-
Notifications
You must be signed in to change notification settings - Fork 78
/
vasp_raman.py
361 lines (349 loc) · 13.5 KB
/
vasp_raman.py
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
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
#!/usr/bin/env python
#
# vasp_raman.py v. 0.6.0
#
# Raman off-resonant activity calculator
# using VASP as a back-end.
#
# Contributors: Alexandr Fonari (Georgia Tech)
# Shannon Stauffer (UT Austin)
#
# URL: http://raman-sc.github.io
#
# MIT license, 2013 - 2016
#
import re
import sys
def MAT_m_VEC(m, v):
p = [ 0.0 for i in range(len(v)) ]
for i in range(len(m)):
assert len(v) == len(m[i]), 'Length of the matrix row is not equal to the length of the vector'
p[i] = sum( [ m[i][j]*v[j] for j in range(len(v)) ] )
return p
def T(m):
p = [[ m[i][j] for i in range(len( m[j] )) ] for j in range(len( m )) ]
return p
def parse_poscar(poscar_fh):
# modified subroutine from phonopy 1.8.3 (New BSD license)
#
poscar_fh.seek(0) # just in case
lines = poscar_fh.readlines()
#
scale = float(lines[1])
if scale < 0.0:
print "[parse_poscar]: ERROR negative scale not implemented."
sys.exit(1)
#
b = []
for i in range(2, 5):
b.append([float(x)*scale for x in lines[i].split()[:3]])
#
vol = b[0][0]*b[1][1]*b[2][2] + b[1][0]*b[2][1]*b[0][2] + b[2][0]*b[0][1]*b[1][2] - \
b[0][2]*b[1][1]*b[2][0] - b[2][1]*b[1][2]*b[0][0] - b[2][2]*b[0][1]*b[1][0]
#
try:
num_atoms = [int(x) for x in lines[5].split()]
line_at = 6
except ValueError:
symbols = [x for x in lines[5].split()]
num_atoms = [int(x) for x in lines[6].split()]
line_at = 7
nat = sum(num_atoms)
#
if lines[line_at][0].lower() == 's':
line_at += 1
#
if (lines[line_at][0].lower() == 'c' or lines[line_at][0].lower() == 'k'):
is_scaled = False
else:
is_scaled = True
#
line_at += 1
#
positions = []
for i in range(line_at, line_at + nat):
pos = [float(x) for x in lines[i].split()[:3]]
#
if is_scaled:
pos = MAT_m_VEC(T(b), pos)
#
positions.append(pos)
#
poscar_header = ''.join(lines[1:line_at-1]) # will add title and 'Cartesian' later
return nat, vol, b, positions, poscar_header
def parse_env_params(params):
tmp = params.strip().split('_')
if len(tmp) != 4:
print "[parse_env_params]: ERROR there should be exactly four parameters"
sys.exit(1)
#
[first, last, nderiv, step_size] = [int(tmp[0]), int(tmp[1]), int(tmp[2]), float(tmp[3])]
#
return first, last, nderiv, step_size
#### subs for the output from VTST tools
def parse_freqdat(freqdat_fh, nat):
freqdat_fh.seek(0) # just in case
#
eigvals = [ 0.0 for i in range(nat*3) ]
#
for i in range(nat*3): # all frequencies should be supplied, regardless of requested to calculate
tmp = freqdat_fh.readline().split()
eigvals[i] = float(tmp[0])
#
return eigvals
#
def parse_modesdat(modesdat_fh, nat):
from math import sqrt
modesdat_fh.seek(0) # just in case
#
eigvecs = [ 0.0 for i in range(nat*3) ]
norms = [ 0.0 for i in range(nat*3) ]
#
for i in range(nat*3): # all frequencies should be supplied, regardless of requested to calculate
eigvec = []
for j in range(nat):
tmp = modesdat_fh.readline().split()
eigvec.append([ float(tmp[x]) for x in range(3) ])
#
modesdat_fh.readline().split() # empty line
eigvecs[i] = eigvec
norms[i] = sqrt( sum( [abs(x)**2 for sublist in eigvec for x in sublist] ) )
#
return eigvecs, norms
#### end subs for VTST
#
def get_modes_from_OUTCAR(outcar_fh, nat):
from math import sqrt
eigvals = [ 0.0 for i in range(nat*3) ]
eigvecs = [ 0.0 for i in range(nat*3) ]
norms = [ 0.0 for i in range(nat*3) ]
#
outcar_fh.seek(0) # just in case
while True:
line = outcar_fh.readline()
if not line:
break
#
if "Eigenvectors after division by SQRT(mass)" in line:
outcar_fh.readline() # empty line
outcar_fh.readline() # Eigenvectors and eigenvalues of the dynamical matrix
outcar_fh.readline() # ----------------------------------------------------
outcar_fh.readline() # empty line
#
for i in range(nat*3): # all frequencies should be supplied, regardless of those requested to calculate
outcar_fh.readline() # empty line
p = re.search(r'^\s*(\d+).+?([\.\d]+) cm-1', outcar_fh.readline())
eigvals[i] = float(p.group(2))
#
outcar_fh.readline() # X Y Z dx dy dz
eigvec = []
#
for j in range(nat):
tmp = outcar_fh.readline().split()
#
eigvec.append([ float(tmp[x]) for x in range(3,6) ])
#
eigvecs[i] = eigvec
norms[i] = sqrt( sum( [abs(x)**2 for sublist in eigvec for x in sublist] ) )
#
return eigvals, eigvecs, norms
#
print "[get_modes_from_OUTCAR]: ERROR Couldn't find 'Eigenvectors after division by SQRT(mass)' in OUTCAR. Use 'NWRITE=3' in INCAR. Exiting..."
sys.exit(1)
#
def get_epsilon_from_OUTCAR(outcar_fh):
epsilon = []
#
outcar_fh.seek(0) # just in case
while True:
line = outcar_fh.readline()
if not line:
break
#
if "MACROSCOPIC STATIC DIELECTRIC TENSOR" in line:
outcar_fh.readline()
epsilon.append([float(x) for x in outcar_fh.readline().split()])
epsilon.append([float(x) for x in outcar_fh.readline().split()])
epsilon.append([float(x) for x in outcar_fh.readline().split()])
return epsilon
#
raise RuntimeError("[get_epsilon_from_OUTCAR]: ERROR Couldn't find dielectric tensor in OUTCAR")
return 1
#
if __name__ == '__main__':
from math import pi
from shutil import move
import os
import datetime
import time
#import argparse
import optparse
#
print ""
print " Raman off-resonant activity calculator,"
print " using VASP as a back-end."
print ""
print " Contributors: Alexandr Fonari (Georgia Tech)"
print " Shannon Stauffer (UT Austin)"
print " MIT License, 2013"
print " URL: http://raman-sc.github.io"
print " Started at: "+datetime.datetime.now().strftime("%Y-%m-%d %H:%M")
print ""
#
description = "Before run, set environment variables:\n"
description += " VASP_RAMAN_RUN='mpirun vasp'\n"
description += " VASP_RAMAN_PARAMS='[first-mode]_[last-mode]_[nderiv]_[step-size]'\n\n"
description += "bash one-liner is:\n"
description += "VASP_RAMAN_RUN='mpirun vasp' VASP_RAMAN_PARAMS='1_2_2_0.01' python vasp_raman.py"
#
parser = optparse.OptionParser(description=description)
parser.add_option('-g', '--gen', help='Generate POSCAR only', action='store_true')
parser.add_option('-u', '--use_poscar', help='Use provided POSCAR in the folder, USE WITH CAUTION!!', action='store_true')
(options, args) = parser.parse_args()
#args = vars(parser.parse_args())
args = vars(options)
#
VASP_RAMAN_RUN = os.environ.get('VASP_RAMAN_RUN')
if VASP_RAMAN_RUN == None:
print "[__main__]: ERROR Set environment variable 'VASP_RAMAN_RUN'"
print ""
parser.print_help()
sys.exit(1)
print "[__main__]: VASP_RAMAN_RUN='"+VASP_RAMAN_RUN+"'"
#
VASP_RAMAN_PARAMS = os.environ.get('VASP_RAMAN_PARAMS')
if VASP_RAMAN_PARAMS == None:
print "[__main__]: ERROR Set environment variable 'VASP_RAMAN_PARAMS'"
print ""
parser.print_help()
sys.exit(1)
print "[__main__]: VASP_RAMAN_PARAMS='"+VASP_RAMAN_PARAMS+"'"
#
first, last, nderiv, step_size = parse_env_params(VASP_RAMAN_PARAMS)
assert first >= 1, '[__main__]: First mode should be equal or larger than 1'
assert last >= first, '[__main__]: Last mode should be equal or larger than first mode'
if args['gen']: assert last == first, "[__main__]: '-gen' mode -> only generation for the one mode makes sense"
assert nderiv == 2, '[__main__]: At this time, nderiv = 2 is the only supported'
disps = [-1, 1] # hardcoded for
coeffs = [-0.5, 0.5] # three point stencil (nderiv=2)
#
try:
poscar_fh = open('POSCAR.phon', 'r')
except IOError:
print "[__main__]: ERROR Couldn't open input file POSCAR.phon, exiting...\n"
sys.exit(1)
#
# nat, vol, b, poscar_header = parse_poscar_header(poscar_fh)
nat, vol, b, pos, poscar_header = parse_poscar(poscar_fh)
print pos
#print poscar_header
#sys.exit(0)
#
# either use modes from vtst tools or VASP
if os.path.isfile('freq.dat') and os.path.isfile('modes_sqrt_amu.dat'):
try:
freqdat_fh = open('freq.dat', 'r')
except IOError:
print "[__main__]: ERROR Couldn't open freq.dat, exiting...\n"
sys.exit(1)
#
eigvals = parse_freqdat(freqdat_fh, nat)
freqdat_fh.close()
#
try:
modes_fh = open('modes_sqrt_amu.dat' , 'r')
except IOError:
print "[__main__]: ERROR Couldn't open modes_sqrt_amu.dat, exiting...\n"
sys.exit(1)
#
eigvecs, norms = parse_modesdat(modes_fh, nat)
modes_fh.close()
#
elif os.path.isfile('OUTCAR.phon'):
try:
outcar_fh = open('OUTCAR.phon', 'r')
except IOError:
print "[__main__]: ERROR Couldn't open OUTCAR.phon, exiting...\n"
sys.exit(1)
#
eigvals, eigvecs, norms = get_modes_from_OUTCAR(outcar_fh, nat)
outcar_fh.close()
#
else:
print "[__main__]: Neither OUTCAR.phon nor freq.dat/modes_sqrt_amu.dat were found, nothing to do, exiting..."
sys.exit(1)
#
output_fh = open('vasp_raman.dat', 'w')
output_fh.write("# mode freq(cm-1) alpha beta2 activity\n")
for i in range(first-1, last):
eigval = eigvals[i]
eigvec = eigvecs[i]
norm = norms[i]
#
print ""
print "[__main__]: Mode #%i: frequency %10.7f cm-1; norm: %10.7f" % ( i+1, eigval, norm )
#
ra = [[0.0 for x in range(3)] for y in range(3)]
for j in range(len(disps)):
disp_filename = 'OUTCAR.%04d.%+d.out' % (i+1, disps[j])
#
try:
outcar_fh = open(disp_filename, 'r')
print "[__main__]: File "+disp_filename+" exists, parsing..."
except IOError:
if args['use_poscar'] != True:
print "[__main__]: File "+disp_filename+" not found, preparing displaced POSCAR"
poscar_fh = open('POSCAR', 'w')
poscar_fh.write("%s %4.1e \n" % (disp_filename, step_size))
poscar_fh.write(poscar_header)
poscar_fh.write("Cartesian\n")
#
for k in range(nat):
pos_disp = [ pos[k][l] + eigvec[k][l]*step_size*disps[j]/norm for l in range(3)]
poscar_fh.write( '%15.10f %15.10f %15.10f\n' % (pos_disp[0], pos_disp[1], pos_disp[2]) )
#print '%10.6f %10.6f %10.6f %10.6f %10.6f %10.6f' % (pos[k][0], pos[k][1], pos[k][2], dis[k][0], dis[k][1], dis[k][2])
poscar_fh.close()
else:
print "[__main__]: Using provided POSCAR"
#
if args['gen']: # only generate POSCARs
poscar_fn = 'POSCAR.%+d.out' % disps[j]
move('POSCAR', poscar_fn)
print "[__main__]: '-gen' mode -> "+poscar_fn+" with displaced atoms have been generated"
#
if j+1 == len(disps): # last iteration for the current displacements list
print "[__main__]: '-gen' mode -> POSCAR files with displaced atoms have been generated, exiting now"
sys.exit(0)
else: # run VASP here
print "[__main__]: Running VASP..."
os.system(VASP_RAMAN_RUN)
try:
move('OUTCAR', disp_filename)
except IOError:
print "[__main__]: ERROR Couldn't find OUTCAR file, exiting..."
sys.exit(1)
#
outcar_fh = open(disp_filename, 'r')
#
try:
eps = get_epsilon_from_OUTCAR(outcar_fh)
outcar_fh.close()
except Exception, err:
print err
print "[__main__]: Moving "+disp_filename+" back to 'OUTCAR' and exiting..."
move(disp_filename, 'OUTCAR')
sys.exit(1)
#
for m in range(3):
for n in range(3):
ra[m][n] += eps[m][n] * coeffs[j]/step_size * norm * vol/(4.0*pi)
#units: A^2/amu^1/2 = dimless * 1/A * 1/amu^1/2 * A^3
#
alpha = (ra[0][0] + ra[1][1] + ra[2][2])/3.0
beta2 = ( (ra[0][0] - ra[1][1])**2 + (ra[0][0] - ra[2][2])**2 + (ra[1][1] - ra[2][2])**2 + 6.0 * (ra[0][1]**2 + ra[0][2]**2 + ra[1][2]**2) )/2.0
print ""
print "! %4i freq: %10.5f alpha: %10.7f beta2: %10.7f activity: %10.7f " % (i+1, eigval, alpha, beta2, 45.0*alpha**2 + 7.0*beta2)
output_fh.write("%03i %10.5f %10.7f %10.7f %10.7f\n" % (i+1, eigval, alpha, beta2, 45.0*alpha**2 + 7.0*beta2))
output_fh.flush()
#
output_fh.close()