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
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
|
""" Read/Write DL_POLY_4 CONFIG files """
import itertools
import re
from typing import IO, Generator, Iterable, List, Optional, Tuple, Union
import numpy as np
from ase.atoms import Atoms
from ase.calculators.singlepoint import SinglePointCalculator
from ase.data import chemical_symbols
from ase.units import _amu, _auf, _auv
from ase.utils import reader, writer
__all__ = ["read_dlp4", "write_dlp4"]
# dlp4 labels will be registered in atoms.arrays[DLP4_LABELS_KEY]
DLP4_LABELS_KEY = "dlp4_labels"
DLP4_DISP_KEY = "dlp4_displacements"
DLP_F_SI = 1.0e-10 * _amu / (1.0e-12 * 1.0e-12) # Å*Da/ps^2
DLP_F_ASE = DLP_F_SI / _auf
DLP_V_SI = 1.0e-10 / 1.0e-12 # Å/ps
DLP_V_ASE = DLP_V_SI / _auv
def _get_frame_positions(fd: IO) -> Tuple[int, int, int, List[int]]:
"""Get positions of frames in HISTORY file."""
init_pos = fd.tell()
fd.seek(0)
record_len = len(fd.readline()) # system name, and record size
items = fd.readline().strip().split()
if len(items) not in (3, 5):
raise RuntimeError("Cannot determine version of HISTORY file format.")
levcfg, imcon, natoms = map(int, items[0:3])
if len(items) == 3: # DLPoly classic
# we have to iterate over the entire file
pos = [fd.tell() for line in fd if "timestep" in line]
else:
nframes = int(items[3])
pos = [((natoms * (levcfg + 2) + 4) * i + 3) * record_len
for i in range(nframes)]
fd.seek(init_pos)
return levcfg, imcon, natoms, pos
@reader
def read_dlp_history(fd: IO,
index: Optional[Union[int, slice]] = None,
symbols: Optional[List[str]] = None) -> List[Atoms]:
"""Read a HISTORY file.
Compatible with DLP4 and DLP_CLASSIC.
*Index* can be integer or a slice.
Provide a list of element strings to symbols to ignore naming
from the HISTORY file.
"""
return list(iread_dlp_history(fd, index, symbols))
@reader
def iread_dlp_history(fd: IO,
index: Optional[Union[int, slice]] = None,
symbols: Optional[List[str]] = None
) -> Generator[Atoms, None, None]:
"""Generator version of read_dlp_history
Compatible with DLP4 and DLP_CLASSIC.
*Index* can be integer or a slice.
Provide a list of element strings to symbols to ignore naming
from the HISTORY file.
"""
levcfg, imcon, natoms, pos = _get_frame_positions(fd)
positions: Iterable[int] = ()
if index is None:
positions = pos
elif isinstance(index, int):
positions = (pos[index],)
elif isinstance(index, slice):
positions = itertools.islice(pos, index.start, index.stop, index.step)
for pos_i in positions:
fd.seek(pos_i + 1)
yield read_single_image(fd, levcfg, imcon, natoms, is_trajectory=True,
symbols=symbols)
@reader
def read_dlp4(fd: IO,
symbols: Optional[List[str]] = None) -> Atoms:
"""Read a DL_POLY_4 config/revcon file.
Typically used indirectly through read("filename", atoms, format="dlp4").
Can be unforgiving with custom chemical element names.
Please complain to alin@elena.space for bugs."""
fd.readline()
levcfg, imcon = map(int, fd.readline().split()[0:2])
position = fd.tell()
is_trajectory = fd.readline().split()[0] == "timestep"
if not is_trajectory:
# Difficult to distinguish between trajectory and non-trajectory
# formats without reading one line too many.
fd.seek(position)
natoms = (int(fd.readline().split()[2]) if is_trajectory else None)
return read_single_image(fd, levcfg, imcon, natoms, is_trajectory,
symbols)
def read_single_image(fd: IO, levcfg: int, imcon: int,
natoms: Optional[int], is_trajectory: bool,
symbols: Optional[List[str]] = None) -> Atoms:
""" Read a DLP frame """
sym = symbols if symbols else []
positions = []
velocities = []
forces = []
charges = []
masses = []
disps = []
labels = []
is_pbc = imcon > 0
cell = np.zeros((3, 3), dtype=np.float64)
if is_pbc or is_trajectory:
for j, line in enumerate(itertools.islice(fd, 3)):
cell[j, :] = np.array(line.split(), dtype=np.float64)
i = 0
for i, line in enumerate(itertools.islice(fd, natoms), 1):
match = re.match(r"\s*([A-Za-z][a-z]?)(\S*)", line)
if not match:
raise OSError(f"Line {line} does not match valid format.")
symbol, label = match.group(1, 2)
symbol = symbol.capitalize()
if is_trajectory:
mass, charge, *disp = map(float, line.split()[2:])
charges.append(charge)
masses.append(mass)
disps.extend(disp if disp else [None]) # type: ignore[list-item]
if not symbols:
if symbol not in chemical_symbols:
raise ValueError(
f"Symbol '{symbol}' not found in chemical symbols table"
)
sym.append(symbol)
# make sure label is not empty
labels.append(label if label else "")
positions.append([float(x) for x in next(fd).split()[:3]])
if levcfg > 0:
velocities.append([float(x) * DLP_V_ASE
for x in next(fd).split()[:3]])
if levcfg > 1:
forces.append([float(x) * DLP_F_ASE
for x in next(fd).split()[:3]])
if symbols and (i != len(symbols)):
raise ValueError(
f"Counter is at {i} but {len(symbols)} symbols provided."
)
if imcon == 0:
pbc = (False, False, False)
elif imcon in (1, 2, 3):
pbc = (True, True, True)
elif imcon == 6:
pbc = (True, True, False)
elif imcon in (4, 5):
raise ValueError(f"Unsupported imcon: {imcon}")
else:
raise ValueError(f"Invalid imcon: {imcon}")
atoms = Atoms(positions=positions,
symbols=sym,
cell=cell,
pbc=pbc,
# Cell is centered around (0, 0, 0) in dlp4:
celldisp=-cell.sum(axis=0) / 2)
if is_trajectory:
atoms.set_masses(masses)
atoms.set_array(DLP4_DISP_KEY, disps, float)
atoms.set_initial_charges(charges)
atoms.set_array(DLP4_LABELS_KEY, labels, str)
if levcfg > 0:
atoms.set_velocities(velocities)
if levcfg > 1:
atoms.calc = SinglePointCalculator(atoms, forces=forces)
return atoms
@writer
def write_dlp4(fd: IO, atoms: Atoms,
levcfg: int = 0,
title: str = "CONFIG generated by ASE"):
"""Write a DL_POLY_4 config file.
Typically used indirectly through write("filename", atoms, format="dlp4").
Can be unforgiven with custom chemical element names.
Please complain to alin@elena.space in case of bugs"""
def float_format(flt):
return format(flt, "20.10f")
natoms = len(atoms)
if tuple(atoms.pbc) == (False, False, False):
imcon = 0
elif tuple(atoms.pbc) == (True, True, True):
imcon = 3
elif tuple(atoms.pbc) == (True, True, False):
imcon = 6
else:
raise ValueError(f"Unsupported pbc: {atoms.pbc}. "
"Supported pbc are 000, 110, and 111.")
print(f"{title:72s}", file=fd)
print(f"{levcfg:10d}{imcon:10d} {natoms}", file=fd)
if imcon > 0:
for row in atoms.get_cell():
print("".join(map(float_format, row)), file=fd)
vels = atoms.get_velocities() / DLP_V_ASE if levcfg > 0 else []
forces = atoms.get_forces() / DLP_F_ASE if levcfg > 1 else []
labels = atoms.arrays.get(DLP4_LABELS_KEY)
for i, atom in enumerate(atoms):
sym = atom.symbol
if labels is not None:
sym += labels[i]
print(f"{sym:8s}{atom.index + 1:10d}", file=fd)
to_write = (atom.x, atom.y, atom.z)
print("".join(map(float_format, to_write)), file=fd)
if levcfg > 0:
to_write = (vels[atom.index, :]
if vels is not None else (0.0, 0.0, 0.0))
print("".join(map(float_format, to_write)), file=fd)
if levcfg > 1:
to_write = (forces[atom.index, :]
if forces is not None else (0.0, 0.0, 0.0))
print("".join(map(float_format, to_write)), file=fd)
|
