Révision 10 ase/calculators/vasp.py
| vasp.py (revision 10) | ||
|---|---|---|
| 151 | 151 |
class Vasp(Calculator): |
| 152 | 152 |
def __init__(self, restart=None, output_template='vasp', track_output=False, write_input = True, |
| 153 | 153 |
**kwargs): |
| 154 |
self.bool_write_input = write_input
|
|
| 154 |
self.write_input = write_input |
|
| 155 | 155 |
self.name = 'Vasp' |
| 156 | 156 |
self.float_params = {}
|
| 157 | 157 |
self.exp_params = {}
|
| ... | ... | |
| 248 | 248 |
# Determine the number of atoms of each atomic species |
| 249 | 249 |
# sorted after atomic species |
| 250 | 250 |
special_setups = [] |
| 251 |
symbols = {}
|
|
| 252 | 251 |
if self.input_params['setups']: |
| 253 | 252 |
for m in self.input_params['setups']: |
| 254 | 253 |
try : |
| ... | ... | |
| 259 | 258 |
continue |
| 260 | 259 |
#print 'special_setups' , special_setups |
| 261 | 260 |
|
| 261 |
#symbols = {}
|
|
| 262 |
#for m,atom in enumerate(atoms): |
|
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# symbol = atom.get_symbol() |
|
| 264 |
# if m in special_setups: |
|
| 265 |
# pass |
|
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# else: |
|
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# if not symbols.has_key(symbol): |
|
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# symbols[symbol] = 1 |
|
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# else: |
|
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# symbols[symbol] += 1 |
|
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|
|
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symbols = [] |
|
| 262 | 273 |
for m,atom in enumerate(atoms): |
| 263 | 274 |
symbol = atom.get_symbol() |
| 264 | 275 |
if m in special_setups: |
| 265 | 276 |
pass |
| 266 | 277 |
else: |
| 267 |
if not symbols.has_key(symbol): |
|
| 268 |
symbols[symbol] = 1 |
|
| 278 |
ind = 0 |
|
| 279 |
bfound = False |
|
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for symbolX, iatom in symbols: |
|
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if symbol == symbolX: |
|
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bfound = True |
|
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break |
|
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ind += 1 |
|
| 285 |
if bfound: |
|
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symbolX, iatom = symbols[ind] |
|
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symbols[ind] = symbolX, iatom+1 |
|
| 269 | 288 |
else: |
| 270 |
symbols[symbol] += 1
|
|
| 289 |
symbols.append((symbol, 1))
|
|
| 271 | 290 |
|
| 272 | 291 |
# Build the sorting list |
| 273 | 292 |
self.sort = [] |
| 274 | 293 |
self.sort.extend(special_setups) |
| 275 | 294 |
|
| 276 |
for symbol in symbols: |
|
| 295 |
for symbol, iatom in symbols:
|
|
| 277 | 296 |
for m,atom in enumerate(atoms): |
| 278 | 297 |
if m in special_setups: |
| 279 | 298 |
pass |
| ... | ... | |
| 284 | 303 |
for n in range(len(self.resort)): |
| 285 | 304 |
self.resort[self.sort[n]] = n |
| 286 | 305 |
self.atoms_sorted = atoms[self.sort] |
| 287 |
|
|
| 306 |
|
|
| 288 | 307 |
# Check if the necessary POTCAR files exists and |
| 289 | 308 |
# create a list of their paths. |
| 290 | 309 |
self.symbol_count = [] |
| 291 | 310 |
for m in special_setups: |
| 292 |
self.symbol_count.append([atomtypes[m],1]) |
|
| 311 |
for symbol, iatom in symbols: |
|
| 312 |
if symbol == m: |
|
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self.symbol_count.append([atomtypes[m],1]) |
|
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#self.symbol_count.append([atomtypes[m],1]) |
|
| 293 | 315 |
for m in symbols: |
| 294 |
self.symbol_count.append([m,symbols[m]]) |
|
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#print 'self.symbol_count',self.symbol_count |
|
| 316 |
for symbol, iatom in symbols: |
|
| 317 |
if symbol == m: |
|
| 318 |
self.symbol_count.append([m,iatom]) |
|
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#self.symbol_count.append([m,symbols[m]]) |
|
| 296 | 320 |
sys.stdout.flush() |
| 297 |
xc = '/' |
|
| 298 |
#print 'p[xc]',p['xc'] |
|
| 299 |
if p['xc'] == 'PW91': |
|
| 300 |
xc = '_gga/' |
|
| 301 |
elif p['xc'] == 'PBE': |
|
| 302 |
xc = '_pbe/' |
|
| 303 |
if 'VASP_PP_PATH' in os.environ: |
|
| 304 |
pppaths = os.environ['VASP_PP_PATH'].split(':')
|
|
| 305 |
else: |
|
| 306 |
pppaths = [] |
|
| 307 |
self.ppp_list = [] |
|
| 308 |
# Setting the pseudopotentials, first special setups and |
|
| 309 |
# then according to symbols |
|
| 310 |
for m in special_setups: |
|
| 311 |
name = 'potpaw'+xc.upper() + p['setups'][str(m)] + '/POTCAR' |
|
| 312 |
found = False |
|
| 313 |
for path in pppaths: |
|
| 314 |
filename = join(path, name) |
|
| 315 |
#print 'filename', filename |
|
| 316 |
if isfile(filename) or islink(filename): |
|
| 317 |
found = True |
|
| 318 |
self.ppp_list.append(filename) |
|
| 319 |
break |
|
| 320 |
elif isfile(filename + '.Z') or islink(filename + '.Z'): |
|
| 321 |
found = True |
|
| 322 |
self.ppp_list.append(filename+'.Z') |
|
| 323 |
break |
|
| 324 |
if not found: |
|
| 325 |
raise RuntimeError('No pseudopotential for %s!' % symbol)
|
|
| 326 |
#print 'symbols', symbols |
|
| 327 |
for symbol in symbols: |
|
| 328 |
try: |
|
| 329 |
name = 'potpaw'+xc.upper()+symbol + p['setups'][symbol] |
|
| 330 |
except (TypeError, KeyError): |
|
| 331 |
name = 'potpaw' + xc.upper() + symbol |
|
| 332 |
name += '/POTCAR' |
|
| 333 |
found = False |
|
| 334 |
for path in pppaths: |
|
| 335 |
filename = join(path, name) |
|
| 336 |
#print 'filename', filename |
|
| 337 |
if isfile(filename) or islink(filename): |
|
| 338 |
found = True |
|
| 339 |
self.ppp_list.append(filename) |
|
| 340 |
break |
|
| 341 |
elif isfile(filename + '.Z') or islink(filename + '.Z'): |
|
| 342 |
found = True |
|
| 343 |
self.ppp_list.append(filename+'.Z') |
|
| 344 |
break |
|
| 345 |
if not found: |
|
| 346 |
raise RuntimeError('No pseudopotential for %s!' % symbol)
|
|
| 321 |
if self.write_input: |
|
| 322 |
xc = '/' |
|
| 323 |
#print 'p[xc]',p['xc'] |
|
| 324 |
if p['xc'] == 'PW91': |
|
| 325 |
xc = '_gga/' |
|
| 326 |
elif p['xc'] == 'PBE': |
|
| 327 |
xc = '_pbe/' |
|
| 328 |
if 'VASP_PP_PATH' in os.environ: |
|
| 329 |
pppaths = os.environ['VASP_PP_PATH'].split(':')
|
|
| 330 |
else: |
|
| 331 |
pppaths = [] |
|
| 332 |
self.ppp_list = [] |
|
| 333 |
# Setting the pseudopotentials, first special setups and |
|
| 334 |
# then according to symbols |
|
| 335 |
for m in special_setups: |
|
| 336 |
name = 'potpaw'+xc.upper() + p['setups'][str(m)] + '/POTCAR' |
|
| 337 |
found = False |
|
| 338 |
for path in pppaths: |
|
| 339 |
filename = join(path, name) |
|
| 340 |
#print 'filename', filename |
|
| 341 |
if isfile(filename) or islink(filename): |
|
| 342 |
found = True |
|
| 343 |
self.ppp_list.append(filename) |
|
| 344 |
break |
|
| 345 |
elif isfile(filename + '.Z') or islink(filename + '.Z'): |
|
| 346 |
found = True |
|
| 347 |
self.ppp_list.append(filename+'.Z') |
|
| 348 |
break |
|
| 349 |
if not found: |
|
| 350 |
raise RuntimeError('No pseudopotential for %s!' % symbol)
|
|
| 351 |
#print 'symbols', symbols |
|
| 352 |
for symbol in symbols: |
|
| 353 |
try: |
|
| 354 |
name = 'potpaw'+xc.upper()+symbol + p['setups'][symbol] |
|
| 355 |
except (TypeError, KeyError): |
|
| 356 |
name = 'potpaw' + xc.upper() + symbol |
|
| 357 |
name += '/POTCAR' |
|
| 358 |
found = False |
|
| 359 |
for path in pppaths: |
|
| 360 |
filename = join(path, name) |
|
| 361 |
#print 'filename', filename |
|
| 362 |
if isfile(filename) or islink(filename): |
|
| 363 |
found = True |
|
| 364 |
self.ppp_list.append(filename) |
|
| 365 |
break |
|
| 366 |
elif isfile(filename + '.Z') or islink(filename + '.Z'): |
|
| 367 |
found = True |
|
| 368 |
self.ppp_list.append(filename+'.Z') |
|
| 369 |
break |
|
| 370 |
if not found: |
|
| 371 |
raise RuntimeError('No pseudopotential for %s!' % symbol)
|
|
| 347 | 372 |
self.converged = None |
| 348 | 373 |
self.setups_changed = None |
| 349 | 374 |
|
| ... | ... | |
| 359 | 384 |
from ase.io.vasp import write_vasp |
| 360 | 385 |
self.initialize(atoms) |
| 361 | 386 |
write_vasp('POSCAR', self.atoms_sorted, symbol_count = self.symbol_count)
|
| 362 |
if self.bool_write_input:
|
|
| 387 |
if self.write_input: |
|
| 363 | 388 |
self.write_incar(atoms) |
| 364 | 389 |
self.write_potcar() |
| 365 | 390 |
self.write_kpoints() |
Formats disponibles : Unified diff