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refactor(abacus): modify poscar2stru in auto_test.lib.abacus #1193

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merged 2 commits into from
Apr 25, 2023
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refactor(abacus): modify poscar2stru in auto_test.lib.abacus #1193

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refactor(abacus): modify poscar2stru in auto_test.lib.abacus
pxlxingliang Apr 24, 2023
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 24, 2023
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23 changes: 16 additions & 7 deletions dpgen/auto_test/lib/abacus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,9 @@

import dpdata
import numpy as np
from dpdata.abacus.scf import make_unlabeled_stru
from dpdata.utils import uniq_atom_names
from dpdata.vasp import poscar as dpdata_poscar
from pymatgen.core.structure import Structure

import dpgen.generator.lib.abacus_scf as abacus_scf
Expand Down Expand Up @@ -242,7 +245,7 @@
]


def poscar2stru(poscar, inter_param, stru):
def poscar2stru(poscar, inter_param, stru="STRU"):
"""
- poscar: POSCAR for input
- inter_param: dictionary of 'interaction' from param.json
Expand All @@ -252,8 +255,12 @@ def poscar2stru(poscar, inter_param, stru):
- deepks_desc: a string of deepks descriptor file
- stru: output filename, usally is 'STRU'
"""
stru = dpdata.System(poscar, fmt="vasp/poscar")
stru_data = stru.data
# if use dpdata.System, the structure will be rotated to make cell to be lower triangular
with open(poscar) as fp:
lines = [line.rstrip("\n") for line in fp]
stru_data = dpdata_poscar.to_system_data(lines)
stru_data = uniq_atom_names(stru_data)

atom_mass = []
pseudo = None
orb = None
Expand Down Expand Up @@ -291,14 +298,16 @@ def poscar2stru(poscar, inter_param, stru):
if "deepks_desc" in inter_param:
deepks_desc = "./pp_orb/%s\n" % inter_param["deepks_desc"]

stru.to(
"stru",
"STRU",
mass=atom_mass,
stru_string = make_unlabeled_stru(
data=stru_data,
frame_idx=0,
pp_file=pseudo,
numerical_orbital=orb,
numerical_descriptor=deepks_desc,
mass=atom_mass,
)
with open(stru, "w") as fp:
fp.write(stru_string)


def stru_fix_atom(struf, fix_atom=[True, True, True]):
Expand Down