"""Extension to ASE: read and write structures in GEN format
Refer to DFTB+ manual for GEN format description.
Note: GEN format only supports single snapshot.
"""
from typing import Dict, Sequence, Union
from ase.atoms import Atoms
from ase.utils import reader, writer
[docs]
@reader
def read_gen(fileobj):
"""Read structure in GEN format (refer to DFTB+ manual).
Multiple snapshot are not allowed. """
image = Atoms()
lines = fileobj.readlines()
line = lines[0].split()
natoms = int(line[0])
pb_flag = line[1]
if line[1] not in ['C', 'F', 'S']:
if line[1] == 'H':
raise OSError('Error in line #1: H (Helical) is valid but not '
'supported. Only C (Cluster), S (Supercell) '
'or F (Fraction) are supported options')
else:
raise OSError('Error in line #1: only C (Cluster), S (Supercell) '
'or F (Fraction) are supported options')
# Read atomic symbols
line = lines[1].split()
symboldict = {symbolid: symb for symbolid, symb in enumerate(line, start=1)}
# Read atoms (GEN format supports only single snapshot)
del lines[:2]
positions = []
symbols = []
for line in lines[:natoms]:
_dummy, symbolid, x, y, z = line.split()[:5]
symbols.append(symboldict[int(symbolid)])
positions.append([float(x), float(y), float(z)])
image = Atoms(symbols=symbols, positions=positions)
del lines[:natoms]
# If Supercell, parse periodic vectors.
# If Fraction, translate into Supercell.
if pb_flag == 'C':
return image
else:
# Dummy line: line after atom positions is not uniquely defined
# in gen implementations, and not necessary in DFTB package
del lines[:1]
image.set_pbc([True, True, True])
p = []
for i in range(3):
x, y, z = lines[i].split()[:3]
p.append([float(x), float(y), float(z)])
image.set_cell([(p[0][0], p[0][1], p[0][2]),
(p[1][0], p[1][1], p[1][2]),
(p[2][0], p[2][1], p[2][2])])
if pb_flag == 'F':
frac_positions = image.get_positions()
image.set_scaled_positions(frac_positions)
return image
[docs]
@writer
def write_gen(
fileobj,
images: Union[Atoms, Sequence[Atoms]],
fractional: bool = False,
):
"""Write structure in GEN format (refer to DFTB+ manual).
Multiple snapshots are not allowed. """
if isinstance(images, (list, tuple)):
# GEN format doesn't support multiple snapshots
if len(images) != 1:
raise ValueError(
'"images" contains more than one structure. '
'GEN format supports only single snapshot output.'
)
atoms = images[0]
else:
atoms = images
symbols = atoms.get_chemical_symbols()
# Define a dictionary with symbols-id
symboldict: Dict[str, int] = {}
for sym in symbols:
if sym not in symboldict:
symboldict[sym] = len(symboldict) + 1
# An ordered symbol list is needed as ordered dictionary
# is just available in python 2.7
orderedsymbols = list(['null'] * len(symboldict.keys()))
for sym, num in symboldict.items():
orderedsymbols[num - 1] = sym
# Check whether the structure is periodic
# GEN cannot describe periodicity in one or two direction,
# a periodic structure is considered periodic in all the
# directions. If your structure is not periodical in all
# the directions, be sure you have set big periodicity
# vectors in the non-periodic directions
if fractional:
pb_flag = 'F'
elif atoms.pbc.any():
pb_flag = 'S'
else:
pb_flag = 'C'
natoms = len(symbols)
ind = 0
fileobj.write(f'{natoms:d} {pb_flag:<5s}\n')
for sym in orderedsymbols:
fileobj.write(f'{sym:<5s}')
fileobj.write('\n')
if fractional:
coords = atoms.get_scaled_positions(wrap=False)
else:
coords = atoms.get_positions(wrap=False)
for sym, (x, y, z) in zip(symbols, coords):
ind += 1
symbolid = symboldict[sym]
fileobj.write(
f'{ind:-6d} {symbolid:d} {x:22.15f} {y:22.15f} {z:22.15f}\n')
if atoms.pbc.any() or fractional:
fileobj.write(f'{0.0:22.15f} {0.0:22.15f} {0.0:22.15f} \n')
cell = atoms.get_cell()
for i in range(3):
for j in range(3):
fileobj.write(f'{cell[i, j]:22.15f} ')
fileobj.write('\n')