/usr/share/pyshared/ase/vibrations.py is in python-ase 3.6.0.2515-1.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 | # -*- coding: utf-8 -*-
"""Vibrational modes."""
import pickle
from math import sin, pi, sqrt
from os import remove
from os.path import isfile
import sys
import numpy as np
import ase.units as units
from ase.io.trajectory import PickleTrajectory
from ase.parallel import rank, paropen
from ase.utils import opencew
class Vibrations:
"""Class for calculating vibrational modes using finite difference.
The vibrational modes are calculated from a finite difference
approximation of the Hessian matrix.
The *summary()*, *get_energies()* and *get_frequencies()* methods all take
an optional *method* keyword. Use method='Frederiksen' to use the method
described in:
T. Frederiksen, M. Paulsson, M. Brandbyge, A. P. Jauho:
"Inelastic transport theory from first-principles: methodology and
applications for nanoscale devices", Phys. Rev. B 75, 205413 (2007)
atoms: Atoms object
The atoms to work on.
indices: list of int
List of indices of atoms to vibrate. Default behavior is
to vibrate all atoms.
name: str
Name to use for files.
delta: float
Magnitude of displacements.
nfree: int
Number of displacements per atom and cartesian coordinate, 2 and 4 are
supported. Default is 2 which will displace each atom +delta and
-delta for each cartesian coordinate.
Example:
>>> from ase import Atoms
>>> from ase.calculators import EMT
>>> from ase.optimize import BFGS
>>> from ase.vibrations import Vibrations
>>> n2 = Atoms('N2', [(0, 0, 0), (0, 0, 1.1)],
... calculator=EMT())
>>> BFGS(n2).run(fmax=0.01)
BFGS: 0 16:01:21 0.440339 3.2518
BFGS: 1 16:01:21 0.271928 0.8211
BFGS: 2 16:01:21 0.263278 0.1994
BFGS: 3 16:01:21 0.262777 0.0088
>>> vib = Vibrations(n2)
>>> vib.run()
Writing vib.eq.pckl
Writing vib.0x-.pckl
Writing vib.0x+.pckl
Writing vib.0y-.pckl
Writing vib.0y+.pckl
Writing vib.0z-.pckl
Writing vib.0z+.pckl
Writing vib.1x-.pckl
Writing vib.1x+.pckl
Writing vib.1y-.pckl
Writing vib.1y+.pckl
Writing vib.1z-.pckl
Writing vib.1z+.pckl
>>> vib.summary()
---------------------
# meV cm^-1
---------------------
0 0.0 0.0
1 0.0 0.0
2 0.0 0.0
3 2.5 20.4
4 2.5 20.4
5 152.6 1230.8
---------------------
Zero-point energy: 0.079 eV
>>> vib.write_mode(-1) # write last mode to trajectory file
"""
def __init__(self, atoms, indices=None, name='vib', delta=0.01, nfree=2):
assert nfree in [2, 4]
self.atoms = atoms
if indices is None:
indices = range(len(atoms))
self.indices = np.asarray(indices)
self.name = name
self.delta = delta
self.nfree = nfree
self.H = None
self.ir = None
def run(self):
"""Run the vibration calculations.
This will calculate the forces for 6 displacements per atom +/-x,
+/-y, +/-z. Only those calculations that are not already done will be
started. Be aware that an interrupted calculation may produce an empty
file (ending with .pckl), which must be deleted before restarting the
job. Otherwise the forces will not be calculated for that
displacement.
Note that the calculations for the different displacements can be done
simultaneously by several independent processes. This feature relies
on the existence of files and the subsequent creation of the file in
case it is not found.
"""
filename = self.name + '.eq.pckl'
fd = opencew(filename)
if fd is not None:
self.calculate(filename, fd)
p = self.atoms.positions.copy()
for a in self.indices:
for i in range(3):
for sign in [-1, 1]:
for ndis in range(1, self.nfree // 2 + 1):
filename = ('%s.%d%s%s.pckl' %
(self.name, a, 'xyz'[i],
ndis * ' +-'[sign]))
fd = opencew(filename)
if fd is not None:
disp = ndis * sign * self.delta
self.atoms.positions[a, i] = p[a, i] + disp
self.calculate(filename, fd)
self.atoms.positions[a, i] = p[a, i]
def calculate(self, filename, fd):
forces = self.atoms.get_forces()
if self.ir:
dipole = self.calc.get_dipole_moment(self.atoms)
if rank == 0:
if self.ir:
pickle.dump([forces, dipole], fd)
sys.stdout.write(
'Writing %s, dipole moment = (%.6f %.6f %.6f)\n' %
(filename, dipole[0], dipole[1], dipole[2]))
else:
pickle.dump(forces, fd)
sys.stdout.write('Writing %s\n' % filename)
fd.close()
sys.stdout.flush()
def clean(self):
if isfile(self.name + '.eq.pckl'):
remove(self.name + '.eq.pckl')
for a in self.indices:
for i in 'xyz':
for sign in '-+':
for ndis in range(1, self.nfree // 2 + 1):
name = '%s.%d%s%s.pckl' % (self.name, a, i,
ndis * sign)
if isfile(name):
remove(name)
def read(self, method='standard', direction='central'):
self.method = method.lower()
self.direction = direction.lower()
assert self.method in ['standard', 'frederiksen']
assert self.direction in ['central', 'forward', 'backward']
n = 3 * len(self.indices)
H = np.empty((n, n))
r = 0
if direction != 'central':
feq = pickle.load(open(self.name + '.eq.pckl'))
for a in self.indices:
for i in 'xyz':
name = '%s.%d%s' % (self.name, a, i)
fminus = pickle.load(open(name + '-.pckl'))
fplus = pickle.load(open(name + '+.pckl'))
if self.method == 'frederiksen':
fminus[a] -= fminus.sum(0)
fplus[a] -= fplus.sum(0)
if self.nfree == 4:
fminusminus = pickle.load(open(name + '--.pckl'))
fplusplus = pickle.load(open(name + '++.pckl'))
if self.method == 'frederiksen':
fminusminus[a] -= fminusminus.sum(0)
fplusplus[a] -= fplusplus.sum(0)
if self.direction == 'central':
if self.nfree == 2:
H[r] = .5 * (fminus - fplus)[self.indices].ravel()
else:
H[r] = H[r] = (-fminusminus +
8 * fminus -
8 * fplus +
fplusplus)[self.indices].ravel() / 12.0
elif self.direction == 'forward':
H[r] = (feq - fplus)[self.indices].ravel()
else:
assert self.direction == 'backward'
H[r] = (fminus - feq)[self.indices].ravel()
H[r] /= 2 * self.delta
r += 1
H += H.copy().T
self.H = H
m = self.atoms.get_masses()
if 0 in [m[index] for index in self.indices]:
raise RuntimeError('Zero mass encountered in one or more of '
'the vibrated atoms. Use Atoms.set_masses()'
' to set all masses to non-zero values.')
self.im = np.repeat(m[self.indices] ** -0.5, 3)
omega2, modes = np.linalg.eigh(self.im[:, None] * H * self.im)
self.modes = modes.T.copy()
# Conversion factor:
s = units._hbar * 1e10 / sqrt(units._e * units._amu)
self.hnu = s * omega2.astype(complex) ** 0.5
def get_energies(self, method='standard', direction='central'):
"""Get vibration energies in eV."""
if (self.H is None or method.lower() != self.method or
direction.lower() != self.direction):
self.read(method, direction)
return self.hnu
def get_frequencies(self, method='standard', direction='central'):
"""Get vibration frequencies in cm^-1."""
s = 0.01 * units._e / units._c / units._hplanck
return s * self.get_energies(method, direction)
def summary(self, method='standard', direction='central', freq=None,
log=sys.stdout):
"""Print a summary of the vibrational frequencies.
Parameters:
method : string
Can be 'standard'(default) or 'Frederiksen'.
direction: string
Direction for finite differences. Can be one of 'central'
(default), 'forward', 'backward'.
freq : numpy array
Optional. Can be used to create a summary on a set of known
frequencies.
log : if specified, write output to a different location than
stdout. Can be an object with a write() method or the name of a
file to create.
"""
if isinstance(log, str):
log = paropen(log, 'a')
write = log.write
s = 0.01 * units._e / units._c / units._hplanck
if freq != None:
hnu = freq / s
else:
hnu = self.get_energies(method, direction)
write('---------------------\n')
write(' # meV cm^-1\n')
write('---------------------\n')
for n, e in enumerate(hnu):
if e.imag != 0:
c = 'i'
e = e.imag
else:
c = ' '
e = e.real
write('%3d %6.1f%s %7.1f%s\n' % (n, 1000 * e, c, s * e, c))
write('---------------------\n')
write('Zero-point energy: %.3f eV\n' %
self.get_zero_point_energy(freq=freq))
def get_zero_point_energy(self, freq=None):
if freq is None:
return 0.5 * self.hnu.real.sum()
else:
s = 0.01 * units._e / units._c / units._hplanck
return 0.5 * freq.real.sum() / s
def get_mode(self, n):
mode = np.zeros((len(self.atoms), 3))
mode[self.indices] = (self.modes[n] * self.im).reshape((-1, 3))
return mode
def write_mode(self, n, kT=units.kB * 300, nimages=30):
"""Write mode to trajectory file."""
mode = self.get_mode(n) * sqrt(kT / abs(self.hnu[n]))
p = self.atoms.positions.copy()
n %= 3 * len(self.indices)
traj = PickleTrajectory('%s.%d.traj' % (self.name, n), 'w')
calc = self.atoms.get_calculator()
self.atoms.set_calculator()
for x in np.linspace(0, 2 * pi, nimages, endpoint=False):
self.atoms.set_positions(p + sin(x) * mode)
traj.write(self.atoms)
self.atoms.set_positions(p)
self.atoms.set_calculator(calc)
traj.close()
def write_jmol(self):
"""Writes file for viewing of the modes with jmol."""
fd = open(self.name + '.xyz', 'w')
symbols = self.atoms.get_chemical_symbols()
f = self.get_frequencies()
for n in range(3 * len(self.indices)):
fd.write('%6d\n' % len(self.atoms))
if f[n].imag != 0:
c = 'i'
f[n] = f[n].imag
else:
c = ' '
fd.write('Mode #%d, f = %.1f%s cm^-1' % (n, f[n], c))
if self.ir:
fd.write(', I = %.4f (D/Å)^2 amu^-1.\n' % self.intensities[n])
else:
fd.write('.\n')
mode = self.get_mode(n)
for i, pos in enumerate(self.atoms.positions):
fd.write('%2s %12.5f %12.5f %12.5f %12.5f %12.5f %12.5f \n' %
(symbols[i], pos[0], pos[1], pos[2],
mode[i, 0], mode[i, 1], mode[i, 2]))
fd.close()
|