From ed40ed4b0153da57c3fadaecc9425569c4aabe47 Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Wed, 21 Jan 2026 21:46:26 -0500 Subject: [PATCH 1/4] Nexus: Restructure for including scripts in package, test_pseudopotential still broken --- nexus/nexus/bin/__init__.py | 0 nexus/{ => nexus}/bin/eshdf | 2 +- nexus/{ => nexus}/bin/nxs-redo | 2 +- nexus/{ => nexus}/bin/nxs-sim | 2 +- nexus/{ => nexus}/bin/nxs-test | 74 +++++++++++++++++-- nexus/{ => nexus}/bin/qdens | 2 +- nexus/{ => nexus}/bin/qdens-radial | 2 +- nexus/{ => nexus}/bin/qmc-fit | 2 +- nexus/{ => nexus}/bin/qmca | 2 +- .../examples/gamess/H2O/h2o_pp_casscf.py | 0 .../examples/gamess/H2O/h2o_pp_cisd.py | 0 .../examples/gamess/H2O/h2o_pp_hf.py | 0 .../H2O/pseudopotentials/H.BFD_V5Z_ANO.gms | 0 .../gamess/H2O/pseudopotentials/O.BFD_V5Z.gms | 0 .../{ => nexus}/examples/generic/bash_demo.py | 0 .../examples/generic/python_demo.py | 0 .../generic/scripts/data_generator.py | 0 .../generic/scripts/data_processor.py | 0 .../generic/scripts/list_directory.sh | 0 .../examples/pyscf/01_h2o_hf/H2O.xyz | 0 .../examples/pyscf/01_h2o_hf/README.rst | 0 .../examples/pyscf/01_h2o_hf/h2o_ae_hf.py | 0 .../examples/pyscf/01_h2o_hf/h2o_pp_hf.py | 0 .../examples/pyscf/01_h2o_hf/scf_template.py | 0 .../examples/pyscf/02_diamond_hf/README.rst | 0 .../02_diamond_hf/diamond_pp_hf_gamma.py | 0 .../pyscf/02_diamond_hf/scf_template.py | 0 nexus/{ => nexus}/examples/pyscf/H2O/H2O.xyz | 0 .../examples/pyscf/H2O/h2o_ae_hf.py | 0 .../examples/pyscf/H2O/h2o_pp_hf.py | 0 .../examples/pyscf/H2O/scf_template.py | 0 .../examples/pyscf/diamond/dft_template.py | 0 .../pyscf/diamond/diamond_pp_dft_gamma.py | 0 .../afqmc_pyscf/01_neon_atom/neon_afqmc.py | 0 .../afqmc_pyscf/01_neon_atom/scf_template.py | 0 .../02_neon_frozen_core/neon_afqmc.py | 0 .../02_neon_frozen_core/scf_template.py | 0 .../03_carbon_triplet_uhf/carbon_afqmc.py | 0 .../03_carbon_triplet_uhf/scf_template.py | 0 .../06_methane_back_prop/methane_afqmc.py | 0 .../06_methane_back_prop/scf_template.py | 0 .../diamond_afqmc.py | 0 .../scf_template.py | 0 .../diamond_afqmc.py | 0 .../scf_template.py | 0 .../qmcpack/pseudopotentials/C.BFD.upf | 0 .../qmcpack/pseudopotentials/C.BFD.xml | 0 .../qmcpack/pseudopotentials/H.BFD.upf | 0 .../qmcpack/pseudopotentials/H.BFD.xml | 0 .../qmcpack/pseudopotentials/O.BFD.upf | 0 .../qmcpack/pseudopotentials/O.BFD.xml | 0 .../examples/qmcpack/rsqmc_misc/H2O/H2O.py | 0 .../examples/qmcpack/rsqmc_misc/H2O/H2O.xyz | 0 .../qmcpack/rsqmc_misc/H2O_pyscf/H2O.xyz | 0 .../rsqmc_misc/H2O_pyscf/h2o_ae_hf_vmc.py | 0 .../rsqmc_misc/H2O_pyscf/scf_template.py | 0 .../examples/qmcpack/rsqmc_misc/LiH/LiH.py | 0 .../LiH/pseudopotentials/H.TN-DF.upf | 0 .../rsqmc_misc/LiH/pseudopotentials/H.pp.data | 0 .../LiH/pseudopotentials/Li.TN-DF.upf | 0 .../LiH/pseudopotentials/Li.pp.data | 0 .../examples/qmcpack/rsqmc_misc/O2_qp/O2.xyz | 0 .../rsqmc_misc/O2_qp/o2_selci_vmc_dmc.py | 0 .../qmcpack/rsqmc_misc/c20/c20.cage.xyz | 0 .../examples/qmcpack/rsqmc_misc/c20/c20.py | 0 .../qmcpack/rsqmc_misc/diamond/d16bulk.POSCAR | 0 .../qmcpack/rsqmc_misc/diamond/d16vac.POSCAR | 0 .../qmcpack/rsqmc_misc/diamond/diamond.py | 0 .../rsqmc_misc/diamond/diamond_vacancy.py | 0 .../rsqmc_misc/diamond_lowdin/diamond.py | 0 .../rsqmc_misc/diamond_lowdin/diamond_spin.py | 0 .../rsqmc_misc/diamond_lowdin/lowdin.py | 0 .../rsqmc_misc/diamond_lowdin/run_lowdin.sh | 0 .../rsqmc_misc/diamond_pyscf/dft_template.py | 0 .../diamond_pyscf/diamond_pp_dft_gamma.py | 0 .../diamond_radial_density/diamond_spin.py | 0 .../diamond_radial_density/qdens-radial.sh | 0 .../diamond_radial_density/qdens.sh | 0 .../qmcpack/rsqmc_misc/estimators/Fe_bcc.xsf | 0 .../qmcpack/rsqmc_misc/estimators/README.rst | 0 .../rsqmc_misc/estimators/iron_ldaU_dmc.py | 0 .../pseudopotentials/Fe.ccECP-soft.upf | 0 .../pseudopotentials/Fe.ccECP-soft.xml | 0 .../estimators/scripts_postproc/get_1rdms.py | 0 .../estimators/scripts_postproc/plot_1rdm.py | 0 .../qmcpack/rsqmc_misc/excited/band.py | 0 .../qmcpack/rsqmc_misc/excited/d16bulk.POSCAR | 0 .../qmcpack/rsqmc_misc/excited/vmc.py | 0 .../excited/vmc_excitation_alternatives.py | 0 .../rsqmc_misc/excited/vmc_opt_tiling.py | 0 .../qmcpack/rsqmc_misc/graphene/graphene.py | 0 .../rsqmc_misc/oxygen_dimer/oxygen_dimer.py | 0 .../qmcpack/rsqmc_pyscf/01_h2o_hf_qmc/H2O.xyz | 0 .../rsqmc_pyscf/01_h2o_hf_qmc/README.rst | 0 .../01_h2o_hf_qmc/h2o_ae_hf_qmc.py | 0 .../rsqmc_pyscf/01_h2o_hf_qmc/scf_template.py | 0 .../rsqmc_pyscf/02_diamond_hf_qmc/README.rst | 0 .../02_diamond_hf_qmc/diamond_pp_hf_gamma.py | 0 .../diamond_pp_hf_twistavg.py | 0 .../diamond_pp_hf_twistavg_prim.py | 0 .../02_diamond_hf_qmc/scf_template.py | 0 .../01_diamond_dft_vmc/README.rst | 0 .../01_diamond_dft_vmc/diamond_lda_vmc.py | 0 .../diamond_lda_vmc_batched.py | 0 .../diamond_lda_vmc_batched_estimators.py | 0 .../02_diamond_dft_vmc_twistavg/README.rst | 0 .../diamond_lda_vmc_twistavg.py | 0 .../03_diamond_dft_dmc_textrap/README.rst | 0 .../diamond_lda_dmc_textrap.py | 0 .../04_iron_dft_dmc_gcta/Fe_bcc.xsf | 0 .../04_iron_dft_dmc_gcta/README.rst | 0 .../iron_ldaU_dmc_gcta.py | 0 .../04_iron_dft_dmc_gcta/pseudopotentials | 0 .../01_h2o_hf_qmc/H2O.xyz | 0 .../01_h2o_hf_qmc/README.rst | 0 .../01_h2o_hf_qmc/h2o_ae_hf_qmc.py | 0 .../02_o2_selci_qmc/O2.xyz | 0 .../02_o2_selci_qmc/README.rst | 0 .../02_o2_selci_qmc/o2_selci_vmc_dmc.py | 0 .../01_diamond_scf/README.rst | 0 .../01_diamond_scf/diamond_lda.py | 0 .../02_diamond_self_consistent_U/README.rst | 0 .../diamond_lda_sc_u.py | 0 .../pseudopotentials/C.BFD.upf | 0 .../pseudopotentials/Ge.pbe-kjpaw.UPF | 0 .../relax_Ge_T_vs_kpoints/Ge_T_16.xyz | 0 .../relax_Ge_T_vs_kpoints/Ge_T_64.xyz | 0 .../relax_vs_kpoints_example.py | 0 .../quantum_package/01_h2o_hf/H2O.xyz | 0 .../quantum_package/01_h2o_hf/README.rst | 0 .../quantum_package/01_h2o_hf/h2o_ae_hf.py | 0 .../quantum_package/02_o2_selci/O2.xyz | 0 .../quantum_package/02_o2_selci/README.rst | 0 .../quantum_package/02_o2_selci/o2_selci.py | 0 .../examples/quantum_package/H2O/H2O.xyz | 0 .../examples/quantum_package/H2O/h2o_ae_hf.py | 0 .../examples/quantum_package/O2/O2.xyz | 0 .../examples/quantum_package/O2/o2_selci.py | 0 .../rmg/01_diamond_scf/diamond_scf.py | 0 nexus/nexus/scripts.py | 44 +++++++++++ nexus/nexus/testing.py | 4 +- nexus/nexus/tests/test_pseudopotential.py | 5 +- nexus/pyproject.toml | 23 +++--- 143 files changed, 135 insertions(+), 29 deletions(-) create mode 100644 nexus/nexus/bin/__init__.py rename nexus/{ => nexus}/bin/eshdf (99%) rename nexus/{ => nexus}/bin/nxs-redo (99%) rename nexus/{ => nexus}/bin/nxs-sim (99%) rename nexus/{ => nexus}/bin/nxs-test (97%) rename nexus/{ => nexus}/bin/qdens (99%) rename nexus/{ => nexus}/bin/qdens-radial (99%) rename nexus/{ => nexus}/bin/qmc-fit (99%) rename nexus/{ => nexus}/bin/qmca (99%) rename nexus/{ => nexus}/examples/gamess/H2O/h2o_pp_casscf.py (100%) rename nexus/{ => nexus}/examples/gamess/H2O/h2o_pp_cisd.py (100%) rename nexus/{ => nexus}/examples/gamess/H2O/h2o_pp_hf.py (100%) rename nexus/{ => nexus}/examples/gamess/H2O/pseudopotentials/H.BFD_V5Z_ANO.gms (100%) rename nexus/{ => nexus}/examples/gamess/H2O/pseudopotentials/O.BFD_V5Z.gms (100%) rename nexus/{ => nexus}/examples/generic/bash_demo.py (100%) rename nexus/{ => nexus}/examples/generic/python_demo.py (100%) rename nexus/{ => nexus}/examples/generic/scripts/data_generator.py (100%) rename nexus/{ => nexus}/examples/generic/scripts/data_processor.py (100%) rename nexus/{ => nexus}/examples/generic/scripts/list_directory.sh (100%) rename nexus/{ => nexus}/examples/pyscf/01_h2o_hf/H2O.xyz (100%) rename nexus/{ => nexus}/examples/pyscf/01_h2o_hf/README.rst (100%) rename nexus/{ => nexus}/examples/pyscf/01_h2o_hf/h2o_ae_hf.py (100%) rename nexus/{ => nexus}/examples/pyscf/01_h2o_hf/h2o_pp_hf.py (100%) rename nexus/{ => nexus}/examples/pyscf/01_h2o_hf/scf_template.py (100%) rename nexus/{ => nexus}/examples/pyscf/02_diamond_hf/README.rst (100%) rename nexus/{ => nexus}/examples/pyscf/02_diamond_hf/diamond_pp_hf_gamma.py (100%) rename nexus/{ => nexus}/examples/pyscf/02_diamond_hf/scf_template.py (100%) rename nexus/{ => nexus}/examples/pyscf/H2O/H2O.xyz (100%) rename nexus/{ => nexus}/examples/pyscf/H2O/h2o_ae_hf.py (100%) rename nexus/{ => nexus}/examples/pyscf/H2O/h2o_pp_hf.py (100%) rename nexus/{ => nexus}/examples/pyscf/H2O/scf_template.py (100%) rename nexus/{ => nexus}/examples/pyscf/diamond/dft_template.py (100%) rename nexus/{ => nexus}/examples/pyscf/diamond/diamond_pp_dft_gamma.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/01_neon_atom/neon_afqmc.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/01_neon_atom/scf_template.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/02_neon_frozen_core/neon_afqmc.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/02_neon_frozen_core/scf_template.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/03_carbon_triplet_uhf/carbon_afqmc.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/03_carbon_triplet_uhf/scf_template.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/06_methane_back_prop/methane_afqmc.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/06_methane_back_prop/scf_template.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/07_diamond_2x2x2_supercell/diamond_afqmc.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/07_diamond_2x2x2_supercell/scf_template.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/08_diamond_2x2x2_kpoint_sym/diamond_afqmc.py (100%) rename nexus/{ => nexus}/examples/qmcpack/afqmc_pyscf/08_diamond_2x2x2_kpoint_sym/scf_template.py (100%) rename nexus/{ => nexus}/examples/qmcpack/pseudopotentials/C.BFD.upf (100%) rename nexus/{ => nexus}/examples/qmcpack/pseudopotentials/C.BFD.xml (100%) rename nexus/{ => 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nexus}/examples/qmcpack/rsqmc_pyscf/01_h2o_hf_qmc/README.rst (100%) rename nexus/{ => nexus}/examples/qmcpack/rsqmc_pyscf/01_h2o_hf_qmc/h2o_ae_hf_qmc.py (100%) rename nexus/{ => nexus}/examples/qmcpack/rsqmc_pyscf/01_h2o_hf_qmc/scf_template.py (100%) rename nexus/{ => nexus}/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/README.rst (100%) rename nexus/{ => nexus}/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_gamma.py (100%) rename nexus/{ => nexus}/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_twistavg.py (100%) rename nexus/{ => nexus}/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_twistavg_prim.py (100%) rename nexus/{ => nexus}/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/scf_template.py (100%) rename nexus/{ => nexus}/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/README.rst (100%) rename nexus/{ => nexus}/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc.py (100%) rename nexus/{ => 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nexus}/examples/quantum_espresso/02_diamond_self_consistent_U/README.rst (100%) rename nexus/{ => nexus}/examples/quantum_espresso/02_diamond_self_consistent_U/diamond_lda_sc_u.py (100%) rename nexus/{ => nexus}/examples/quantum_espresso/pseudopotentials/C.BFD.upf (100%) rename nexus/{ => nexus}/examples/quantum_espresso/pseudopotentials/Ge.pbe-kjpaw.UPF (100%) rename nexus/{ => nexus}/examples/quantum_espresso/relax_Ge_T_vs_kpoints/Ge_T_16.xyz (100%) rename nexus/{ => nexus}/examples/quantum_espresso/relax_Ge_T_vs_kpoints/Ge_T_64.xyz (100%) rename nexus/{ => nexus}/examples/quantum_espresso/relax_Ge_T_vs_kpoints/relax_vs_kpoints_example.py (100%) rename nexus/{ => nexus}/examples/quantum_package/01_h2o_hf/H2O.xyz (100%) rename nexus/{ => nexus}/examples/quantum_package/01_h2o_hf/README.rst (100%) rename nexus/{ => nexus}/examples/quantum_package/01_h2o_hf/h2o_ae_hf.py (100%) rename nexus/{ => nexus}/examples/quantum_package/02_o2_selci/O2.xyz (100%) rename nexus/{ => nexus}/examples/quantum_package/02_o2_selci/README.rst (100%) rename nexus/{ => nexus}/examples/quantum_package/02_o2_selci/o2_selci.py (100%) rename nexus/{ => nexus}/examples/quantum_package/H2O/H2O.xyz (100%) rename nexus/{ => nexus}/examples/quantum_package/H2O/h2o_ae_hf.py (100%) rename nexus/{ => nexus}/examples/quantum_package/O2/O2.xyz (100%) rename nexus/{ => nexus}/examples/quantum_package/O2/o2_selci.py (100%) rename nexus/{ => nexus}/examples/rmg/01_diamond_scf/diamond_scf.py (100%) create mode 100644 nexus/nexus/scripts.py diff --git a/nexus/nexus/bin/__init__.py b/nexus/nexus/bin/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nexus/bin/eshdf b/nexus/nexus/bin/eshdf similarity index 99% rename from nexus/bin/eshdf rename to nexus/nexus/bin/eshdf index 0a4525bc0c..190d37e33f 100755 --- a/nexus/bin/eshdf +++ b/nexus/nexus/bin/eshdf @@ -12,7 +12,7 @@ import numpy as np def find_nexus_modules(): import os import sys - nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..','nexus')) + nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..')) assert(os.path.exists(nexus_lib)) sys.path.insert(0,nexus_lib) import nexus diff --git a/nexus/bin/nxs-redo b/nexus/nexus/bin/nxs-redo similarity index 99% rename from nexus/bin/nxs-redo rename to nexus/nexus/bin/nxs-redo index b8294ceb4d..3c2cedd657 100755 --- a/nexus/bin/nxs-redo +++ b/nexus/nexus/bin/nxs-redo @@ -7,7 +7,7 @@ from optparse import OptionParser def find_nexus_modules(): import os import sys - nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..','nexus')) + nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..')) assert(os.path.exists(nexus_lib)) sys.path.insert(0,nexus_lib) import nexus diff --git a/nexus/bin/nxs-sim b/nexus/nexus/bin/nxs-sim similarity index 99% rename from nexus/bin/nxs-sim rename to nexus/nexus/bin/nxs-sim index 2d42084c00..153cbe645b 100755 --- a/nexus/bin/nxs-sim +++ b/nexus/nexus/bin/nxs-sim @@ -7,7 +7,7 @@ from optparse import OptionParser def find_nexus_modules(): import os import sys - nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..','nexus')) + nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..')) assert(os.path.exists(nexus_lib)) sys.path.insert(0,nexus_lib) import nexus diff --git a/nexus/bin/nxs-test b/nexus/nexus/bin/nxs-test similarity index 97% rename from nexus/bin/nxs-test rename to nexus/nexus/bin/nxs-test index ed0671f5c7..2c49dfe249 100755 --- a/nexus/bin/nxs-test +++ b/nexus/nexus/bin/nxs-test @@ -17,13 +17,75 @@ if host_dir is not None: #end if # save nexus directories -library_dir = parent_dir -test_dir = os.path.join(parent_dir,'nexus/tests') -reference_dir = os.path.join(parent_dir,'nexus/tests/reference') +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 = ['examples','bin','nexus','nexus/tests','nexus/tests/reference'] +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", + "scripts.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): @@ -1788,7 +1850,7 @@ def user_examples(label): # remove prexisting example files nenter(tpath,relative=True) # copy over nexus examples files just for this example - epath = os.path.join(example_dir,path) + epath = os.path.realpath(os.path.join(example_dir,path)) command = 'rsync -av {0}/* ./'.format(epath) out,err,rc = execute(command) if rc>0: @@ -2223,7 +2285,7 @@ if __name__=='__main__': testing_wrong_nexus_install = False try: import nexus - nexus_file = os.path.realpath(os.path.join(nexus.__file__,'../..')) + 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: diff --git a/nexus/bin/qdens b/nexus/nexus/bin/qdens similarity index 99% rename from nexus/bin/qdens rename to nexus/nexus/bin/qdens index 1d5e97cebe..62a2dc23eb 100755 --- a/nexus/bin/qdens +++ b/nexus/nexus/bin/qdens @@ -8,7 +8,7 @@ from optparse import OptionParser def find_nexus_modules(): import os import sys - nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..','nexus')) + nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..')) assert(os.path.exists(nexus_lib)) sys.path.insert(0,nexus_lib) import nexus diff --git a/nexus/bin/qdens-radial b/nexus/nexus/bin/qdens-radial similarity index 99% rename from nexus/bin/qdens-radial rename to nexus/nexus/bin/qdens-radial index d5fbc2ea06..afa73f67cc 100755 --- a/nexus/bin/qdens-radial +++ b/nexus/nexus/bin/qdens-radial @@ -6,7 +6,7 @@ from optparse import OptionParser def find_nexus_modules(): import os import sys - nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..','nexus')) + nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..')) assert(os.path.exists(nexus_lib)) sys.path.insert(0,nexus_lib) import nexus diff --git a/nexus/bin/qmc-fit b/nexus/nexus/bin/qmc-fit similarity index 99% rename from nexus/bin/qmc-fit rename to nexus/nexus/bin/qmc-fit index 5cbca4df53..037ae1264e 100755 --- a/nexus/bin/qmc-fit +++ b/nexus/nexus/bin/qmc-fit @@ -31,7 +31,7 @@ except (ImportError,RuntimeError): def find_nexus_modules(): import os import sys - nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..','nexus')) + nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..')) assert(os.path.exists(nexus_lib)) sys.path.insert(0,nexus_lib) import nexus diff --git a/nexus/bin/qmca b/nexus/nexus/bin/qmca similarity index 99% rename from nexus/bin/qmca rename to nexus/nexus/bin/qmca index 9e9baf62d5..ceea23e8e6 100755 --- a/nexus/bin/qmca +++ b/nexus/nexus/bin/qmca @@ -8,7 +8,7 @@ from optparse import OptionParser def find_nexus_modules(): import os import sys - nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..','nexus')) + nexus_lib = os.path.realpath(os.path.join(__file__,'..','..','..')) assert(os.path.exists(nexus_lib)) sys.path.insert(0,nexus_lib) import nexus diff --git a/nexus/examples/gamess/H2O/h2o_pp_casscf.py b/nexus/nexus/examples/gamess/H2O/h2o_pp_casscf.py similarity index 100% rename from nexus/examples/gamess/H2O/h2o_pp_casscf.py rename to nexus/nexus/examples/gamess/H2O/h2o_pp_casscf.py diff --git a/nexus/examples/gamess/H2O/h2o_pp_cisd.py b/nexus/nexus/examples/gamess/H2O/h2o_pp_cisd.py similarity index 100% rename from nexus/examples/gamess/H2O/h2o_pp_cisd.py rename to nexus/nexus/examples/gamess/H2O/h2o_pp_cisd.py diff --git a/nexus/examples/gamess/H2O/h2o_pp_hf.py b/nexus/nexus/examples/gamess/H2O/h2o_pp_hf.py similarity index 100% rename from nexus/examples/gamess/H2O/h2o_pp_hf.py rename to nexus/nexus/examples/gamess/H2O/h2o_pp_hf.py diff --git a/nexus/examples/gamess/H2O/pseudopotentials/H.BFD_V5Z_ANO.gms b/nexus/nexus/examples/gamess/H2O/pseudopotentials/H.BFD_V5Z_ANO.gms similarity index 100% rename from nexus/examples/gamess/H2O/pseudopotentials/H.BFD_V5Z_ANO.gms rename to nexus/nexus/examples/gamess/H2O/pseudopotentials/H.BFD_V5Z_ANO.gms diff --git a/nexus/examples/gamess/H2O/pseudopotentials/O.BFD_V5Z.gms b/nexus/nexus/examples/gamess/H2O/pseudopotentials/O.BFD_V5Z.gms similarity index 100% rename from nexus/examples/gamess/H2O/pseudopotentials/O.BFD_V5Z.gms rename to nexus/nexus/examples/gamess/H2O/pseudopotentials/O.BFD_V5Z.gms diff --git a/nexus/examples/generic/bash_demo.py b/nexus/nexus/examples/generic/bash_demo.py similarity index 100% rename from nexus/examples/generic/bash_demo.py rename to nexus/nexus/examples/generic/bash_demo.py diff --git a/nexus/examples/generic/python_demo.py b/nexus/nexus/examples/generic/python_demo.py similarity index 100% rename from nexus/examples/generic/python_demo.py rename to nexus/nexus/examples/generic/python_demo.py diff --git a/nexus/examples/generic/scripts/data_generator.py b/nexus/nexus/examples/generic/scripts/data_generator.py similarity index 100% rename from nexus/examples/generic/scripts/data_generator.py rename to nexus/nexus/examples/generic/scripts/data_generator.py diff --git a/nexus/examples/generic/scripts/data_processor.py b/nexus/nexus/examples/generic/scripts/data_processor.py similarity index 100% rename from nexus/examples/generic/scripts/data_processor.py rename to nexus/nexus/examples/generic/scripts/data_processor.py diff --git a/nexus/examples/generic/scripts/list_directory.sh b/nexus/nexus/examples/generic/scripts/list_directory.sh similarity index 100% rename from nexus/examples/generic/scripts/list_directory.sh rename to nexus/nexus/examples/generic/scripts/list_directory.sh diff --git a/nexus/examples/pyscf/01_h2o_hf/H2O.xyz b/nexus/nexus/examples/pyscf/01_h2o_hf/H2O.xyz similarity index 100% rename from nexus/examples/pyscf/01_h2o_hf/H2O.xyz rename to nexus/nexus/examples/pyscf/01_h2o_hf/H2O.xyz diff --git a/nexus/examples/pyscf/01_h2o_hf/README.rst b/nexus/nexus/examples/pyscf/01_h2o_hf/README.rst similarity index 100% rename from nexus/examples/pyscf/01_h2o_hf/README.rst rename to nexus/nexus/examples/pyscf/01_h2o_hf/README.rst diff --git a/nexus/examples/pyscf/01_h2o_hf/h2o_ae_hf.py b/nexus/nexus/examples/pyscf/01_h2o_hf/h2o_ae_hf.py similarity index 100% rename from nexus/examples/pyscf/01_h2o_hf/h2o_ae_hf.py rename to nexus/nexus/examples/pyscf/01_h2o_hf/h2o_ae_hf.py diff --git a/nexus/examples/pyscf/01_h2o_hf/h2o_pp_hf.py b/nexus/nexus/examples/pyscf/01_h2o_hf/h2o_pp_hf.py similarity index 100% rename from nexus/examples/pyscf/01_h2o_hf/h2o_pp_hf.py rename to nexus/nexus/examples/pyscf/01_h2o_hf/h2o_pp_hf.py diff --git a/nexus/examples/pyscf/01_h2o_hf/scf_template.py b/nexus/nexus/examples/pyscf/01_h2o_hf/scf_template.py similarity index 100% rename from nexus/examples/pyscf/01_h2o_hf/scf_template.py rename to nexus/nexus/examples/pyscf/01_h2o_hf/scf_template.py diff --git a/nexus/examples/pyscf/02_diamond_hf/README.rst b/nexus/nexus/examples/pyscf/02_diamond_hf/README.rst similarity index 100% rename from nexus/examples/pyscf/02_diamond_hf/README.rst rename to nexus/nexus/examples/pyscf/02_diamond_hf/README.rst diff --git a/nexus/examples/pyscf/02_diamond_hf/diamond_pp_hf_gamma.py b/nexus/nexus/examples/pyscf/02_diamond_hf/diamond_pp_hf_gamma.py similarity index 100% rename from nexus/examples/pyscf/02_diamond_hf/diamond_pp_hf_gamma.py rename to nexus/nexus/examples/pyscf/02_diamond_hf/diamond_pp_hf_gamma.py diff --git a/nexus/examples/pyscf/02_diamond_hf/scf_template.py b/nexus/nexus/examples/pyscf/02_diamond_hf/scf_template.py similarity index 100% rename from nexus/examples/pyscf/02_diamond_hf/scf_template.py rename to nexus/nexus/examples/pyscf/02_diamond_hf/scf_template.py diff --git a/nexus/examples/pyscf/H2O/H2O.xyz b/nexus/nexus/examples/pyscf/H2O/H2O.xyz similarity index 100% rename from nexus/examples/pyscf/H2O/H2O.xyz rename to nexus/nexus/examples/pyscf/H2O/H2O.xyz diff --git a/nexus/examples/pyscf/H2O/h2o_ae_hf.py b/nexus/nexus/examples/pyscf/H2O/h2o_ae_hf.py similarity index 100% rename from nexus/examples/pyscf/H2O/h2o_ae_hf.py rename to nexus/nexus/examples/pyscf/H2O/h2o_ae_hf.py diff --git a/nexus/examples/pyscf/H2O/h2o_pp_hf.py b/nexus/nexus/examples/pyscf/H2O/h2o_pp_hf.py similarity index 100% rename from nexus/examples/pyscf/H2O/h2o_pp_hf.py rename to nexus/nexus/examples/pyscf/H2O/h2o_pp_hf.py diff --git a/nexus/examples/pyscf/H2O/scf_template.py b/nexus/nexus/examples/pyscf/H2O/scf_template.py similarity index 100% rename from nexus/examples/pyscf/H2O/scf_template.py rename to nexus/nexus/examples/pyscf/H2O/scf_template.py diff --git a/nexus/examples/pyscf/diamond/dft_template.py b/nexus/nexus/examples/pyscf/diamond/dft_template.py similarity index 100% rename from nexus/examples/pyscf/diamond/dft_template.py rename to nexus/nexus/examples/pyscf/diamond/dft_template.py diff --git a/nexus/examples/pyscf/diamond/diamond_pp_dft_gamma.py b/nexus/nexus/examples/pyscf/diamond/diamond_pp_dft_gamma.py similarity index 100% rename from nexus/examples/pyscf/diamond/diamond_pp_dft_gamma.py rename to nexus/nexus/examples/pyscf/diamond/diamond_pp_dft_gamma.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/01_neon_atom/neon_afqmc.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/01_neon_atom/neon_afqmc.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/01_neon_atom/neon_afqmc.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/01_neon_atom/neon_afqmc.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/01_neon_atom/scf_template.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/01_neon_atom/scf_template.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/01_neon_atom/scf_template.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/01_neon_atom/scf_template.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/02_neon_frozen_core/neon_afqmc.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/02_neon_frozen_core/neon_afqmc.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/02_neon_frozen_core/neon_afqmc.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/02_neon_frozen_core/neon_afqmc.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/02_neon_frozen_core/scf_template.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/02_neon_frozen_core/scf_template.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/02_neon_frozen_core/scf_template.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/02_neon_frozen_core/scf_template.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/03_carbon_triplet_uhf/carbon_afqmc.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/03_carbon_triplet_uhf/carbon_afqmc.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/03_carbon_triplet_uhf/carbon_afqmc.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/03_carbon_triplet_uhf/carbon_afqmc.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/03_carbon_triplet_uhf/scf_template.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/03_carbon_triplet_uhf/scf_template.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/03_carbon_triplet_uhf/scf_template.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/03_carbon_triplet_uhf/scf_template.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/06_methane_back_prop/methane_afqmc.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/06_methane_back_prop/methane_afqmc.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/06_methane_back_prop/methane_afqmc.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/06_methane_back_prop/methane_afqmc.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/06_methane_back_prop/scf_template.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/06_methane_back_prop/scf_template.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/06_methane_back_prop/scf_template.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/06_methane_back_prop/scf_template.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/07_diamond_2x2x2_supercell/diamond_afqmc.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/07_diamond_2x2x2_supercell/diamond_afqmc.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/07_diamond_2x2x2_supercell/diamond_afqmc.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/07_diamond_2x2x2_supercell/diamond_afqmc.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/07_diamond_2x2x2_supercell/scf_template.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/07_diamond_2x2x2_supercell/scf_template.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/07_diamond_2x2x2_supercell/scf_template.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/07_diamond_2x2x2_supercell/scf_template.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/08_diamond_2x2x2_kpoint_sym/diamond_afqmc.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/08_diamond_2x2x2_kpoint_sym/diamond_afqmc.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/08_diamond_2x2x2_kpoint_sym/diamond_afqmc.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/08_diamond_2x2x2_kpoint_sym/diamond_afqmc.py diff --git a/nexus/examples/qmcpack/afqmc_pyscf/08_diamond_2x2x2_kpoint_sym/scf_template.py b/nexus/nexus/examples/qmcpack/afqmc_pyscf/08_diamond_2x2x2_kpoint_sym/scf_template.py similarity index 100% rename from nexus/examples/qmcpack/afqmc_pyscf/08_diamond_2x2x2_kpoint_sym/scf_template.py rename to nexus/nexus/examples/qmcpack/afqmc_pyscf/08_diamond_2x2x2_kpoint_sym/scf_template.py diff --git a/nexus/examples/qmcpack/pseudopotentials/C.BFD.upf b/nexus/nexus/examples/qmcpack/pseudopotentials/C.BFD.upf similarity index 100% rename from nexus/examples/qmcpack/pseudopotentials/C.BFD.upf rename to nexus/nexus/examples/qmcpack/pseudopotentials/C.BFD.upf diff --git a/nexus/examples/qmcpack/pseudopotentials/C.BFD.xml b/nexus/nexus/examples/qmcpack/pseudopotentials/C.BFD.xml similarity index 100% rename from nexus/examples/qmcpack/pseudopotentials/C.BFD.xml rename to nexus/nexus/examples/qmcpack/pseudopotentials/C.BFD.xml diff --git a/nexus/examples/qmcpack/pseudopotentials/H.BFD.upf b/nexus/nexus/examples/qmcpack/pseudopotentials/H.BFD.upf similarity index 100% rename from nexus/examples/qmcpack/pseudopotentials/H.BFD.upf rename to nexus/nexus/examples/qmcpack/pseudopotentials/H.BFD.upf diff --git 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nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_gamma.py rename to nexus/nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_gamma.py diff --git a/nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_twistavg.py b/nexus/nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_twistavg.py similarity index 100% rename from nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_twistavg.py rename to nexus/nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_twistavg.py diff --git a/nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_twistavg_prim.py b/nexus/nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_twistavg_prim.py similarity index 100% rename from nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_twistavg_prim.py rename to nexus/nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/diamond_pp_hf_twistavg_prim.py diff --git a/nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/scf_template.py b/nexus/nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/scf_template.py similarity index 100% rename from nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/scf_template.py rename to nexus/nexus/examples/qmcpack/rsqmc_pyscf/02_diamond_hf_qmc/scf_template.py diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/README.rst b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/README.rst similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/README.rst rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/README.rst diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc.py b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc.py similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc.py rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc.py diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc_batched.py b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc_batched.py similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc_batched.py rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc_batched.py diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc_batched_estimators.py b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc_batched_estimators.py similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc_batched_estimators.py rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/01_diamond_dft_vmc/diamond_lda_vmc_batched_estimators.py diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/02_diamond_dft_vmc_twistavg/README.rst b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/02_diamond_dft_vmc_twistavg/README.rst similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/02_diamond_dft_vmc_twistavg/README.rst rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/02_diamond_dft_vmc_twistavg/README.rst diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/02_diamond_dft_vmc_twistavg/diamond_lda_vmc_twistavg.py b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/02_diamond_dft_vmc_twistavg/diamond_lda_vmc_twistavg.py similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/02_diamond_dft_vmc_twistavg/diamond_lda_vmc_twistavg.py rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/02_diamond_dft_vmc_twistavg/diamond_lda_vmc_twistavg.py diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/03_diamond_dft_dmc_textrap/README.rst b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/03_diamond_dft_dmc_textrap/README.rst similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/03_diamond_dft_dmc_textrap/README.rst rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/03_diamond_dft_dmc_textrap/README.rst diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/03_diamond_dft_dmc_textrap/diamond_lda_dmc_textrap.py b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/03_diamond_dft_dmc_textrap/diamond_lda_dmc_textrap.py similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/03_diamond_dft_dmc_textrap/diamond_lda_dmc_textrap.py rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/03_diamond_dft_dmc_textrap/diamond_lda_dmc_textrap.py diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/Fe_bcc.xsf b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/Fe_bcc.xsf similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/Fe_bcc.xsf rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/Fe_bcc.xsf diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/README.rst b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/README.rst similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/README.rst rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/README.rst diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/iron_ldaU_dmc_gcta.py b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/iron_ldaU_dmc_gcta.py similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/iron_ldaU_dmc_gcta.py rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/iron_ldaU_dmc_gcta.py diff --git a/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/pseudopotentials b/nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/pseudopotentials similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/pseudopotentials rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_espresso/04_iron_dft_dmc_gcta/pseudopotentials diff --git a/nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/H2O.xyz b/nexus/nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/H2O.xyz similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/H2O.xyz rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/H2O.xyz diff --git a/nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/README.rst b/nexus/nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/README.rst similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/README.rst rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/README.rst diff --git a/nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/h2o_ae_hf_qmc.py b/nexus/nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/h2o_ae_hf_qmc.py similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/h2o_ae_hf_qmc.py rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_package/01_h2o_hf_qmc/h2o_ae_hf_qmc.py diff --git a/nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/O2.xyz b/nexus/nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/O2.xyz similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/O2.xyz rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/O2.xyz diff --git a/nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/README.rst b/nexus/nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/README.rst similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/README.rst rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/README.rst diff --git a/nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/o2_selci_vmc_dmc.py b/nexus/nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/o2_selci_vmc_dmc.py similarity index 100% rename from nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/o2_selci_vmc_dmc.py rename to nexus/nexus/examples/qmcpack/rsqmc_quantum_package/02_o2_selci_qmc/o2_selci_vmc_dmc.py diff --git a/nexus/examples/quantum_espresso/01_diamond_scf/README.rst b/nexus/nexus/examples/quantum_espresso/01_diamond_scf/README.rst similarity index 100% rename from nexus/examples/quantum_espresso/01_diamond_scf/README.rst rename to nexus/nexus/examples/quantum_espresso/01_diamond_scf/README.rst diff --git a/nexus/examples/quantum_espresso/01_diamond_scf/diamond_lda.py b/nexus/nexus/examples/quantum_espresso/01_diamond_scf/diamond_lda.py similarity index 100% rename from nexus/examples/quantum_espresso/01_diamond_scf/diamond_lda.py rename to nexus/nexus/examples/quantum_espresso/01_diamond_scf/diamond_lda.py diff --git a/nexus/examples/quantum_espresso/02_diamond_self_consistent_U/README.rst b/nexus/nexus/examples/quantum_espresso/02_diamond_self_consistent_U/README.rst similarity index 100% rename from nexus/examples/quantum_espresso/02_diamond_self_consistent_U/README.rst rename to nexus/nexus/examples/quantum_espresso/02_diamond_self_consistent_U/README.rst diff --git a/nexus/examples/quantum_espresso/02_diamond_self_consistent_U/diamond_lda_sc_u.py b/nexus/nexus/examples/quantum_espresso/02_diamond_self_consistent_U/diamond_lda_sc_u.py similarity index 100% rename from nexus/examples/quantum_espresso/02_diamond_self_consistent_U/diamond_lda_sc_u.py rename to nexus/nexus/examples/quantum_espresso/02_diamond_self_consistent_U/diamond_lda_sc_u.py diff --git a/nexus/examples/quantum_espresso/pseudopotentials/C.BFD.upf b/nexus/nexus/examples/quantum_espresso/pseudopotentials/C.BFD.upf similarity index 100% rename from nexus/examples/quantum_espresso/pseudopotentials/C.BFD.upf rename to nexus/nexus/examples/quantum_espresso/pseudopotentials/C.BFD.upf diff --git a/nexus/examples/quantum_espresso/pseudopotentials/Ge.pbe-kjpaw.UPF b/nexus/nexus/examples/quantum_espresso/pseudopotentials/Ge.pbe-kjpaw.UPF similarity index 100% rename from nexus/examples/quantum_espresso/pseudopotentials/Ge.pbe-kjpaw.UPF rename to nexus/nexus/examples/quantum_espresso/pseudopotentials/Ge.pbe-kjpaw.UPF diff --git a/nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/Ge_T_16.xyz b/nexus/nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/Ge_T_16.xyz similarity index 100% rename from nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/Ge_T_16.xyz rename to nexus/nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/Ge_T_16.xyz diff --git a/nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/Ge_T_64.xyz b/nexus/nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/Ge_T_64.xyz similarity index 100% rename from nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/Ge_T_64.xyz rename to nexus/nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/Ge_T_64.xyz diff --git a/nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/relax_vs_kpoints_example.py b/nexus/nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/relax_vs_kpoints_example.py similarity index 100% rename from nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/relax_vs_kpoints_example.py rename to nexus/nexus/examples/quantum_espresso/relax_Ge_T_vs_kpoints/relax_vs_kpoints_example.py diff --git a/nexus/examples/quantum_package/01_h2o_hf/H2O.xyz b/nexus/nexus/examples/quantum_package/01_h2o_hf/H2O.xyz similarity index 100% rename from nexus/examples/quantum_package/01_h2o_hf/H2O.xyz rename to nexus/nexus/examples/quantum_package/01_h2o_hf/H2O.xyz diff --git a/nexus/examples/quantum_package/01_h2o_hf/README.rst b/nexus/nexus/examples/quantum_package/01_h2o_hf/README.rst similarity index 100% rename from nexus/examples/quantum_package/01_h2o_hf/README.rst rename to nexus/nexus/examples/quantum_package/01_h2o_hf/README.rst diff --git a/nexus/examples/quantum_package/01_h2o_hf/h2o_ae_hf.py b/nexus/nexus/examples/quantum_package/01_h2o_hf/h2o_ae_hf.py similarity index 100% rename from nexus/examples/quantum_package/01_h2o_hf/h2o_ae_hf.py rename to nexus/nexus/examples/quantum_package/01_h2o_hf/h2o_ae_hf.py diff --git a/nexus/examples/quantum_package/02_o2_selci/O2.xyz b/nexus/nexus/examples/quantum_package/02_o2_selci/O2.xyz similarity index 100% rename from nexus/examples/quantum_package/02_o2_selci/O2.xyz rename to nexus/nexus/examples/quantum_package/02_o2_selci/O2.xyz diff --git a/nexus/examples/quantum_package/02_o2_selci/README.rst b/nexus/nexus/examples/quantum_package/02_o2_selci/README.rst similarity index 100% rename from nexus/examples/quantum_package/02_o2_selci/README.rst rename to nexus/nexus/examples/quantum_package/02_o2_selci/README.rst diff --git a/nexus/examples/quantum_package/02_o2_selci/o2_selci.py b/nexus/nexus/examples/quantum_package/02_o2_selci/o2_selci.py similarity index 100% rename from nexus/examples/quantum_package/02_o2_selci/o2_selci.py rename to nexus/nexus/examples/quantum_package/02_o2_selci/o2_selci.py diff --git a/nexus/examples/quantum_package/H2O/H2O.xyz b/nexus/nexus/examples/quantum_package/H2O/H2O.xyz similarity index 100% rename from nexus/examples/quantum_package/H2O/H2O.xyz rename to nexus/nexus/examples/quantum_package/H2O/H2O.xyz diff --git a/nexus/examples/quantum_package/H2O/h2o_ae_hf.py b/nexus/nexus/examples/quantum_package/H2O/h2o_ae_hf.py similarity index 100% rename from nexus/examples/quantum_package/H2O/h2o_ae_hf.py rename to nexus/nexus/examples/quantum_package/H2O/h2o_ae_hf.py diff --git a/nexus/examples/quantum_package/O2/O2.xyz b/nexus/nexus/examples/quantum_package/O2/O2.xyz similarity index 100% rename from nexus/examples/quantum_package/O2/O2.xyz rename to nexus/nexus/examples/quantum_package/O2/O2.xyz diff --git a/nexus/examples/quantum_package/O2/o2_selci.py b/nexus/nexus/examples/quantum_package/O2/o2_selci.py similarity index 100% rename from nexus/examples/quantum_package/O2/o2_selci.py rename to nexus/nexus/examples/quantum_package/O2/o2_selci.py diff --git a/nexus/examples/rmg/01_diamond_scf/diamond_scf.py b/nexus/nexus/examples/rmg/01_diamond_scf/diamond_scf.py similarity index 100% rename from nexus/examples/rmg/01_diamond_scf/diamond_scf.py rename to nexus/nexus/examples/rmg/01_diamond_scf/diamond_scf.py diff --git a/nexus/nexus/scripts.py b/nexus/nexus/scripts.py new file mode 100644 index 0000000000..c5a504d35a --- /dev/null +++ b/nexus/nexus/scripts.py @@ -0,0 +1,44 @@ +import subprocess +import sys +from os import PathLike +from pathlib import Path + +bin_dir = Path(__file__).parent/"bin" + +def run(script_name: PathLike): + script_path = bin_dir/script_name + result = subprocess.run([script_path] + sys.argv[1:]) + sys.exit(result.returncode) +#end def run + +def eshdf(): + run("eshdf") +#end def eshdf + +def nxs_redo(): + run("nxs-redo") +#end def nxs_redo + +def nxs_sim(): + run("nxs-sim") +#end def nxs_sim + +def nxs_test(): + run("nxs-test") +#end def nxs_test + +def qdens(): + run("qdens") +#end def qdens + +def qdens_radial(): + run("qdens-radial") +#end def qdens_radial + +def qmca(): + run("qmca") +#end def qmca + +def qmc_fit(): + run("qmc-fit") +#end def qmc_fit diff --git a/nexus/nexus/testing.py b/nexus/nexus/testing.py index 9e58463c33..ea0b7791a9 100644 --- a/nexus/nexus/testing.py +++ b/nexus/nexus/testing.py @@ -290,16 +290,14 @@ def nexus_path(append=None,location=None): assert(len(tokens)>=3) assert(tokens[-1].startswith('testing.py')) assert(tokens[-2]=='nexus') - assert(tokens[-3]=='nexus') path = os.path.dirname(testing_path) - path = os.path.dirname(path) assert(path.endswith('/nexus')) if location is not None: if location=='unit': - append = 'nexus/tests' + append = 'tests' elif location=='bin': append = 'bin' else: diff --git a/nexus/nexus/tests/test_pseudopotential.py b/nexus/nexus/tests/test_pseudopotential.py index 3645724b24..03c9a40f7f 100644 --- a/nexus/nexus/tests/test_pseudopotential.py +++ b/nexus/nexus/tests/test_pseudopotential.py @@ -234,8 +234,11 @@ def test_pseudopotential_classes(): 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.join(pp_path,pp_relpath) + print(os.path.realpath(pp_path)) + print(os.path.realpath(pp_relpath)) + filepath = os.path.realpath(os.path.join(pp_path,pp_relpath)) f.close() + print(os.path.realpath(filepath)) qpp = QmcpackPP(filepath) diff --git a/nexus/pyproject.toml b/nexus/pyproject.toml index b8a2ab77fa..90f5ad7d27 100644 --- a/nexus/pyproject.toml +++ b/nexus/pyproject.toml @@ -17,16 +17,15 @@ dependencies = [ "numpy (>=2.3.0, !=2.4.0) ; python_version >= '3.14.0'", # ] -# TODO Restructure to support including the scripts with the package distribution -# [project.scripts] -# eshdf = "nexus.scripts:eshdf" -# nxs-redo = "nexus.scripts:nxs_redo" -# nxs-sim = "nexus.scripts:nxs_sim" -# nxs-test = "nexus.scripts:nxs_test" -# qdens = "nexus.scripts:qdens" -# qdens-radial = "nexus.scripts:qdens_radial" -# qmca = "nexus.scripts:qmca" -# qmc-fit = "nexus.scripts:qmc_fit" +[project.scripts] +eshdf = "nexus.scripts:eshdf" +nxs-redo = "nexus.scripts:nxs_redo" +nxs-sim = "nexus.scripts:nxs_sim" +nxs-test = "nexus.scripts:nxs_test" +qdens = "nexus.scripts:qdens" +qdens-radial = "nexus.scripts:qdens_radial" +qmca = "nexus.scripts:qmca" +qmc-fit = "nexus.scripts:qmc_fit" [build-system] requires = ["hatchling"] @@ -34,8 +33,8 @@ build-backend = "hatchling.build" [dependency-groups] dev = [ - "pytest>=9.0.2", - "pytest-cov>=7.0.0", + "pytest>=9.0.2 ; python_version >= '3.10.0'", + "pytest-cov>=7.0.0 ; python_version >= '3.10.0'", ] [project.optional-dependencies] From 74144563ccd851600fddb0e366c4e22dc176bb73 Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Wed, 28 Jan 2026 16:26:35 -0500 Subject: [PATCH 2/4] Nexus: Fix pseudopotential tests and fix CMake pathing for Nexus tests --- nexus/nexus/tests/CMakeLists.txt | 8 ++++---- nexus/nexus/tests/test_pseudopotential_files/C.BFD.upf | 2 +- nexus/nexus/tests/test_pseudopotential_files/C.BFD.xml | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/nexus/nexus/tests/CMakeLists.txt b/nexus/nexus/tests/CMakeLists.txt index 0165563eec..272c3df2f7 100644 --- a/nexus/nexus/tests/CMakeLists.txt +++ b/nexus/nexus/tests/CMakeLists.txt @@ -5,13 +5,13 @@ include("${PROJECT_SOURCE_DIR}/CMake/python.cmake") check_python_reqs(numpy "nexus base" ADD_TEST) if(ADD_TEST) - file(TIMESTAMP ${qmcpack_SOURCE_DIR}/nexus/bin/nxs-test NEXUS_TESTLIST_TIMESTAMP) + 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/bin/nxs-test --ctestlist + 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} ${qmcpack_SOURCE_DIR}/nexus/bin/nxs-test --ctestlist' failed!") + message(FATAL_ERROR "Command line '${Python3_EXECUTABLE} ${qmcpack_SOURCE_DIR}/nexus/nexus/bin/nxs-test --ctestlist' failed!") endif() set(CACHE_NEXUS_TESTLIST @@ -31,7 +31,7 @@ if(ADD_TEST) endif() foreach(TESTNAME ${NEXUS_TESTLIST}) #message("Adding test ntest_nexus_${TESTNAME}") - set(NTEST "${qmcpack_SOURCE_DIR}/nexus/bin/nxs-test") + set(NTEST "${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}) diff --git a/nexus/nexus/tests/test_pseudopotential_files/C.BFD.upf b/nexus/nexus/tests/test_pseudopotential_files/C.BFD.upf index 02c521cf75..79413db7b0 100644 --- a/nexus/nexus/tests/test_pseudopotential_files/C.BFD.upf +++ b/nexus/nexus/tests/test_pseudopotential_files/C.BFD.upf @@ -1 +1 @@ -../../../examples/qmcpack/pseudopotentials/C.BFD.upf \ No newline at end of file +../../examples/qmcpack/pseudopotentials/C.BFD.upf \ No newline at end of file diff --git a/nexus/nexus/tests/test_pseudopotential_files/C.BFD.xml b/nexus/nexus/tests/test_pseudopotential_files/C.BFD.xml index 52629c190a..74db3b1ba4 100644 --- a/nexus/nexus/tests/test_pseudopotential_files/C.BFD.xml +++ b/nexus/nexus/tests/test_pseudopotential_files/C.BFD.xml @@ -1 +1 @@ -../../../examples/qmcpack/pseudopotentials/C.BFD.xml \ No newline at end of file +../../examples/qmcpack/pseudopotentials/C.BFD.xml \ No newline at end of file From f41688520b0995a55a758a2ee50f995d781c8aff Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Fri, 6 Feb 2026 12:07:39 -0500 Subject: [PATCH 3/4] Nexus: Remove print statements leftover from debugging --- nexus/nexus/tests/test_pseudopotential.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/nexus/nexus/tests/test_pseudopotential.py b/nexus/nexus/tests/test_pseudopotential.py index 03c9a40f7f..ce95142c8a 100644 --- a/nexus/nexus/tests/test_pseudopotential.py +++ b/nexus/nexus/tests/test_pseudopotential.py @@ -234,11 +234,8 @@ def test_pseudopotential_classes(): f = open(files['C.BFD.xml'],'r') pp_relpath = f.read().strip() pp_path = os.path.split(files['C.BFD.xml'])[0] - print(os.path.realpath(pp_path)) - print(os.path.realpath(pp_relpath)) filepath = os.path.realpath(os.path.join(pp_path,pp_relpath)) f.close() - print(os.path.realpath(filepath)) qpp = QmcpackPP(filepath) From 40543921241833d8871aca4efdb06612bba26fae Mon Sep 17 00:00:00 2001 From: brockdyer03 Date: Thu, 12 Mar 2026 15:02:31 -0400 Subject: [PATCH 4/4] Nexus: Update installation docs to reflect bin packaging --- nexus/docs/installation.rst | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/nexus/docs/installation.rst b/nexus/docs/installation.rst index 0cee290717..deb572b205 100644 --- a/nexus/docs/installation.rst +++ b/nexus/docs/installation.rst @@ -11,10 +11,6 @@ to development or (currently) if any scripts/"binaries" are needed. Administrati Note that while many supercomputer systems have an outdated system Python, a recent Python version is usually provided via a loadable module: check the local documentation or discuss with your system administrators to find the simplest installation route. -.. important:: - Currently, Nexus installed via ``pip`` or ``uv`` does not include any scripts (``qmca``, ``nxs-test``, etc.) which are readily available in QMCPACK installations. - Users may install them by following the manual installation method described in :ref:`manual_install`. - .. contents:: Installation using ``pip`` @@ -54,8 +50,11 @@ To subsequently use the environment: cd $HOME/somewhere # Wherever you created the environment source nexusenv/bin/activate -Note that any versions of Nexus found via the ``PYTHONPATH`` environment variable will take precedence over a ``pip`` installed -version. +Note that any versions of Nexus found via the ``PYTHONPATH`` environment variable will take precedence over a ``pip`` installed version. + +.. important:: + If you install Nexus into a virtual environment, the Nexus executables (e.g. ``qmca``, ``nxs-sim``, etc.) will only be accessible if you have activated that virtual environment. + System-wide installation (not recommended in general) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -114,7 +113,6 @@ minimum set of dependencies. You can also install the full set of optional depen uv pip install "nexus[full]@git+https://github.com/QMCPACK/qmcpack.git@main#subdirectory=nexus" - Note that when using ``uv`` as a package manager, your Python scripts can optionally use a modified `shebang `__ that tells it to use ``uv`` to run it. For example