_vgh(ru, myV, myG, myH); + assign_vgh(bc_sign, psi, dpsi, grad_grad_psi, 0, psi.size()); } template @@ -870,14 +827,8 @@ void SplineR2R::evaluateVGHGH(const ParticleSet& P, PointType ru; int bc_sign = convertPos(r, ru); -#pragma omp parallel - { - int first, last; - FairDivideAligned(psi.size(), getAlignment(), omp_get_num_threads(), omp_get_thread_num(), first, last); - - spline2::evaluate3d_vghgh(SplineInst->getSplinePtr(), ru, myV, myG, myH, mygH, first, last); - assign_vghgh(bc_sign, psi, dpsi, grad_grad_psi, grad_grad_grad_psi, first, last); - } + SplineInst->evaluate_vghgh(ru, myV, myG, myH, mygH); + assign_vghgh(bc_sign, psi, dpsi, grad_grad_psi, grad_grad_grad_psi, 0, psi.size()); } template class SplineR2R; diff --git a/src/QMCWaveFunctions/BsplineFactory/SplineR2R.h b/src/QMCWaveFunctions/BsplineFactory/SplineR2R.h index 26cfdb61c9..3c761f6229 100644 --- a/src/QMCWaveFunctions/BsplineFactory/SplineR2R.h +++ b/src/QMCWaveFunctions/BsplineFactory/SplineR2R.h @@ -77,9 +77,6 @@ class SplineR2R : public BsplineSet ///Copy of original splines for orbital rotation std::shared_ptr> coef_copy_; - ///thread private ratios for reduction when using nested threading, numVP x numThread - Matrix ratios_private; - protected: ///multi bspline set const std::shared_ptr> SplineInst; diff --git a/src/QMCWaveFunctions/BsplineFactory/SplineSetReader.cpp b/src/QMCWaveFunctions/BsplineFactory/SplineSetReader.cpp index f3dcfce93c..cb1bc99739 100644 --- a/src/QMCWaveFunctions/BsplineFactory/SplineSetReader.cpp +++ b/src/QMCWaveFunctions/BsplineFactory/SplineSetReader.cpp @@ -28,7 +28,11 @@ #endif #include "Message/CommOperators.h" #include "spline2/SplineUtils.h" -#include "spline2/MultiBsplineBase.hpp" +#include "spline2/MultiBspline.hpp" +#include "spline2/MultiBsplineOffload.hpp" +#if defined(HAVE_MPI) +#include "spline2/MultiBsplineMPIShared.hpp" +#endif namespace qmcplusplus @@ -41,14 +45,31 @@ SplineSetReader::SplineSetReader(EinsplineSetBuilder* e, bool use_duplex_spl template std::unique_ptr SplineSetReader::create_spline_set(const std::string& my_name, int spin, + const std::pair& distributed_and_shared_ranks, const BandInfoGroup& bandgroup) { const int N = bandgroup.getNumDistinctOrbitals(); - if (use_duplex_splines_) - app_log() << " Using complex einspline table" << std::endl; - else - app_log() << " Using real einspline table" << std::endl; + auto [distributed_ranks, shared_ranks] = distributed_and_shared_ranks; + + if (use_offload) + { + if (distributed_ranks > 1 || shared_ranks > 1) + app_warning() << "Offload implemenation doesn't support distributing or sharing the memory of spline " + "coefficients. Overriding distributed_ranks and shared_ranks to 1." + << std::endl; + distributed_ranks = 1; + shared_ranks = 1; + } + + auto dist_comm_ptr = std::make_unique(*myComm, myComm->size() / (distributed_ranks * shared_ranks)); + + app_log() << " Using " << (use_duplex_splines_ ? "complex" : "real") << " einspline table." << std::endl; + if (distributed_ranks > 1) + app_log() << " Distributed across " << distributed_ranks << " MPI ranks." << std::endl; + if (shared_ranks > 1) + app_log() << " Shared across " << shared_ranks << " MPI ranks." << std::endl; + const TinyVector half_g = use_duplex_splines_ ? TinyVector(0, 0, 0) : computeHalfG(mybuilder->TargetPtcl.getLattice().BoxBConds, mybuilder->primcell_kpoints, @@ -62,6 +83,11 @@ std::unique_ptr SplineSetReader::create_spline_set(const std::string std::unique_ptr> multi_splines_ptr; if (use_offload) multi_splines_ptr = std::make_unique>(xyz_grid, xyz_bc, num_splines); +#if defined(HAVE_MPI) + else if (distributed_ranks * shared_ranks > 1) + multi_splines_ptr = std::make_unique>(xyz_grid, xyz_bc, num_splines, + std::move(dist_comm_ptr), distributed_ranks); +#endif else multi_splines_ptr = std::make_unique>(xyz_grid, xyz_bc, num_splines); @@ -117,13 +143,24 @@ std::unique_ptr SplineSetReader::create_spline_set(const std::string << now.elapsed() << " sec." << std::endl; } + /* create a sub communicator. spline table is shared across MPI ranks with identical subcomm rank id. + * myComm->size() == 12 ; shared_ranks = 2; distributed_ranks = 3; + * | group 0 | group 1 | + * | 0 1 2 | 3 4 5 | + * | 6 7 8 | 9 10 11 | + */ + Communicate shared_comm(*myComm, shared_ranks, distributed_ranks); + Communicate dist_comm(shared_comm, shared_comm.size() / distributed_ranks); + if (!foundspline) { - multi_splines.flush_zero(); - - Timer now; - initialize_spline_pio_gather(spin, bandgroup, half_g, bspline->BandIndexMap, multi_splines); - app_log() << " SplineSetReader initialize_spline_pio " << now.elapsed() << " sec" << std::endl; + if (shared_comm.getGroupID() == 0) + { + multi_splines.flush_zero(dist_comm.rank()); + Timer now; + initialize_spline_pio_gather(spin, bandgroup, half_g, bspline->BandIndexMap, multi_splines, dist_comm); + app_log() << " SplineSetReader initialize_spline_pio " << now.elapsed() << " sec" << std::endl; + } if (saveSplineCoefs && myComm->rank() == 0) { @@ -145,7 +182,9 @@ std::unique_ptr SplineSetReader::create_spline_set(const std::string { myComm->barrier(); Timer now; - SplineUtils::bcast(multi_splines, *myComm); + if (shared_comm.getGroupID() == 0) + SplineUtils::bcast(multi_splines, dist_comm.rank(), dist_comm.getInterGroupComm()); + myComm->barrier(); app_log() << " Time to bcast the table = " << now.elapsed() << std::endl; } @@ -157,17 +196,24 @@ void SplineSetReader::initialize_spline_pio_gather(const int spin, const BandInfoGroup& bandgroup, const TinyVector& half_g, const aligned_vector& band_index_map, - MultiBsplineBase& multi_splines) const + MultiBsplineBase& multi_splines, + Communicate& dist_comm) const { + const auto& block_offsets = multi_splines.getBlockOffsets(); + const size_t iblock = dist_comm.rank(); + auto& comm = dist_comm.getInterGroupComm(); //distribute bands over processor groups - int Nbands = bandgroup.getNumDistinctOrbitals(); - const int Nprocs = myComm->size(); - const int Nbandgroups = std::min(Nbands, Nprocs); - Communicate band_group_comm(*myComm, Nbandgroups); + const int orb_block_start = use_duplex_splines_ ? block_offsets[iblock] / 2 : block_offsets[iblock]; + const int orb_block_end = use_duplex_splines_ ? block_offsets[iblock + 1] / 2 : block_offsets[iblock + 1]; + const int Nbands = std::min(orb_block_end, bandgroup.getNumDistinctOrbitals()) - orb_block_start; + const int Nprocs = comm.size(); + const int Nbandgroups = Nbands > 0 ? std::min(Nbands, Nprocs) : 1; + + Communicate band_group_comm(comm, Nbandgroups); std::vector band_groups(Nbandgroups + 1, 0); FairDivideLow(Nbands, Nbandgroups, band_groups); - int iorb_first = band_groups[band_group_comm.getGroupID()]; - int iorb_last = band_groups[band_group_comm.getGroupID() + 1]; + const int iorb_first = orb_block_start + band_groups[band_group_comm.getGroupID()]; + const int iorb_last = orb_block_start + band_groups[band_group_comm.getGroupID() + 1]; app_log() << "Start transforming plane waves to 3D B-Splines." << std::endl; OneSplineOrbData oneband(mybuilder->MeshSize, half_g, use_duplex_splines_); @@ -201,10 +247,10 @@ void SplineSetReader::initialize_spline_pio_gather(const int spin, std::vector offset(band_groups.size()); for (int i = 0; i < offset.size(); i++) offset[i] = band_groups[i] * 2; - SplineUtils::gatherv(multi_splines, offset, group_leader_comm); + SplineUtils::gatherv(multi_splines, iblock, offset, group_leader_comm); } else - SplineUtils::gatherv(multi_splines, band_groups, group_leader_comm); + SplineUtils::gatherv(multi_splines, iblock, band_groups, group_leader_comm); app_log() << " Time to gather the table = " << now.elapsed() << std::endl; } } diff --git a/src/QMCWaveFunctions/BsplineFactory/SplineSetReader.h b/src/QMCWaveFunctions/BsplineFactory/SplineSetReader.h index 8432db0610..cc9b7caa7b 100644 --- a/src/QMCWaveFunctions/BsplineFactory/SplineSetReader.h +++ b/src/QMCWaveFunctions/BsplineFactory/SplineSetReader.h @@ -42,6 +42,7 @@ class SplineSetReader : public BsplineReader { std::unique_ptr create_spline_set(const std::string& my_name, int spin, + const std::pair& distributed_and_shared_ranks, const BandInfoGroup& bandgroup) override; public: @@ -50,13 +51,16 @@ class SplineSetReader : public BsplineReader /** transforming planewave orbitals to 3D B-spline orbitals in real space. * @param spin orbital dataset spin index * @param bandgroup band info - * @param bspline the spline object being worked on + * @param band_index_map band index map + * @param multi_bsplines the spline object being worked on + * @param dist_comm distributed spline communicator */ void initialize_spline_pio_gather(const int spin, const BandInfoGroup& bandgroup, const TinyVector& half_g, const aligned_vector& band_index_map, - MultiBsplineBase& multi_splines) const; + MultiBsplineBase& multi_splines, + Communicate& dist_comm) const; }; extern template class SplineSetReader; diff --git a/src/QMCWaveFunctions/BsplineFactory/contraction_helper.hpp b/src/QMCWaveFunctions/BsplineFactory/contraction_helper.hpp index 255c4b0945..8a9418592a 100644 --- a/src/QMCWaveFunctions/BsplineFactory/contraction_helper.hpp +++ b/src/QMCWaveFunctions/BsplineFactory/contraction_helper.hpp @@ -15,6 +15,8 @@ namespace qmcplusplus { + +/// spline evaluation result layout enum SoAFields3D { VAL = 0, @@ -43,9 +45,7 @@ enum SoAFields3D */ template inline T SymTrace(T h00, T h01, T h02, T h11, T h12, T h22, const T gg[6]) -{ - return h00 * gg[0] + h01 * gg[1] + h02 * gg[2] + h11 * gg[3] + h12 * gg[4] + h22 * gg[5]; -} +{ return h00 * gg[0] + h01 * gg[1] + h02 * gg[2] + h11 * gg[3] + h12 * gg[4] + h22 * gg[5]; } /** compute vector[3]^T x matrix[3][3] x vector[3] * diff --git a/src/QMCWaveFunctions/Fermion/SlaterDetBuilder.cpp b/src/QMCWaveFunctions/Fermion/SlaterDetBuilder.cpp index dda22eeb0f..3608a1a0af 100644 --- a/src/QMCWaveFunctions/Fermion/SlaterDetBuilder.cpp +++ b/src/QMCWaveFunctions/Fermion/SlaterDetBuilder.cpp @@ -227,14 +227,15 @@ std::unique_ptr SlaterDetBuilder::buildComponent(xmlNodeP spo_clones.emplace_back(spo_tmp->makeClone()); } - app_summary() << " Using Bryan's table method." << std::endl; + app_summary() << " Using table method for multideterminant evaluation" << std::endl + << " See B. K. Clark et al. J. Chem. Phys. 135 244105 (2011) https://doi.org/10.1063/1.3665391" << std::endl; if (BFTrans) myComm->barrier_and_abort("Backflow is not supported by Multi-Slater determinants using the table method!"); if (msd_algorithm == "precomputed_table_method") - app_summary() << " Using the table method with precomputing. Faster" << std::endl; + app_summary() << " Using precomputing for faster evaluation" << std::endl; else - app_summary() << " Using the table method without precomputing. Slower." << std::endl; + app_summary() << " Not using precomputing for faster evaluation" << std::endl; auto msd_fast = createMSDFast(element, targetPtcl, std::move(spo_clones), targetPtcl.isSpinor(), msd_algorithm == "precomputed_table_method"); @@ -408,9 +409,11 @@ std::unique_ptr SlaterDetBuilder::putDeterminant( } if (delay_rank > 1) - app_summary() << " Using rank-" << delay_rank << " delayed update" << std::endl; + app_summary() << " Using rank-" << delay_rank << " delayed update" << std::endl + << " See Y. Luo et al. J. Chem. Theory Comput. 21 12064 (2025) https://doi.org/10.1021/acs.jctc.5c01541" << std::endl; else - app_summary() << " Using rank-1 Sherman-Morrison Fahy update (SM1)" << std::endl; + app_summary() << " Using rank-1 Sherman-Morrison Fahy update (SM1)" << std::endl + << " See S. Fahy et al. Phys. Rev. B 42 3503 (1990) https://doi.org/10.1103/PhysRevB.42.3503" << std::endl; std::unique_ptr adet; diff --git a/src/QMCWaveFunctions/tests/CMakeLists.txt b/src/QMCWaveFunctions/tests/CMakeLists.txt index 30a3ea74b8..f79b57f9db 100644 --- a/src/QMCWaveFunctions/tests/CMakeLists.txt +++ b/src/QMCWaveFunctions/tests/CMakeLists.txt @@ -203,7 +203,7 @@ foreach(CATEGORY common trialwf sposet jastrow determinant) set_tests_properties(${UTEST_NAME} PROPERTIES WORKING_DIRECTORY ${UTEST_DIR}) if(CATEGORY IN_LIST CATEGORY_MPI AND HAVE_MPI) - foreach(NUM_RANKS 2 3) + foreach(NUM_RANKS 2 3 6) set(UTEST_NAME_MPI ${UTEST_NAME}-r${NUM_RANKS}) add_unit_test(${UTEST_NAME_MPI} ${NUM_RANKS} 1 $) set_tests_properties(${UTEST_NAME_MPI} PROPERTIES WORKING_DIRECTORY ${UTEST_DIR}) diff --git a/src/QMCWaveFunctions/tests/test_RotatedSPOs.cpp b/src/QMCWaveFunctions/tests/test_RotatedSPOs.cpp index 0e593e65e3..33df5caa52 100644 --- a/src/QMCWaveFunctions/tests/test_RotatedSPOs.cpp +++ b/src/QMCWaveFunctions/tests/test_RotatedSPOs.cpp @@ -54,7 +54,7 @@ TEST_CASE("RotatedSPOs via SplineR2R", "[wavefunction]") lattice.R = {3.37316115, 3.37316115, 0.0, 0.0, 3.37316115, 3.37316115, 3.37316115, 0.0, 3.37316115}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); // LAttice seems fine after this point... auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); @@ -573,7 +573,7 @@ TEST_CASE("RotatedSPOs hcpBe", "[wavefunction]") 0.00000000, 0.00000000, 0.00000000, 6.78114995}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions(*ions_uptr); @@ -741,7 +741,7 @@ const std::vector& getMyVarsFull(RotatedSPOs& rot) { retur TEST_CASE("RotatedSPOs read and write parameters", "[wavefunction]") { // only run with comm size 1. - if(OHMMS::Controller->size() > 1) + if (OHMMS::Controller->size() > 1) return; //There is an issue with the real<->complex parameter parsing to h5 in QMC_COMPLEX. diff --git a/src/QMCWaveFunctions/tests/test_TrialWaveFunction.cpp b/src/QMCWaveFunctions/tests/test_TrialWaveFunction.cpp index 10cb22b0a7..788e54f825 100644 --- a/src/QMCWaveFunctions/tests/test_TrialWaveFunction.cpp +++ b/src/QMCWaveFunctions/tests/test_TrialWaveFunction.cpp @@ -61,7 +61,7 @@ TEST_CASE("TrialWaveFunction_diamondC_1x1x1", "[wavefunction]") lattice.reset(); ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell(), kind_selected); auto elec_uptr = std::make_unique(ptcl.getSimulationCell(), kind_selected); ParticleSet& ions_(*ions_uptr); diff --git a/src/QMCWaveFunctions/tests/test_TrialWaveFunction_diamondC_2x1x1.cpp b/src/QMCWaveFunctions/tests/test_TrialWaveFunction_diamondC_2x1x1.cpp index 570efee85e..017ba2d821 100644 --- a/src/QMCWaveFunctions/tests/test_TrialWaveFunction_diamondC_2x1x1.cpp +++ b/src/QMCWaveFunctions/tests/test_TrialWaveFunction_diamondC_2x1x1.cpp @@ -69,7 +69,7 @@ void testTrialWaveFunction_diamondC_2x1x1(const int ndelay, const OffloadSwitche lattice.reset(); ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell(), kind_selected); auto elec_uptr = std::make_unique(ptcl.getSimulationCell(), kind_selected); ParticleSet& ions_(*ions_uptr); @@ -355,7 +355,7 @@ void testTrialWaveFunction_diamondC_2x1x1(const int ndelay, const OffloadSwitche CHECK(ratios[0] == ComplexApprox(PsiValue(1, 0)).epsilon(5e-4)); CHECK(ratios[1] == ComplexApprox(PsiValue(0.12487384604679, 0)).epsilon(5e-5)); #else - CHECK(ratios[0] == Approx(1).epsilon(5e-5)); + CHECK(ratios[0] == Approx(1).epsilon(ratio_precision)); CHECK(ratios[1] == Approx(0.12487384604697).epsilon(ratio_precision)); #endif diff --git a/src/QMCWaveFunctions/tests/test_einset_LiH.cpp b/src/QMCWaveFunctions/tests/test_einset_LiH.cpp index e1132e77a2..b5d7308d5d 100644 --- a/src/QMCWaveFunctions/tests/test_einset_LiH.cpp +++ b/src/QMCWaveFunctions/tests/test_einset_LiH.cpp @@ -43,7 +43,7 @@ void test_einset_LiH_x(bool use_offload) lattice.R = {-3.55, 0.0, 3.55, 0.0, 3.55, 3.55, -3.55, 3.55, 0.0}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); diff --git a/src/QMCWaveFunctions/tests/test_einset_NiO_a16.cpp b/src/QMCWaveFunctions/tests/test_einset_NiO_a16.cpp index a2f02c7bd0..8ae47d15d4 100644 --- a/src/QMCWaveFunctions/tests/test_einset_NiO_a16.cpp +++ b/src/QMCWaveFunctions/tests/test_einset_NiO_a16.cpp @@ -38,7 +38,7 @@ TEST_CASE("Einspline SPO from HDF NiO a16 97 electrons", "[wavefunction]") lattice.R = {3.94055, 3.94055, 7.8811, 3.94055, 3.94055, -7.8811, -7.8811, 7.8811, 0}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); diff --git a/src/QMCWaveFunctions/tests/test_einset_diamondC.cpp b/src/QMCWaveFunctions/tests/test_einset_diamondC.cpp index 8578f90024..402a6c1bd9 100644 --- a/src/QMCWaveFunctions/tests/test_einset_diamondC.cpp +++ b/src/QMCWaveFunctions/tests/test_einset_diamondC.cpp @@ -30,7 +30,7 @@ using std::string; namespace qmcplusplus { -void test_einset_diamond_1x1x1(bool use_offload) +void test_einset_diamond_1x1x1(bool use_offload, int distributed_ranks = 1, int shared_ranks = 1) { Communicate* c = OHMMS::Controller; @@ -42,7 +42,7 @@ void test_einset_diamond_1x1x1(bool use_offload) lattice.R = {3.37316115, 3.37316115, 0.0, 0.0, 3.37316115, 3.37316115, 3.37316115, 0.0, 3.37316115}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); @@ -71,12 +71,17 @@ void test_einset_diamond_1x1x1(bool use_offload) // add save_coefs="yes" to create an HDF file of spline coefficients for the eval_bspline_spo.py script std::string spo_xml = R"XML( - + + + )XML"; if (!use_offload) spo_xml = std::regex_replace(spo_xml, std::regex("omptarget"), "no"); + spo_xml = std::regex_replace(spo_xml, std::regex("DISTRIBUTED_RANKS"), std::to_string(distributed_ranks)); + spo_xml = std::regex_replace(spo_xml, std::regex("SHARED_RANKS"), std::to_string(shared_ranks)); + Libxml2Document doc; REQUIRE(doc.parseFromString(spo_xml)); @@ -300,6 +305,21 @@ TEST_CASE("Einspline SPO from HDF diamond_1x1x1", "[wavefunction]") { test_einset_diamond_1x1x1(true); test_einset_diamond_1x1x1(false); + Communicate* c = OHMMS::Controller; + if (c->size() % 2 == 0) + { + test_einset_diamond_1x1x1(true, 2, 1); + test_einset_diamond_1x1x1(false, 2, 1); + test_einset_diamond_1x1x1(true, 1, 2); + test_einset_diamond_1x1x1(false, 1, 2); + } + if (c->size() % 6 == 0) + { + test_einset_diamond_1x1x1(true, 2, 3); + test_einset_diamond_1x1x1(false, 2, 3); + test_einset_diamond_1x1x1(true, 3, 2); + test_einset_diamond_1x1x1(false, 3, 2); + } } TEST_CASE("Einspline SPO from HDF diamond_2x1x1 5 electrons", "[wavefunction]") @@ -311,7 +331,7 @@ TEST_CASE("Einspline SPO from HDF diamond_2x1x1 5 electrons", "[wavefunction]") lattice.R = {6.7463223, 6.7463223, 0.0, 0.0, 3.37316115, 3.37316115, 3.37316115, 0.0, 3.37316115}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); diff --git a/src/QMCWaveFunctions/tests/test_einset_spinor.cpp b/src/QMCWaveFunctions/tests/test_einset_spinor.cpp index 13bdf993b7..3a2a7f446e 100644 --- a/src/QMCWaveFunctions/tests/test_einset_spinor.cpp +++ b/src/QMCWaveFunctions/tests/test_einset_spinor.cpp @@ -54,7 +54,7 @@ TEST_CASE("Einspline SpinorSet from HDF", "[wavefunction]") 0.00000000, -6.49690625, 0.00000000, 7.08268015}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); @@ -675,8 +675,8 @@ TEST_CASE("Einspline SpinorSet from HDF", "[wavefunction]") inv_row = {0.1, 0.2, 0.3}; inv_row.updateTo(); std::vector inv_row_ptr(2, spo->isOMPoffload() ? inv_row.device_data() : inv_row.data()); - const auto& ei_table1 = elec_.getDistTableAB(elec_.addTable(ions_)); - const auto& ei_table2 = elec_2.getDistTableAB(elec_2.addTable(ions_)); + const auto& ei_table1 = elec_.getDistTableAB(elec_.addTable(ions_)); + const auto& ei_table2 = elec_2.getDistTableAB(elec_2.addTable(ions_)); ParticleSet::mw_update(p_list); for (int iat = 0; iat < 3; iat++) { diff --git a/src/QMCWaveFunctions/tests/test_hybridrep.cpp b/src/QMCWaveFunctions/tests/test_hybridrep.cpp index 50e64e0f48..a3206a9646 100644 --- a/src/QMCWaveFunctions/tests/test_hybridrep.cpp +++ b/src/QMCWaveFunctions/tests/test_hybridrep.cpp @@ -40,7 +40,7 @@ TEST_CASE("Hybridrep SPO from HDF diamond_1x1x1", "[wavefunction]") lattice.R = {3.37316115, 3.37316115, 0.0, 0.0, 3.37316115, 3.37316115, 3.37316115, 0.0, 3.37316115}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); @@ -199,7 +199,7 @@ TEST_CASE("Hybridrep SPO from HDF diamond_2x1x1", "[wavefunction]") lattice.R = {6.7463223, 6.7463223, 0.0, 0.0, 3.37316115, 3.37316115, 3.37316115, 0.0, 3.37316115}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); diff --git a/src/QMCWaveFunctions/tests/test_pw.cpp b/src/QMCWaveFunctions/tests/test_pw.cpp index 6343ebf604..39e9e0bca6 100644 --- a/src/QMCWaveFunctions/tests/test_pw.cpp +++ b/src/QMCWaveFunctions/tests/test_pw.cpp @@ -36,7 +36,7 @@ TEST_CASE("PlaneWave SPO from HDF for BCC H", "[wavefunction]") lattice.reset(); ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions(*ions_uptr); @@ -137,7 +137,7 @@ TEST_CASE("PlaneWave SPO from HDF for LiH arb", "[wavefunction]") lattice.reset(); ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions(*ions_uptr); diff --git a/src/QMCWaveFunctions/tests/test_spline_applyrotation.cpp b/src/QMCWaveFunctions/tests/test_spline_applyrotation.cpp index 36ba45bf9b..b34e8b3bce 100644 --- a/src/QMCWaveFunctions/tests/test_spline_applyrotation.cpp +++ b/src/QMCWaveFunctions/tests/test_spline_applyrotation.cpp @@ -39,7 +39,7 @@ TEST_CASE("Spline applyRotation zero rotation", "[wavefunction]") lattice.R = {3.37316115, 3.37316115, 0.0, 0.0, 3.37316115, 3.37316115, 3.37316115, 0.0, 3.37316115}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); @@ -176,7 +176,7 @@ TEST_CASE("Spline applyRotation one rotation", "[wavefunction]") lattice.R = {3.37316115, 3.37316115, 0.0, 0.0, 3.37316115, 3.37316115, 3.37316115, 0.0, 3.37316115}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); @@ -386,7 +386,7 @@ TEST_CASE("Spline applyRotation two rotations", "[wavefunction]") lattice.R = {3.37316115, 3.37316115, 0.0, 0.0, 3.37316115, 3.37316115, 3.37316115, 0.0, 3.37316115}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); @@ -691,7 +691,7 @@ TEST_CASE("Spline applyRotation complex rotation", "[wavefunction]") lattice.R = {3.37316115, 3.37316115, 0.0, 0.0, 3.37316115, 3.37316115, 3.37316115, 0.0, 3.37316115}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); diff --git a/src/QMCWaveFunctions/tests/test_spo_collection_input_spline.cpp b/src/QMCWaveFunctions/tests/test_spo_collection_input_spline.cpp index 0aa814592b..b250776300 100644 --- a/src/QMCWaveFunctions/tests/test_spo_collection_input_spline.cpp +++ b/src/QMCWaveFunctions/tests/test_spo_collection_input_spline.cpp @@ -36,7 +36,7 @@ void test_diamond_2x1x1_xml_input(const std::string& spo_xml_string) lattice.R = {6.7463223, 6.7463223, 0.0, 0.0, 3.37316115, 3.37316115, 3.37316115, 0.0, 3.37316115}; ParticleSetPool ptcl = ParticleSetPool(c); - ptcl.setSimulationCell(lattice); + ptcl.createSimulationCellByLattice(lattice); auto ions_uptr = std::make_unique(ptcl.getSimulationCell()); auto elec_uptr = std::make_unique(ptcl.getSimulationCell()); ParticleSet& ions_(*ions_uptr); diff --git a/src/Sandbox/diff_distancetables.cpp b/src/Sandbox/diff_distancetables.cpp index 402e1f04a0..1b5b094206 100644 --- a/src/Sandbox/diff_distancetables.cpp +++ b/src/Sandbox/diff_distancetables.cpp @@ -88,7 +88,8 @@ int main(int argc, char** argv) auto super_lattice(createSuperLattice(create_prim_lattice(), tmat)); super_lattice.LR_rc = 5; - ParticleSet ions(super_lattice), els(super_lattice); + SimulationCell supercell(super_lattice); + ParticleSet ions(supercell), els(supercell); ions.setName("ion0"); els.setName("e"); diff --git a/src/Sandbox/einspline_spo.cpp b/src/Sandbox/einspline_spo.cpp index 5a4893fe7f..77548f316d 100644 --- a/src/Sandbox/einspline_spo.cpp +++ b/src/Sandbox/einspline_spo.cpp @@ -112,9 +112,9 @@ int main(int argc, char** argv) spo_type spo_main; int nTiles = 1; - auto super_lattice(createSuperLattice(create_prim_lattice(), tmat)); + SimulationCell supercell(createSuperLattice(create_prim_lattice(), tmat)); { - ParticleSet ions(super_lattice); + ParticleSet ions(supercell); tile_cell(ions, tmat); const int nions = ions.getTotalNum(); const int nels = count_electrons(ions) / 2; @@ -124,7 +124,7 @@ int main(int argc, char** argv) cout << "\nNumber of orbitals/splines = " << nels << " and Tile size = " << tileSize << " and Number of tiles = " << nTiles << " and Iterations = " << nsteps << endl; spo_main.set(nx, ny, nz, nels, nTiles); - spo_main.Lattice.set(super_lattice.R); + spo_main.Lattice.set(supercell.getLattice().R); } double tInit = 0.0; @@ -156,7 +156,7 @@ int main(int argc, char** argv) //create generator within the thread RandomGenerator random_th(MakeSeed(teamID, np)); - ParticleSet ions(super_lattice), els(super_lattice); + ParticleSet ions(supercell), els(supercell); tile_cell(ions, tmat); const int nions = ions.getTotalNum(); diff --git a/src/Sandbox/einspline_spo_nested.cpp b/src/Sandbox/einspline_spo_nested.cpp index ce29dc9817..ffb453b516 100644 --- a/src/Sandbox/einspline_spo_nested.cpp +++ b/src/Sandbox/einspline_spo_nested.cpp @@ -102,9 +102,9 @@ int main(int argc, char** argv) spo_type spo_main; int nTiles = 1; - auto super_lattice(createSuperLattice(create_prim_lattice(), tmat)); + SimulationCell supercell(createSuperLattice(create_prim_lattice(), tmat)); { - ParticleSet ions(super_lattice); + ParticleSet ions(supercell); tile_cell(ions, tmat); const int nions = ions.getTotalNum(); const int nels = count_electrons(ions) / 2; @@ -114,7 +114,7 @@ int main(int argc, char** argv) cout << "\nNumber of orbitals/splines = " << nels << " and Tile size = " << tileSize << " and Number of tiles = " << nTiles << " and Iterations = " << nsteps << endl; spo_main.set(nx, ny, nz, nels, nTiles); - spo_main.Lattice.set(super_lattice.R); + spo_main.Lattice.set(supercell.getLattice().R); } double tInit = 0.0; @@ -134,7 +134,7 @@ int main(int argc, char** argv) //create generator within the thread RandomGenerator random_th(MakeSeed(ip, np)); - ParticleSet ions(super_lattice), els(super_lattice); + ParticleSet ions(supercell), els(supercell); tile_cell(ions, tmat); const int nions = ions.getTotalNum(); diff --git a/src/Sandbox/input/graphite.hpp b/src/Sandbox/input/graphite.hpp index 71d1b8a4a4..c024b0c21c 100644 --- a/src/Sandbox/input/graphite.hpp +++ b/src/Sandbox/input/graphite.hpp @@ -33,10 +33,10 @@ inline auto create_prim_lattice() */ void tile_cell(ParticleSet& ions, Tensor& tmat) { - auto prim_lat(create_prim_lattice()); + SimulationCell sim_cell(create_prim_lattice()); // create Ni and O by group std::vector graphite_group{4}; - ParticleSet prim_ions(prim_lat); + ParticleSet prim_ions(sim_cell); // create particles by groups prim_ions.create(graphite_group); // using lattice coordinates diff --git a/src/Sandbox/restart.cpp b/src/Sandbox/restart.cpp index ffbb5b861d..8bfdeb28ef 100644 --- a/src/Sandbox/restart.cpp +++ b/src/Sandbox/restart.cpp @@ -128,14 +128,14 @@ int main(int argc, char** argv) int nptcl = 0; double t0 = 0.0, t1 = 0.0; - auto super_lattice(createSuperLattice(create_prim_lattice(), tmat)); - ParticleSet ions(super_lattice); + SimulationCell supercell(createSuperLattice(create_prim_lattice(), tmat)); + ParticleSet ions(supercell); tile_cell(ions, tmat); auto& rnc_children = RandomNumberControl::getChildren(); std::vector mt(Random.state_size(), 0); std::vector> mt_children(NumThreads, mt); - std::vector elecs(NumThreads, MCWalkerConfiguration(super_lattice)); + std::vector elecs(NumThreads, MCWalkerConfiguration(supercell)); #pragma omp parallel reduction(+ : t0) { diff --git a/src/Utilities/for_testing/NativeInitializerPrint.hpp b/src/Utilities/for_testing/NativeInitializerPrint.hpp index 2c92fb61fc..5802b63b6d 100644 --- a/src/Utilities/for_testing/NativeInitializerPrint.hpp +++ b/src/Utilities/for_testing/NativeInitializerPrint.hpp @@ -89,8 +89,8 @@ inline std::ostream& operator<<(std::ostream& out, const NativePrint -inline std::ostream& operator<<(std::ostream& out, const NativePrint>& np_vec) +template +inline std::ostream& operator<<(std::ostream& out, const NativePrint>& np_vec) { out << "{ "; auto vec = np_vec.get_obj(); @@ -103,6 +103,7 @@ inline std::ostream& operator<<(std::ostream& out, const NativePrint>& return out; } + template inline std::ostream& operator<<( std::ostream& out, diff --git a/src/integration_testing/MockGoldWalkerElements.cpp b/src/integration_testing/MockGoldWalkerElements.cpp index acb8e6642c..d80fe81f2c 100644 --- a/src/integration_testing/MockGoldWalkerElements.cpp +++ b/src/integration_testing/MockGoldWalkerElements.cpp @@ -37,6 +37,15 @@ MockGoldWalkerElements makeGoldWalkerElementsWithEE(Communicate* comm, RuntimeOp return MockGoldWalkerElements(comm, runtime_opt, wfp_diamondC, hamp_ee); } +MockGoldWalkerElements makeGoldWalkerElementsWithEI(Communicate* comm, RuntimeOptions runtime_opt) +{ + using namespace std::placeholders; + MockGoldWalkerElements::WaveFunctionPoolFactoryFunc wfp_diamondC = + std::bind(MinimalWaveFunctionPool::make_diamondC_1x1x1, _1, _2, _3); + MockGoldWalkerElements::HamPoolFactoryFunc hamp_ei = std::bind(MinimalHamiltonianPool::makeHamWithEI, _1, _2, _3); + return MockGoldWalkerElements(comm, runtime_opt, wfp_diamondC, hamp_ei); +} + MockGoldWalkerElements makeGoldWalkerElementsWithEEEI(Communicate* comm, RuntimeOptions runtime_opt) { using namespace std::placeholders; diff --git a/src/integration_testing/MockGoldWalkerElements.h b/src/integration_testing/MockGoldWalkerElements.h index 6e616fd8c2..5abe74e2f2 100644 --- a/src/integration_testing/MockGoldWalkerElements.h +++ b/src/integration_testing/MockGoldWalkerElements.h @@ -55,6 +55,10 @@ class MockGoldWalkerElements * electron interaction and electron ion interaction */ MockGoldWalkerElements makeGoldWalkerElementsWithEE(Communicate*, RuntimeOptions run_time_opt); +/** make walker elements with primary hamiltonian with Coulombic electron + * ion interaction + */ +MockGoldWalkerElements makeGoldWalkerElementsWithEI(Communicate*, RuntimeOptions run_time_opt); /** make walker elements with a primary hamiltonian with Coulombic electron * electron interaction and electron ion interaction and ion ion interaction. */ diff --git a/src/spline2/CMakeLists.txt b/src/spline2/CMakeLists.txt index 52003db406..231265d9de 100644 --- a/src/spline2/CMakeLists.txt +++ b/src/spline2/CMakeLists.txt @@ -10,7 +10,7 @@ #////////////////////////////////////////////////////////////////////////////////////// -add_library(spline2_omptarget OBJECT MultiBsplineOffload.cpp) +add_library(spline2_omptarget OBJECT MultiBsplineOffload.cpp MultiBsplineOffloadMapper.cpp) target_link_libraries(spline2_omptarget PUBLIC einspline platform_runtime) set(SPLINE2_SRC MultiBspline.cpp MultiBspline1D.cpp SplineUtils.cpp) diff --git a/src/spline2/MultiBsplineBase.hpp b/src/spline2/MultiBsplineBase.hpp index 2c28515cd4..aeda20b184 100644 --- a/src/spline2/MultiBsplineBase.hpp +++ b/src/spline2/MultiBsplineBase.hpp @@ -45,7 +45,7 @@ class MultiBsplineBase using BoundaryCondition = typename bspline_traits::BCType; ///actual vector of einspline multi-bspline objects std::vector spline_blocks; - + ///index offsets of spline_blocks. const std::vector offsets_; MultiBsplineBase(const std::vector& offsets) : offsets_(offsets) {} @@ -128,12 +128,14 @@ class MultiBsplineBase } public: - MultiBsplineBase() = default; MultiBsplineBase(const MultiBsplineBase& in) = delete; MultiBsplineBase& operator=(const MultiBsplineBase& in) = delete; virtual ~MultiBsplineBase() = default; + size_t getNumBlocks() const { return spline_blocks.size(); } + const auto& getBlockOffsets() const { return offsets_; } + SplineType* getSplinePtr() { if (spline_blocks.size() != 1) @@ -141,11 +143,11 @@ class MultiBsplineBase return spline_blocks[0]; } - void flush_zero() const - { - for (auto spline_m : spline_blocks) - std::fill(spline_m->coefs, spline_m->coefs + spline_m->coefs_size, T(0)); - } + SplineType& getBlock(size_t iblock) { return *spline_blocks[iblock]; } + const SplineType& getBlock(size_t iblock) const { return *spline_blocks[iblock]; } + + void flush_zero(size_t iblock = 0) const + { std::fill(spline_blocks[iblock]->coefs, spline_blocks[iblock]->coefs + spline_blocks[iblock]->coefs_size, T(0)); } size_t num_splines() const { @@ -167,7 +169,7 @@ class MultiBsplineBase { size_t num_T = 0; for (auto spline_m : spline_blocks) - num_T += spline_m->coefs_size * sizeof(T); + num_T += spline_m->coefs_size; return num_T * sizeof(T); } diff --git a/src/spline2/MultiBsplineEval.hpp b/src/spline2/MultiBsplineEval.hpp index afb8327544..2549644f02 100644 --- a/src/spline2/MultiBsplineEval.hpp +++ b/src/spline2/MultiBsplineEval.hpp @@ -41,22 +41,16 @@ namespace spline2 /// evaluate values optionally in the range [first,last) template inline void evaluate3d(const SPLINET& spline, const PT& r, VT& psi) -{ - evaluate_v_impl(spline, r[0], r[1], r[2], psi.data(), 0, psi.size()); -} +{ evaluate_v_impl(spline, r[0], r[1], r[2], psi.data(), 0, psi.size()); } template inline void evaluate3d(const SPLINET& spline, const PT& r, VT& psi, int first, int last) -{ - evaluate_v_impl(spline, r[0], r[1], r[2], psi.data() + first, first, last); -} +{ evaluate_v_impl(spline, r[0], r[1], r[2], psi.data() + first, first, last); } /// evaluate values, gradients, laplacians optionally in the range [first,last) template inline void evaluate3d_vgl(const SPLINET& spline, const PT& r, VT& psi, GT& grad, LT& lap) -{ - evaluate_vgl_impl(spline, r[0], r[1], r[2], psi.data(), grad.data(), lap.data(), psi.size(), 0, psi.size()); -} +{ evaluate_vgl_impl(spline, r[0], r[1], r[2], psi.data(), grad.data(), lap.data(), psi.size(), 0, psi.size()); } template inline void evaluate3d_vgl(const SPLINET& spline, const PT& r, VT& psi, GT& grad, LT& lap, int first, int last) @@ -68,9 +62,7 @@ inline void evaluate3d_vgl(const SPLINET& spline, const PT& r, VT& psi, GT& grad /// evaluate values, gradients, hessians optionally in the range [first,last) template inline void evaluate3d_vgh(const SPLINET& spline, const PT& r, VT& psi, GT& grad, HT& hess) -{ - evaluate_vgh_impl(spline, r[0], r[1], r[2], psi.data(), grad.data(), hess.data(), psi.size(), 0, psi.size()); -} +{ evaluate_vgh_impl(spline, r[0], r[1], r[2], psi.data(), grad.data(), hess.data(), psi.size(), 0, psi.size()); } template inline void evaluate3d_vgh(const SPLINET& spline, const PT& r, VT& psi, GT& grad, HT& hess, int first, int last) @@ -88,13 +80,13 @@ inline void evaluate3d_vghgh(const SPLINET& spline, const PT& r, VT& psi, GT& gr template inline void evaluate3d_vghgh(const SPLINET& spline, - const PT& r, - VT& psi, - GT& grad, - HT& hess, - GHT& ghess, - int first, - int last) + const PT& r, + VT& psi, + GT& grad, + HT& hess, + GHT& ghess, + int first, + int last) { evaluate_vghgh_impl(spline, r[0], r[1], r[2], psi.data() + first, grad.data() + first, hess.data() + first, ghess.data() + first, psi.size(), first, last); diff --git a/src/spline2/MultiBsplineMPIShared.hpp b/src/spline2/MultiBsplineMPIShared.hpp index 195e4f7b16..b3d6eb1bce 100644 --- a/src/spline2/MultiBsplineMPIShared.hpp +++ b/src/spline2/MultiBsplineMPIShared.hpp @@ -35,26 +35,31 @@ class MultiBsplineMPIShared : public MultiBsplineBase private: using Base = MultiBsplineBase; using Alloc = aligned_allocator; - ///use allocator - Alloc coefs_allocator; - + /// communicator covering all the ranks included distributed and shared. ranks with distributed splines are contiguous. const std::unique_ptr comm_; MPI_Win win; + /// number of ranks among which splines are distributed. + const unsigned distributed_ranks_; using Base::offsets_; public: template - MultiBsplineMPIShared(const Ugrid grid[3], const BCT& bc, size_t num_splines, std::unique_ptr&& comm_distributed) - : Base(FairDivideAligned>(num_splines, getAlignment(), comm_distributed->size())), comm_(std::move(comm_distributed)) + MultiBsplineMPIShared(const Ugrid grid[3], + const BCT& bc, + size_t num_splines, + std::unique_ptr&& comm_distributed_and_shared, + unsigned distributed_ranks) + : Base(FairDivideAligned>(num_splines, getAlignment(), distributed_ranks)), + comm_(std::move(comm_distributed_and_shared)), + distributed_ranks_(distributed_ranks) { - auto& comm = *comm_; + auto& comm = *comm_; const auto comm_rank = comm.rank(); - const auto comm_size = comm.size(); - Base::spline_blocks.resize(comm_size, nullptr); - for (int i = 0; i < comm_size; i++) + Base::spline_blocks.resize(distributed_ranks_, nullptr); + for (int i = 0; i < distributed_ranks_; i++) { const auto num_splines = offsets_[i + 1] - offsets_[i]; auto* spline_m = new typename Base::SplineType; @@ -63,23 +68,25 @@ class MultiBsplineMPIShared : public MultiBsplineBase getAlignedSize(num_splines)); } - MPI_Info info; MPI_Info_create(&info); MPI_Info_set(info, "alloc_shared_noncontig", "true"); MPI_Info_set(info, "mpi_minimum_memory_alignment", std::to_string(Alloc::alignment).c_str()); - auto& spline_owned = *Base::spline_blocks[comm_rank]; + auto& spline_owned = *Base::spline_blocks[comm_rank % distributed_ranks_]; + // Only the members of the first group of distributed ranks allocate memory. + // Other ranks are considered references and hence size = 0 is valid. + const MPI_Aint allocation_size = + comm_rank < distributed_ranks_ ? spline_owned.coefs_size * sizeof(T) + Alloc::alignment : 0; void* coefs = nullptr; - auto err = MPI_Win_allocate_shared(spline_owned.coefs_size * sizeof(T) + Alloc::alignment, sizeof(T), info, - comm.getMPI(), &coefs, &win); + auto err = MPI_Win_allocate_shared(allocation_size, sizeof(T), info, comm.getMPI(), &coefs, &win); MPI_Info_free(&info); if (err != MPI_SUCCESS) throw UniformCommunicateError("MultiBsplineMPIShared::MultiBsplineMPIShared MPI_Win_allocate_shared failed!"); spline_owned.coefs = (T*)coefs; - for (int i = 0; i < comm_size; i++) + for (int i = 0; i < distributed_ranks_; i++) { MPI_Aint size; int disp_unit; diff --git a/src/spline2/MultiBsplineOffloadMapper.cpp b/src/spline2/MultiBsplineOffloadMapper.cpp new file mode 100644 index 0000000000..566bf2995f --- /dev/null +++ b/src/spline2/MultiBsplineOffloadMapper.cpp @@ -0,0 +1,151 @@ +////////////////////////////////////////////////////////////////////////////////////// +// This file is distributed under the University of Illinois/NCSA Open Source License. +// See LICENSE file in top directory for details. +// +// Copyright (c) 2026 QMCPACK developers. +// +// File developed by: Ye Luo, yeluo@anl.gov, Argonne National Laboratory +// +// File created by: Ye Luo, yeluo@anl.gov, Argonne National Laboratory +////////////////////////////////////////////////////////////////////////////////////// + + +#include "MultiBsplineOffloadMapper.hpp" +#include "MultiBsplineEval_OMPoffload.hpp" +#include "OMPTarget/OMPTargetMath.hpp" + +namespace qmcplusplus +{ +template +MultiBsplineOffloadMapper::MultiBsplineOffloadMapper(const HostBspline& host_bsplines) + : host_bsplines_(host_bsplines) +{ + block_coefs_.reserve(host_bsplines_.getNumBlocks()); + for (int ib = 0; ib < host_bsplines_.getNumBlocks(); ib++) + { + auto* coefs = host_bsplines_.getBlock(ib).coefs; + block_coefs_.push_back(coefs); + } +} + +template +void MultiBsplineOffloadMapper::mapToDevice() +{ + for (int ib = 0; ib < host_bsplines_.getNumBlocks(); ib++) + { + auto* spline_m = &host_bsplines_.getBlock(ib); + auto* coefs = block_coefs_[ib]; + PRAGMA_OFFLOAD("omp target enter data map(to: spline_m[:1]) map(alloc: coefs[:spline_m->coefs_size])") + } +} + +template +MultiBsplineOffloadMapper::~MultiBsplineOffloadMapper() +{ + for (int ib = 0; ib < host_bsplines_.getNumBlocks(); ib++) + { + auto* spline_m = &host_bsplines_.getBlock(ib); + auto* coefs = block_coefs_[ib]; + PRAGMA_OFFLOAD("omp target exit data map(delete: spline_m[:1]) map(delete: coefs[:spline_m->coefs_size])") + } +} + +template +void MultiBsplineOffloadMapper::updateToDevice() +{ + for (int ib = 0; ib < host_bsplines_.getNumBlocks(); ib++) + { + auto* spline_m = &host_bsplines_.getBlock(ib); + auto* coefs = block_coefs_[ib]; + PRAGMA_OFFLOAD("omp target update to(coefs[:spline_m->coefs_size])") + } +} + +template +void MultiBsplineOffloadMapper::mw_evaluate_v(int num_pos, T* pos_arr, T* spline_v, size_t walker_stride) +{ + const auto block_offsets = host_bsplines_.getBlockOffsets(); + for (size_t ib = 0; ib < host_bsplines_.getNumBlocks(); ib++) + { + const auto& host_block = host_bsplines_.getBlock(ib); + if (host_block.num_splines == 0) + continue; + + const size_t num_splines = host_block.num_splines; + const size_t ChunkSizePerTeam = 512; + const int NumTeams = (num_splines + ChunkSizePerTeam - 1) / ChunkSizePerTeam; + + // Ye: need to extract sizes and pointers before entering target region + const auto* spline_ptr = &host_block; + const auto* spline_coefs = block_coefs_[ib]; + const auto block_offset = block_offsets[ib]; + + PRAGMA_OFFLOAD("omp target teams distribute collapse(2) num_teams(NumTeams * num_pos)") + for (int iw = 0; iw < num_pos; iw++) + for (int team_id = 0; team_id < NumTeams; team_id++) + { + const size_t first = ChunkSizePerTeam * team_id; + const size_t last = omptarget::min(first + ChunkSizePerTeam, num_splines); + + auto* spline_v_iw = spline_v + walker_stride * iw; + int ix, iy, iz; + T a[4], b[4], c[4]; + spline2::computeLocationAndFractional(spline_ptr, pos_arr[iw * 3], pos_arr[iw * 3 + 1], pos_arr[iw * 3 + 2], ix, + iy, iz, a, b, c); + + PRAGMA_OFFLOAD("omp parallel for") + for (int index = 0; index < last - first; index++) + spline2offload::evaluate_v_impl_v2(spline_ptr, spline_coefs, ix, iy, iz, first + index, a, b, c, + spline_v_iw + block_offset + first + index); + } + } +} + +template +void MultiBsplineOffloadMapper::mw_evaluate_vgh(int num_pos, + T* pos_arr, + T* spline_vgh, + size_t walker_stride, + size_t field_stride) +{ + const auto block_offsets = host_bsplines_.getBlockOffsets(); + for (size_t ib = 0; ib < host_bsplines_.getNumBlocks(); ib++) + { + const auto& host_block = host_bsplines_.getBlock(ib); + if (host_block.num_splines == 0) + continue; + + const size_t num_splines = host_block.num_splines; + const size_t ChunkSizePerTeam = 512; + const int NumTeams = (num_splines + ChunkSizePerTeam - 1) / ChunkSizePerTeam; + + // Ye: need to extract sizes and pointers before entering target region + const auto* spline_ptr = &host_block; + const auto* spline_coefs = block_coefs_[ib]; + const auto block_offset = block_offsets[ib]; + + PRAGMA_OFFLOAD("omp target teams distribute collapse(2) num_teams(NumTeams * num_pos)") + for (int iw = 0; iw < num_pos; iw++) + for (int team_id = 0; team_id < NumTeams; team_id++) + { + const size_t first = ChunkSizePerTeam * team_id; + const size_t last = omptarget::min(first + ChunkSizePerTeam, num_splines); + + auto* spline_vgh_iw = spline_vgh + walker_stride * iw; + int ix, iy, iz; + T a[4], b[4], c[4], da[4], db[4], dc[4], d2a[4], d2b[4], d2c[4]; + spline2::computeLocationAndFractional(spline_ptr, pos_arr[iw * 3], pos_arr[iw * 3 + 1], pos_arr[iw * 3 + 2], ix, + iy, iz, a, b, c, da, db, dc, d2a, d2b, d2c); + + PRAGMA_OFFLOAD("omp parallel for") + for (int index = 0; index < last - first; index++) + spline2offload::evaluate_vgh_impl_v2(spline_ptr, spline_coefs, ix, iy, iz, first + index, a, b, c, da, db, dc, + d2a, d2b, d2c, spline_vgh_iw + block_offset + first + index, + field_stride); + } + } +} + +template class MultiBsplineOffloadMapper; +template class MultiBsplineOffloadMapper; +} // namespace qmcplusplus diff --git a/src/spline2/MultiBsplineOffloadMapper.hpp b/src/spline2/MultiBsplineOffloadMapper.hpp new file mode 100644 index 0000000000..597f562b29 --- /dev/null +++ b/src/spline2/MultiBsplineOffloadMapper.hpp @@ -0,0 +1,66 @@ +////////////////////////////////////////////////////////////////////////////////////// +// This file is distributed under the University of Illinois/NCSA Open Source License. +// See LICENSE file in top directory for details. +// +// Copyright (c) 2026 QMCPACK developers. +// +// File developed by: Ye Luo, yeluo@anl.gov, Argonne National Laboratory +// +// File created by: Ye Luo, yeluo@anl.gov, Argonne National Laboratory +////////////////////////////////////////////////////////////////////////////////////// + + +#ifndef QMCPLUSPLUS_MULTIEINSPLINEOFFLOADMAPPER_HPP +#define QMCPLUSPLUS_MULTIEINSPLINEOFFLOADMAPPER_HPP + +#include "MultiBsplineBase.hpp" +#include + +namespace qmcplusplus +{ +/** A mapper class to map host spline coeficients to devices and handle multi-walker evaluation. + * @tparam T the precision of splines + */ +template +class MultiBsplineOffloadMapper +{ + using HostBspline = MultiBsplineBase; + + /// reference to a host spline object. + const HostBspline& host_bsplines_; + /// array of host coefficient pointers for all the blocks. + std::vector block_coefs_; + +public: + MultiBsplineOffloadMapper(const HostBspline& host_bsplines); + + ~MultiBsplineOffloadMapper(); + + /// map host coefficients to devices + virtual void mapToDevice(); + + /// update device coeficients + void updateToDevice(); + + /** evaluate spline values + * @param num_pos, number of electron positions + * @param pos_arr, array of electron positions [num_pos, 3] + * @param spline_v, result pointer + * @param walker_stride, result distance between two positions + */ + void mw_evaluate_v(int num_pos, T* pos_arr, T* spline_v, size_t walker_stride); + /** evaluate spline value, gradients and hessian. + * @param num_pos, number of electron positions + * @param pos_arr, array of electron positions [num_pos, 3] + * @param spline_vgh, result pointer + * @param walker_stride, result distance between two positions + * @param filed_stride, result distance of value, gradients and hessian fields for a given electron position. + */ + void mw_evaluate_vgh(int num_pos, T* pos_arr, T* spline_vgh, size_t walker_stride, size_t field_stride); +}; + +extern template class MultiBsplineOffloadMapper; +extern template class MultiBsplineOffloadMapper; +} // namespace qmcplusplus + +#endif diff --git a/src/spline2/MultiBsplineVGLH_OMPoffload.hpp b/src/spline2/MultiBsplineVGLH_OMPoffload.hpp index 03f7115ecd..b13bd0d159 100644 --- a/src/spline2/MultiBsplineVGLH_OMPoffload.hpp +++ b/src/spline2/MultiBsplineVGLH_OMPoffload.hpp @@ -267,6 +267,7 @@ inline void evaluate_vgh_impl(const typename qmcplusplus::bspline_traits:: */ template inline void evaluate_vgh_impl_v2(const typename qmcplusplus::bspline_traits::SplineType* restrict spline_m, + const T* restrict spline_coefs, int ix, int iy, int iz, @@ -301,7 +302,7 @@ inline void evaluate_vgh_impl_v2(const typename qmcplusplus::bspline_traitscoefs + ((ix + i) * xs + (iy + j) * ys + iz * zs); + const T* restrict coefs = spline_coefs + ((ix + i) * xs + (iy + j) * ys + iz * zs); const T coefsv = coefs[index]; const T coefsvzs = coefs[index + zs]; const T coefsv2zs = coefs[index + 2 * zs]; diff --git a/src/spline2/MultiBsplineValue_OMPoffload.hpp b/src/spline2/MultiBsplineValue_OMPoffload.hpp index 9604343e4a..c4a59ec2d7 100644 --- a/src/spline2/MultiBsplineValue_OMPoffload.hpp +++ b/src/spline2/MultiBsplineValue_OMPoffload.hpp @@ -70,6 +70,7 @@ inline void evaluate_v_impl(const typename qmcplusplus::bspline_traits::Sp */ template inline void evaluate_v_impl_v2(const typename qmcplusplus::bspline_traits::SplineType* restrict spline_m, + const T* restrict spline_coefs, int ix, int iy, int iz, @@ -87,7 +88,7 @@ inline void evaluate_v_impl_v2(const typename qmcplusplus::bspline_traits: for (int i = 0; i < 4; i++) for (int j = 0; j < 4; j++) { - const T* restrict coefs = spline_m->coefs + ((ix + i) * xs + (iy + j) * ys + iz * zs); + const T* restrict coefs = spline_coefs + ((ix + i) * xs + (iy + j) * ys + iz * zs); val += a[i] * b[j] * (c[0] * coefs[index] + c[1] * coefs[index + zs] + c[2] * coefs[index + zs * 2] + c[3] * coefs[index + zs * 3]); diff --git a/src/spline2/SplineUtils.cpp b/src/spline2/SplineUtils.cpp index 19c5e580e2..09325c080e 100644 --- a/src/spline2/SplineUtils.cpp +++ b/src/spline2/SplineUtils.cpp @@ -11,6 +11,8 @@ #include "SplineUtils.h" #include +#include "spline2/MultiBsplineBase.hpp" +#include "spline2/MultiBspline1D.hpp" #include "spline2/einspline_engine.hpp" #include "spline2/einspline_util.hpp" @@ -20,18 +22,32 @@ template bool SplineUtils::read(MultiBsplineBase& spline, hdf_archive& h5f) { std::ostringstream o; - o << "spline_" << my_index; - einspline_engine bigtable(*spline.getSplinePtr()); - return h5f.readEntry(bigtable, o.str()); + bool success = true; + int my_index = 0; + do + { + o << "spline_" << my_index; + einspline_engine bigtable(spline.getBlock(my_index)); + success = h5f.readEntry(bigtable, o.str()); + my_index++; + } while (my_index < spline.getNumBlocks() && success); + return success; } template bool SplineUtils::write(MultiBsplineBase& spline, hdf_archive& h5f) { std::ostringstream o; - o << "spline_" << my_index; - einspline_engine bigtable(*spline.getSplinePtr()); - return h5f.writeEntry(bigtable, o.str()); + bool success = true; + int my_index = 0; + do + { + o << "spline_" << my_index; + einspline_engine bigtable(spline.getBlock(my_index)); + success = h5f.writeEntry(bigtable, o.str()); + my_index++; + } while (my_index < spline.getNumBlocks() && success); + return success; } template @@ -49,19 +65,23 @@ bool SplineUtils::write(MultiBspline1D& spline, hdf_archive& h5f) } template -void SplineUtils::gatherv(MultiBsplineBase& spline, const std::vector& offset, Communicate& comm) +void SplineUtils::gatherv(MultiBsplineBase& spline, + size_t iblock, + const std::vector& offset, + Communicate& comm) { if (comm.size() == 1) return; - qmcplusplus::gatherv(&comm, spline.getSplinePtr(), spline.getSplinePtr()->z_stride, offset); + auto& spline_block = spline.getBlock(iblock); + qmcplusplus::gatherv(&comm, &spline_block, spline_block.z_stride, offset); } template -void SplineUtils::bcast(MultiBsplineBase& spline, Communicate& comm) +void SplineUtils::bcast(MultiBsplineBase& spline, size_t iblock, Communicate& comm) { if (comm.size() == 1) return; - chunked_bcast(&comm, spline.getSplinePtr()); + chunked_bcast(&comm, &spline.getBlock(iblock)); } template diff --git a/src/spline2/SplineUtils.h b/src/spline2/SplineUtils.h index 3401072090..0fae2daabe 100644 --- a/src/spline2/SplineUtils.h +++ b/src/spline2/SplineUtils.h @@ -14,17 +14,18 @@ #define QMCPLUSPLUS_SPLINE_UTILS_H #include "hdf/hdf_archive.h" -#include "spline2/MultiBsplineBase.hpp" -#include "spline2/MultiBspline1D.hpp" #include "Message/Communicate.h" namespace qmcplusplus { +template +class MultiBsplineBase; +template +class MultiBspline1D; + template class SplineUtils { - static constexpr size_t my_index = 0; - public: static bool read(MultiBsplineBase& spline, hdf_archive& h5f); static bool write(MultiBsplineBase& spline, hdf_archive& h5f); @@ -32,8 +33,8 @@ class SplineUtils static bool read(MultiBspline1D& spline, hdf_archive& h5f); static bool write(MultiBspline1D& spline, hdf_archive& h5f); - static void gatherv(MultiBsplineBase& spline, const std::vector& offset, Communicate& comm); - static void bcast(MultiBsplineBase& spline, Communicate& comm); + static void gatherv(MultiBsplineBase& spline, size_t iblock, const std::vector& offset, Communicate& comm); + static void bcast(MultiBsplineBase& spline, size_t iblock, Communicate& comm); static void gatherv(MultiBspline1D& spline, size_t stride, const std::vector& offset, Communicate& comm); static void bcast(MultiBspline1D& spline, Communicate& comm); diff --git a/src/spline2/tests/CMakeLists.txt b/src/spline2/tests/CMakeLists.txt index c26171e995..a6915cda33 100644 --- a/src/spline2/tests/CMakeLists.txt +++ b/src/spline2/tests/CMakeLists.txt @@ -23,5 +23,8 @@ if(HAVE_MPI) target_link_libraries(${UTEST_EXE} message) endif() target_link_libraries(${UTEST_EXE} catch_main spline2 einspline qmcutil) +if(USE_OBJECT_TARGET) + target_link_libraries(${UTEST_EXE} spline2_omptarget) +endif() add_unit_test(${UTEST_NAME} 1 1 $) diff --git a/src/spline2/tests/bspline_funcs.py b/src/spline2/tests/bspline_funcs.py index 15bc9b688d..97bdfccbf4 100644 --- a/src/spline2/tests/bspline_funcs.py +++ b/src/spline2/tests/bspline_funcs.py @@ -1,86 +1,157 @@ +"""Collection of routines for generating symbolic spline functions +Some of these routines should be common with QMCWavefunctions/tests/gen_bspline_jastrow.py +""" -from sympy import * from collections import defaultdict -# Collection of routines for generating symbolic spline functions -# Some of these routines should be common with QMCWavefunctions/tests/gen_bspline_jastrow.py +from sympy import ( + And, + Expr, + IndexedBase, + Interval, + Piecewise, + Symbol, + bspline_basis_set, +) + + +def _infer_position_symbol(ival: And) -> Symbol: + """Infer the spline coordinate from an interval condition.""" + symbols = sorted([s for s in ival.free_symbols if s.name != "Delta"], key=lambda s: s.name) + if len(symbols) != 1: + raise ValueError(f"expected one spline coordinate in {ival}, found {symbols}") + return symbols[0] + + +def to_interval(ival: And, xs: Symbol | None = None) -> Interval: + """Convert relational expression to an Interval.""" + if xs is None: + xs = _infer_position_symbol(ival) -def to_interval(ival): - """Convert relational expression to an Interval""" min_val = None - lower_open = False max_val = None - upper_open = True - if isinstance(ival, And): - for rel in ival.args: - if isinstance(rel, StrictGreaterThan): - min_val = rel.args[1] - #lower_open = True - elif isinstance(rel, GreaterThan): - min_val = rel.args[1] - #lower_open = False - elif isinstance(rel, StrictLessThan): - max_val = rel.args[1] - #upper_open = True - elif isinstance(rel, LessThan): - max_val = rel.args[1] - #upper_open = False + rels = ival.args if isinstance(ival, And) else (ival,) + + for rel in rels: + expr = (rel.lhs - rel.rhs).expand() + coeff = expr.coeff(xs) + if coeff == 0: + raise ValueError(f"relation does not constrain {xs}: {rel}") + + rest = (expr - coeff * xs).expand() + bound = (-rest / coeff).simplify() + + if coeff.is_positive: + if rel.rel_op in ("<", "<="): + max_val = bound + elif rel.rel_op in (">", ">="): + min_val = bound else: - print('unhandled ',rel) + raise ValueError(f"unhandled relation: {rel}") + elif coeff.is_negative: + if rel.rel_op in ("<", "<="): + min_val = bound + elif rel.rel_op in (">", ">="): + max_val = bound + else: + raise ValueError(f"unhandled relation: {rel}") + else: + raise ValueError(f"could not determine coefficient sign for {xs}: {rel}") + + if min_val is None or max_val is None: + raise ValueError(f"could not determine interval bounds from {ival}") + return Interval(min_val, max_val, False, True) - if min_val == None or max_val == None: - print('error',ival) - return Interval(min_val, max_val, lower_open, upper_open) -# Transpose the interval and coefficients -# Note that interval [0,1) has the polynomial coefficients found in the einspline code -# The other intervals could be shifted, and they would also have the same polynomials -def transpose_interval_and_coefficients(sym_basis): +def transpose_interval_and_coefficients( + sym_basis: list[Piecewise], xs: Symbol | None = None +) -> defaultdict[Interval, tuple[int, Expr] | list]: + """Transpose the interval and coefficients. + + Parameters + ---------- + sym_basis : list of Piecewise + 3rd-order bspline basis. + (output of ``sympy.bspline_basis_set(d, knots, x)`` with ``d=3``) + + Notes + ----- + The interval [0,1) has the polynomial coefficients found in the + einspline code. The other intervals could be shifted, and they would + also have the same polynomials. + """ cond_map = defaultdict(list) - i1 = Interval(0,5, False, False) # interval for evaluation + i1 = Interval(0, 5, False, False) # Interval for evaluation for idx, s0 in enumerate(sym_basis): for expr, cond in s0.args: - if cond != True: - i2 = to_interval(cond) - if not i1.is_disjoint(i2): - cond_map[i2].append( (idx, expr) ) + if cond == True: + continue + + i2 = to_interval(cond, xs) + if not i1.is_disjoint(i2): + cond_map[i2].append((idx, expr)) return cond_map -# Create piecewise expression from the transposed intervals -# basis_map - map of interval to list of spline expressions for that interval -# c - coefficient symbol (needs to allow indexing) -# xs - symbol for the position variable ('x') -def recreate_piecewise(basis_map, c, xs): + +def recreate_piecewise(basis_map: dict, c: IndexedBase, xs: Symbol) -> Piecewise: + """Create piecewise expression from the transposed intervals. + + Parameters + ---------- + basis_map : dict + Map of interval to list of spline expressions for that interval. + c : IndexedBase + Coefficient symbol (needs to allow indexing). + xs : Symbol + Symbol for the position variable ('x'). + + See Also + -------- + transpose_interval_and_coefficients + """ + args = [] for cond, exprs in basis_map.items(): e = 0 for idx, b in exprs: e += c[idx] * b - args.append( (e, cond.as_relational(xs))) + args.append((e, cond.as_relational(xs))) args.append((0, True)) return Piecewise(*args) -# Get the values corresponding to the interval starting at 0 -# basis_map - map of interval to list of spline expressions for that interval -def get_base_interval(basis_map): +def get_base_interval( + basis_map: dict[Interval, tuple[int, Expr]] +) -> tuple[int, Expr] | None: + """Get the values corresponding to the interval starting at 0. + + Parameters + ---------- + basis_map : dict + Map of interval to list of spline expressions for that interval. + """ for cond, exprs in basis_map.items(): if cond.start == 0: return exprs return None -# Create a set of spline functions -def create_spline(nknots, xs, c, Delta): - Delta = Symbol('Delta', positive=True) - all_knots = [i*Delta for i in range(-3, nknots+3)] - - # Third-order bspline - sym_basis = bspline_basis_set(3, all_knots, xs) - cond_map = transpose_interval_and_coefficients(sym_basis) - spline = recreate_piecewise(cond_map, c, xs) +def create_spline( + nknots: int, + xs: Symbol, + c: IndexedBase, + Delta: Symbol | None = None, +) -> Piecewise: + """Create a set of spline functions.""" + if Delta is None: + Delta = Symbol('Delta', positive=True) + all_knots = [i*Delta for i in range(-3, nknots+3)] - return spline + # Third-order bspline + sym_basis = bspline_basis_set(3, all_knots, xs) + cond_map = transpose_interval_and_coefficients(sym_basis, xs) + spline = recreate_piecewise(cond_map, c, xs) + return spline diff --git a/src/spline2/tests/gen_bspline_values.py b/src/spline2/tests/gen_bspline_values.py index 3664a43478..b7be7ddda5 100644 --- a/src/spline2/tests/gen_bspline_values.py +++ b/src/spline2/tests/gen_bspline_values.py @@ -6,7 +6,14 @@ # This file can get slow when computing the 3D coefficients - run under Pypy to speed it up -from sympy import * +from sympy import ( + Symbol, + IndexedBase, + Matrix, + S, + sin, + diff +) from bspline_funcs import create_spline @@ -37,15 +44,15 @@ def gen_coeffs_1D(): subslist[c[k]] = 0 subslist[xs] = j*Delta - print 'subslist',subslist + print('subslist',subslist) e = spline.subs(subslist) - print j,i,e + print(j,i,e) mat[j,i] = e #print mat for i in range(m): - print mat.row(i) + print(mat.row(i)) tpi = 2*S.Pi delta = 1.0/nknots @@ -53,13 +60,13 @@ def gen_coeffs_1D(): for i in range(m): x = delta*(i%(nknots)) val = sin(tpi*x).evalf() - print i%nknots,x,val + print(i%nknots,x,val) rhs.append(val) b = Matrix(rhs) - print 'Function values = ',b + print('Function values = ',b) res = mat.LUsolve(b) - print 'Coefficients = ',res + print('Coefficients = ',res) # Construct and solve the matrix equation for coefficients @@ -99,7 +106,7 @@ def gen_coeffs_3D(): subslist_x[cx[k]] = 0 subslist_x[xs] = jx*Delta - #print 'subslist',subslist + #print('subslist',subslist) subslist_y = {} for k in range(nknots+3): @@ -125,11 +132,11 @@ def gen_coeffs_3D(): e = spline_x.subs(subslist_x) * spline_y.subs(subslist_y) * spline_z.subs(subslist_z) #print j,i,e mat[j,i] = e - print j,i,e + print(j,i,e) #print mat for i in range(m): - print mat.row(i) + print(mat.row(i)) tpi = 2*S.Pi delta = 1.0/nknots @@ -145,11 +152,11 @@ def gen_coeffs_3D(): rhs.append(val) b = Matrix(rhs) - print 'b = ',b + print('b = ',b) res = mat.LUsolve(b) mp = nknots + 3 subslist = dict() - #print 'coefficients =',res + #print('coefficients =',res) for ix in range(m): for iy in range(m): for iz in range(m): @@ -225,84 +232,84 @@ def evaluate_spline_3D(): e = (spline_x * spline_y * spline_z).subs(Delta, delta) - print - print '// Code from here to the end of the function is generated by gen_bspline_values.py' - print + print() + print('// Code from here to the end of the function is generated by gen_bspline_values.py') + print() pos = {xs:0, ys:0, zs:0} - print ' TinyVector pos = {%g, %g, %g};'%(pos[xs], pos[ys], pos[zs]) - print - print ' // symbolic value at pos = ',e.subs(pos) - print - print ' aligned_vector v(npad);' - print ' bs.evaluate(pos, v);' + print(' TinyVector pos = {%g, %g, %g};'%(pos[xs], pos[ys], pos[zs])) + print() + print(' // symbolic value at pos = ',e.subs(pos)) + print() + print(' aligned_vector v(npad);') + print(' bs.evaluate(pos, v);') # the 'expand' after substituting pos is necessary for the triples of coefficients (cx*cy*cz) to # be formed so the substitution of coefficients works val = e.subs(pos).expand().subs(subslist) - print ' CHECK(v[0] == Approx(%15.10g));'%(val) - print + print(' CHECK(v[0] == Approx(%15.10g));'%(val)) + print() - print ' VectorSoaContainer dv(npad);' - print ' VectorSoaContainer hess(npad); // 6 - number of unique hessian components' - print ' bs.evaluate_vgh(pos, v, dv, hess);' + print(' VectorSoaContainer dv(npad);') + print(' VectorSoaContainer hess(npad); // 6 - number of unique hessian components') + print(' bs.evaluate_vgh(pos, v, dv, hess);') ex = diff(e, xs).subs(pos).expand().subs(subslist) ey = diff(e, ys).subs(pos).expand().subs(subslist) ez = diff(e, zs).subs(pos).expand().subs(subslist) - print ' // Gradient' - print ' CHECK(dv[0][%d] == Approx(%15.10g));'%(0,ex) - print ' CHECK(dv[0][%d] == Approx(%15.10g));'%(1,ey) - print ' CHECK(dv[0][%d] == Approx(%15.10g));'%(2,ez) + print(' // Gradient') + print(' CHECK(dv[0][%d] == Approx(%15.10g));'%(0,ex)) + print(' CHECK(dv[0][%d] == Approx(%15.10g));'%(1,ey)) + print(' CHECK(dv[0][%d] == Approx(%15.10g));'%(2,ez)) - print - print ' // Hessian' - print ' for (int i = 0; i < 6; i++) {' - print ' CHECK(hess[0][i] == Approx(0.0));' - print ' }' + print() + print(' // Hessian') + print(' for (int i = 0; i < 6; i++) {') + print(' CHECK(hess[0][i] == Approx(0.0));') + print(' }') - print + print() pos1 = {xs:0.1, ys:0.2, zs:0.3} - print ' pos = {%g, %g, %g};'%(pos1[xs], pos1[ys], pos1[zs]) - print ' bs.evaluate(pos, v);' - print + print(' pos = {%g, %g, %g};'%(pos1[xs], pos1[ys], pos1[zs])) + print(' bs.evaluate(pos, v);') + print() val = e.subs(pos1).expand().subs(subslist) - print ' // Value' - print ' CHECK(v[0] == Approx(%15.10g));'%(val) - print - print ' bs.evaluate_vgh(pos, v, dv, hess);' - print ' // Value' - print ' CHECK(v[0] == Approx(%15.10g));'%(val) + print(' // Value') + print(' CHECK(v[0] == Approx(%15.10g));'%(val)) + print() + print(' bs.evaluate_vgh(pos, v, dv, hess);') + print(' // Value') + print(' CHECK(v[0] == Approx(%15.10g));'%(val)) ex = diff(e, xs).subs(pos1).expand().subs(subslist) ey = diff(e, ys).subs(pos1).expand().subs(subslist) ez = diff(e, zs).subs(pos1).expand().subs(subslist) - print ' // Gradient' - print ' CHECK(dv[0][%d] == Approx(%15.10g));'%(0,ex) - print ' CHECK(dv[0][%d] == Approx(%15.10g));'%(1,ey) - print ' CHECK(dv[0][%d] == Approx(%15.10g));'%(2,ez) + print(' // Gradient') + print(' CHECK(dv[0][%d] == Approx(%15.10g));'%(0,ex)) + print(' CHECK(dv[0][%d] == Approx(%15.10g));'%(1,ey)) + print(' CHECK(dv[0][%d] == Approx(%15.10g));'%(2,ez)) - print ' // Hessian' + print(' // Hessian') for idx,(d1,d2) in enumerate([(xs,xs), (xs,ys), (xs,zs), (ys, ys), (ys, zs), (zs, zs)]): hess = diff(diff(e,d1), d2).subs(pos1).expand().subs(subslist) - print ' CHECK(hess[0][%d] == Approx(%15.10g));'%(idx, hess) + print(' CHECK(hess[0][%d] == Approx(%15.10g));'%(idx, hess)) #print d1,d2,hess - print - print - print ' VectorSoaContainer lap(npad);' - print ' bs.evaluate_vgl(pos, v, dv, lap);' + print() + print() + print(' VectorSoaContainer lap(npad);') + print(' bs.evaluate_vgl(pos, v, dv, lap);') lap = diff(e,xs,2) + diff(e,ys,2) + diff(e,zs,2) lap_val = lap.subs(pos1).expand().subs(subslist) - print ' // Value' - print ' CHECK(v[0] == Approx(%15.10g));'%(val) - print ' // Gradient' - print ' CHECK(dv[0][%d] == Approx(%15.10g));'%(0,ex) - print ' CHECK(dv[0][%d] == Approx(%15.10g));'%(1,ey) - print ' CHECK(dv[0][%d] == Approx(%15.10g));'%(2,ez) - print ' // Laplacian' - print ' CHECK(lap[0][0] == Approx(%15.10g));'%(lap_val) + print(' // Value') + print(' CHECK(v[0] == Approx(%15.10g));'%(val)) + print(' // Gradient') + print(' CHECK(dv[0][%d] == Approx(%15.10g));'%(0,ex)) + print(' CHECK(dv[0][%d] == Approx(%15.10g));'%(1,ey)) + print(' CHECK(dv[0][%d] == Approx(%15.10g));'%(2,ez)) + print(' // Laplacian') + print(' CHECK(lap[0][0] == Approx(%15.10g));'%(lap_val)) if __name__ == '__main__': diff --git a/src/spline2/tests/gen_prefactor.py b/src/spline2/tests/gen_prefactor.py index 110c6a369f..da9867293d 100644 --- a/src/spline2/tests/gen_prefactor.py +++ b/src/spline2/tests/gen_prefactor.py @@ -4,7 +4,11 @@ # For code in test_prefactors() in test_multi_spline.cpp -from sympy import * +from sympy import ( + Symbol, + bspline_basis_set, + diff, +) from bspline_funcs import transpose_interval_and_coefficients, get_base_interval @@ -20,7 +24,7 @@ def gen_prefactor(): sym_basis = bspline_basis_set(3, all_knots, xs) #print("Number of basis functions = ",len(sym_basis)) - cond_map = transpose_interval_and_coefficients(sym_basis) + cond_map = transpose_interval_and_coefficients(sym_basis, xs) spline_exprs = get_base_interval(cond_map) spline_exprs = [(idx,s.subs(Delta, 1)) for idx,s in spline_exprs] @@ -29,23 +33,23 @@ def gen_prefactor(): # Adjust xval (between 0.0 and 1.0) and re-run the script xval = 0.1 - print ' // Code from here to the end the of function generated by gen_prefactor.py' - print + print(' // Code from here to the end the of function generated by gen_prefactor.py') + print() # For values - print ' tx = %g;'%xval - print ' bd.compute_prefactors(a, tx);' + print(' tx = %g;'%xval) + print(' bd.compute_prefactors(a, tx);') for idx,s in spline_exprs: - print ' CHECK(a[%d] == Approx(%g));'%(idx, s.subs(xs,xval)) + print(' CHECK(a[%d] == Approx(%g));'%(idx, s.subs(xs,xval))) - print + print() xval = 0.8 # For values, first and second derivatives - print ' tx = %g;'%xval - print ' bd.compute_prefactors(a, da, d2a, tx);' + print(' tx = %g;'%xval) + print(' bd.compute_prefactors(a, da, d2a, tx);') for idx,s in spline_exprs: - print ' CHECK(a[%d] == Approx(%g));'%(idx, s.subs(xs,xval)) - print ' CHECK(da[%d] == Approx(%g));'%(idx, diff(s,xs).subs(xs,xval)) - print ' CHECK(d2a[%d] == Approx(%g));'%(idx, diff(s,xs,2).subs(xs,xval)) + print(' CHECK(a[%d] == Approx(%g));'%(idx, s.subs(xs,xval))) + print(' CHECK(da[%d] == Approx(%g));'%(idx, diff(s,xs).subs(xs,xval))) + print(' CHECK(d2a[%d] == Approx(%g));'%(idx, diff(s,xs,2).subs(xs,xval))) if __name__ == '__main__': gen_prefactor() diff --git a/src/spline2/tests/gen_trace.py b/src/spline2/tests/gen_trace.py index f3aff110a6..b56abe7481 100644 --- a/src/spline2/tests/gen_trace.py +++ b/src/spline2/tests/gen_trace.py @@ -1,5 +1,11 @@ -from sympy import * +from sympy import ( + IndexedBase, + Matrix, + MatrixSymbol, + Symbol, + Trace, +) # Verify SymTrace in MultiBspline.hpp @@ -12,16 +18,16 @@ H = MatrixSymbol('H', 3, 3) h1 = Matrix(H) -print 'H = ',h1 +print('H = ',h1) # Symmetrize H h1 = h1.subs(H[1,0], H[0,1]) h1 = h1.subs(H[2,1], H[1,2]) h1 = h1.subs(H[2,0], H[0,2]) -print 'Symmetrized H = ',h1 -print +print('Symmetrized H = ',h1) +print() e = Trace(h1*Matrix(G)).doit() -print 'Trace = ',e +print('Trace = ',e) h00 = Symbol('h00') h01 = Symbol('h01') @@ -29,17 +35,17 @@ h11 = Symbol('h11') h12 = Symbol('h12') h22 = Symbol('h22') -print +print() e = e.subs(H[0,0], h00) e = e.subs(H[0,1], h01) e = e.subs(H[0,2], h02) e = e.subs(H[1,1], h11) e = e.subs(H[1,2], h12) e = e.subs(H[2,2], h22) -print 'Trace = ',e -print +print('Trace = ',e) +print() e2 = e.collect([h00,h01,h02,h12,h11,h22]) -print 'Trace =',e2 +print('Trace =',e2) g = IndexedBase('g') e2 = e2.subs(G[0,0], g[0]) @@ -48,9 +54,9 @@ e2 = e2.subs(G[1,1], g[1]) e2 = e2.subs(G[1,2]+G[2,1], g[4]) e2 = e2.subs(G[2,2], g[5]) -print -print 'Replace with symmetrized G' -print 'Trace =',e2 +print() +print('Replace with symmetrized G') +print('Trace =',e2) vH = Matrix([[1.0, 2.0, 3.0], [2.0, 4.4, 1.1], @@ -60,22 +66,22 @@ [0.9, 1.4, 2.3]]) tr = Trace(vH*vG).doit() -print 'Trace = ',tr +print('Trace = ',tr) -print -print 'Concrete values for unit test' -print '// Code from here to the end of the function generate by gen_trace.py' -print -print ' double h00 = %g;'%vH[0,0] -print ' double h01 = %g;'%vH[0,1] -print ' double h02 = %g;'%vH[0,2] -print ' double h11 = %g;'%vH[1,1] -print ' double h12 = %g;'%vH[1,2] -print ' double h22 = %g;'%vH[2,2] -print -print ' double gg[6] = {%g, %g, %g, %g, %g, %g};'%(vG[0,0], vG[0,1] + vG[1,0], vG[0,2] + vG[2,0], vG[1,1], vG[1,2] + vG[2,1], vG[2,2]) -print -print ' double tr = SymTrace(h00, h01, h02, h11, h12, h22, gg);' -print ' CHECK(tr == Approx(%g));'%tr -print +print() +print('Concrete values for unit test') +print('// Code from here to the end of the function generate by gen_trace.py') +print() +print(' double h00 = %g;'%vH[0,0]) +print(' double h01 = %g;'%vH[0,1]) +print(' double h02 = %g;'%vH[0,2]) +print(' double h11 = %g;'%vH[1,1]) +print(' double h12 = %g;'%vH[1,2]) +print(' double h22 = %g;'%vH[2,2]) +print() +print(' double gg[6] = {%g, %g, %g, %g, %g, %g};'%(vG[0,0], vG[0,1] + vG[1,0], vG[0,2] + vG[2,0], vG[1,1], vG[1,2] + vG[2,1], vG[2,2])) +print() +print(' double tr = SymTrace(h00, h01, h02, h11, h12, h22, gg);') +print(' CHECK(tr == Approx(%g));'%tr) +print() diff --git a/src/spline2/tests/test_multi_spline.cpp b/src/spline2/tests/test_multi_spline.cpp index 3d092764b2..e38727201a 100644 --- a/src/spline2/tests/test_multi_spline.cpp +++ b/src/spline2/tests/test_multi_spline.cpp @@ -14,10 +14,12 @@ #include "OhmmsSoA/VectorSoaContainer.h" #include "spline2/MultiBspline.hpp" +#include "spline2/MultiBsplineOffloadMapper.hpp" #include "spline2/SingleBsplineAllocator.hpp" #include "spline2/MultiBsplineEval.hpp" #include "QMCWaveFunctions/BsplineFactory/contraction_helper.hpp" #include "config/stdlib/Constants.h" +#include "OMPTarget/OffloadAlignedAllocators.hpp" namespace qmcplusplus { @@ -294,7 +296,6 @@ struct test_splines : public test_splines_base CHECK(hess[0][1] == Approx(1.174505743e-09)); CHECK(hess[0][2] == Approx(-1.1483271e-09)); CHECK(hess[0][3] == Approx(133.9204891)); - CHECK(hess[0][4] == Approx(-2.15319293e-09)); CHECK(hess[0][5] == Approx(34.53786329)); @@ -313,6 +314,39 @@ struct test_splines : public test_splines_base CHECK(ghess[0][7] == Approx(-2.575826885e-09).epsilon(eps)); CHECK(ghess[0][8] == Approx(-4.683496702e-09).epsilon(eps)); CHECK(ghess[0][9] == Approx(-81.53283531)); + + MultiBsplineOffloadMapper mapped_bs(bs); + mapped_bs.mapToDevice(); + mapped_bs.updateToDevice(); + + const int num_pos = 3; + Vector> pos_arr{0.1, 0.2, 0.3, 0.3, 0.1, 0.2, 0.1, 0.2, 0.3}; + pos_arr.updateTo(); + + auto num_splines_padded = bs.num_splines_padded(); + + Vector> spline_v_vals(num_pos * num_splines_padded); + mapped_bs.mw_evaluate_v(num_pos, pos_arr.data(), spline_v_vals.data(), num_splines_padded); + spline_v_vals.updateFrom(); + + CHECK(spline_v_vals[0] == Approx(-0.9476393279)); + CHECK(spline_v_vals[num_splines_padded * 2] == Approx(-0.9476393279)); + + Vector> spline_vgh_vals(num_pos * num_splines_padded * SoAFields3D::NUM_FIELDS); + mapped_bs.mw_evaluate_vgh(num_pos, pos_arr.data(), spline_vgh_vals.data(), + num_splines_padded * SoAFields3D::NUM_FIELDS, num_splines_padded); + spline_vgh_vals.updateFrom(); + + CHECK(spline_vgh_vals[0] == Approx(-0.9476393279)); + CHECK(spline_vgh_vals[num_splines_padded * SoAFields3D::GRAD1] == Approx(5.989106342)); + CHECK(spline_vgh_vals[num_splines_padded * SoAFields3D::HESS22] == Approx(34.53786329)); + + Vector> + spline_vgh_vals_w2(spline_vgh_vals, &spline_vgh_vals[num_splines_padded * SoAFields3D::NUM_FIELDS * 2], + num_splines_padded * SoAFields3D::NUM_FIELDS); + CHECK(spline_vgh_vals_w2[0] == Approx(-0.9476393279)); + CHECK(spline_vgh_vals_w2[num_splines_padded * SoAFields3D::GRAD1] == Approx(5.989106342)); + CHECK(spline_vgh_vals_w2[num_splines_padded * SoAFields3D::HESS22] == Approx(34.53786329)); } }; diff --git a/src/spline2/tests/test_multi_spline_MPI_shared.cpp b/src/spline2/tests/test_multi_spline_MPI_shared.cpp index e8d9001303..e1523b9797 100644 --- a/src/spline2/tests/test_multi_spline_MPI_shared.cpp +++ b/src/spline2/tests/test_multi_spline_MPI_shared.cpp @@ -14,10 +14,12 @@ #include "OhmmsSoA/VectorSoaContainer.h" #include "spline2/MultiBsplineMPIShared.hpp" +#include "spline2/MultiBsplineOffloadMapper.hpp" #include "spline2/SingleBsplineAllocator.hpp" #include "spline2/MultiBsplineEval.hpp" #include "QMCWaveFunctions/BsplineFactory/contraction_helper.hpp" #include "config/stdlib/Constants.h" +#include "OMPTarget/OffloadAlignedAllocators.hpp" namespace qmcplusplus { @@ -150,11 +152,17 @@ struct test_splines : public test_splines_base using base::grid; using base::N; - void test(size_t num_splines) + void test(size_t num_splines, unsigned shared_ranks) { auto comm_distributed = std::make_unique(*OHMMS::Controller, OHMMS::Controller->size()); + auto& comm(*comm_distributed); - MultiBsplineMPIShared bs(grid, bc, num_splines, std::move(comm_distributed)); + + // need sufficient number of ranks to test the distributing and/or sharing feature. + if (comm.size() % shared_ranks > 0) + return; + + MultiBsplineMPIShared bs(grid, bc, num_splines, std::move(comm_distributed), comm.size() / shared_ranks); const size_t npad = getAlignedSize(num_splines); REQUIRE(bs.num_splines_padded() == getAlignedSize(num_splines)); @@ -257,11 +265,54 @@ struct test_splines : public test_splines_base CHECK(ghess[0][7] == Approx(-2.575826885e-09).epsilon(eps)); CHECK(ghess[0][8] == Approx(-4.683496702e-09).epsilon(eps)); CHECK(ghess[0][9] == Approx(-81.53283531)); + + MultiBsplineOffloadMapper mapped_bs(bs); + mapped_bs.mapToDevice(); + mapped_bs.updateToDevice(); + + const int num_pos = 3; + Vector> pos_arr{0.1, 0.2, 0.3, 0.3, 0.1, 0.2, 0.1, 0.2, 0.3}; + pos_arr.updateTo(); + + auto num_splines_padded = bs.num_splines_padded(); + + Vector> spline_v_vals(num_pos * num_splines_padded); + mapped_bs.mw_evaluate_v(num_pos, pos_arr.data(), spline_v_vals.data(), num_splines_padded); + spline_v_vals.updateFrom(); + + CHECK(spline_v_vals[0] == Approx(-0.9476393279)); + CHECK(spline_v_vals[num_splines_padded * 2] == Approx(-0.9476393279)); + + Vector> spline_vgh_vals(num_pos * num_splines_padded * SoAFields3D::NUM_FIELDS); + mapped_bs.mw_evaluate_vgh(num_pos, pos_arr.data(), spline_vgh_vals.data(), + num_splines_padded * SoAFields3D::NUM_FIELDS, num_splines_padded); + spline_vgh_vals.updateFrom(); + + CHECK(spline_vgh_vals[0] == Approx(-0.9476393279)); + CHECK(spline_vgh_vals[num_splines_padded * SoAFields3D::GRAD1] == Approx(5.989106342)); + CHECK(spline_vgh_vals[num_splines_padded * SoAFields3D::HESS22] == Approx(34.53786329)); + + Vector> + spline_vgh_vals_w2(spline_vgh_vals, &spline_vgh_vals[num_splines_padded * SoAFields3D::NUM_FIELDS * 2], + num_splines_padded * SoAFields3D::NUM_FIELDS); + CHECK(spline_vgh_vals_w2[0] == Approx(-0.9476393279)); + CHECK(spline_vgh_vals_w2[num_splines_padded * SoAFields3D::GRAD1] == Approx(5.989106342)); + CHECK(spline_vgh_vals_w2[num_splines_padded * SoAFields3D::HESS22] == Approx(34.53786329)); } }; -TEST_CASE("MultiBsplineMPIShared periodic double", "[spline2]") { test_splines().test(13); } +TEST_CASE("MultiBsplineMPIShared periodic double", "[spline2]") +{ + test_splines().test(13, 1); + test_splines().test(13, 2); + test_splines().test(13, 3); +} -//TEST_CASE("MultiBsplineMPIShared periodic float", "[spline2]") { test_splines().test(11); } +TEST_CASE("MultiBsplineMPIShared periodic float", "[spline2]") +{ + test_splines().test(11, 1); + test_splines().test(11, 2); + test_splines().test(11, 3); +} } // namespace qmcplusplus diff --git a/tests/molecules/Li2_STO_ae/UNR_timestep_comparison/E_DMC_vs_tau.py b/tests/molecules/Li2_STO_ae/UNR_timestep_comparison/E_DMC_vs_tau.py index c3e38a192e..80fed3c623 100755 --- a/tests/molecules/Li2_STO_ae/UNR_timestep_comparison/E_DMC_vs_tau.py +++ b/tests/molecules/Li2_STO_ae/UNR_timestep_comparison/E_DMC_vs_tau.py @@ -1,10 +1,10 @@ #! /usr/bin/env python3 -from matplotlib.pyplot import figure,plot,xlabel,ylabel,title,show,ylim,legend,xlim,rcParams,savefig,xticks,yticks,errorbar,tight_layout +import matplotlib.pyplot as plt params = {'legend.fontsize':14,'figure.facecolor':'white','figure.subplot.hspace':0., 'axes.labelsize':16,'xtick.labelsize':14,'ytick.labelsize':14} -rcParams.update(params) +plt.rcParams.update(params) from numpy import array from numpy import polyfit,polyval,linspace @@ -36,7 +36,7 @@ 0.010 -14.9894693877551 0.010 -14.989117346938775'''.split(),dtype=float) -d.shape = len(d)/2,2 +d = d.reshape((len(d) // 2, 2)) tau = d[::2,0] # UNR timesteps E_unr = d[::2,1] # UNR DMC energy means @@ -49,25 +49,25 @@ Efit = polyval(p_unr,tfit) # print out UNR Fig 7 means and error bars -print -print 'Extracted Emix data from UNR Fig. 7' +print() +print('Extracted Emix data from UNR Fig. 7') for i in range(len(tau)): - print '{0:6.4f} {1:12.6f} +/- {2:12.6f}'.format(tau[i],E_unr[i],Ee_unr[i]) + print('{0:6.4f} {1:12.6f} +/- {2:12.6f}'.format(tau[i],E_unr[i],Ee_unr[i])) #end for # recreate UNR Figure 7 (mixed estimator only) -figure(tight_layout=True) -plot(tfit,Efit,'k-') -errorbar(tau,E_unr,Ee_unr,fmt='bs',capsize=5,markerfacecolor='white') -xlim([0,0.25]) -xticks([0,0.05,0.1,0.15,0.2,0.25]) -ylim([-14.996,-14.988]) -yticks([-14.996,-14.994,-14.992,-14.990,-14.988]) -xlabel('Time Step $\\tau$ (Hartree$^{-1}$)') -ylabel('Energy (Hartrees)') -title('Reconstruction of UNR Figure 7',fontsize=16) -savefig('UNR_Fig7_reconstructed.pdf') +plt.figure(layout="constrained") +plt.plot(tfit,Efit,'k-') +plt.errorbar(tau,E_unr,Ee_unr,fmt='bs',capsize=5,markerfacecolor='white') +plt.xlim([0,0.25]) +plt.xticks([0,0.05,0.1,0.15,0.2,0.25]) +plt.ylim([-14.996,-14.988]) +plt.yticks([-14.996,-14.994,-14.992,-14.990,-14.988]) +plt.xlabel('Time Step $\\tau$ (Hartree$^{-1}$)') +plt.ylabel('Energy (Hartrees)') +plt.title('Reconstruction of UNR Figure 7',fontsize=16) +plt.savefig('UNR_Fig7_reconstructed.pdf') # QMCPACK data, generated on 29 Sep 2017 with version 3.2.0 @@ -105,7 +105,7 @@ 0.010 -14.989505 0.000078 0.005 -14.989772 0.000067 '''.split(),dtype=float) -qd.shape = len(qd)/3,3 +qd = qd.reshape((len(qd) // 3, 3)) # extract timestep, mean and errorbar qtau = qd[:,0] @@ -118,32 +118,32 @@ # Plot QMCPACK v3.2.0 data alongside UNR results -figure(tight_layout=True) -plot(tfit,Efit,'k-') -errorbar(tau,E_unr,Ee_unr,fmt='ks',capsize=5,markerfacecolor='white',label='UNR') -plot(tfit,Efit_v320,'g-') -errorbar(qtau,E_v320,Ee_v320,fmt='g^',capsize=5,label='QMCPACK') -xlim([0,0.27]) -xlabel('Time Step $\\tau$ (Ha$^{-1}$)') -ylabel('DMC Energy (Ha)') -legend(loc='lower left') -title('UNR vs. QMCPACK',fontsize=16) -savefig('UNR_vs_QMCPACK.pdf') +plt.figure(layout="constrained") +plt.plot(tfit,Efit,'k-') +plt.errorbar(tau,E_unr,Ee_unr,fmt='ks',capsize=5,markerfacecolor='white',label='UNR') +plt.plot(tfit,Efit_v320,'g-') +plt.errorbar(qtau,E_v320,Ee_v320,fmt='g^',capsize=5,label='QMCPACK') +plt.xlim([0,0.27]) +plt.xlabel('Time Step $\\tau$ (Ha$^{-1}$)') +plt.ylabel('DMC Energy (Ha)') +plt.legend(loc='lower left') +plt.title('UNR vs. QMCPACK',fontsize=16) +plt.savefig('UNR_vs_QMCPACK.pdf') # Make a zoomed version of the plot -figure(tight_layout=True) -plot(tfit,Efit,'k-') -errorbar(tau,E_unr,Ee_unr,fmt='ks',capsize=5,markerfacecolor='white',label='UNR') -plot(tfit,Efit_v320,'g-') -errorbar(qtau,E_v320,Ee_v320,fmt='g^',capsize=5,label='QMCPACK') -xlim([0,0.15]) -ylim([-14.996,-14.988]) -xlabel('Time Step $\\tau$ (Ha$^{-1}$)') -ylabel('DMC Energy (Ha)') -legend(loc='lower left') -title('UNR vs. QMCPACK (zoomed)',fontsize=16) -savefig('UNR_vs_QMCPACK_zoomed.pdf') - - -show() +plt.figure(layout="constrained") +plt.plot(tfit,Efit,'k-') +plt.errorbar(tau,E_unr,Ee_unr,fmt='ks',capsize=5,markerfacecolor='white',label='UNR') +plt.plot(tfit,Efit_v320,'g-') +plt.errorbar(qtau,E_v320,Ee_v320,fmt='g^',capsize=5,label='QMCPACK') +plt.xlim([0,0.15]) +plt.ylim([-14.996,-14.988]) +plt.xlabel('Time Step $\\tau$ (Ha$^{-1}$)') +plt.ylabel('DMC Energy (Ha)') +plt.legend(loc='lower left') +plt.title('UNR vs. QMCPACK (zoomed)',fontsize=16) +plt.savefig('UNR_vs_QMCPACK_zoomed.pdf') + + +plt.show() diff --git a/tests/solids/LiH_solid_1x1x1_pp/CMakeLists.txt b/tests/solids/LiH_solid_1x1x1_pp/CMakeLists.txt index b6ab2d9c08..940a69fc6f 100644 --- a/tests/solids/LiH_solid_1x1x1_pp/CMakeLists.txt +++ b/tests/solids/LiH_solid_1x1x1_pp/CMakeLists.txt @@ -256,14 +256,14 @@ qmc_run_and_check( # Deterministic test if(QMC_MIXED_PRECISION) - list(APPEND DET_LIH_GAMMA_SCALARS "totenergy" "-8.99301725 0.00001597") + list(APPEND DET_LIH_GAMMA_SCALARS "totenergy" "-8.99301725 0.00002") list(APPEND DET_LIH_GAMMA_SCALARS "kinetic" "7.42550431 0.00001588") list(APPEND DET_LIH_GAMMA_SCALARS "potential" "-16.41852156 0.000005") list(APPEND DET_LIH_GAMMA_SCALARS "eeenergy" "-1.39002015 0.000001") list(APPEND DET_LIH_GAMMA_SCALARS "ionion" "-3.68928007 0.000001") list(APPEND DET_LIH_GAMMA_SCALARS "localecp" "-11.33922134 0.000005") list(APPEND DET_LIH_GAMMA_SCALARS "samples" "9 0.0") - list(APPEND DET_LIH_GAMMA_SCALARS "flux" "0.04160754 0.00002925") + list(APPEND DET_LIH_GAMMA_SCALARS "flux" "0.04160754 0.00004") else() list(APPEND DET_LIH_GAMMA_SCALARS "totenergy" "-8.99302939 0.000001") list(APPEND DET_LIH_GAMMA_SCALARS "kinetic" "7.42549769 0.000001") diff --git a/tests/solids/NiO_a4_e48_pp/CMakeLists.txt b/tests/solids/NiO_a4_e48_pp/CMakeLists.txt index 279fc4ca23..a9dc3ba0c4 100644 --- a/tests/solids/NiO_a4_e48_pp/CMakeLists.txt +++ b/tests/solids/NiO_a4_e48_pp/CMakeLists.txt @@ -291,7 +291,7 @@ else() list(APPEND DET_NIO_A4_E48_SCALARS "potential" "-660.30813251 0.02") list(APPEND DET_NIO_A4_E48_SCALARS "eeenergy" "80.56139080 0.003") list(APPEND DET_NIO_A4_E48_SCALARS "ionion" "-239.29802821 0.000004") - list(APPEND DET_NIO_A4_E48_SCALARS "localecp" "-392.26503661 0.001") + list(APPEND DET_NIO_A4_E48_SCALARS "localecp" "-392.26503661 0.0015") list(APPEND DET_NIO_A4_E48_SCALARS "nonlocalecp" "-109.30472876 0.02") list(APPEND DET_NIO_A4_E48_SCALARS "samples" "9 0.0") endif() diff --git a/tests/solids/bccH_1x1x1_ae/CMakeLists.txt b/tests/solids/bccH_1x1x1_ae/CMakeLists.txt index 1e9a4d40bd..b883b6f1e1 100644 --- a/tests/solids/bccH_1x1x1_ae/CMakeLists.txt +++ b/tests/solids/bccH_1x1x1_ae/CMakeLists.txt @@ -79,7 +79,7 @@ qmc_run_and_check( ) # Deterministic correlated sampling test -list(APPEND DET_BCC_H_CSVMC_SCALARS "totenergy_A" "-1.5879406376 0.00001") +list(APPEND DET_BCC_H_CSVMC_SCALARS "totenergy_A" "-1.5879406376 0.000015") list(APPEND DET_BCC_H_CSVMC_SCALARS "totenergy_B" "-1.5845867400 0.00002") list(APPEND DET_BCC_H_CSVMC_SCALARS "dtotenergy_AB" "-0.0033713724 0.00002") list(APPEND DET_BCC_H_CSVMC_SCALARS "ionion_A" "-0.9628996202 0.0000001") diff --git a/tests/solids/diamondC_1x1x1-Gaussian_pp/dft-inputs/diamondC_1x1x1_pp.py b/tests/solids/diamondC_1x1x1-Gaussian_pp/dft-inputs/diamondC_1x1x1_pp.py index 02df6706a0..107f9df8d0 100755 --- a/tests/solids/diamondC_1x1x1-Gaussian_pp/dft-inputs/diamondC_1x1x1_pp.py +++ b/tests/solids/diamondC_1x1x1-Gaussian_pp/dft-inputs/diamondC_1x1x1_pp.py @@ -57,7 +57,7 @@ ener = open('e_scf','w') ener.write('%s\n' % (e_scf)) -print 'e_scf',e_scf +print('e_scf', e_scf) title="C_Diamond" diff --git a/tests/solids/diamondC_1x1x1_pp/CMakeLists.txt b/tests/solids/diamondC_1x1x1_pp/CMakeLists.txt index f691826919..5619f4e116 100644 --- a/tests/solids/diamondC_1x1x1_pp/CMakeLists.txt +++ b/tests/solids/diamondC_1x1x1_pp/CMakeLists.txt @@ -1501,7 +1501,7 @@ if(QMC_MIXED_PRECISION) list(APPEND DET_DIAMOND_DMC_MULTI2_SCALARS "eeenergy" "-2.89879032 0.00000133") list(APPEND DET_DIAMOND_DMC_MULTI2_SCALARS "ionion" "-12.77566507 0.000001") list(APPEND DET_DIAMOND_DMC_MULTI2_SCALARS "localecp" "-15.41387689 0.00001471") - list(APPEND DET_DIAMOND_DMC_MULTI2_SCALARS "nonlocalecp" "6.10588419 0.00001448") + list(APPEND DET_DIAMOND_DMC_MULTI2_SCALARS "nonlocalecp" "6.10590756 0.00001448") list(APPEND DET_DIAMOND_DMC_MULTI2_SCALARS "mpc" "-2.61905471 0.00000179") list(APPEND DET_DIAMOND_DMC_MULTI2_SCALARS "samples" "9 0.0") # DMC cycle 3 @@ -1800,7 +1800,7 @@ if(QMC_MIXED_PRECISION) list(APPEND DET_DIAMOND_DMC_TM1_BATCH_SCALARS "kinetic" "9.94328567 0.00003064") list(APPEND DET_DIAMOND_DMC_TM1_BATCH_SCALARS "potential" "-20.29185640 0.00000232") list(APPEND DET_DIAMOND_DMC_TM1_BATCH_SCALARS "eeenergy" "-2.70623197 0.00000776") - list(APPEND DET_DIAMOND_DMC_TM1_BATCH_SCALARS "ionion" "-12.77566333 0.000001") + list(APPEND DET_DIAMOND_DMC_TM1_BATCH_SCALARS "ionion" "-12.77566533 0.000001") list(APPEND DET_DIAMOND_DMC_TM1_BATCH_SCALARS "localecp" "-5.26283000 0.00001536") list(APPEND DET_DIAMOND_DMC_TM1_BATCH_SCALARS "nonlocalecp" "0.45287649 0.00000689") list(APPEND DET_DIAMOND_DMC_TM1_BATCH_SCALARS "mpc" "-2.43479306 0.00000857") diff --git a/tests/solids/diamondC_2x1x1-Gaussian_pp/CMakeLists.txt b/tests/solids/diamondC_2x1x1-Gaussian_pp/CMakeLists.txt index e083284f88..cab83251cb 100644 --- a/tests/solids/diamondC_2x1x1-Gaussian_pp/CMakeLists.txt +++ b/tests/solids/diamondC_2x1x1-Gaussian_pp/CMakeLists.txt @@ -141,7 +141,7 @@ if(QMC_MIXED_PRECISION) list(APPEND DET_DIAMOND-r1-t4_SCALARS "kinetic" "18.72979475 0.000516") list(APPEND DET_DIAMOND-r1-t4_SCALARS "potential" "-40.85806527 0.000025") list(APPEND DET_DIAMOND-r1-t4_SCALARS "eeenergy" "-4.65173512 0.000009") - list(APPEND DET_DIAMOND-r1-t4_SCALARS "ionion" "-25.55132413 0.000001") + list(APPEND DET_DIAMOND-r1-t4_SCALARS "ionion" "-25.55132413 0.000002") list(APPEND DET_DIAMOND-r1-t4_SCALARS "localecp" "-12.55060882 0.000051") list(APPEND DET_DIAMOND-r1-t4_SCALARS "nonlocalecp" "1.89561077 0.000026") else() @@ -172,7 +172,7 @@ if(QMC_MIXED_PRECISION) list(APPEND DET_DIAMOND-r2-t2_SCALARS "kinetic" "20.18278052 0.000516") list(APPEND DET_DIAMOND-r2-t2_SCALARS "potential" "-42.43359884 0.000025") list(APPEND DET_DIAMOND-r2-t2_SCALARS "eeenergy" "-5.10111755 0.000009") - list(APPEND DET_DIAMOND-r1-t4_SCALARS "ionion" "-25.55132413 0.000001") + list(APPEND DET_DIAMOND-r1-t4_SCALARS "ionion" "-25.55132413 0.000002") list(APPEND DET_DIAMOND-r2-t2_SCALARS "localecp" "-13.23969275 0.000051") list(APPEND DET_DIAMOND-r2-t2_SCALARS "nonlocalecp" "1.45854374 0.000026") else() @@ -211,7 +211,7 @@ if(QMC_MIXED_PRECISION) list(APPEND DET_DIAMOND-r2-t3_SCALARS "kinetic" "17.83517172 0.000516") list(APPEND DET_DIAMOND-r2-t3_SCALARS "potential" "-39.52299737 0.000025") list(APPEND DET_DIAMOND-r2-t3_SCALARS "eeenergy" "-5.26867544 0.000009") - list(APPEND DET_DIAMOND-r1-t4_SCALARS "ionion" "-25.55132413 0.000001") + list(APPEND DET_DIAMOND-r1-t4_SCALARS "ionion" "-25.55132413 0.000002") list(APPEND DET_DIAMOND-r2-t3_SCALARS "localecp" "-10.28363113 0.000051") list(APPEND DET_DIAMOND-r2-t3_SCALARS "nonlocalecp" "1.58064151 0.000026") else() diff --git a/tests/solids/diamondC_2x1x1-Gaussian_pp/dft-inputs/diamondC_2x1x1_pp.py b/tests/solids/diamondC_2x1x1-Gaussian_pp/dft-inputs/diamondC_2x1x1_pp.py index c6b8121556..31850f799c 100755 --- a/tests/solids/diamondC_2x1x1-Gaussian_pp/dft-inputs/diamondC_2x1x1_pp.py +++ b/tests/solids/diamondC_2x1x1-Gaussian_pp/dft-inputs/diamondC_2x1x1_pp.py @@ -57,7 +57,7 @@ ener = open('e_scf','w') ener.write('%s\n' % (e_scf)) -print 'e_scf',e_scf +print('e_scf', e_scf) title="C_Diamond" diff --git a/tests/test_automation/containers/Dockerfile_gcc_mpi_develop_complete b/tests/test_automation/containers/Dockerfile_gcc_mpi_develop_complete index 6311f31c10..279d9e7651 100644 --- a/tests/test_automation/containers/Dockerfile_gcc_mpi_develop_complete +++ b/tests/test_automation/containers/Dockerfile_gcc_mpi_develop_complete @@ -1,10 +1,10 @@ -FROM ubuntu:latest +FROM ubuntu:24.04 LABEL Description="Development version of QMCPACK and Nexus configured for use with complete source codes, plus Quantum ESPRESSO" SHELL ["/bin/bash", "-c"] ENV QE_VERSION="7.5" -ENV PYSCF_VERSION=2.12.0 +ENV PYSCF_VERSION=2.13.0 #ENV QMCPACK_VERSION="4.1.0" ARG USERNAME=qmcuser @@ -28,7 +28,8 @@ RUN groupadd --gid $USER_GID $USERNAME \ RUN apt-get install -y --no-install-recommends \ ca-certificates make ninja-build git cmake wget bzip2 rsync g++ gfortran openmpi-bin libopenmpi-dev libboost-dev \ libopenblas-openmp-dev libhdf5-dev libxml2-dev libfftw3-dev \ - python3-numpy python3-scipy python3-pandas python3-h5py python3-matplotlib + python3-numpy python3-scipy python3-pandas python3-h5py python3-matplotlib \ + python3-coverage python3-pytest python3-pytest-cov python3-pytest-order # Convenience feature to setup certificates for behind firewall builds. # * Copy any provided certificates into the container and update the SSL config @@ -65,12 +66,12 @@ RUN git clone https://github.com/sunqm/libcint.git && cd libcint && git checkout mkdir build && cd build && \ cmake -DWITH_F12=1 -DWITH_RANGE_COULOMB=1 -DWITH_COULOMB_ERF=1 -DCMAKE_INSTALL_PREFIX:PATH=/opt -DCMAKE_INSTALL_LIBDIR:PATH=lib .. && \ make -j 4 && make install && cd ../.. && rm -rf /scratch/libcint -RUN wget https://gitlab.com/libxc/libxc/-/archive/6.0.0/libxc-6.0.0.tar.gz && tar xvzf libxc-6.0.0.tar.gz && \ - cd libxc-6.0.0 && mkdir build && cd build && \ +RUN wget https://gitlab.com/libxc/libxc/-/archive/7.0.0/libxc-7.0.0.tar.gz && tar xvzf libxc-7.0.0.tar.gz && \ + cd libxc-7.0.0 && mkdir build && cd build && \ cmake -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_SHARED_LIBS=1 \ -DENABLE_FORTRAN=0 -DDISABLE_KXC=0 -DDISABLE_LXC=1 \ -DCMAKE_INSTALL_PREFIX:PATH=/opt -DCMAKE_INSTALL_LIBDIR:PATH=lib .. && \ - make -j 4 && make install && cd ../.. && rm -rf /scratch/libxc-6.0.0 libxc-6.0.0.tar.gz + make -j 4 && make install && cd ../.. && rm -rf /scratch/libxc-7.0.0 libxc-7.0.0.tar.gz RUN wget -O xcfun.tar.gz https://github.com/fishjojo/xcfun/archive/refs/tags/cmake-3.5.tar.gz && tar xvzf xcfun.tar.gz && \ cd xcfun-cmake-3.5 && mkdir build && cd build && \ cmake -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_SHARED_LIBS=1 -DXCFUN_MAX_ORDER=3 -DXCFUN_ENABLE_TESTS=0 \ diff --git a/tests/test_automation/github-actions/ci/run_step.sh b/tests/test_automation/github-actions/ci/run_step.sh index 2a18089e15..dd0c9da2f5 100755 --- a/tests/test_automation/github-actions/ci/run_step.sh +++ b/tests/test_automation/github-actions/ci/run_step.sh @@ -163,9 +163,17 @@ case "$1" in ;; *"GCC"*"-Gcov"*) echo 'Configure for code coverage with gcc and gcovr -DENABLE_GCOV=TRUE and upload reports to Codecov' + + # For consistency with other compiler usage, while usually the default, specify gcc to OpenMPI wrappers. + export OMPI_CC=gcc + export OMPI_CXX=g++ + # Make current environment variables available to subsequent steps + echo "OMPI_CC=gcc" >> $GITHUB_ENV + echo "OMPI_CXX=g++" >> $GITHUB_ENV + cmake -GNinja $CMAKE_OPTIONS \ - -DMPI_C_COMPILER=mpicc \ - -DMPI_CXX_COMPILER=mpicxx \ + -DCMAKE_C_COMPILER=mpicc \ + -DCMAKE_CXX_COMPILER=mpicxx \ -DENABLE_GCOV=TRUE \ -DENABLE_PYCOV=TRUE \ ${GITHUB_WORKSPACE} @@ -234,6 +242,7 @@ case "$1" in "need built-from-source OpenBLAS due to bug in rpm" source /opt/intel/oneapi/setvars.sh + unset CPATH C_INCLUDE_PATH CPLUS_INCLUDE_PATH LIBRARY_PATH export OMPI_CC=/opt/intel/oneapi/compiler/2023.0.0/linux/bin/intel64/icc export OMPI_CXX=/opt/intel/oneapi/compiler/2023.0.0/linux/bin/intel64/icpc @@ -355,7 +364,9 @@ case "$1" in cd ${GITHUB_WORKSPACE}/../qmcpack-build # filter unreachable branches with gcovr # see https://gcovr.com/en/stable/faq.html#why-does-c-code-have-so-many-uncovered-branches - gcovr --exclude-unreachable-branches --exclude-throw-branches --root=${GITHUB_WORKSPACE}/.. --xml-pretty -o coverage.xml + # set suspicious hits threshold=2^40 + # see https://gcovr.com/en/stable/manpage.html#gcov-options + gcovr --exclude-unreachable-branches --exclude-throw-branches --gcov-ignore-parse-errors=suspicious_hits.warn_once_per_file --gcov-suspicious-hits-threshold=1099511627776 --root=${GITHUB_WORKSPACE}/.. --xml-pretty -o coverage.xml du -hs coverage.xml #cat coverage.xml python3-coverage combine nexus/nexus/tests/.coverage* diff --git a/tests/test_automation/github-actions/ci/run_step_ornl-sulfur-1.sh b/tests/test_automation/github-actions/ci/run_step_ornl-sulfur-1.sh index 311dfc053e..5dfad14254 100755 --- a/tests/test_automation/github-actions/ci/run_step_ornl-sulfur-1.sh +++ b/tests/test_automation/github-actions/ci/run_step_ornl-sulfur-1.sh @@ -53,6 +53,7 @@ case "$1" in echo 'Configure for building with GCC and Intel MKL' source /opt/intel/oneapi/setvars.sh + unset CPATH C_INCLUDE_PATH CPLUS_INCLUDE_PATH LIBRARY_PATH cmake -GNinja \ -DCMAKE_C_COMPILER=/usr/lib64/openmpi/bin/mpicc \ diff --git a/tests/test_automation/nightly_test_scripts/nightly_ornl.sh b/tests/test_automation/nightly_test_scripts/nightly_ornl.sh index e1ad314e4e..790babdd1e 100755 --- a/tests/test_automation/nightly_test_scripts/nightly_ornl.sh +++ b/tests/test_automation/nightly_test_scripts/nightly_ornl.sh @@ -78,9 +78,13 @@ case "$ourhostname" in clangoffloadnompi_offloadcuda_mixed_complex \ clangoffloadnompi_offloadcuda_debug \ clangoffloadnompi_offloadcuda_complex_debug \ + clangoffloadnompi_offloadcpu \ + clangnewmpi clangnewmpi_mixed clangnewmpi_complex clangnewmpi_mixed_complex \ + clangnewnompi_debug clangnewnompi_debug_asan \ gccnewnompi_debug_asan gccnewnompi_debug_ubsan \ - gccnewmpi_mkl clangnewmpi gccnewnompi gccnewmpi gccoldmpi clangnewmpi_complex gccnewnompi_complex gccnewmpi_complex \ - clangnewmpi_mixed gccnewnompi_mixed gccnewmpi_mixed clangnewmpi_mixed_complex gccnewnompi_mixed_complex gccnewmpi_mixed_complex" + gccnewmpi gccnewmpi_mkl gccnewnompi gccnewnompi_complex gccnewmpi_complex \ + gccnewnompi_mixed gccnewmpi_mixed gccnewnompi_mixed_complex gccnewmpi_mixed_complex \ + gccoldmpi" else buildsys="gccnewmpi_mkl clangnewmpi gccnewmpi clangnewmpi_complex clangnewmpi_mixed clangnewmpi_mixed_complex clangoffloadmpi_offloadcuda" fi @@ -88,14 +92,16 @@ case "$ourhostname" in ;; nitrogen2 ) if [[ $jobtype == "nightly" ]]; then - buildsys="amdclangnompi_offloadhip_complex \ - amdclangnompi_offloadhip amdclangnompi_offloadhip_debug \ - amdclangnompi_offloadhip_complex_debug \ - amdclangnompi_offloadhip_mixed amdclangnompi_offloadhip_mixed_debug \ - amdclangnompi_offloadhip_mixed_complex amdclangnompi_offloadhip_mixed_complex_debug \ - gccnewnompi gccnewnompi_aocl gccnewnompi_complex gccnewnompi_debug gccnewnompi_complex_debug \ - gccnewnompi_mixed_debug gccnewnompi_mixed_complex_debug gccnewnompi_aocl_mixed_complex_debug gccnewmpi gccnewmpi_aocl clangnewmpi \ - amdclangnompi amdclangnompi_debug" + buildsys="gccoldmpi_aocl gccoldnompi_aocl_mixed_complex_debug gccoldnompi gccoldnompi_debug \ + amdclangnompi_offloadhip_complex \ + amdclangnompi_offloadhip amdclangnompi_offloadhip_debug \ + amdclangnompi_offloadhip_complex_debug \ + amdclangnompi_offloadhip_mixed amdclangnompi_offloadhip_mixed_debug \ + amdclangnompi_offloadhip_mixed_complex amdclangnompi_offloadhip_mixed_complex_debug \ + gccnewnompi gccnewnompi_complex gccnewnompi_debug gccnewnompi_complex_debug \ + gccnewnompi_mixed_debug gccnewnompi_mixed_complex_debug gccnewmpi \ + clangnewmpi \ + amdclangnompi amdclangnompi_debug" else buildsys="gccnewmpi gccnewmpi_aocl amdclangnompi gccnewnompi gccnewnompi_aocl clangnewmpi amdclangnompi_offloadhip" fi @@ -179,7 +185,7 @@ module() { eval `/usr/bin/modulecmd bash $*`; } export SPACK_USER_CONFIG_PATH=$HOME/apps/spack_user_config # Avoid using $HOME/.spack export SPACK_ROOT=$HOME/apps/spack -export PATH=$SPACK_ROOT/bin:$PATH +#export PATH=$SPACK_ROOT/bin:$PATH . $SPACK_ROOT/share/spack/setup-env.sh @@ -216,7 +222,8 @@ fi # Sanity check cmake config file present if [ -e qmcpack/CMakeLists.txt ]; then -export PYTHONPATH=${test_dir}/qmcpack/nexus +# TODO: Update PYTHONPATH for modern tool location +#export PYTHONPATH=${test_dir}/qmcpack/nexus/lib echo --- PYTHONPATH=$PYTHONPATH echo --- Starting test builds and tests @@ -242,29 +249,33 @@ cd build_$sys ourenv=env${syscompilermpi} echo --- Activating environment $ourenv spack env activate $ourenv -echo --- Sourcing environment $ourenv -if [ ! -e $HOME/apps/spack/var/spack/environments/$ourenv/loads ]; then - echo Loads file missing for environment $ourenv - exit 1 -fi -source $HOME/apps/spack/var/spack/environments/$ourenv/loads +#MAR26retcode=$? +#MAR26if (( rc != 0 )); then +#MAR26 echo "FAILED to activate $ourenv (exit code $rc)" +#MAR26 break +#MAR26else +#MAR26 echo "Successfully activated $ourenv" +#MAR26fi +#MAR26 TODO: Verify views work +#MAR26echo --- Sourcing environment $ourenv +#MAR26if [ ! -e $HOME/apps/spack/var/spack/environments/$ourenv/loads ]; then +#MAR26 echo Loads file missing for environment $ourenv +#MAR26 exit 1 +#MAR26fi +#MAR26 source $HOME/apps/spack/var/spack/environments/$ourenv/loads # Compiler sanity check: -which gcc -which clang -which mpicc +echo "gcc is `which gcc`" +echo "clang is `which clang`" +echo "mpicc is `which mpicc`" # Extra configuration for this build # All base sw should be available via the environments # Ensure GNU C++ library available. Problem symptoms: # $ bin/qmcpack # bin/qmcpack: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by bin/qmcpack) - -echo LD_LIBRARY_PATH=$LD_LIBRARY_PATH -export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`which gcc|sed 's/bin\/gcc/lib64/g'` -echo LD_LIBRARY_PATH=$LD_LIBRARY_PATH - - - +#MAR26#echo LD_LIBRARY_PATH=$LD_LIBRARY_PATH +#MAR26#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`which gcc|sed 's/bin\/gcc/lib64/g'` +#MAR26#echo LD_LIBRARY_PATH=$LD_LIBRARY_PATH # Setup additional python paths when gccnew and therefore pyscf available. TO DO: test for module availability case "$sys" in @@ -364,14 +375,21 @@ if [[ $sys == *"clang"* ]]; then # Clang OpenMP offload CUDA builds. Setup here due to clang specific arguments if [[ $sys == *"offloadcuda"* ]]; then - QMCPACK_TEST_SUBMIT_NAME=${QMCPACK_TEST_SUBMIT_NAME}-NVGPU + # Default OpenMP offload with CUDA support + QMCPACK_TEST_SUBMIT_NAME=${QMCPACK_TEST_SUBMIT_NAME}-Offload-NVGPU CMCFG="$CMCFG -DCMAKE_CXX_FLAGS=-Wno-unknown-cuda-version" QMC_OPTIONS="${QMC_OPTIONS};-DQMC_GPU_ARCHS=sm_70" fi if [[ $sys == *"offloadhip"* ]]; then - QMCPACK_TEST_SUBMIT_NAME=${QMCPACK_TEST_SUBMIT_NAME}-AMDGPU + # Default OpenMP offload with ROCm/HIP support + QMCPACK_TEST_SUBMIT_NAME=${QMCPACK_TEST_SUBMIT_NAME}-Offload-AMDGPU QMC_OPTIONS="${QMC_OPTIONS};-DQMC_GPU_ARCHS=$amdgpuarch" fi + if [[ $sys == *"offloadcpu"* ]]; then + # Pure OpenMP offload to host cpu (i.e. no GPU required) + QMCPACK_TEST_SUBMIT_NAME=${QMCPACK_TEST_SUBMIT_NAME}-Offload-CPU + QMC_OPTIONS="${QMC_OPTIONS};-DQMC_GPU=openmp;-DOFFLOAD_TARGET=x86_64-pc-linux-gnu" + fi fi @@ -442,6 +460,16 @@ else fi fi +# END of compiler setup +if [[ $sys == *"nompi"* ]]; then +echo MPI is disabled +else + echo MPI is enabled + echo OMPI_CC=$OMPI_CC + echo OMPI_CXX=$OMPI_CXX +fi + + # Complex if [[ $sys == *"complex"* ]]; then QMCPACK_TEST_SUBMIT_NAME=${QMCPACK_TEST_SUBMIT_NAME}-Complex diff --git a/tests/test_automation/nightly_test_scripts/ornl_setup.sh b/tests/test_automation/nightly_test_scripts/ornl_setup.sh index a42d498128..843e087a45 100755 --- a/tests/test_automation/nightly_test_scripts/ornl_setup.sh +++ b/tests/test_automation/nightly_test_scripts/ornl_setup.sh @@ -45,9 +45,6 @@ ourhostname=`hostname|sed 's/\..*//g'` echo --- Host is $ourhostname export SPACK_ROOT=$HOME/apps/spack -if [ -e $SPACK_ROOT ]; then - rm -r -f $SPACK_ROOT -fi export SPACK_USER_CONFIG_PATH=$HOME/apps/spack_user_config # Avoid using $HOME/.spack if [ ! -e $SPACK_USER_CONFIG_PATH ]; then mkdir $SPACK_USER_CONFIG_PATH @@ -59,6 +56,26 @@ if [ -e $HOME/.spack ]; then rm -r -f $HOME/.spack fi + +# Pin the version of the package repository for reproducibility +# Docs: https://spack.readthedocs.io/en/latest/repositories.html#updating-and-pinning +# The package repo will be at something like ~/.spack/package_repos/fncqgg4/ + +cat >>$SPACK_USER_CONFIG_PATH/repos.yaml< develop, origin/develop) +#Author: Alec Scott +#Date: Wed Apr 8 16:29:47 2026 -0700 +# +# helm: new package (#4179) +# +# Signed-off-by: Alec Scott +EOF + + # Setup build multiplicity and preferred directories for spack # Choose the fastest filesytem. Don't abuse shared nodes. case "$ourhostname" in @@ -85,7 +102,6 @@ packages: externals: - spec: openssl@1.1.1k prefix: /usr - buildable: False EOF ;; nitrogen ) @@ -111,7 +127,6 @@ packages: externals: - spec: openssl@1.1.1k prefix: /usr - buildable: False EOF ;; sulfur ) @@ -137,7 +152,6 @@ packages: externals: - spec: openssl@1.1.1k prefix: /usr - buildable: False EOF ;; *) @@ -178,30 +192,35 @@ fi cd $HOME/apps -if [ -e $HOME/apps/spack ]; then - rm -r -f $HOME/apps/spack +if [ -e spack ]; then + cd spack + echo -- Resetting existing spack git repo + git checkout -f + git clean -fd + git checkout develop + git pull + cd .. +else + git clone https://github.com/spack/spack.git fi -git clone https://github.com/spack/spack.git - if [ ! -e spack/CHANGELOG.md ]; then echo "--- FAILED TO FIND spack/CHANGELOG.md . BAD CLONE or I/O PROBLEMS. ABORTING" exit 1 fi -cd $HOME/apps/spack - +cd $SPACK_ROOT # For reproducibility, use a specific version of Spack # Prefer to use tagged releases https://github.com/spack/spack/releases -git checkout b8c31b22a5d1619d0137bc3fc69e24389ca436fb -#commit b8c31b22a5d1619d0137bc3fc69e24389ca436fb (HEAD -> develop, origin/develop, origin/HEAD) +git checkout 45b9069e4997f4b453b2770886b1e8ba790980f4 +#commit 45b9069e4997f4b453b2770886b1e8ba790980f4 (HEAD -> develop, origin/develop, origin/HEAD) #Author: Harmen Stoppels -#Date: Fri May 16 12:09:20 2025 +0200 +#Date: Wed Apr 8 14:38:32 2026 +0200 # -# builtin: crlf -> lf (#50505) +# new_installer.py: sub_process < /dev/null (#52221) # Limit overly strong rmg boost dependency to allow concretizer:unify:true -sed -ibak 's/boost@1.61.0:1.82.0/boost@1.61.0:1.82.0", when="@:6.1.2/g' var/spack/repos/spack_repo/builtin/packages/rmgdft/package.py +#sed -ibak 's/boost@1.61.0:1.82.0/boost@1.61.0:1.82.0", when="@:6.1.2/g' var/spack/repos/spack_repo/builtin/packages/rmgdft/package.py echo --- Git version and last log entry git log -1 @@ -213,70 +232,107 @@ cd bin # Consider using a GCC toolset on Red Hat systems to use # recent compilers with better architecture support. # e.g. dnf install gcc-toolset-14 -if [ -e /opt/rh/gcc-toolset-14/enable ]; then - echo --- Using gcc-toolset-14 for newer compilers - source /opt/rh/gcc-toolset-14/enable -fi +#if [ -e /opt/rh/gcc-toolset-14/enable ]; then +# echo --- Using gcc-toolset-14 for newer compilers +# source /opt/rh/gcc-toolset-14/enable +#fi export DISPLAY="" -export SPACK_ROOT=$HOME/apps/spack -export SPACK_USER_CONFIG_PATH=$HOME/apps/spack_user_config # Avoid using $HOME/.spack +# SPACK_ROOT & SPACK_USER_CONFIG_PATH already set export PATH=$SPACK_ROOT/bin:$PATH . $SPACK_ROOT/share/spack/setup-env.sh echo --- Bootstrap spack bootstrap now +spack gpg init + +echo --- Setup/use mirror in /scratch/$USER/spack_mirror +if [ ! -e /scratch/$USER/spack_mirror ];then + mkdir /scratch/$USER/spack_mirror + #spack mirror create -d /scratch/$USER/spack_mirror # Will error due to no packages +else + echo --- Mirror already exists. Carefully consider if refresh needed after major spack updates. + du -ksh /scratch/$USER/spack_mirror +fi +spack mirror add localmirror /scratch/$USER/spack_mirror +spack buildcache update-index /scratch/$USER/spack_mirror +spack mirror set --autopush localmirror # enable automatic push for an existing mirror +spack mirror set --unsigned localmirror # disable signing and verification echo --- Spack list spack find +echo --- Spack compilers +spack compilers +echo --- Spack compiler find +spack compiler find +echo --- Spack compilers +spack compilers echo --- Modules list module list echo --- End listings -echo --- gcc@${gcc_vnew} `date` -spack install gcc@${gcc_vnew} -echo --- load gcc@${gcc_vnew} -spack load gcc@${gcc_vnew} -module list -spack compiler find -spack unload gcc@${gcc_vnew} +#DEBUGecho --- Screen llvm compilations +#DEBUGecho --- Trying without cuda_arch +#DEBUGecho --- llvm@22 for offload `date` +#DEBUGspack spec llvm@22 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack install llvm@22 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack load llvm@22 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack unload llvm +#DEBUGecho --- llvm@21 for offload `date` +#DEBUGspack spec llvm@21 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack install llvm@21 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack load llvm@21 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack unload llvm +#DEBUGecho --- llvm@20 for offload `date` +#DEBUGspack spec llvm@20 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack install llvm@20 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack load llvm@20 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack unload llvm +#DEBUGecho --- llvm@19 for offload `date` +#DEBUGspack spec llvm@19 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack install llvm@19 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack load llvm@19 +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +#DEBUGspack unload llvm + +# 2026-03-28: Install LLVM first. Will use system gcc and avoid problems/spack bugs with newer gcc, binutils etc. +echo --- llvm@${llvm_voffload} for offload `date` + +spack spec llvm@${llvm_voffload} openmp=project +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +spack install llvm@${llvm_voffload} openmp=project +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +spack load llvm@${llvm_voffload} openmp=project +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +allow-unsupported-compilers +spack unload llvm + +echo --- llvm@${llvm_vnew} `date` +if [ "${llvm_vnew}" == "${llvm_voffload}" ]; then + echo Skipping: Offload and New LLVM versions are identical +else + spack install llvm@${llvm_vnew} openmp=project + spack load llvm@${llvm_vnew} openmp=project + spack compiler find + spack unload llvm@${llvm_vnew} +fi + echo --- gcc@${gcc_vold} `date` -spack install gcc@${gcc_vold} -echo --- load gcc@${gcc_vold} -spack load gcc@${gcc_vold} -module list -spack compiler find -spack unload gcc@${gcc_vold} -echo --- gcc@${gcc_vcuda} -spack install gcc@${gcc_vcuda} -spack load gcc@${gcc_vcuda} -spack compiler find -spack unload gcc@${gcc_vcuda} -if [ "$ourplatform" == "Intel" ]; then -echo --- gcc@${gcc_vintel} `date` -spack install gcc@${gcc_vintel} -spack load gcc@${gcc_vintel} -spack compiler find -spack unload gcc@${gcc_vintel} +if [ "${gcc_vllvmoffload}" == "${gcc_vold}" ]; then + echo Skipping: Already available via offload version +else + spack install gcc@${gcc_vold} + spack load gcc@${gcc_vold} + module list + spack compiler find + spack unload gcc@${gcc_vold} fi -echo --- gcc@${gcc_vnvhpc} `date` -spack install gcc@${gcc_vnvhpc} -spack load gcc@${gcc_vnvhpc} -spack compiler find -spack unload gcc@${gcc_vnvhpc} -echo --- llvm@${llvm_vnew} `date` -spack install llvm@${llvm_vnew} -spack load llvm@${llvm_vnew} -spack compiler find -spack unload llvm@${llvm_vnew} -echo --- llvm@${llvm_voffload} for offload `date` -spack install gcc@${gcc_vllvmoffload} -spack install cuda@${cuda_voffload} +allow-unsupported-compilers -spack load cuda@${cuda_voffload} +allow-unsupported-compilers -spack install llvm@${llvm_voffload} targets=all ^gcc@${gcc_vllvmoffload} -spack load llvm@${llvm_voffload} targets=all ^gcc@${gcc_vllvmoffload} -spack compiler find -spack unload llvm@${llvm_voffload} -spack unload cuda@${cuda_voffload} + +echo --- gcc@${gcc_vnew} `date` +if [ "${gcc_vllvmoffload}" == "${gcc_vnew}" ] || [ "${gcc_vold}" == "${gcc_vnew}" ] ; then + echo Skipping: Already available via offload or old versions +else + spack install gcc@${gcc_vnew} + spack load gcc@${gcc_vnew} + module list + spack compiler find + spack unload gcc@${gcc_vnew} +fi + echo --- Spack compilers `date` spack compilers echo --- Modules list diff --git a/tests/test_automation/nightly_test_scripts/ornl_setup_environments.sh b/tests/test_automation/nightly_test_scripts/ornl_setup_environments.sh index f548a32c95..be6efa4e43 100755 --- a/tests/test_automation/nightly_test_scripts/ornl_setup_environments.sh +++ b/tests/test_automation/nightly_test_scripts/ornl_setup_environments.sh @@ -2,12 +2,15 @@ echo --- START environment setup `date` +command -v spack >/dev/null 2>&1 || { echo "Error: spack not found on PATH." >&2; exit 1; } + # serial : single install # 8up : 8 installs # par48 : install -j 48 # makefile : make -j parallelmode=par48 +#parallelmode=makefile install_environment () { case "$parallelmode" in @@ -34,7 +37,7 @@ case "$parallelmode" in echo --- Install via parallel make spack concretize spack env depfile >Makefile - make -j + make -j 48 SPACK_COLOR=always --output-sync=recurse ;; * ) echo Unknown parallelmode @@ -76,45 +79,63 @@ echo --- Host is $ourhostname echo --- Using spack `which spack` echo --- SPACK_USER_CONFIG_PATH=$SPACK_USER_CONFIG_PATH -theenv=envgccnewmpi +for havempi in mpi nompi +do + +theenv=envgccnew${havempi} echo --- Setting up $theenv `date` spack env create $theenv -#spack -e $theenv config add "concretizer:unify:when_possible" spack -e $theenv config add "concretizer:unify:true" spack env activate $theenv spack add gcc@${gcc_vnew} +spack add hwloc spack add git spack add ninja -spack add cmake@${cmake_vnew} -spack add libxml2@${libxml2_v}^gcc@${gcc_vnew} +spack add cmake@${cmake_vnew}^gcc@${gcc_vnew} +spack add libxml2 spack add boost@${boost_vnew}^gcc@${gcc_vnew} spack add util-linux-uuid^gcc@${gcc_vnew} spack add python^gcc@${gcc_vnew} -spack add openmpi@${ompi_vnew}^gcc@${gcc_vnew} -spack add hdf5@${hdf5_vnew} +fortran +hl +mpi -spack add fftw@${fftw_vnew} -mpi #Avoid MPI for simplicity -spack add openblas threads=openmp -if [ "$ourplatform" == "AMD" ]; then -spack add amdblis; spack add amdlibflame; #spack add amd-aocl +if [ "$havempi" == "mpi" ]; then + spack add openmpi@${ompi_vnew}^gcc@${gcc_vnew} fi + +if [ "$havempi" == "mpi" ]; then + spack add hdf5@${hdf5_vnew} +fortran +hl +mpi ^gcc@${gcc_vnew} +else + spack add hdf5@${hdf5_vnew} +fortran +hl ~mpi ^gcc@${gcc_vnew} +fi + +spack add fftw@${fftw_vnew} -mpi ^gcc@${gcc_vnew} #Avoid MPI for simplicity +spack add openblas threads=openmp ^gcc@${gcc_vnew} +#PK: amdlibflame@5.2 will fail with gcc 15.2.0 as of 2026-03-24.f Link error +#if [ "$ourplatform" == "AMD" ]; then +#spack add amdblis; spack add amdlibflame; #spack add amd-aocl +#fi if [ "$ourplatform" == "Intel" ]; then spack add intel-oneapi-mkl fi - spack add py-lxml spack add py-matplotlib spack add py-pandas -spack add py-mpi4py +if [ "$havempi" == "mpi" ]; then + spack add py-mpi4py +fi + spack add py-numpy@${numpy_vnew} spack add py-scipy spack add py-h5py ^hdf5@${hdf5_vnew} + +if [ "$havempi" == "mpi" ]; then +# Complete install only for MPI environments: spack add quantum-espresso +mpi +qmcpack export CMAKE_BUILD_PARALLEL_LEVEL=8 # For PySCF -spack add py-pyscf -spack add dftd4 -spack add rmgdft +#spack add py-pyscf # Does not work with gccnew=15.2 +#spack add dftd4 +#spack add rmgdft@develop # Use develop version to avoid vendored SCALPACK compilation bugs (20250324) +#spack add rmgdft #Luxury options for actual science use: spack add py-requests # for pseudo helper @@ -127,106 +148,70 @@ spack add py-pydot # NEXUS optional #spack add py-seekpath # NEXUS optional #spack add py-pycifrw # NEXUS optional #NOT IN SPACK spack add py-cif2cell # NEXUS optional +fi install_environment unset CMAKE_BUILD_PARALLEL_LEVEL spack env deactivate -theenv=envgccnewnompi -echo --- Setting up $theenv `date` -spack env create $theenv -spack -e $theenv config add "concretizer:unify:when_possible" -#spack -e $theenv config add "concretizer:unify:true" -spack env activate $theenv - -spack add gcc@${gcc_vnew} -spack add git -spack add ninja -spack add cmake@${cmake_vnew} -spack add libxml2@${libxml2_v}^gcc@${gcc_vnew} -spack add boost@${boost_vnew}^gcc@${gcc_vnew} -spack add util-linux-uuid^gcc@${gcc_vnew} -spack add python^gcc@${gcc_vnew} -spack add hdf5@${hdf5_vnew} +fortran +hl ~mpi -spack add fftw@${fftw_vnew} -mpi #Avoid MPI for simplicity -spack add openblas threads=openmp -if [ "$ourplatform" == "AMD" ]; then -spack add amdblis; spack add amdlibflame; #spack add amd-aocl -fi -if [ "$ourplatform" == "Intel" ]; then -spack add intel-oneapi-mkl -fi +done +for havempi in mpi nompi +do -spack add py-lxml -spack add py-matplotlib -spack add py-pandas -spack add py-numpy@${numpy_vnew} -spack add py-scipy -spack add py-h5py ^hdf5@${hdf5_vnew} - -install_environment -spack env deactivate - -theenv=envgccoldnompi +theenv=envgccold${havempi} echo --- Setting up $theenv `date` spack env create $theenv -#spack -e $theenv config add "concretizer:unify:when_possible" spack -e $theenv config add "concretizer:unify:true" spack env activate $theenv spack add gcc@${gcc_vold} -spack add cmake@${cmake_vold}^gcc@${gcc_vold} -spack add libxml2@${libxml2_v}^gcc@${gcc_vold} -spack add boost@${boost_vold}^gcc@${gcc_vold} -spack add util-linux-uuid^gcc@${gcc_vold} -spack add python^gcc@${gcc_vold} -spack add hdf5@${hdf5_vold} +fortran +hl ~mpi -spack add fftw@${fftw_vold} -mpi #Avoid MPI for simplicity -spack add openblas threads=openmp +spack add hwloc spack add git spack add ninja - -spack add py-lxml -spack add py-matplotlib -spack add py-pandas -spack add py-numpy@${numpy_vold} -spack add py-scipy -spack add py-h5py ^hdf5@${hdf5_vnew} -install_environment -spack env deactivate - -theenv=envgccoldmpi -echo --- Setting up $theenv `date` -spack env create $theenv -#spack -e $theenv config add "concretizer:unify:when_possible" -spack -e $theenv config add "concretizer:unify:true" -spack env activate $theenv - -spack add gcc@${gcc_vold} spack add cmake@${cmake_vold}^gcc@${gcc_vold} -spack add libxml2@${libxml2_v}^gcc@${gcc_vold} +spack add libxml2 spack add boost@${boost_vold}^gcc@${gcc_vold} spack add util-linux-uuid^gcc@${gcc_vold} spack add python^gcc@${gcc_vold} -spack add openmpi@${ompi_vnew}^gcc@${gcc_vold} -spack add hdf5@${hdf5_vold} +fortran +hl +mpi -spack add fftw@${fftw_vold} -mpi #Avoid MPI for simplicity -spack add openblas threads=openmp -spack add git -spack add ninja +if [ "$havempi" == "mpi" ]; then + spack add openmpi@${ompi_vnew}^gcc@${gcc_vold} +fi + +if [ "$havempi" == "mpi" ]; then + spack add hdf5@${hdf5_vold} +fortran +hl +mpi ^gcc@${gcc_vold} +else + spack add hdf5@${hdf5_vold} +fortran +hl ~mpi ^gcc@${gcc_vold} +fi + +spack add fftw@${fftw_vold} -mpi ^gcc@${gcc_vold} #Avoid MPI for simplicity +spack add openblas threads=openmp ^gcc@${gcc_vold} +if [ "$ourplatform" == "AMD" ]; then +spack add amdblis; spack add amdlibflame; #spack add amd-aocl +fi +if [ "$ourplatform" == "Intel" ]; then +spack add intel-oneapi-mkl +fi spack add py-lxml spack add py-matplotlib spack add py-pandas -spack add py-mpi4py +if [ "$havempi" == "mpi" ]; then + spack add py-mpi4py +fi + spack add py-numpy@${numpy_vold} spack add py-scipy spack add py-h5py ^hdf5@${hdf5_vnew} -#spack add quantum-espresso +mpi +qmcpack # Skip QE, will crash GCC 12.4.0 + +if [ "$havempi" == "mpi" ]; then +# Complete install only for MPI environments: +spack add quantum-espresso +mpi +qmcpack export CMAKE_BUILD_PARALLEL_LEVEL=8 # For PySCF spack add py-pyscf -spack add rmgdft +#spack add dftd4 +#spack add rmgdft@develop # Use develop version to avoid vendored SCALPACK compilation bugs (20250324) +#spack add rmgdft #Luxury options for actual science use: spack add py-requests # for pseudo helper @@ -234,159 +219,140 @@ spack add py-ase # full Atomic Simulation Environment spack add libffi spack add graphviz +pangocairo # NEXUS requires optional PNG support in dot spack add py-pydot # NEXUS optional + #spack add py-spglib # NEXUS optional #spack add py-seekpath # NEXUS optional #spack add py-pycifrw # NEXUS optional #NOT IN SPACK spack add py-cif2cell # NEXUS optional +fi install_environment unset CMAKE_BUILD_PARALLEL_LEVEL spack env deactivate +done - theenv=envclangnewmpi - echo --- Setting up $theenv `date` - spack env create $theenv - #spack -e $theenv config add "concretizer:unify:when_possible" - spack -e $theenv config add "concretizer:unify:true" - spack env activate $theenv - - spack add llvm@${llvm_vnew} - spack add gcc@${gcc_vnew} - spack add git - spack add ninja - spack add cmake@${cmake_vnew} - spack add libxml2@${libxml2_v}^gcc@${gcc_vnew} - spack add boost@${boost_vnew}^gcc@${gcc_vnew} - spack add util-linux-uuid^gcc@${gcc_vnew} - spack add python^gcc@${gcc_vnew} - spack add openmpi@${ompi_vnew}^gcc@${gcc_vnew} - spack add hdf5@${hdf5_vnew} +fortran +hl +mpi - spack add fftw@${fftw_vnew} -mpi #Avoid MPI for simplicity - spack add openblas threads=openmp - if [ "$ourplatform" == "AMD" ]; then - spack add amdblis; spack add amdlibflame; #spack add amd-aocl - fi - if [ "$ourplatform" == "Intel" ]; then - spack add intel-oneapi-mkl - fi - - spack add py-lxml - spack add py-matplotlib - spack add py-pandas - spack add py-mpi4py - spack add py-numpy@${numpy_vold} - spack add py-scipy - spack add py-h5py ^hdf5@${hdf5_vnew} - install_environment - spack env deactivate - - theenv=envclangnewnompi - echo --- Setting up $theenv `date` - spack env create $theenv - #spack -e $theenv config add "concretizer:unify:when_possible" - spack -e $theenv config add "concretizer:unify:true" - spack env activate $theenv - - spack add llvm@${llvm_vnew}^gcc@${gcc_vnew} - spack add gcc@${gcc_vnew} - spack add git - spack add ninja - spack add cmake@${cmake_vnew} - spack add libxml2@${libxml2_v}^gcc@${gcc_vnew} - spack add boost@${boost_vnew}^gcc@${gcc_vnew} - spack add util-linux-uuid^gcc@${gcc_vnew} - spack add python^gcc@${gcc_vnew} - spack add hdf5@${hdf5_vnew} +fortran +hl ~mpi - spack add fftw@${fftw_vnew} -mpi #Avoid MPI for simplicity - spack add openblas threads=openmp - if [ "$ourplatform" == "AMD" ]; then - spack add amdblis; spack add amdlibflame; #spack add amd-aocl - fi - if [ "$ourplatform" == "Intel" ]; then - spack add intel-oneapi-mkl - fi - - spack add py-lxml - spack add py-matplotlib - spack add py-pandas - spack add py-numpy@${numpy_vold} - spack add py-scipy - spack add py-h5py ^hdf5@${hdf5_vnew} - install_environment - spack env deactivate - - -# TO DO: Match chosen cuda with version installed on system -theenv=envclangoffloadmpi +for havempi in mpi nompi +do + +theenv=envclangnew${havempi} echo --- Setting up $theenv `date` spack env create $theenv -#spack -e $theenv config add "concretizer:unify:when_possible" spack -e $theenv config add "concretizer:unify:true" spack env activate $theenv -spack add gcc@${gcc_vllvmoffload} -spack add cuda@${cuda_voffload} +allow-unsupported-compilers -spack add llvm@${llvm_voffload} - +spack add llvm@${llvm_vnew} +#spack add gcc@${gcc_vold} +spack add hwloc spack add git spack add ninja +#spack add cmake@${cmake_vnew}^gcc@${gcc_vold} spack add cmake@${cmake_vnew} -spack add libxml2@${libxml2_v}^gcc@${gcc_vllvmoffload} -spack add boost@${boost_vold}^gcc@${gcc_vllvmoffload} -spack add util-linux-uuid^gcc@${gcc_vllvmoffload} -spack add python^gcc@${gcc_vllvmoffload} -spack add openmpi@${ompi_vnew}^gcc@${gcc_vllvmoffload} -spack add hdf5@${hdf5_vold} +fortran +hl +mpi -spack add fftw@${fftw_vold} -mpi #Avoid MPI for simplicity -spack add openblas threads=openmp +spack add libxml2 +#spack add boost@${boost_vnew}^gcc@${gcc_vold} +spack add boost@${boost_vnew} +#spack add util-linux-uuid^gcc@${gcc_vold} +spack add util-linux-uuid +#spack add python^gcc@${gcc_vold} +spack add python +if [ "$havempi" == "mpi" ]; then +#spack add openmpi@${ompi_vnew}^gcc@${gcc_vold} +spack add openmpi@${ompi_vnew} +fi +if [ "$havempi" == "mpi" ]; then +#spack add hdf5@${hdf5_vnew} +fortran +hl +mpi ^gcc@${gcc_vold} +spack add hdf5@${hdf5_vnew} +fortran +hl +mpi +else +#spack add hdf5@${hdf5_vnew} +fortran +hl ~mpi ^gcc@${gcc_vold} +spack add hdf5@${hdf5_vnew} +fortran +hl ~mpi +fi +#spack add fftw@${fftw_vnew} -mpi ^gcc@${gcc_vold} #Avoid MPI for simplicity +spack add fftw@${fftw_vnew} -mpi #Avoid MPI for simplicity +#spack add openblas threads=openmp ^gcc@${gcc_vold} +spack add openblas threads=openmp +#PK: amdlibflame@5.2 will fail as of 2026-03-24 +#if [ "$ourplatform" == "AMD" ]; then +#spack add amdblis; spack add amdlibflame; #spack add amd-aocl +#fi +if [ "$ourplatform" == "Intel" ]; then +spack add intel-oneapi-mkl +fi + spack add py-lxml spack add py-matplotlib spack add py-pandas -spack add py-mpi4py +if [ "$havempi" == "mpi" ]; then + spack add py-mpi4py +fi spack add py-numpy@${numpy_vold} spack add py-scipy -spack add py-h5py ^hdf5@${hdf5_vold} +spack add py-h5py ^hdf5@${hdf5_vnew} install_environment spack env deactivate +done -theenv=envclangoffloadnompi +# Build LLVM offload with preferred GCC since CUDA may not support new GCC +# Build with new CMake +# TO DO: Match chosen cuda with version installed on system +for havempi in mpi nompi +do +theenv=envclangoffload${havempi} echo --- Setting up $theenv `date` spack env create $theenv -#spack -e $theenv config add "concretizer:unify:when_possible" spack -e $theenv config add "concretizer:unify:true" spack env activate $theenv spack add gcc@${gcc_vllvmoffload} spack add cuda@${cuda_voffload} +allow-unsupported-compilers -spack add llvm@${llvm_voffload} targets=all +spack add llvm@${llvm_voffload} openmp=project +libomptarget +libomptarget_debug ^cuda@${cuda_voffload} +spack add hwloc # Try hwloc to solve duplicate 2026-03-24 spack add git spack add ninja -spack add cmake@${cmake_vnew} -spack add libxml2@${libxml2_v}^gcc@${gcc_vllvmoffload} +spack add cmake@${cmake_vnew}^gcc@${gcc_vllvmoffload} +spack add libxml2 spack add boost@${boost_vold}^gcc@${gcc_vllvmoffload} spack add util-linux-uuid^gcc@${gcc_vllvmoffload} spack add python^gcc@${gcc_vllvmoffload} -spack add hdf5@${hdf5_vold} +fortran +hl ~mpi -spack add fftw@${fftw_vold} -mpi #Avoid MPI for simplicity -spack add openblas threads=openmp +spack add openmpi@${ompi_vnew}^gcc@${gcc_vllvmoffload} +if [ "$havempi" == "mpi" ]; then +spack add hdf5@${hdf5_vold} +fortran +hl +mpi ^gcc@${gcc_vllvmoffload} +else +spack add hdf5@${hdf5_vold} +fortran +hl ~mpi ^gcc@${gcc_vllvmoffload} +fi +spack add fftw@${fftw_vold} -mpi ^gcc@${gcc_vllvmoffload} #Avoid MPI for simplicity +spack add openblas threads=openmp ^gcc@${gcc_vllvmoffload} +#PK: amdlibflame@5.2 will fail 2026-03-24. Link error +#if [ "$ourplatform" == "AMD" ]; then +#spack add amdblis; spack add amdlibflame; #spack add amd-aocl +#fi +if [ "$ourplatform" == "Intel" ]; then +spack add intel-oneapi-mkl +fi spack add py-lxml spack add py-matplotlib spack add py-pandas + +if [ "$havempi" == "mpi" ]; then +spack add py-mpi4py +fi + spack add py-numpy@${numpy_vold} spack add py-scipy spack add py-h5py ^hdf5@${hdf5_vold} install_environment spack env deactivate - +done if [ "$ourplatform" == "AMD" ]; then -theenv=envamdclangmpi + +for havempi in mpi nompi +do + +theenv=envamdclang${havempi} echo --- Setting up $theenv `date` spack env create $theenv -#spack -e $theenv config add "concretizer:unify:when_possible" spack -e $theenv config add "concretizer:unify:true" spack env activate $theenv @@ -395,126 +361,108 @@ spack add gcc@${gcc_vllvmoffload} spack add git spack add ninja spack add cmake@${cmake_vnew} -spack add libxml2@${libxml2_v}^gcc@${gcc_vllvmoffload} +spack add libxml2 spack add boost@${boost_vold}^gcc@${gcc_vllvmoffload} spack add util-linux-uuid^gcc@${gcc_vllvmoffload} spack add python^gcc@${gcc_vllvmoffload} + +if [ "$havempi" == "mpi" ]; then spack add openmpi@${ompi_vnew}^gcc@${gcc_vllvmoffload} +fi +#spack add hdf5@${hdf5_vold}%gcc@${gcc_vllvmoffload} +fortran +hl +mpi +if [ "$havempi" == "mpi" ]; then spack add hdf5@${hdf5_vold} +fortran +hl +mpi -spack add fftw@${fftw_vold} -mpi #Avoid MPI for simplicity -spack add openblas threads=openmp -spack add amdblis; spack add amdlibflame; #spack add amd-aocl +else +spack add hdf5@${hdf5_vold} +fortran +hl ~mpi +fi +spack add fftw@${fftw_vold} -mpi ^gcc@${gcc_vllvmoffload} #Avoid MPI for simplicity +spack add openblas threads=openmp ^gcc@${gcc_vllvmoffload} +#MAR26spack add amdblis^gcc@${gcc_vold}; spack add amdlibflame^gcc@${gcc_vold}; #spack add amd-aocl spack add py-lxml spack add py-matplotlib spack add py-pandas +if [ "$havempi" == "mpi" ]; then spack add py-mpi4py +fi spack add py-numpy@${numpy_vold} spack add py-scipy spack add py-h5py ^hdf5@${hdf5_vold} +if [ "$havempi" == "mpi" ]; then spack add quantum-espresso +mpi +qmcpack -spack add rmgdft@develop # Use develop version to avoid vendored SCALPACK compilation bugs (20250324) -install_environment -spack env deactivate - -theenv=envamdclangnompi -echo --- Setting up $theenv `date` -spack env create $theenv -#spack -e $theenv config add "concretizer:unify:when_possible" -spack -e $theenv config add "concretizer:unify:true" -spack env activate $theenv - -spack add gcc@${gcc_vllvmoffload} -spack add git -spack add ninja -spack add cmake@${cmake_vnew} -spack add libxml2@${libxml2_v}^gcc@${gcc_vllvmoffload} -spack add boost@${boost_vold}^gcc@${gcc_vllvmoffload} -spack add util-linux-uuid^gcc@${gcc_vllvmoffload} -spack add python^gcc@${gcc_vllvmoffload} -spack add hdf5@${hdf5_vold} +fortran +hl ~mpi -spack add fftw@${fftw_vold} -mpi #Avoid MPI for simplicity -spack add openblas threads=openmp -spack add amdblis; spack add amdlibflame; #spack add amd-aocl - -spack add py-lxml -spack add py-matplotlib -spack add py-pandas -spack add py-numpy@${numpy_vold} -spack add py-scipy -spack add py-h5py ^hdf5@${hdf5_vold} +fi install_environment spack env deactivate +done fi - -#if [ "$ourplatform" == "Intel" ]; then -#theenv=envinteloneapinompi -#echo --- Setting up $theenv `date` -#spack env create $theenv -##spack -e $theenv config add "concretizer:unify:when_possible" -#spack -e $theenv config add "concretizer:unify:true" -#spack env activate $theenv -# -#spack add gcc@${gcc_vintel} -#spack add git -#spack add ninja -#spack add cmake@${cmake_vnew} -#spack add libxml2@${libxml2_v}%gcc@${gcc_vintel} -#spack add boost@${boost_vnew}%gcc@${gcc_vintel} -#spack add util-linux-uuid%gcc@${gcc_vintel} -#spack add python%gcc@${gcc_vintel} -#spack add hdf5@${hdf5_vnew}%gcc@${gcc_vintel} +fortran +hl ~mpi -#spack add fftw@${fftw_vnew}%gcc@${gcc_vintel} -mpi #Avoid MPI for simplicity -# -#spack add py-lxml -#spack add py-matplotlib -#spack add py-pandas -#spack add py-numpy@${numpy_vold} -#spack add py-scipy -#spack add py-h5py ^hdf5@${hdf5_vnew}%gcc@${gcc_vintel} +fortran +hl ~mpi -#install_environment -#spack env deactivate -# -#theenv=envinteloneapimpi -#echo --- Setting up $theenv `date` -#spack env create $theenv -##spack -e $theenv config add "concretizer:unify:when_possible" -#spack -e $theenv config add "concretizer:unify:true" -#spack env activate $theenv -# -#spack add gcc@${gcc_vintel} -#spack add git -#spack add ninja -#spack add cmake@${cmake_vnew} -#spack add libxml2@${libxml2_v}%gcc@${gcc_vintel} -#spack add boost@${boost_vnew}%gcc@${gcc_vintel} -#spack add util-linux-uuid%gcc@${gcc_vintel} -#spack add python%gcc@${gcc_vintel} -#spack add hdf5@${hdf5_vnew}%gcc@${gcc_vintel} +fortran +hl ~mpi -#spack add fftw@${fftw_vnew}%gcc@${gcc_vintel} -mpi #Avoid MPI for simplicity -# -#spack add py-lxml -#spack add py-matplotlib -#spack add py-pandas -#spack add py-numpy@${numpy_vold} -#spack add py-scipy -#spack add py-h5py ^hdf5@${hdf5_vnew}%gcc@${gcc_vintel} +fortran +hl ~mpi -#install_environment -#spack env deactivate -#fi - -# CAUTION: Removing build deps reveals which spack packages do not have correct runtime deps specified and may result in breakage -#echo --- Removing build deps -#for f in `spack env list` -#do -# spack env activate $f -# spack gc --yes-to-all -# echo --- Software for environment $f -# spack env status -# spack find -# spack env deactivate -#done +#MAR26#if [ "$ourplatform" == "Intel" ]; then +#MAR26#theenv=envinteloneapinompi +#MAR26#echo --- Setting up $theenv `date` +#MAR26#spack env create $theenv +#MAR26##spack -e $theenv config add "concretizer:unify:when_possible" +#MAR26#spack -e $theenv config add "concretizer:unify:true" +#MAR26#spack env activate $theenv +#MAR26# +#MAR26#spack add gcc@${gcc_vintel} +#MAR26#spack add git +#MAR26#spack add ninja +#MAR26#spack add cmake@${cmake_vnew} +#MAR26#spack add libxml2%gcc@${gcc_vintel} +#MAR26#spack add boost@${boost_vnew}%gcc@${gcc_vintel} +#MAR26#spack add util-linux-uuid%gcc@${gcc_vintel} +#MAR26#spack add python%gcc@${gcc_vintel} +#MAR26#spack add hdf5@${hdf5_vnew}%gcc@${gcc_vintel} +fortran +hl ~mpi +#MAR26#spack add fftw@${fftw_vnew}%gcc@${gcc_vintel} -mpi #Avoid MPI for simplicity +#MAR26# +#MAR26#spack add py-lxml +#MAR26#spack add py-matplotlib +#MAR26#spack add py-pandas +#MAR26#spack add py-numpy@${numpy_vold} +#MAR26#spack add py-scipy +#MAR26#spack add py-h5py ^hdf5@${hdf5_vnew}%gcc@${gcc_vintel} +fortran +hl ~mpi +#MAR26#install_environment +#MAR26#spack env deactivate +#MAR26# +#MAR26#theenv=envinteloneapimpi +#MAR26#echo --- Setting up $theenv `date` +#MAR26#spack env create $theenv +#MAR26##spack -e $theenv config add "concretizer:unify:when_possible" +#MAR26#spack -e $theenv config add "concretizer:unify:true" +#MAR26#spack env activate $theenv +#MAR26# +#MAR26#spack add gcc@${gcc_vintel} +#MAR26#spack add git +#MAR26#spack add ninja +#MAR26#spack add cmake@${cmake_vnew} +#MAR26#spack add libxml2%gcc@${gcc_vintel} +#MAR26#spack add boost@${boost_vnew}%gcc@${gcc_vintel} +#MAR26#spack add util-linux-uuid%gcc@${gcc_vintel} +#MAR26#spack add python%gcc@${gcc_vintel} +#MAR26#spack add hdf5@${hdf5_vnew}%gcc@${gcc_vintel} +fortran +hl ~mpi +#MAR26#spack add fftw@${fftw_vnew}%gcc@${gcc_vintel} -mpi #Avoid MPI for simplicity +#MAR26# +#MAR26#spack add py-lxml +#MAR26#spack add py-matplotlib +#MAR26#spack add py-pandas +#MAR26#spack add py-numpy@${numpy_vold} +#MAR26#spack add py-scipy +#MAR26#spack add py-h5py ^hdf5@${hdf5_vnew}%gcc@${gcc_vintel} +fortran +hl ~mpi +#MAR26#install_environment +#MAR26#spack env deactivate +#MAR26#fi +#MAR26 +#MAR26# CAUTION: Removing build deps reveals which spack packages do not have correct runtime deps specified and may result in breakage +#MAR26#echo --- Removing build deps +#MAR26#for f in `spack env list` +#MAR26#do +#MAR26# spack env activate $f +#MAR26# spack gc --yes-to-all +#MAR26# echo --- Software for environment $f +#MAR26# spack env status +#MAR26# spack find +#MAR26# spack env deactivate +#MAR26#done echo --- Making loads files for f in `spack env list` diff --git a/tests/test_automation/nightly_test_scripts/ornl_versions.sh b/tests/test_automation/nightly_test_scripts/ornl_versions.sh index c6e143df4f..d900688cb1 100755 --- a/tests/test_automation/nightly_test_scripts/ornl_versions.sh +++ b/tests/test_automation/nightly_test_scripts/ornl_versions.sh @@ -4,42 +4,37 @@ # GCC # Dates at https://gcc.gnu.org/releases.html -#gcc_vnew=15.1.0 # Released 2025-04-25 # Too ambituous 2025-05-02 -gcc_vnew=14.2.0 # Released 2024-08-01 -gcc_vold=12.4.0 # Released 2024-06-20 +gcc_vnew=15.2.0 # Released 2025-08-08 +gcc_vold=13.4.0 # Released 2025-06-06 -gcc_vcuda=${gcc_vold} -gcc_vintel=${gcc_vold} -gcc_vnvhpc=${gcc_vold} -gcc_vllvmoffload=${gcc_vold} +# Verify vs cuda_voffload release notes e.g. +# https://docs.nvidia.com/cuda/archive/12.9.0/cuda-installation-guide-linux/index.html#host-compiler-support-policy +#gcc_vllvmoffload=13.4.0 +gcc_vllvmoffload=11.5.0 # Must match RHEL system supplied gcc # LLVM # Dates at https://releases.llvm.org/ -llvm_vnew=20.1.4 # Released 2025-05-02 -llvm_voffload=${llvm_vnew} -cuda_voffload=12.6.0 # https://releases.llvm.org/20.1.0/tools/clang/docs/ReleaseNotes.html#cuda-support #12.6 is limit for LLVM 20.1.0 +llvm_vnew=22.1.2 # Released 2026-03-25 +llvm_voffload=21.1.8 # 22.1.1 not working as of 2026-04-03 +cuda_voffload=12.6.0 # Same as system installed version # HDF5 # Dates at https://portal.hdfgroup.org/display/support/Downloads -#hdf5_vnew=1.14.6 # Released 2025-02-05 -hdf5_vnew=1.14.5 +hdf5_vnew=1.14.6 # Released 2025-02-05 +#hdf5_vnew=1.14.5 hdf5_vold=${hdf5_vnew} # CMake # Dates at https://cmake.org/files/ #cmake_vnew=3.30.8 # Try older version for py-pyscf build -cmake_vnew=3.31.6 -cmake_vold=${cmake_vnew} +cmake_vnew=4.2.3 +cmake_vold=3.27.9 # OpenMPI # Dates at https://www.open-mpi.org/software/ompi/v5.0/ -ompi_vnew=5.0.6 # Released 2024-11-15 -#ompi_vnew=5.0.7 # Released 2025-02-014 +ompi_vnew=5.0.10 # Released 2026-02-23 ompi_vold=${ompi_vold} -# Libxml2 -libxml2_v=2.13.5 # Released 2024-11-12 See https://gitlab.gnome.org/GNOME/libxml2/-/releases - # FFTW # Dates at http://www.fftw.org/release-notes.html fftw_vnew=3.3.10 # Released 2021-09-15 @@ -47,14 +42,15 @@ fftw_vold=${fftw_vnew} # Released 2018-05-28 # BOOST # Dates at https://www.boost.org/users/history/ -boost_vnew=1.88.0 # Released 2025-04-10 -boost_vold=1.82.0 # Released 2023-08-11 +boost_vnew=1.90.0 # Released 2025-12-10 +boost_vold=1.84.0 # Released 2023-12-06 # Python # Use a single version to reduce dependencies. Ideally the spack prefered version. -python_version=3.13.2 +python_version=3.14.3 -numpy_vnew=2.2.5 -numpy_vold=2.2.5 -#numpy_vold=1.26.4 +#numpy_vnew=2.4.3 +#numpy_vold=2.4.3 +numpy_vnew=2.3.5 # PySCF < v2.12.1 is incompatible with >=2.4.0 +numpy_vold=2.3.5 diff --git a/utils/ncjf_gen.py b/utils/ncjf_gen.py index 4b3651ed3f..f373d3cd57 100755 --- a/utils/ncjf_gen.py +++ b/utils/ncjf_gen.py @@ -4,6 +4,7 @@ import sys import numpy as np from copy import deepcopy +from functools import reduce import xml.etree.ElementTree as et @@ -182,7 +183,7 @@ def __imul__(self, other): return self # g / c or g1 / g2 - def __div__(self,other): + def __truediv__(self,other): try: A = self.A - other.A B = self.B - other.B @@ -199,7 +200,7 @@ def __div__(self,other): return gaussian("none",A,B,C) # c / g - def __rdiv__(self,other): + def __rtruediv__(self,other): A = self.A B = self.B C = self.C - np.log(other) @@ -209,7 +210,7 @@ def __rdiv__(self,other): # g /= c or g1 /= g2 - def __idiv__(self,other): + def __itruediv__(self,other): # other is another gaussian try: self.A -= other.A @@ -274,8 +275,8 @@ def atomic_coords(ptclfile): posnode = ptclroot.find(".//particleset[@name='ion0']/attrib[@name='position']") posblock = posnode.text pts = [] - re_num = "(-?\d\.\d+e[+-]\d\d)" - re_pos = "{re_num}\s+{re_num}\s+{re_num}".format(re_num=re_num) + re_num = r"(-?\d\.\d+e[+-]\d\d)" + re_pos = r"{re_num}\s+{re_num}\s+{re_num}".format(re_num=re_num) for pos in re.finditer(re_pos, posblock): pts.append( np.array(pos.groups(), dtype=np.float64) ) return pts @@ -328,12 +329,12 @@ def write_ncjf(outpath, g_list, F, ncjf_name, gref = None): region_tag.append(gaussian_tag) # indent and write to file indent(cjf_tag) - print " writing cjf tags to file: {}".format(outpath) + print(" writing cjf tags to file: {}".format(outpath)) et.ElementTree(cjf_tag).write(outpath) if __name__ == "__main__": if len(sys.argv) < 3: - print "usage: ncjf_gen.py qmc.ptcl.xml cjf.xml" + print("usage: ncjf_gen.py qmc.ptcl.xml cjf.xml") sys.exit(0) ptclfile = sys.argv[1] cjffile = sys.argv[2] From 314c272c59600a4bb0a888672a0d6c43175e956e Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Sun, 14 Jun 2026 11:48:01 -0400 Subject: [PATCH 10/10] Nexus: Clean up some docstrings, remove temp files --- nexus/nexus/pwscf_input_new.py | 140 +++++++++++---------------------- nexus/nxs_pw_inp_arrays.txt | 24 ------ nexus/nxs_pw_inp_bools.txt | 43 ---------- nexus/nxs_pw_inp_floats.txt | 138 -------------------------------- nexus/nxs_pw_inp_ints.txt | 70 ----------------- nexus/nxs_pw_inp_strs.txt | 45 ----------- 6 files changed, 45 insertions(+), 415 deletions(-) delete mode 100644 nexus/nxs_pw_inp_arrays.txt delete mode 100644 nexus/nxs_pw_inp_bools.txt delete mode 100644 nexus/nxs_pw_inp_floats.txt delete mode 100644 nexus/nxs_pw_inp_ints.txt delete mode 100644 nexus/nxs_pw_inp_strs.txt diff --git a/nexus/nexus/pwscf_input_new.py b/nexus/nexus/pwscf_input_new.py index e7b42fa19a..e85c3437dd 100644 --- a/nexus/nexus/pwscf_input_new.py +++ b/nexus/nexus/pwscf_input_new.py @@ -1,11 +1,30 @@ +"""Module for generating input files for Quantum ESPRESSO. + +A majority of the code in this module was auto-generated by a Python script that +uses the intermediate XML representation of QE's ``pw.x`` input +description files. + +A description of how to turn QE's ``.def`` documentation files into ``.xml`` +is given in QE's repository, at ``q-e/dev-tools/README.helpdoc``. + +Notes +----- +If you wish to add a new variable to a namelist enum, you +can simply append the variable to the end of the definitions. +The only required attributes that you must define are ``datatype`` +and ``default``, however it is ***strongly encouraged*** to specify +the remaining information so that the various checks present +throughout the rest of the code base can be utilized properly. +""" + + from __future__ import annotations -import os from os import PathLike from collections.abc import Sequence from abc import ABC, abstractmethod from dataclasses import dataclass from pathlib import Path -from typing import ClassVar, Self, TypeVar +from typing import ClassVar, Self, TypeAlias from enum import Enum import builtins @@ -17,9 +36,9 @@ from .structure import kmesh -PwscfInputType = str | bool | int | float | Sequence +PwscfInputType: TypeAlias = str | bool | int | float | Sequence # For structured array inputs (k-points, weights, reciprocal lattice, etc.) -PwscfArrayInput = npt.NDArray[np.floating] | Sequence[Sequence[float]] | Sequence[float] +PwscfArrayInput: TypeAlias = npt.NDArray[np.floating] | Sequence[Sequence[float]] | Sequence[float] @dataclass(frozen=True) # We generally don't want any of these to be modified @@ -61,18 +80,7 @@ def __new__( #end class NamelistEnumBase class ControlDefinitions(NamelistParamDefinition, NamelistEnumBase): - """Class representing all variables that belongs to the - &CONTROL input namelist for ``pw.x``. - - Notes - ----- - If you wish to add a new variable to the &CONTROL namelist, you - can simply append the variable to the end of the definitions. - The only required attributes that you must define are ``datatype`` - and ``default``, however it is ***strongly encouraged*** to specify - the remaining information so that the various checks present - throughout the rest of the code base can be utilized properly. - """ + """All variables belonging to the &CONTROL input namelist for ``pw.x``.""" calculation = str, False, (1,), ('scf', 'nscf', 'bands', 'relax', 'md', 'vc-relax', 'vc-md') title = str, False, (1,), None @@ -108,18 +116,7 @@ class ControlDefinitions(NamelistParamDefinition, NamelistEnumBase): #end class ControlDefinitions class SystemVariables(NamelistParamDefinition, NamelistEnumBase): - """Class representing all variables that belongs to the - &SYSTEM input namelist for ``pw.x``. - - Notes - ----- - If you wish to add a new variable to the &CONTROL namelist, you - can simply append the variable to the end of the definitions. - The only required attributes that you must define are ``datatype`` - and ``default``, however it is ***strongly encouraged*** to specify - the remaining information so that the various checks present - throughout the rest of the code base can be utilized properly. - """ + """All variables belonging to the &SYSTEM input namelist for ``pw.x``.""" ibrav = int, True, (1,), None nat = int, True, (1,), None @@ -236,18 +233,7 @@ class SystemVariables(NamelistParamDefinition, NamelistEnumBase): #end class SystemVariables class ElectronsVariables(NamelistParamDefinition, NamelistEnumBase): - """Class representing all variables that belongs to the - &ELECTRONS input namelist for ``pw.x``. - - Notes - ----- - If you wish to add a new variable to the &CONTROL namelist, you - can simply append the variable to the end of the definitions. - The only required attributes that you must define are ``datatype`` - and ``default``, however it is ***strongly encouraged*** to specify - the remaining information so that the various checks present - throughout the rest of the code base can be utilized properly. - """ + """All variables belonging to the &ELECTRONS input namelist for ``pw.x``.""" electron_maxstep = int, False, (1,), None exx_maxstep = int, False, (1,), None @@ -278,18 +264,7 @@ class ElectronsVariables(NamelistParamDefinition, NamelistEnumBase): #end class ElectronsVariables class IonsVariables(NamelistParamDefinition, NamelistEnumBase): - """Class representing all variables that belongs to the - &IONS input namelist for ``pw.x``. - - Notes - ----- - If you wish to add a new variable to the &CONTROL namelist, you - can simply append the variable to the end of the definitions. - The only required attributes that you must define are ``datatype`` - and ``default``, however it is ***strongly encouraged*** to specify - the remaining information so that the various checks present - throughout the rest of the code base can be utilized properly. - """ + """All variables belonging to the &IONS input namelist for ``pw.x``.""" ion_positions = str, False, (1,), ('default', 'from_input') ion_velocities = str, False, (1,), ('default', 'from_input') @@ -326,18 +301,7 @@ class IonsVariables(NamelistParamDefinition, NamelistEnumBase): #end class IonsVariables class CellVariables(NamelistParamDefinition, NamelistEnumBase): - """Class representing all variables that belongs to the - &CELL input namelist for ``pw.x``. - - Notes - ----- - If you wish to add a new variable to the &CONTROL namelist, you - can simply append the variable to the end of the definitions. - The only required attributes that you must define are ``datatype`` - and ``default``, however it is ***strongly encouraged*** to specify - the remaining information so that the various checks present - throughout the rest of the code base can be utilized properly. - """ + """All variables belonging to the &CELL input namelist for ``pw.x``.""" cell_dynamics = str, False, (1,), ('none', 'sd', 'damp-pr', 'damp-w', 'bfgs', 'none', 'pr', 'w') press = float, False, (1,), None @@ -348,18 +312,7 @@ class CellVariables(NamelistParamDefinition, NamelistEnumBase): #end class CellVariables class FCPVariables(NamelistParamDefinition, NamelistEnumBase): - """Class representing all variables that belongs to the - &FCP input namelist for ``pw.x``. - - Notes - ----- - If you wish to add a new variable to the &CONTROL namelist, you - can simply append the variable to the end of the definitions. - The only required attributes that you must define are ``datatype`` - and ``default``, however it is ***strongly encouraged*** to specify - the remaining information so that the various checks present - throughout the rest of the code base can be utilized properly. - """ + """All variables belonging to the &FCP input namelist for ``pw.x``.""" fcp_mu = float, True, (1,), None fcp_dynamics = str, False, (1,), ('bfgs', 'newton', 'damp', 'lm', 'velocity-verlet', 'verlet') @@ -376,18 +329,7 @@ class FCPVariables(NamelistParamDefinition, NamelistEnumBase): #end class FCPVariables class RismVariables(NamelistParamDefinition, NamelistEnumBase): - """Class representing all variables that belongs to the - &RISM input namelist for ``pw.x``. - - Notes - ----- - If you wish to add a new variable to the &CONTROL namelist, you - can simply append the variable to the end of the definitions. - The only required attributes that you must define are ``datatype`` - and ``default``, however it is ***strongly encouraged*** to specify - the remaining information so that the various checks present - throughout the rest of the code base can be utilized properly. - """ + """All variables belonging to the &RISM input namelist for ``pw.x``.""" nsolv = int, True, (1,), None closure = str, False, (1,), ('kh', 'hnc') @@ -454,7 +396,7 @@ def value(self, val: PwscfInputType): f"Can not set {self.name} to None, it is required!" ) elif not isinstance(val, self.datatype): - return TypeError( + raise TypeError( f"Expected a value of type {self.datatype} for {self.name} but got {type(val)} instead!" ) else: @@ -506,6 +448,7 @@ def write(self, card: PWscfCardBase) -> str: def read(self, body: str, **kwargs) -> PWscfCardBase: """Read the card body (excluding header line). Returns the card instance.""" ... +#end class PWscfCardBaseIO class PWscfCardBase(ABC): @@ -519,7 +462,6 @@ def write(self) -> str: ... @classmethod @abstractmethod def read(cls, card: str): ... - #end class PWscfCardBase @@ -543,6 +485,7 @@ def from_physical_system(cls, system: PhysicalSystem, pseudos: str) -> Self: Nexus ``PhysicalSystem``. Must have elements and be pseudized. """ ... +#end class AtomicSpecies _PWSCF_ARRAY_FORMAT = '{0:16.8f}' # could be imported from somewhere else to be more general @@ -560,6 +503,7 @@ def _array_to_string( return rowsep.join( pad + ' '.join(fmt.format(v) for v in row) for row in a ) +#end def _array_to_string # Kpoints Card class KPointsGammaIO(PWscfCardBaseIO): @@ -570,6 +514,7 @@ def write(self, card: KPoints) -> str: @staticmethod def read(lines: list[str]) -> KPoints: return KPoints(specifier='gamma') +#end class KPointsGammaIO class KPointsAutomaticIO(PWscfCardBaseIO): """IO for K_POINTS {automatic} - Monkhorst-Pack grid.""" @@ -588,7 +533,7 @@ def read(self, lines: list[str]) -> KPoints: grid = a[0:3] shift = a[3:] return KPoints(specifier='automatic', grid=grid, shift=shift) - +#end class KPointsAutomaticIO class KPointsExplicitIO(PWscfCardBaseIO): """IO for K_POINTS {tpiba,crystal,tpiba_b,crystal_b,tpiba_c,crystal_c}. @@ -620,6 +565,7 @@ def read(self, lines: list[str], specifier: str = 'crystal', **kwargs) -> KPoint kpoints = arr[:, :3] weights = arr[:, 3] if arr.shape[1] > 3 else np.ones(len(kpoints)) return KPoints(specifier=specifier, kpoints=kpoints, weights=weights) +#end class KPointsExplicitIO class KPoints(PWscfCardBase): """K_POINTS card with strategy-pattern writers for specifier-dependent formats. @@ -855,6 +801,7 @@ def from_physical_system( elif spec in ('crystal_b', 'crystal_c'): card.specifier = spec # same coords as crystal, different specifier return card +#end class KPoints # Hubbard Card @dataclass(frozen=True) @@ -870,6 +817,7 @@ class HubbardOnSite: def __post_init__(self): if self.param not in self._allowed_params: raise ValueError(f"Invalid on-site parameter: {self.param}") +#end class HubbardOnSite @dataclass(frozen=True) class HubbardOrbitalResolved(HubbardOnSite): @@ -878,6 +826,7 @@ class HubbardOrbitalResolved(HubbardOnSite): """ param: str orbitals: tuple[int, ...] # orbital indices in manifold +#end class HubbardOrbitalResolved @dataclass(frozen=True) class HubbardInterSite: @@ -895,9 +844,9 @@ class HubbardInterSite: def __post_init__(self): if self.param not in self._allowed_params: raise ValueError(f"Invalid inter-site parameter: {self.param}") +#end class HubbardInterSite - -HubbardEntry = HubbardOnSite | HubbardInterSite | HubbardOrbitalResolved +HubbardEntry: TypeAlias = HubbardOnSite | HubbardInterSite | HubbardOrbitalResolved class HubbardIO(PWscfCardBaseIO): @@ -950,7 +899,7 @@ def read(self, lines: list[str], specifier: str = 'atomic', **kwargs) -> Hubbard orbitals = tuple(int(t) for t in tokens[3:]) entries.append(HubbardOrbitalResolved(param, label, val, orbitals)) return Hubbard(entries=entries, specifier=specifier) - +#end class HubbardIO class Hubbard(PWscfCardBase): """HUBBARD card with strategy-pattern writers for line types 1, 2, 3. @@ -1117,4 +1066,5 @@ def from_hp_output(cls, text: str) -> Self: def from_hubbard_dat_file(self, file: PathLike) -> Self: """Create HUBBARD card from a hubbard.dat file.""" with Path(file).open() as f: - return self.from_hp_output(f.read()) \ No newline at end of file + return self.from_hp_output(f.read()) +#end class Hubbard diff --git a/nexus/nxs_pw_inp_arrays.txt b/nexus/nxs_pw_inp_arrays.txt deleted file mode 100644 index 9a95d88414..0000000000 --- a/nexus/nxs_pw_inp_arrays.txt +++ /dev/null @@ -1,24 +0,0 @@ -"celldm", -!"starting_magnetization", -!"hubbard_alpha", # Removed? -!"hubbard_u", # Removed? -!"hubbard_j0", # Removed? -!"hubbard_beta", -!"hubbard_j", # Removed? -"starting_ns_eigenvalue", -!"angle1", -!"angle2", -"fixed_magnetization", -"fe_step", # Removed? -"efield_cart", -!"london_c6", -!"london_rvdw", -!"starting_charge" - - -fnhscl -start 1 -end ntyp REAL -solute_epsilon -start 1 -end ntyp REAL -solute_sigma -start 1 -end ntyp REAL -Hubbard_occ -start 1,1 -end ntyp,3 -indexes ityp,i REAL -nhgrp -start 1 -end ntyp INTEGER -solute_lj -start 1 -end ntyp CHARACTER \ No newline at end of file diff --git a/nexus/nxs_pw_inp_bools.txt b/nexus/nxs_pw_inp_bools.txt deleted file mode 100644 index ba67a43093..0000000000 --- a/nexus/nxs_pw_inp_bools.txt +++ /dev/null @@ -1,43 +0,0 @@ -"wf_collect", -"tstress", -"tprnfor", -"lkpoint_dir", -"tefield", -"dipfield", -"lelfield", -"lberry", -"nosym", -"nosym_evc", -"noinv", -"force_symmorphic", -"noncolin", # Removed? -"lda_plus_u", # Removed? -"lspinorb", -"do_ee", # Removed? -"london", -"diago_full_acc", -"tqr", -"remove_rigid_rot", -"refold_pos", -"first_last_opt", # Removed? -"use_masses", # Removed? -"use_freezing", # Removed? -"la2F", # Removed? -"lorbm", -"lfcpopt", # Removed? -"scf_must_converge", -"adaptive_thr", -"no_t_rev", -"use_all_frac", -"one_atom_occupations", -"starting_spin_angle", -"x_gamma_extrapolation", -"xdm", -"uniqueb", -"rhombohedral", -"gate", -"block", -"relaxz", -"dftd3_threebody", -"ts_vdw_isolated", # Removed? -"lforcet", diff --git a/nexus/nxs_pw_inp_floats.txt b/nexus/nxs_pw_inp_floats.txt deleted file mode 100644 index 54e6525445..0000000000 --- a/nexus/nxs_pw_inp_floats.txt +++ /dev/null @@ -1,138 +0,0 @@ -"dt", -"max_seconds", -"etot_conv_thr", -"forc_conv_thr", -"celldm", -"A", -"B", -"C", -"cosAB", -"cosAC", -"cosBC", -"nelec", # Removed? -"ecutwfc", -"ecutrho", -"degauss", -"tot_charge", -"tot_magnetization", -"starting_magnetization", -"nelup", # Removed? -"neldw", # Removed? -"ecfixed", -"qcutz", -"q2sigma", -"Hubbard_alpha", # Removed? -"Hubbard_U", # Removed? -"Hubbard_J", # Removed? -"starting_ns_eigenvalue", -"emaxpos", -"eopreg", -"eamp", -"angle1", -"angle2", -"fixed_magnetization", -"lambda", -"london_s6", -"london_rcut", -"conv_thr", -"mixing_beta", -"diago_thr_init", -"efield", -"tempw", -"tolp", -"delta_t", -"upscale", -"trust_radius_max", -"trust_radius_min", -"trust_radius_ini", -"w_1", -"w_2", -"temp_req", # Removed? -"ds", # Removed? -"k_max", # Removed? -"k_min", # Removed? -"path_thr", # Removed? -"fe_step", # Removed? -"g_amplitude", # Removed? -"press", -"wmass", -"cell_factor", -"press_conv_thr", -"xqq", # Removed? -"ecutcoarse", # Removed? -"mixing_charge_compensation", # Removed? -"comp_thr", # Removed? -"exx_fraction", -"ecutfock", -"conv_thr_init", -"conv_thr_multi", -"efield_cart", -"screening_parameter", -"ecutvcut", -"Hubbard_J0", # Removed? -"Hubbard_beta", -"Hubbard_J", # Removed? -"esm_w", -"esm_efield", -"fcp_mu", -"london_c6", -"london_rvdw", -"xdm_a1", -"xdm_a2", -"block_1", -"block_2", -"block_height", -"zgate", -"ts_vdw_econv_thr", -"starting_charge" - - - -"degauss_cond", # New? -"nelec_cond", # New? -"sic_gamma", # New? -"sci_vb", # New? -"sci_cb", # New? -"localization_thr", # New? -"gcscf_mu", # New? -"gcscf_conv_thr", # New? -"gcscf_beta", # New? -"fnosep", # New? -"fire_alpha_init", # New? -"fire_falpha", # New? -"fire_f_inc", # New? -"fire_f_dec", # New? -"fire_dtmax", # New? -"fcp_conv_thr", # New? -"fcp_mass", # New? -"fcp_velocity", # New? -"fcp_tempw", # New? -"fcp_tolp", # New? -"fcp_delta_t", # New? -"tempv", # New? -"ecutsolv", # New? -"smear1d", # New? -"smear3d", # New? -"rism1d_conv_thr", # New? -"rism3d_conv_thr", # New? -"mdiis1d_step", # New? -"mdiis3d_step", # New? -"rism1d_bond_width", # New? -"rism1d_dielectric", # New? -"rism1d_molesize", # New? -"rism3d_conv_level", # New? -"laue_expand_right", # New? -"laue_expand_left", # New? -"laue_starting_right", # New? -"laue_starting_left", # New? -"laue_buffer_right", # New? -"laue_buffer_left", # New? -"laue_wall_z", # New? -"laue_wall_rho", # New? -"laue_wall_epsilon", # New? -"laue_wall_sigma", # New? -"constr_tol", # New? -"Hubbard_occ", # New? -"fnhscl", # New? -"solute_epsilon", # New? -"solute_sigma", # New? \ No newline at end of file diff --git a/nexus/nxs_pw_inp_ints.txt b/nexus/nxs_pw_inp_ints.txt deleted file mode 100644 index 75215d2bea..0000000000 --- a/nexus/nxs_pw_inp_ints.txt +++ /dev/null @@ -1,70 +0,0 @@ -"nstep" -"iprint" -"gdir" -"nppstr" -"nberrycyc" -"ibrav" -"nat" -"ntyp" -"nbnd" -"nr1" -"nr2" -"nr3" -"nr1s" -"nr2s" -"nr3s" -"nspin" -"multiplicity" # Removed? -"edir" -"report" -"electron_maxstep" -"mixing_ndim" -"mixing_fixed_ns" -"ortho_para" # Removed? -"diago_cg_maxiter" -"diago_david_ndim" -"nraise" -"bfgs_ndim" -"num_of_images" # Removed? -"fe_nstep" # Removed? -"sw_nstep" # Removed? -"modenum" # Removed? -"n_charge_compensation" # Removed? -"nlev" # Removed? -"lda_plus_u_kind" # Removed? -"nqx1" -"nqx2" -"nqx3" -"esm_nfit" -"space_group" -"origin_choice" -"dftd3_version" - - -"nextffield", # New? -"exx_maxstep", # New? -"diago_rmm_ndim", # New? -"diago_gs_nblock", # New? -"nhpcl", # New? -"nhptyp", # New? -"ndega", # New? -"fire_nmin", # New? -"fcp_ndiis", # New? -"fcp_nraise", # New? -"nsolv", # New? -"rism1d_maxstep", # New? -"rism3d_maxstep", # New? -"mdiis1d_size", # New? -"mdiis3d_size", # New? -"rism1d_nproc", # New? -"laue_nfit", # New? -"nks", # New? -"nks_add", # New? -"nconstr", # New? -"nbnd_cond", # New? -"nk1", # New? -"nk2", # New? -"nk3", # New? -"sk1", # New? -"sk2", # New? -"sk3", # New? \ No newline at end of file diff --git a/nexus/nxs_pw_inp_strs.txt b/nexus/nxs_pw_inp_strs.txt deleted file mode 100644 index 25bc23c0ff..0000000000 --- a/nexus/nxs_pw_inp_strs.txt +++ /dev/null @@ -1,45 +0,0 @@ -"calculation", -"title", -"verbosity", -"restart_mode", -"outdir", -"wfcdir", -"prefix", -"disk_io", -"pseudo_dir", -"occupations", -"smearing", -"input_dft", -"U_projection_type", # Removed? -"constrained_magnetization", -"mixing_mode", -"diagonalization", -"startingpot", -"startingwfc", -"ion_dynamics", -"ion_positions", -"phase_space", # Removed? -"pot_extrapolation", -"wfc_extrapolation", -"ion_temperature", -"opt_scheme", # Removed? -"CI_scheme", # Removed? -"cell_dynamics", -"cell_dofree", -"which_compensation", # Removed? -"assume_isolated", -"exxdiv_treatment", -"esm_bc", -"vdw_corr", -"efield_phase", - - -"pol_type", # New? -"dmft_prefix", # New? -"ion_velocities", # New? -"fcp_dynamics", # New? -"fcp_temperature", # New? -"closure", # New? -"starting1d", # New? -"starting3d", # New? -"laue_wall", # New? \ No newline at end of file