/usr/share/pyshared/ase/io/gen.py is in python-ase 3.6.0.2515-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 | """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 ase.atoms import Atoms
from ase.parallel import paropen
def read_gen(fileobj):
"""Read structure in GEN format (refer to DFTB+ manual).
Multiple snapshot are not allowed. """
if isinstance(fileobj, str):
fileobj = open(fileobj)
image = Atoms()
lines = fileobj.readlines()
line = lines[0].split()
natoms = int(line[0])
if line[1] == 'S':
supercell = True
elif line[1] == 'C':
supercell = False
else:
raise IOError('Error in line #1: only C (Cluster) or S (Supercell) ' +
'are valid options')
# Read atomic symbols
line = lines[1].split()
# Define a dictionary with symbols-id
symboldict = dict()
symbolid = 1
for symb in line:
symboldict[symbolid] = symb
symbolid += 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 not supercell:
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])])
return image
def write_gen(fileobj, images):
"""Write structure in GEN format (refer to DFTB+ manual).
Multiple snapshots are not allowed. """
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
if not isinstance(images, (list, tuple)):
images = [images]
# Images is kept in a list but a size > 0 is not allowed
# as GEN format doesn't support multiple snapshots.
# Images is used as a list for consistency with the other
# output modules
if len(images) != 1:
raise ValueError('images contains more than one structure\n' +
'GEN format supports only single snapshot output')
symbols = images[0].get_chemical_symbols()
# Define a dictionary with symbols-id
symboldict = dict()
for sym in symbols:
if not (sym 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 in symboldict.keys():
orderedsymbols[symboldict[sym] - 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 images[0].pbc.any():
pb_flag = 'S'
else:
pb_flag = 'C'
natoms = len(symbols)
ind = 0
for atoms in images:
fileobj.write('%d %-5s\n' % (natoms, pb_flag))
for s in orderedsymbols:
fileobj.write('%-5s' % s)
fileobj.write('\n')
for sym, (x, y, z) in zip(symbols, atoms.get_positions()):
ind += 1
symbolid = symboldict[sym]
fileobj.write('%-6d %d %22.15f %22.15f %22.15f\n' % (ind,
symbolid, x, y, z))
if images[0].pbc.any():
fileobj.write('%22.15f %22.15f %22.15f \n' % (0.0, 0.0, 0.0))
fileobj.write('%22.15f %22.15f %22.15f \n' %
(images[0].get_cell()[0][0],
images[0].get_cell()[0][1],
images[0].get_cell()[0][2]))
fileobj.write('%22.15f %22.15f %22.15f \n' %
(images[0].get_cell()[1][0],
images[0].get_cell()[1][1],
images[0].get_cell()[1][2]))
fileobj.write('%22.15f %22.15f %22.15f \n' %
(images[0].get_cell()[2][0],
images[0].get_cell()[2][1],
images[0].get_cell()[2][2]))
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