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
|
# Copyright (C) 2012, Jesper Friis, SINTEF
# (see accompanying license files for ASE).
"""Module to read and write atoms EON reactant.con files.
See http://theory.cm.utexas.edu/eon/index.html for a description of EON.
"""
import os
from warnings import warn
from glob import glob
import numpy as np
from ase.atoms import Atoms
from ase.constraints import FixAtoms
from ase.geometry import cellpar_to_cell, cell_to_cellpar
from ase.utils import writer
def read_eon(fileobj, index=-1):
"""Reads an EON reactant.con file. If *fileobj* is the name of a
"states" directory created by EON, all the structures will be read."""
if isinstance(fileobj, str):
if (os.path.isdir(fileobj)):
return read_states(fileobj)
else:
f = open(fileobj)
else:
f = fileobj
more_images_to_read = True
images = []
first_line = f.readline()
while more_images_to_read:
comment = first_line.strip()
f.readline() # 0.0000 TIME (??)
cell_lengths = f.readline().split()
cell_angles = f.readline().split()
# Different order of angles in EON.
cell_angles = [cell_angles[2], cell_angles[1], cell_angles[0]]
cellpar = [float(x) for x in cell_lengths + cell_angles]
f.readline() # 0 0 (??)
f.readline() # 0 0 0 (??)
ntypes = int(f.readline()) # number of atom types
natoms = [int(n) for n in f.readline().split()]
atommasses = [float(m) for m in f.readline().split()]
symbols = []
coords = []
masses = []
fixed = []
for n in range(ntypes):
symbol = f.readline().strip()
symbols.extend([symbol] * natoms[n])
masses.extend([atommasses[n]] * natoms[n])
f.readline() # Coordinates of Component n
for i in range(natoms[n]):
row = f.readline().split()
coords.append([float(x) for x in row[:3]])
fixed.append(bool(int(row[3])))
atoms = Atoms(symbols=symbols,
positions=coords,
masses=masses,
cell=cellpar_to_cell(cellpar),
constraint=FixAtoms(mask=fixed),
info=dict(comment=comment))
images.append(atoms)
first_line = f.readline()
if first_line == '':
more_images_to_read = False
if isinstance(fileobj, str):
f.close()
if not index:
return images
else:
return images[index]
def read_states(states_dir):
"""Read structures stored by EON in the states directory *states_dir*."""
subdirs = glob(os.path.join(states_dir, '[0123456789]*'))
subdirs.sort(key=lambda d: int(os.path.basename(d)))
images = [read_eon(os.path.join(subdir, 'reactant.con'))
for subdir in subdirs]
return images
@writer
def write_eon(fileobj, images):
"""Writes structure to EON reactant.con file
Multiple snapshots are allowed."""
if isinstance(images, Atoms):
atoms = images
elif len(images) == 1:
atoms = images[0]
else:
raise ValueError('Can only write one configuration to EON '
'reactant.con file')
out = []
out.append(atoms.info.get('comment', 'Generated by ASE'))
out.append('0.0000 TIME') # ??
a, b, c, alpha, beta, gamma = cell_to_cellpar(atoms.cell)
out.append('%-10.6f %-10.6f %-10.6f' % (a, b, c))
out.append('%-10.6f %-10.6f %-10.6f' % (gamma, beta, alpha))
out.append('0 0') # ??
out.append('0 0 0') # ??
symbols = atoms.get_chemical_symbols()
massdict = dict(list(zip(symbols, atoms.get_masses())))
atomtypes = sorted(massdict.keys())
atommasses = [massdict[at] for at in atomtypes]
natoms = [symbols.count(at) for at in atomtypes]
ntypes = len(atomtypes)
out.append(str(ntypes))
out.append(' '.join([str(n) for n in natoms]))
out.append(' '.join([str(n) for n in atommasses]))
atom_id = 0
for n in range(ntypes):
fixed = np.array([False] * len(atoms))
out.append(atomtypes[n])
out.append('Coordinates of Component %d' % (n + 1))
indices = [i for i, at in enumerate(symbols) if at == atomtypes[n]]
a = atoms[indices]
coords = a.positions
for c in a.constraints:
if not isinstance(c, FixAtoms):
warn('Only FixAtoms constraints are supported by con files. '
'Dropping %r', c)
continue
if c.index.dtype.kind == 'b':
fixed = np.array(c.index, dtype=int)
else:
fixed = np.zeros((natoms[n], ), dtype=int)
for i in c.index:
fixed[i] = 1
for xyz, fix in zip(coords, fixed):
out.append('%22.17f %22.17f %22.17f %d %4d' %
(tuple(xyz) + (fix, atom_id)))
atom_id += 1
fileobj.write('\n'.join(out))
fileobj.write('\n')
|
