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fix a bug when reading the key block of STRU #591

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Merged
wanghan-iapcm merged 2 commits into from
Dec 25, 2023
Merged

fix a bug when reading the key block of STRU #591

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b8196c5
fix a bug when reading the key block of STRU
pxlxingliang Dec 25, 2023
8e13d7d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 25, 2023
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39 changes: 36 additions & 3 deletions dpdata/abacus/scf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,16 @@
ry2ev = EnergyConversion("rydberg", "eV").value()
kbar2evperang3 = PressureConversion("kbar", "eV/angstrom^3").value()

ABACUS_STRU_KEYS = [
"ATOMIC_SPECIES",
"NUMERICAL_ORBITAL",
"LATTICE_CONSTANT",
"LATTICE_VECTORS",
"ATOMIC_POSITIONS",
"NUMERICAL_DESCRIPTOR",
"PAW_FILES",
]


def CheckFile(ifile):
if not os.path.isfile(ifile):
Expand Down Expand Up @@ -43,6 +53,29 @@ def get_block(lines, keyword, skip=0, nlines=None):
return ret


def get_stru_block(lines, keyword):
# return the block of lines after keyword in STRU file, and skip the blank lines

def clean_comment(line):
return re.split("[#]", line)[0]

ret = []
found = False
for i in range(len(lines)):
if clean_comment(lines[i]).strip() == keyword:
found = True
for j in range(i + 1, len(lines)):
if clean_comment(lines[j]).strip() == "":
continue
elif clean_comment(lines[j]).strip() in ABACUS_STRU_KEYS:
break
else:
ret.append(clean_comment(lines[j]))
if not found:
return None
return ret


def get_geometry_in(fname, inlines):
geometry_path_in = os.path.join(fname, "STRU")
for line in inlines:
Expand All @@ -64,8 +97,8 @@ def get_path_out(fname, inlines):


def get_cell(geometry_inlines):
cell_lines = get_block(geometry_inlines, "LATTICE_VECTORS", skip=0, nlines=3)
celldm_lines = get_block(geometry_inlines, "LATTICE_CONSTANT", skip=0, nlines=1)
cell_lines = get_stru_block(geometry_inlines, "LATTICE_VECTORS")
celldm_lines = get_stru_block(geometry_inlines, "LATTICE_CONSTANT")

celldm = float(celldm_lines[0].split()[0]) * bohr2ang # lattice const is in Bohr
cell = []
Expand All @@ -76,7 +109,7 @@ def get_cell(geometry_inlines):


def get_coords(celldm, cell, geometry_inlines, inlines=None):
coords_lines = get_block(geometry_inlines, "ATOMIC_POSITIONS", skip=0)
coords_lines = get_stru_block(geometry_inlines, "ATOMIC_POSITIONS")
# assuming that ATOMIC_POSITIONS is at the bottom of the STRU file
coord_type = coords_lines[0].split()[0].lower() # cartisan or direct
atom_names = [] # element abbr in periodic table
Expand Down