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
|
from __future__ import print_function
import os
import pickle
import numpy as np
from ase.atoms import Atoms
from ase.parallel import rank
def ensemble(energy, contributions, xc, verbose=False):
"""Returns an array of ensemble total energies."""
ensemble = BEEFEnsemble(None, energy, contributions, xc, verbose)
return ensemble.get_ensemble_energies()
class BEEFEnsemble:
"""BEEF type ensemble error estimation"""
def __init__(self, atoms=None, e=None, contribs=None, xc=None,
verbose=True):
if (atoms is not None or contribs is not None or xc is not None):
if atoms is None:
assert e is not None
assert contribs is not None
assert xc is not None
else:
if isinstance(atoms, Atoms):
calc = atoms.get_calculator()
self.atoms = atoms
else:
calc = atoms
self.atoms = calc.atoms
self.calc = calc
xc = self.calc.get_xc_functional()
self.e = e
self.contribs = contribs
self.xc = xc
self.verbose = verbose
self.done = False
if self.xc in ['BEEF-vdW', 'BEEF', 'PBE']:
self.beef_type = 'beefvdw'
elif self.xc == 'mBEEF':
self.beef_type = 'mbeef'
elif self.xc == 'mBEEF-vdW':
self.beef_type = 'mbeefvdw'
else:
raise NotImplementedError('No ensemble for xc = %s' % self.xc)
def get_ensemble_energies(self, size=2000, seed=0):
"""Returns an array of ensemble total energies"""
self.seed = seed
if rank == 0 and self.verbose:
print(self.beef_type, 'ensemble started')
if self.contribs is None:
self.contribs = self.calc.get_nonselfconsistent_energies(
self.beef_type)
self.e = self.calc.get_potential_energy(self.atoms)
if self.beef_type == 'beefvdw':
assert len(self.contribs) == 32
coefs = self.get_beefvdw_ensemble_coefs(size, seed)
elif self.beef_type == 'mbeef':
assert len(self.contribs) == 64
coefs = self.get_mbeef_ensemble_coefs(size, seed)
elif self.beef_type == 'mbeefvdw':
assert len(self.contribs) == 28
coefs = self.get_mbeefvdw_ensemble_coefs(size, seed)
self.de = np.dot(coefs, self.contribs)
self.done = True
if rank == 0 and self.verbose:
print(self.beef_type, 'ensemble finished')
return self.e + self.de
def get_beefvdw_ensemble_coefs(self, size=2000, seed=0):
"""Perturbation coefficients of the BEEF-vdW ensemble"""
from ase.dft.pars_beefvdw import uiOmega as omega
assert np.shape(omega) == (31, 31)
W, V, generator = self.eigendecomposition(omega, seed)
RandV = generator.randn(31, size)
for j in range(size):
v = RandV[:, j]
coefs_i = (np.dot(np.dot(V, np.diag(np.sqrt(W))), v)[:])
if j == 0:
ensemble_coefs = coefs_i
else:
ensemble_coefs = np.vstack((ensemble_coefs, coefs_i))
PBEc_ens = -ensemble_coefs[:, 30]
return (np.vstack((ensemble_coefs.T, PBEc_ens))).T
def get_mbeef_ensemble_coefs(self, size=2000, seed=0):
"""Perturbation coefficients of the mBEEF ensemble"""
from ase.dft.pars_mbeef import uiOmega as omega
assert np.shape(omega) == (64, 64)
W, V, generator = self.eigendecomposition(omega, seed)
mu, sigma = 0.0, 1.0
rand = np.array(generator.normal(mu, sigma, (len(W), size)))
return (np.sqrt(2) * np.dot(np.dot(V, np.diag(np.sqrt(W))),
rand)[:]).T
def get_mbeefvdw_ensemble_coefs(self, size=2000, seed=0):
"""Perturbation coefficients of the mBEEF-vdW ensemble"""
from ase.dft.pars_mbeefvdw import uiOmega as omega
assert np.shape(omega) == (28, 28)
W, V, generator = self.eigendecomposition(omega, seed)
mu, sigma = 0.0, 1.0
rand = np.array(generator.normal(mu, sigma, (len(W), size)))
return (np.sqrt(2) * np.dot(np.dot(V, np.diag(np.sqrt(W))), rand)[:]).T
def eigendecomposition(self, omega, seed=0):
u, s, v = np.linalg.svd(omega) # unsafe: W, V = np.linalg.eig(omega)
generator = np.random.RandomState(seed)
return s, v.T, generator
def write(self, fname):
"""Write ensemble data file"""
if not fname.endswith('.bee'):
fname += '.bee'
assert self.done
if rank == 0:
if os.path.isfile(fname):
os.rename(fname, fname + '.old')
obj = [self.e, self.de, self.contribs, self.seed, self.xc]
with open(fname, 'wb') as f:
pickle.dump(obj, f)
def readbee(fname, all=False):
if not fname.endswith('.bee'):
fname += '.bee'
with open(fname, 'rb') as f:
e, de, contribs, seed, xc = pickle.load(f)
if all:
return e, de, contribs, seed, xc
else:
return e + de
def BEEF_Ensemble(*args, **kwargs):
import warnings
warnings.warn('Please use BEEFEnsemble instead of BEEF_Ensemble.')
return BEEFEnsemble(*args, **kwargs)
|
