def STRU_to_POSCAR(cls, srcfile: str_PathLike, tofile: str_PathLike,
ntype: int) -> None:
"""Convert STRU of ABACUS to POSCAR of VASP
:params srcfile: str_PathLike, source file
:params tofile: str_PathLike, converted file
"""
def convert_pos(elements: list, positions: dict):
newpos = []
for elem in elements:
for pos in positions[elem]:
newpos.append(' ' + ''.ljust(20).join(list_elem2str(pos)))
return newpos
stru = read_stru(ntype, srcfile)
line = [f"From {srcfile}"]
line.append(str(stru.lat0 * BOHR_TO_A))
for i in stru.cell:
line.append('\t' + '\t'.join(list_elem2str(i)))
line.append(' ' + ''.ljust(10).join(stru.elements))
line.append(' ' +
''.ljust(10).join(list_elem2str(stru.numbers.values())))
line.append(stru._ctype)
if stru._ctype == "Direct":
line.append('\n'.join(
convert_pos(stru.elements, stru.scaled_positions)))
if stru._ctype == "Cartesian":
line.append('\n'.join(convert_pos(stru.elements, stru.positions)))
else:
ValueError(f"Type {stru._ctype} is not supported for VASP.")
with open(tofile, 'w') as file:
file.write('\n'.join(line))
def get_kpt(self) -> str:
"""Return the `KPT` file as a string"""
line = []
line.append("K_POINTS")
if self.mode in ["Gamma", "MP"]:
line.append("0")
line.append(self.mode)
line.append(" ".join(list_elem2str(self.numbers + self.offset)))
elif self.mode == "Line":
line.append(str(len(self.special_k)))
line.append(self.mode)
for i, k in enumerate(self.special_k):
if self.klabel:
line.append(" ".join(list_elem2str(k +
[self.numbers[i]])) +
'\t#' + self.klabel[i])
else:
line.append(" ".join(list_elem2str(k + [self.numbers[i]])))
return '\n'.join(line)
def _prepare(self, **kwargs):
"""Prepare input files for optimizing ABFs e.g. input.json"""
self.folder_opt = Path("opt_orb_" + "-".join(list_elem2str(self.Nu)))
self.folder_opt.mkdir(exist_ok=False)
if not Path("folders").exists():
raise FileNotFoundError(
"'folders' which is a out file of `SetDimers` calculations not found."
)
with open(self.folder_opt / "input.json", 'w') as file:
json.dump(self.set_input(), file, indent=4)
def get_stru(self) -> str:
"""Return the `STRU` file as a string"""
empty_line = ''
line = []
line.append("ATOMIC_SPECIES")
for elem in self.elements:
line.append(f"{elem}\t{self.masses[elem]}\t{self.pps[elem]}")
line.append(empty_line)
if self.orbitals:
line.append("NUMERICAL_ORBITAL")
for elem in self.elements:
line.append(f"{self.orbitals[elem]}")
line.append(empty_line)
if self.abfs:
line.append("ABFS_ORBITAL")
for elem in self.elements:
line.append(f"{self.abfs[elem]}")
line.append(empty_line)
line.append("LATTICE_CONSTANT")
line.append(str(self.lat0))
line.append(empty_line)
line.append("LATTICE_VECTORS")
for i in range(3):
line.append(" ".join(list_elem2str(self.cell[i])))
line.append(empty_line)
line.append("ATOMIC_POSITIONS")
line.append(self._ctype)
line.append(empty_line)
for elem in self.elements:
line.append(f"{elem}\n{self.magmoms[elem]}\n{self.numbers[elem]}")
for j in range(self.numbers[elem]):
if self._ctype == "Cartesian":
line.append(
" ".join(list_elem2str(self.positions[elem][j])) +
" " + " ".join(list_elem2str(self.move[elem][j])))
elif self._ctype == "Direct":
line.append(" ".join(
list_elem2str(self.scaled_positions[elem][j])) + " " +
" ".join(list_elem2str(self.move[elem][j])))
elif self._ctype == "Cartesian_angstrom":
line.append(" ".join(
list_elem2str(self.positions_angstrom_lat0[elem][j])) +
" " +
" ".join(list_elem2str(self.move[elem][j])))
line.append(empty_line)
return '\n'.join(line)
def convert_pos(elements: list, positions: dict):
newpos = []
for elem in elements:
for pos in positions[elem]:
newpos.append(' ' + ''.ljust(20).join(list_elem2str(pos)))
return newpos
def convert_path_to_string(path=[[]]):
line = []
for i in path:
line.append(' '.join(list_elem2str(i)))
return '\t'.join(line)