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
|
import sys
from typing import Dict, Any
import numpy as np
from ase.calculators.calculator import (get_calculator_class,
names as calcnames,
PropertyNotImplementedError)
from ase.constraints import FixAtoms, UnitCellFilter
from ase.eos import EquationOfState
from ase.io import read, write, Trajectory
from ase.optimize import LBFGS
import ase.db as db
class CLICommand:
"""Run calculation with one of ASE's calculators.
Four types of calculations can be done:
* single point
* atomic relaxations
* unit cell + atomic relaxations
* equation-of-state
Examples of the four types of calculations:
ase run emt h2o.xyz
ase run emt h2o.xyz -f 0.01
ase run emt cu.traj -s 0.01
ase run emt cu.traj -E 5,2.0
"""
@staticmethod
def add_arguments(parser):
parser.add_argument('calculator',
help='Name of calculator to use. '
'Must be one of: {}.'
.format(', '.join(calcnames)))
CLICommand.add_more_arguments(parser)
@staticmethod
def add_more_arguments(parser):
add = parser.add_argument
add('name', nargs='?', default='-',
help='Read atomic structure from this file.')
add('-p', '--parameters', default='',
metavar='key=value,...',
help='Comma-separated key=value pairs of ' +
'calculator specific parameters.')
add('-t', '--tag',
help='String tag added to filenames.')
add('--properties', default='efsdMm',
help='Default value is "efsdMm" meaning calculate energy, ' +
'forces, stress, dipole moment, total magnetic moment and ' +
'atomic magnetic moments.')
add('-f', '--maximum-force', type=float,
help='Relax internal coordinates.')
add('--constrain-tags',
metavar='T1,T2,...',
help='Constrain atoms with tags T1, T2, ...')
add('-s', '--maximum-stress', type=float,
help='Relax unit-cell and internal coordinates.')
add('-E', '--equation-of-state',
help='Use "-E 5,2.0" for 5 lattice constants ranging from '
'-2.0 %% to +2.0 %%.')
add('--eos-type', default='sjeos', help='Selects the type of eos.')
add('-o', '--output', help='Write result to file (append mode).')
add('--modify', metavar='...',
help='Modify atoms with Python statement. ' +
'Example: --modify="atoms.positions[-1,2]+=0.1".')
add('--after', help='Perform operation after calculation. ' +
'Example: --after="atoms.calc.write(...)"')
@staticmethod
def run(args):
runner = Runner()
runner.parse(args)
runner.run()
class Runner:
def __init__(self):
self.args = None
self.calculator_name = None
def parse(self, args):
self.calculator_name = args.calculator
self.args = args
def run(self):
args = self.args
atoms = self.build(args.name)
if args.modify:
exec(args.modify, {'atoms': atoms, 'np': np})
if args.name == '-':
args.name = 'stdin'
self.set_calculator(atoms, args.name)
self.calculate(atoms, args.name)
def calculate(self, atoms, name):
args = self.args
if args.maximum_force or args.maximum_stress:
self.optimize(atoms, name)
if args.equation_of_state:
self.eos(atoms, name)
self.calculate_once(atoms)
if args.after:
exec(args.after, {'atoms': atoms})
if args.output:
write(args.output, atoms, append=True)
def build(self, name):
if name == '-':
con = db.connect(sys.stdin, 'json')
return con.get_atoms(add_additional_information=True)
else:
atoms = read(name)
if isinstance(atoms, list):
assert len(atoms) == 1
atoms = atoms[0]
return atoms
def set_calculator(self, atoms, name):
cls = get_calculator_class(self.calculator_name)
parameters = str2dict(self.args.parameters)
if getattr(cls, 'nolabel', False):
atoms.calc = cls(**parameters)
else:
atoms.calc = cls(label=self.get_filename(name), **parameters)
def calculate_once(self, atoms):
args = self.args
for p in args.properties or 'efsdMm':
property, method = {'e': ('energy', 'get_potential_energy'),
'f': ('forces', 'get_forces'),
's': ('stress', 'get_stress'),
'd': ('dipole', 'get_dipole_moment'),
'M': ('magmom', 'get_magnetic_moment'),
'm': ('magmoms', 'get_magnetic_moments')}[p]
try:
getattr(atoms, method)()
except PropertyNotImplementedError:
pass
def optimize(self, atoms, name):
args = self.args
if args.constrain_tags:
tags = [int(t) for t in args.constrain_tags.split(',')]
mask = [t in tags for t in atoms.get_tags()]
atoms.constraints = FixAtoms(mask=mask)
logfile = self.get_filename(name, 'log')
if args.maximum_stress:
optimizer = LBFGS(UnitCellFilter(atoms), logfile=logfile)
fmax = args.maximum_stress
else:
optimizer = LBFGS(atoms, logfile=logfile)
fmax = args.maximum_force
trajectory = Trajectory(self.get_filename(name, 'traj'), 'w', atoms)
optimizer.attach(trajectory)
optimizer.run(fmax=fmax)
def eos(self, atoms, name):
args = self.args
traj = Trajectory(self.get_filename(name, 'traj'), 'w', atoms)
N, eps = args.equation_of_state.split(',')
N = int(N)
eps = float(eps) / 100
strains = np.linspace(1 - eps, 1 + eps, N)
v1 = atoms.get_volume()
volumes = strains**3 * v1
energies = []
cell1 = atoms.cell
for s in strains:
atoms.set_cell(cell1 * s, scale_atoms=True)
energies.append(atoms.get_potential_energy())
traj.write(atoms)
traj.close()
eos = EquationOfState(volumes, energies, args.eos_type)
v0, e0, B = eos.fit()
atoms.set_cell(cell1 * (v0 / v1)**(1 / 3), scale_atoms=True)
from ase.parallel import parprint as p
p('volumes:', volumes)
p('energies:', energies)
p('fitted energy:', e0)
p('fitted volume:', v0)
p('bulk modulus:', B)
p('eos type:', args.eos_type)
def get_filename(self, name: str, ext: str = '') -> str:
if '.' in name:
name = name.rsplit('.', 1)[0]
if self.args.tag is not None:
name += '-' + self.args.tag
if ext:
name += '.' + ext
return name
def str2dict(s: str, namespace={}, sep: str = '=') -> Dict[str, Any]:
"""Convert comma-separated key=value string to dictionary.
Examples:
>>> str2dict('xc=PBE,nbands=200,parallel={band:4}')
{'xc': 'PBE', 'nbands': 200, 'parallel': {'band': 4}}
>>> str2dict('a=1.2,b=True,c=ab,d=1,2,3,e={f:42,g:cd}')
{'a': 1.2, 'c': 'ab', 'b': True, 'e': {'g': 'cd', 'f': 42}, 'd': (1, 2, 3)}
"""
def myeval(value):
try:
value = eval(value, namespace)
except (NameError, SyntaxError):
pass
return value
dct = {}
strings = (s + ',').split(sep)
for i in range(len(strings) - 1):
key = strings[i]
m = strings[i + 1].rfind(',')
value: Any = strings[i + 1][:m]
if value[0] == '{':
assert value[-1] == '}'
value = str2dict(value[1:-1], namespace, ':')
elif value[0] == '(':
assert value[-1] == ')'
value = [myeval(t) for t in value[1:-1].split(',')]
else:
value = myeval(value)
dct[key] = value
strings[i + 1] = strings[i + 1][m + 1:]
return dct
|
