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support to read coord/cell from STRU_ION*_D in abacus/relax #957

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33b6364
support to read coord/cell from STRU_ION*_D in abacus/relax
Mar 18, 2026
bf5cf3e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 18, 2026
e3ae51c
fix the bug of unit of cell/coord
Mar 18, 2026
2168483
update coords.npy
Mar 18, 2026
30797b5
Merge branch 'abacus-relax' of https://github.com/pxlxingliang/dpdata…
Mar 18, 2026
5f4745c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 18, 2026
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70 changes: 61 additions & 9 deletions dpdata/abacus/relax.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from __future__ import annotations

import glob
import os

import numpy as np
Expand Down Expand Up @@ -31,7 +32,23 @@ def get_log_file(fname, inlines):
return logf


def get_coords_from_log(loglines, natoms):
def get_relax_stru_files(output_dir):
"""Find the STRU files in the output directory.

Args:
output_dir (str): output directory

Returns
-------
strus: list of STRU files

example:
["STRU_ION1_D", "STRU_ION2_D"]
"""
return glob.glob(os.path.join(output_dir, "STRU_ION*_D"))


def get_coords_from_log(loglines, natoms, stru_files=None):
"""NOTICE: unit of coords and cells is Angstrom
order:
coordinate
Expand Down Expand Up @@ -72,7 +89,12 @@ def get_coords_from_log(loglines, natoms):
coord_direct.append(False)
for k in range(2, 2 + natoms):
coords[-1].append(
list(map(lambda x: float(x) * a0, loglines[i + k].split()[1:4]))
list(
map(
lambda x: float(x) * a0 * bohr2ang,
loglines[i + k].split()[1:4],
)
)
)
else:
assert False, "Unrecongnized coordinate type, %s, line:%d" % ( # noqa: UP031
Expand All @@ -91,7 +113,12 @@ def get_coords_from_log(loglines, natoms):
cells.append([])
for k in range(1, 4):
cells[-1].append(
list(map(lambda x: float(x) * a0, loglines[i + k].split()[0:3]))
list(
map(
lambda x: float(x) * a0 * bohr2ang,
loglines[i + k].split()[0:3],
)
)
)

elif line[1:14] == "final etot is" or "#TOTAL ENERGY#" in line:
Expand All @@ -101,6 +128,27 @@ def get_coords_from_log(loglines, natoms):
# get the energy of current structure
energy.append(float(line.split()[-2]))

# in some relax method (like: bfgs_trad), the coordinate is not outputed in running_relax.log
# but if out_stru is true, then STRU_ION*_D will be outputed in OUT.ABACUS
# we should read cell and coord from STRU_ION*_D files
if len(energy) > 1 and len(coords) == 1:
# the energies of all structrues are collected, but coords have only the first structure
if (
stru_files is not None and len(stru_files) > 1
): # if stru_files are not only STRU_ION_D
stru_file_name = [os.path.basename(i) for i in stru_files]
coords = coords[:1] + [np.nan for i in range(len(energy) - 1)]
coord_direct = coord_direct[:1] + [False for i in range(len(energy) - 1)]
cells = cells[:1] + [np.nan for i in range(len(energy) - 1)]
for iframe in range(1, len(energy)):
if f"STRU_ION{iframe}_D" in stru_file_name:
# read the structure from STRU_ION*_D
stru_data = get_frame_from_stru(
stru_files[stru_file_name.index(f"STRU_ION{iframe}_D")]
)
coords[iframe] = stru_data["coords"][0]
cells[iframe] = stru_data["cells"][0]

force = collect_force(loglines)
stress = collect_stress(loglines)

Expand Down Expand Up @@ -133,7 +181,11 @@ def get_coords_from_log(loglines, natoms):

# delete structures whose energy is np.nan
for i in range(minl):
if np.isnan(energy[i - minl]):
if (
np.isnan(energy[i - minl])
or np.any(np.isnan(coords[i - minl]))
or np.any(np.isnan(cells[i - minl]))
):
del energy[i - minl]
del coords[i - minl]
del cells[i - minl]
Expand All @@ -154,10 +206,6 @@ def get_coords_from_log(loglines, natoms):
if coord_direct[i]:
coords[i] = coords[i].dot(cells[i])

# transfer bohrium to angstrom
cells *= bohr2ang
coords *= bohr2ang

if len(stress) > 0:
virial = np.zeros([len(cells), 3, 3])
for i in range(len(cells)):
Expand Down Expand Up @@ -191,7 +239,11 @@ def get_frame(fname):
with open_file(logf) as f1:
lines = f1.readlines()

energy, cells, coords, force, stress, virial = get_coords_from_log(lines, natoms)
relax_stru_files = get_relax_stru_files(os.path.dirname(logf))

energy, cells, coords, force, stress, virial = get_coords_from_log(
lines, natoms, stru_files=relax_stru_files
)

magmom, magforce = get_mag_force(lines)

Expand Down
54 changes: 54 additions & 0 deletions tests/abacus.relax.readFromSTRUIOND/INPUT
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@@ -0,0 +1,54 @@
INPUT_PARAMETERS RUNNING ABACUS-DFT

#Parameters (1.General)
suffix ABACUS # suffix of OUTPUT DIR
nspin 1 # 1/2/4
symmetry 0 # 0/1
esolver_type ksdft # ksdft/ofdft/sdft/tddft/lj/dp
dft_functional pbe # lda/pbe/scan/hf/pbe0/hse/libxc
ks_solver genelpa # genelpa/scalapack_avx for lcao, cg/dav for pw
vdw_method none # d3/d3_bj/none

#Parameters (2.Iteration)
calculation cell-relax # scf/relax/cell-relax/md
ecutwfc 100 # Rydberg, in lcao is for grid density
scf_thr 1e-7 # Rydberg
scf_nmax 100
#printe 300 # default eq scf_nmax
relax_nmax 30
relax_method bfgs_trad # cg/bfgs/bfgs_trad/sd/"fire"
force_thr_ev 0.05
# stress_thr 1 # GPa

#Parameters (3.Basis)
basis_type lcao # lcao or pw
# kspacing 0.14 0.50 0.14 # replace KPT
gamma_only 1 # 0/1, replace KPT

#Parameters (4.Smearing)
smearing_method mp # mp/gauss/fixed/mp-n/fd
smearing_sigma 0.008 # Rydberg

#Parameters (5.Mixing)
mixing_type broyden # pulay/broyden
mixing_ndim 20
#mixing_beta 0.4 # use default
#mixing_gg0 1.0 # use default

#Parameters (6.Calculation)
cal_force 1
cal_stress 1
#init_chg atomic # atomic/auto/file
#init_wfc atomic # atomic/file
out_stru 1 # print STRU in OUT
out_chg -1 # -1 no, 0 binary, 1 cube, more number as cube prec
out_bandgap 1
out_mul 1 # print charge and mag of atom in mulliken.txt
# out_wfc_lcao 0 # 0 no, 1 txt, 2 dat


# #Parameters (7. Dipole Correction)
# efield_flag 1 # open added potential, if 0, all below useless
# dip_cor_flag 1 # open dipole correction
# efield_dir 1 # direction of dipole correction, 0,1,2 for x,y,z

4 changes: 4 additions & 0 deletions tests/abacus.relax.readFromSTRUIOND/KPT
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@@ -0,0 +1,4 @@
K_POINTS
0
Gamma
1 1 1 0 0 0
34 changes: 34 additions & 0 deletions tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION1_D
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ATOMIC_SPECIES
Ga 69.7230 Ga.upf upf201
As 74.9216 As.PD04.PBE.UPF upf201

NUMERICAL_ORBITAL
Ga_gga_7au_100Ry_2s2p2d1f.orb
As_gga_8au_100Ry_2s2p1d.orb

LATTICE_CONSTANT
1.8897160000

LATTICE_VECTORS
5.9515362652 -0.0000000000 0.0000000000
-0.0000000000 5.9515362652 -0.0000000000
0.0000000000 -0.0000000000 5.9515362652

ATOMIC_POSITIONS
Direct

Ga #label
0.0000 #magnetism
4 #number of atoms
1.0000000000 0.0000000000 1.0000000000 m 1 1 1
1.0000000000 0.5000000000 0.5000000000 m 1 1 1
0.5000000000 0.0000000000 0.5000000000 m 1 1 1
0.5000000000 0.5000000000 1.0000000000 m 1 1 1

As #label
0.0000 #magnetism
4 #number of atoms
0.2500000000 0.2500000000 0.2500000000 m 1 1 1
0.2500000000 0.7500000000 0.7500000000 m 1 1 1
0.7500000000 0.2500000000 0.7500000000 m 1 1 1
0.7500000000 0.7500000000 0.2500000000 m 1 1 1
34 changes: 34 additions & 0 deletions tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION2_D
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ATOMIC_SPECIES
Ga 69.7230 Ga.upf upf201
As 74.9216 As.PD04.PBE.UPF upf201

NUMERICAL_ORBITAL
Ga_gga_7au_100Ry_2s2p2d1f.orb
As_gga_8au_100Ry_2s2p1d.orb

LATTICE_CONSTANT
1.8897160000

LATTICE_VECTORS
6.5556050607 -0.0000000000 0.0000000000
-0.0000000000 6.5556050607 -0.0000000000
0.0000000000 -0.0000000000 6.5556050607

ATOMIC_POSITIONS
Direct

Ga #label
0.0000 #magnetism
4 #number of atoms
1.0000000000 0.0000000000 1.0000000000 m 1 1 1
1.0000000000 0.5000000000 0.5000000000 m 1 1 1
0.5000000000 0.0000000000 0.5000000000 m 1 1 1
0.5000000000 0.5000000000 1.0000000000 m 1 1 1

As #label
0.0000 #magnetism
4 #number of atoms
0.2500000000 0.2500000000 0.2500000000 m 1 1 1
0.2500000000 0.7500000000 0.7500000000 m 1 1 1
0.7500000000 0.2500000000 0.7500000000 m 1 1 1
0.7500000000 0.7500000000 0.2500000000 m 1 1 1
34 changes: 34 additions & 0 deletions tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION3_D
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ATOMIC_SPECIES
Ga 69.7230 Ga.upf upf201
As 74.9216 As.PD04.PBE.UPF upf201

NUMERICAL_ORBITAL
Ga_gga_7au_100Ry_2s2p2d1f.orb
As_gga_8au_100Ry_2s2p1d.orb

LATTICE_CONSTANT
1.8897160000

LATTICE_VECTORS
6.3401004195 -0.0000000000 0.0000000000
-0.0000000000 6.3401004195 -0.0000000000
0.0000000000 -0.0000000000 6.3401004195

ATOMIC_POSITIONS
Direct

Ga #label
0.0000 #magnetism
4 #number of atoms
1.0000000000 0.0000000000 1.0000000000 m 1 1 1
1.0000000000 0.5000000000 0.5000000000 m 1 1 1
0.5000000000 0.0000000000 0.5000000000 m 1 1 1
0.5000000000 0.5000000000 1.0000000000 m 1 1 1

As #label
0.0000 #magnetism
4 #number of atoms
0.2500000000 0.2500000000 0.2500000000 m 1 1 1
0.2500000000 0.7500000000 0.7500000000 m 1 1 1
0.7500000000 0.2500000000 0.7500000000 m 1 1 1
0.7500000000 0.7500000000 0.2500000000 m 1 1 1
34 changes: 34 additions & 0 deletions tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION4_D
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ATOMIC_SPECIES
Ga 69.7230 Ga.upf upf201
As 74.9216 As.PD04.PBE.UPF upf201

NUMERICAL_ORBITAL
Ga_gga_7au_100Ry_2s2p2d1f.orb
As_gga_8au_100Ry_2s2p1d.orb

LATTICE_CONSTANT
1.8897160000

LATTICE_VECTORS
6.1458183424 -0.0000000000 0.0000000000
-0.0000000000 6.1458183424 -0.0000000000
0.0000000000 -0.0000000000 6.1458183424

ATOMIC_POSITIONS
Direct

Ga #label
0.0000 #magnetism
4 #number of atoms
1.0000000000 0.0000000000 1.0000000000 m 1 1 1
1.0000000000 0.5000000000 0.5000000000 m 1 1 1
0.5000000000 0.0000000000 0.5000000000 m 1 1 1
0.5000000000 0.5000000000 1.0000000000 m 1 1 1

As #label
0.0000 #magnetism
4 #number of atoms
0.2500000000 0.2500000000 0.2500000000 m 1 1 1
0.2500000000 0.7500000000 0.7500000000 m 1 1 1
0.7500000000 0.2500000000 0.7500000000 m 1 1 1
0.7500000000 0.7500000000 0.2500000000 m 1 1 1
34 changes: 34 additions & 0 deletions tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION5_D
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ATOMIC_SPECIES
Ga 69.7230 Ga.upf upf201
As 74.9216 As.PD04.PBE.UPF upf201

NUMERICAL_ORBITAL
Ga_gga_7au_100Ry_2s2p2d1f.orb
As_gga_8au_100Ry_2s2p1d.orb

LATTICE_CONSTANT
1.8897160000

LATTICE_VECTORS
6.2881167169 -0.0000000039 -0.0000000010
-0.0000000039 6.2881167169 0.0000000005
-0.0000000010 0.0000000005 6.2881167191

ATOMIC_POSITIONS
Direct

Ga #label
0.0000 #magnetism
4 #number of atoms
0.0000000081 0.9999999941 0.9999999959 m 1 1 1
0.0000000081 0.5000000079 0.5000000109 m 1 1 1
0.4999999941 0.9999999941 0.5000000109 m 1 1 1
0.4999999941 0.5000000079 0.9999999959 m 1 1 1

As #label
0.0000 #magnetism
4 #number of atoms
0.2499999989 0.2499999990 0.2499999966 m 1 1 1
0.2499999989 0.7499999990 0.7499999966 m 1 1 1
0.7499999989 0.2499999990 0.7499999966 m 1 1 1
0.7499999989 0.7499999990 0.2499999966 m 1 1 1
34 changes: 34 additions & 0 deletions tests/abacus.relax.readFromSTRUIOND/OUT.ABACUS/STRU_ION_D
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Original file line number Diff line number Diff line change
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ATOMIC_SPECIES
Ga 69.7230 Ga.upf upf201
As 74.9216 As.PD04.PBE.UPF upf201

NUMERICAL_ORBITAL
Ga_gga_7au_100Ry_2s2p2d1f.orb
As_gga_8au_100Ry_2s2p1d.orb

LATTICE_CONSTANT
1.8897160000

LATTICE_VECTORS
6.2881167169 -0.0000000039 -0.0000000010
-0.0000000039 6.2881167169 0.0000000005
-0.0000000010 0.0000000005 6.2881167191

ATOMIC_POSITIONS
Direct

Ga #label
0.0000 #magnetism
4 #number of atoms
0.0000000081 0.9999999941 0.9999999959 m 1 1 1
0.0000000081 0.5000000079 0.5000000109 m 1 1 1
0.4999999941 0.9999999941 0.5000000109 m 1 1 1
0.4999999941 0.5000000079 0.9999999959 m 1 1 1

As #label
0.0000 #magnetism
4 #number of atoms
0.2499999989 0.2499999990 0.2499999966 m 1 1 1
0.2499999989 0.7499999990 0.7499999966 m 1 1 1
0.7499999989 0.2499999990 0.7499999966 m 1 1 1
0.7499999989 0.7499999990 0.2499999966 m 1 1 1
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