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support to read coord/cell from STRU_ION*_D in abacus/relax
1 parent 26171f2 commit 33b6364

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Lines changed: 2559 additions & 4 deletions

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‎dpdata/abacus/relax.py‎

Lines changed: 39 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
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from __future__ import annotations
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3-
import os
3+
import os, glob
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55
import numpy as np
66

@@ -30,8 +30,22 @@ def get_log_file(fname, inlines):
3030
logf = os.path.join(fname, f"OUT.{suffix}/running_{calculation}.log")
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return logf
3232

33+
def get_relax_stru_files(output_dir):
34+
"""Find the STRU files in the output directory.
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Args:
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output_dir (str): output directory
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returns:
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strus: list of STRU files
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example:
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["STRU_ION1_D", "STRU_ION2_D"]
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"""
45+
return glob.glob(os.path.join(output_dir, "STRU_ION*_D"))
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3347

34-
def get_coords_from_log(loglines, natoms):
48+
def get_coords_from_log(loglines, natoms, stru_files=[]):
3549
"""NOTICE: unit of coords and cells is Angstrom
3650
order:
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coordinate
@@ -101,6 +115,24 @@ def get_coords_from_log(loglines, natoms):
101115
# get the energy of current structure
102116
energy.append(float(line.split()[-2]))
103117

118+
# in some relax method (like: bfgs_trad), the coordinate is not outputed in running_relax.log
119+
# but if out_stru is true, then STRU_ION*_D will be outputed in OUT.ABACUS
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# we should read cell and coord from STRU_ION*_D files
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if len(energy) > 1 and len(coords) == 1:
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# the energies of all structrues are collected, but coords have only the first structure
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if len(stru_files) > 1: # if stru_files are not only STRU_ION_D
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stru_file_name = [os.path.basename(i) for i in stru_files]
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coords = coords[:1] + [np.nan for i in range(len(energy)-1)]
126+
coord_direct = coord_direct[:1] + [False for i in range(len(energy)-1)]
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cells = cells[:1] + [np.nan for i in range(len(energy)-1)]
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for iframe in range(1, len(energy)):
129+
if f"STRU_ION{iframe}_D" in stru_file_name:
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# read the structure from STRU_ION*_D
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stru_data = get_frame_from_stru(stru_files[stru_file_name.index(f"STRU_ION{iframe}_D")])
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coords[iframe] = stru_data["coords"][0]
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cells[iframe] = stru_data["cells"][0]
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135+
104136
force = collect_force(loglines)
105137
stress = collect_stress(loglines)
106138

@@ -133,7 +165,7 @@ def get_coords_from_log(loglines, natoms):
133165

134166
# delete structures whose energy is np.nan
135167
for i in range(minl):
136-
if np.isnan(energy[i - minl]):
168+
if np.isnan(energy[i - minl]) or np.any(np.isnan(coords[i - minl])) or np.any(np.isnan(cells[i - minl])):
137169
del energy[i - minl]
138170
del coords[i - minl]
139171
del cells[i - minl]
@@ -191,7 +223,10 @@ def get_frame(fname):
191223
with open_file(logf) as f1:
192224
lines = f1.readlines()
193225

194-
energy, cells, coords, force, stress, virial = get_coords_from_log(lines, natoms)
226+
relax_stru_files = get_relax_stru_files(os.path.dirname(logf))
227+
228+
energy, cells, coords, force, stress, virial = get_coords_from_log(lines, natoms, stru_files=relax_stru_files)
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195230

196231
magmom, magforce = get_mag_force(lines)
197232

‎tests/abacus.relax.readFromSTRUIOND/INPUT‎

Lines changed: 54 additions & 0 deletions
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INPUT_PARAMETERS RUNNING ABACUS-DFT
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#Parameters (1.General)
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suffix ABACUS # suffix of OUTPUT DIR
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nspin 1 # 1/2/4
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symmetry 0 # 0/1
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esolver_type ksdft # ksdft/ofdft/sdft/tddft/lj/dp
8+
dft_functional pbe # lda/pbe/scan/hf/pbe0/hse/libxc
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ks_solver genelpa # genelpa/scalapack_avx for lcao, cg/dav for pw
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vdw_method none # d3/d3_bj/none
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#Parameters (2.Iteration)
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calculation cell-relax # scf/relax/cell-relax/md
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ecutwfc 100 # Rydberg, in lcao is for grid density
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scf_thr 1e-7 # Rydberg
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scf_nmax 100
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#printe 300 # default eq scf_nmax
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relax_nmax 30
19+
relax_method bfgs_trad # cg/bfgs/bfgs_trad/sd/"fire"
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force_thr_ev 0.05
21+
# stress_thr 1 # GPa
22+
23+
#Parameters (3.Basis)
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basis_type lcao # lcao or pw
25+
# kspacing 0.14 0.50 0.14 # replace KPT
26+
gamma_only 1 # 0/1, replace KPT
27+
28+
#Parameters (4.Smearing)
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smearing_method mp # mp/gauss/fixed/mp-n/fd
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smearing_sigma 0.008 # Rydberg
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32+
#Parameters (5.Mixing)
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mixing_type broyden # pulay/broyden
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mixing_ndim 20
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#mixing_beta 0.4 # use default
36+
#mixing_gg0 1.0 # use default
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38+
#Parameters (6.Calculation)
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cal_force 1
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cal_stress 1
41+
#init_chg atomic # atomic/auto/file
42+
#init_wfc atomic # atomic/file
43+
out_stru 1 # print STRU in OUT
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out_chg -1 # -1 no, 0 binary, 1 cube, more number as cube prec
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out_bandgap 1
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out_mul 1 # print charge and mag of atom in mulliken.txt
47+
# out_wfc_lcao 0 # 0 no, 1 txt, 2 dat
48+
49+
50+
# #Parameters (7. Dipole Correction)
51+
# efield_flag 1 # open added potential, if 0, all below useless
52+
# dip_cor_flag 1 # open dipole correction
53+
# efield_dir 1 # direction of dipole correction, 0,1,2 for x,y,z
54+

‎tests/abacus.relax.readFromSTRUIOND/KPT‎

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1+
K_POINTS
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0
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Gamma
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1 1 1 0 0 0

‎tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION1_D‎

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ATOMIC_SPECIES
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Ga 69.7230 Ga.upf upf201
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As 74.9216 As.PD04.PBE.UPF upf201
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5+
NUMERICAL_ORBITAL
6+
Ga_gga_7au_100Ry_2s2p2d1f.orb
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As_gga_8au_100Ry_2s2p1d.orb
8+
9+
LATTICE_CONSTANT
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1.8897160000
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12+
LATTICE_VECTORS
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5.9515362652 -0.0000000000 0.0000000000
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-0.0000000000 5.9515362652 -0.0000000000
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0.0000000000 -0.0000000000 5.9515362652
16+
17+
ATOMIC_POSITIONS
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Direct
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Ga #label
21+
0.0000 #magnetism
22+
4 #number of atoms
23+
1.0000000000 0.0000000000 1.0000000000 m 1 1 1
24+
1.0000000000 0.5000000000 0.5000000000 m 1 1 1
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0.5000000000 0.0000000000 0.5000000000 m 1 1 1
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0.5000000000 0.5000000000 1.0000000000 m 1 1 1
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As #label
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0.0000 #magnetism
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4 #number of atoms
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0.2500000000 0.2500000000 0.2500000000 m 1 1 1
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0.2500000000 0.7500000000 0.7500000000 m 1 1 1
33+
0.7500000000 0.2500000000 0.7500000000 m 1 1 1
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0.7500000000 0.7500000000 0.2500000000 m 1 1 1

‎tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION2_D‎

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ATOMIC_SPECIES
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Ga 69.7230 Ga.upf upf201
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As 74.9216 As.PD04.PBE.UPF upf201
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5+
NUMERICAL_ORBITAL
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Ga_gga_7au_100Ry_2s2p2d1f.orb
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As_gga_8au_100Ry_2s2p1d.orb
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LATTICE_CONSTANT
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1.8897160000
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LATTICE_VECTORS
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6.5556050607 -0.0000000000 0.0000000000
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-0.0000000000 6.5556050607 -0.0000000000
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0.0000000000 -0.0000000000 6.5556050607
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ATOMIC_POSITIONS
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Direct
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Ga #label
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0.0000 #magnetism
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4 #number of atoms
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1.0000000000 0.0000000000 1.0000000000 m 1 1 1
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1.0000000000 0.5000000000 0.5000000000 m 1 1 1
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0.5000000000 0.0000000000 0.5000000000 m 1 1 1
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0.5000000000 0.5000000000 1.0000000000 m 1 1 1
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As #label
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0.0000 #magnetism
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4 #number of atoms
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0.2500000000 0.2500000000 0.2500000000 m 1 1 1
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0.2500000000 0.7500000000 0.7500000000 m 1 1 1
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0.7500000000 0.2500000000 0.7500000000 m 1 1 1
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0.7500000000 0.7500000000 0.2500000000 m 1 1 1

‎tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION3_D‎

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ATOMIC_SPECIES
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Ga 69.7230 Ga.upf upf201
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As 74.9216 As.PD04.PBE.UPF upf201
4+
5+
NUMERICAL_ORBITAL
6+
Ga_gga_7au_100Ry_2s2p2d1f.orb
7+
As_gga_8au_100Ry_2s2p1d.orb
8+
9+
LATTICE_CONSTANT
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1.8897160000
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12+
LATTICE_VECTORS
13+
6.3401004195 -0.0000000000 0.0000000000
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-0.0000000000 6.3401004195 -0.0000000000
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0.0000000000 -0.0000000000 6.3401004195
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17+
ATOMIC_POSITIONS
18+
Direct
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Ga #label
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0.0000 #magnetism
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4 #number of atoms
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1.0000000000 0.0000000000 1.0000000000 m 1 1 1
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1.0000000000 0.5000000000 0.5000000000 m 1 1 1
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0.5000000000 0.0000000000 0.5000000000 m 1 1 1
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0.5000000000 0.5000000000 1.0000000000 m 1 1 1
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As #label
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0.0000 #magnetism
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4 #number of atoms
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0.2500000000 0.2500000000 0.2500000000 m 1 1 1
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0.2500000000 0.7500000000 0.7500000000 m 1 1 1
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0.7500000000 0.2500000000 0.7500000000 m 1 1 1
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0.7500000000 0.7500000000 0.2500000000 m 1 1 1

‎tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION4_D‎

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ATOMIC_SPECIES
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Ga 69.7230 Ga.upf upf201
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As 74.9216 As.PD04.PBE.UPF upf201
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5+
NUMERICAL_ORBITAL
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Ga_gga_7au_100Ry_2s2p2d1f.orb
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As_gga_8au_100Ry_2s2p1d.orb
8+
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LATTICE_CONSTANT
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1.8897160000
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12+
LATTICE_VECTORS
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6.1458183424 -0.0000000000 0.0000000000
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-0.0000000000 6.1458183424 -0.0000000000
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0.0000000000 -0.0000000000 6.1458183424
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ATOMIC_POSITIONS
18+
Direct
19+
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Ga #label
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0.0000 #magnetism
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4 #number of atoms
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1.0000000000 0.0000000000 1.0000000000 m 1 1 1
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1.0000000000 0.5000000000 0.5000000000 m 1 1 1
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0.5000000000 0.0000000000 0.5000000000 m 1 1 1
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0.5000000000 0.5000000000 1.0000000000 m 1 1 1
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As #label
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0.0000 #magnetism
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4 #number of atoms
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0.2500000000 0.2500000000 0.2500000000 m 1 1 1
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0.2500000000 0.7500000000 0.7500000000 m 1 1 1
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0.7500000000 0.2500000000 0.7500000000 m 1 1 1
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0.7500000000 0.7500000000 0.2500000000 m 1 1 1

‎tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION5_D‎

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ATOMIC_SPECIES
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Ga 69.7230 Ga.upf upf201
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As 74.9216 As.PD04.PBE.UPF upf201
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5+
NUMERICAL_ORBITAL
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Ga_gga_7au_100Ry_2s2p2d1f.orb
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As_gga_8au_100Ry_2s2p1d.orb
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9+
LATTICE_CONSTANT
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1.8897160000
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12+
LATTICE_VECTORS
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6.2881167169 -0.0000000039 -0.0000000010
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-0.0000000039 6.2881167169 0.0000000005
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-0.0000000010 0.0000000005 6.2881167191
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17+
ATOMIC_POSITIONS
18+
Direct
19+
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Ga #label
21+
0.0000 #magnetism
22+
4 #number of atoms
23+
0.0000000081 0.9999999941 0.9999999959 m 1 1 1
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0.0000000081 0.5000000079 0.5000000109 m 1 1 1
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0.4999999941 0.9999999941 0.5000000109 m 1 1 1
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0.4999999941 0.5000000079 0.9999999959 m 1 1 1
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As #label
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0.0000 #magnetism
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4 #number of atoms
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0.2499999989 0.2499999990 0.2499999966 m 1 1 1
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0.2499999989 0.7499999990 0.7499999966 m 1 1 1
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0.7499999989 0.2499999990 0.7499999966 m 1 1 1
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0.7499999989 0.7499999990 0.2499999966 m 1 1 1

‎tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION_D‎

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ATOMIC_SPECIES
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Ga 69.7230 Ga.upf upf201
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As 74.9216 As.PD04.PBE.UPF upf201
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5+
NUMERICAL_ORBITAL
6+
Ga_gga_7au_100Ry_2s2p2d1f.orb
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As_gga_8au_100Ry_2s2p1d.orb
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9+
LATTICE_CONSTANT
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1.8897160000
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12+
LATTICE_VECTORS
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6.2881167169 -0.0000000039 -0.0000000010
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-0.0000000039 6.2881167169 0.0000000005
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-0.0000000010 0.0000000005 6.2881167191
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17+
ATOMIC_POSITIONS
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Direct
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Ga #label
21+
0.0000 #magnetism
22+
4 #number of atoms
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0.0000000081 0.9999999941 0.9999999959 m 1 1 1
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0.0000000081 0.5000000079 0.5000000109 m 1 1 1
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0.4999999941 0.9999999941 0.5000000109 m 1 1 1
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0.4999999941 0.5000000079 0.9999999959 m 1 1 1
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As #label
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0.0000 #magnetism
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4 #number of atoms
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0.2499999989 0.2499999990 0.2499999966 m 1 1 1
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0.2499999989 0.7499999990 0.7499999966 m 1 1 1
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0.7499999989 0.2499999990 0.7499999966 m 1 1 1
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0.7499999989 0.7499999990 0.2499999966 m 1 1 1

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