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
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
|
# fmt: off
"""
A module for reading and writing crystal structures from JSV
See http://www.jcrystal.com/steffenweber/JAVA/JSV/jsv.html
By Jesper Friis, Jan. 2012
"""
import re
import numpy as np
import ase
from ase.geometry import cell_to_cellpar, cellpar_to_cell
from ase.spacegroup import Spacegroup, crystal
def read_jsv(f):
"""Reads a JSV file."""
natom = nbond = npoly = 0
symbols = []
labels = []
cellpar = basis = title = bonds = poly = origin = shell_numbers = None
spacegroup = 1
headline = f.readline().strip()
while True:
line = f.readline()
if not line:
break
line = line.strip()
m = re.match(r'^\[([^]]+)\]\s*(.*)', line)
if m is None or not line:
continue
tag = m.groups()[0].lower()
if len(m.groups()) > 1:
args = m.groups()[1].split()
else:
args = []
if tag == 'cell':
cellpar = [float(x) for x in args]
elif tag == 'natom':
natom = int(args[0])
elif tag == 'nbond':
nbond = int(args[0])
# optional margin of the bondlengths
elif tag == 'npoly':
npoly = int(args[0])
elif tag == 'space_group':
spacegroup = Spacegroup(*tuple(int(x) for x in args))
elif tag == 'title':
title = m.groups()[1]
elif tag == 'atoms':
symbols = []
basis = np.zeros((natom, 3), dtype=float)
shell_numbers = -np.ones((natom, ), dtype=int) # float?
for i in range(natom):
tokens = f.readline().strip().split()
labels.append(tokens[0])
symbols.append(ase.data.chemical_symbols[int(tokens[1])])
basis[i] = [float(x) for x in tokens[2:5]]
if len(tokens) > 5:
shell_numbers[i] = float(tokens[5]) # float?
elif tag == 'bonds':
for _ in range(nbond):
f.readline()
bonds = NotImplemented
elif tag == 'poly':
for _ in range(npoly):
f.readline()
poly = NotImplemented
elif tag == 'origin':
origin = NotImplemented
else:
raise ValueError(f'Unknown tag: "{tag}"')
if headline == 'asymmetric_unit_cell':
atoms = crystal(symbols=symbols,
basis=basis,
spacegroup=spacegroup,
cellpar=cellpar,
)
elif headline == 'full_unit_cell':
atoms = ase.Atoms(symbols=symbols,
scaled_positions=basis,
cell=cellpar_to_cell(cellpar),
)
atoms.info['spacegroup'] = Spacegroup(spacegroup)
elif headline == 'cartesian_cell':
atoms = ase.Atoms(symbols=symbols,
positions=basis,
cell=cellpar_to_cell(cellpar),
)
atoms.info['spacegroup'] = Spacegroup(spacegroup)
else:
raise ValueError(f'Invalid JSV file type: "{headline}"')
atoms.info['title'] = title
atoms.info['labels'] = labels
if bonds is not None:
atoms.info['bonds'] = bonds
if poly is not None:
atoms.info['poly'] = poly
if origin is not None:
atoms.info['origin'] = origin
if shell_numbers is not None:
atoms.info['shell_numbers'] = shell_numbers
return atoms
def write_jsv(fd, atoms):
"""Writes JSV file."""
fd.write('asymmetric_unit_cell\n')
fd.write('[cell]')
for v in cell_to_cellpar(atoms.cell):
fd.write(' %g' % v)
fd.write('\n')
fd.write('[natom] %d\n' % len(atoms))
fd.write('[nbond] 0\n') # FIXME
fd.write('[npoly] 0\n') # FIXME
if 'spacegroup' in atoms.info:
sg = Spacegroup(atoms.info['spacegroup'])
fd.write('[space_group] %d %d\n' % (sg.no, sg.setting))
else:
fd.write('[space_group] 1 1\n')
fd.write('[title] %s\n' % atoms.info.get('title', 'untitled'))
fd.write('\n')
fd.write('[atoms]\n')
if 'labels' in atoms.info:
labels = atoms.info['labels']
else:
labels = ['%s%d' % (s, i + 1) for i, s in
enumerate(atoms.get_chemical_symbols())]
numbers = atoms.get_atomic_numbers()
scaled = atoms.get_scaled_positions()
for label, n, p in zip(labels, numbers, scaled):
fd.write('%-4s %2d %9.6f %9.6f %9.6f\n'
% (label, n, p[0], p[1], p[2]))
fd.write('Label AtomicNumber x y z (repeat natom times)\n')
fd.write('\n')
fd.write('[bonds]\n')
fd.write('\n')
fd.write('[poly]\n')
fd.write('\n')
|
