Révision 50
| database/import_vasp_calc (revision 50) | ||
|---|---|---|
| 13 | 13 |
import multiprocessing |
| 14 | 14 |
import traceback |
| 15 | 15 |
|
| 16 |
xc_dict = {'1':'LDA(HL)',
|
|
| 17 |
'2':'LDA(CA/PZ)', |
|
| 18 |
'3':'LDA(WI)', |
|
| 19 |
'4':'GGA(PB)', |
|
| 20 |
'5':'GGA(PW86)', |
|
| 21 |
'6':'LM', |
|
| 22 |
'7':'PW91', |
|
| 23 |
'8':'PBE', |
|
| 24 |
'9':'RPBE', |
|
| 25 |
'10':'VWN', |
|
| 26 |
'11':'B3LYP(VWN3 correction)', |
|
| 27 |
'12':'B3LYP(VWN5 correction)', |
|
| 28 |
'13':'AM05', |
|
| 29 |
'14':'PBEsol', |
|
| 30 |
'17':'BEEF', |
|
| 31 |
'100':'CO'} |
|
| 16 | 32 |
def error(msg, *args): |
| 17 | 33 |
return multiprocessing.get_logger().error(msg, *args) |
| 18 | 34 |
|
| ... | ... | |
| 39 | 55 |
#log = open('scan.log','w')
|
| 40 | 56 |
_all = os.walk(os.path.abspath(path)) |
| 41 | 57 |
calculator=None |
| 42 |
xc_dict = {'8': 'PBE', '91': 'PW91', 'CA': 'LDA'}
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|
| 43 | 58 |
read_all_dir = 0 |
| 44 | 59 |
filenames = [] |
| 45 | 60 |
if os.path.exists(db): |
| ... | ... | |
| 90 | 105 |
t2 = time() |
| 91 | 106 |
print 'timing: ', t2-t1 |
| 92 | 107 |
if use_poscar: |
| 93 |
constraints = read(path+'/POSCAR').constraints |
|
| 108 |
try: |
|
| 109 |
constraints = read(path+'/POSCAR').constraints |
|
| 110 |
except IOError: |
|
| 111 |
try: |
|
| 112 |
constraints = read(path+'/POSCAR.gz').constraints |
|
| 113 |
except IOError: |
|
| 114 |
try: |
|
| 115 |
constraints = read(path+'/POSCAR.bz2').constraints |
|
| 116 |
except IOError: |
|
| 117 |
constraints = None |
|
| 94 | 118 |
Atoms.set_constraint(constraints) |
| 95 | 119 |
print 'get constraint from poscar', filetoread |
| 96 |
else:
|
|
| 120 |
if not constraints:
|
|
| 97 | 121 |
Atoms0 = read(filetoread, index=0) |
| 98 | 122 |
pos0 = Atoms0.positions |
| 99 | 123 |
pos = Atoms.positions |
| ... | ... | |
| 138 | 162 |
pot = 'PAW' |
| 139 | 163 |
else: |
| 140 | 164 |
pot = line[1] |
| 165 |
elif line.startswith(' exchange correlation table for LEXCH ='):
|
|
| 166 |
xc_flag = line.split()[-1].upper() |
|
| 167 |
if xc_flag not in xc_dict.keys(): |
|
| 168 |
raise ValueError('Unknown xc-functional flag found in POTCAR,'
|
|
| 169 |
' LEXCH=%s' % xc_flag) |
|
| 170 |
xc = xc_dict[xc_flag] |
|
| 141 | 171 |
elif line.startswith(' Dimension of arrays'):
|
| 142 | 172 |
#if line.startswith(' Dimension of arrays'):
|
| 143 | 173 |
read_para = 1 |
| 144 | 174 |
elif read_para: |
| 145 |
if 'LEXCH' in line: |
|
| 146 |
xc_flag = line.split()[2].upper() |
|
| 147 |
if xc_flag not in xc_dict.keys(): |
|
| 148 |
raise ValueError('Unknown xc-functional flag found in POTCAR,'
|
|
| 149 |
' LEXCH=%s' % xc_flag) |
|
| 150 |
xc = xc_dict[xc_flag] |
|
| 151 |
elif 'NKPTS' in line: |
|
| 152 |
#if 'NKPTS' in line:
|
|
| 175 |
#if 'LEXCH' in line:
|
|
| 176 |
# xc_flag = line.split()[2].upper()
|
|
| 177 |
# if xc_flag not in xc_dict.keys():
|
|
| 178 |
# raise ValueError('Unknown xc-functional flag found in POTCAR,'
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|
| 179 |
# ' LEXCH=%s' % xc_flag)
|
|
| 180 |
# xc = xc_dict[xc_flag]
|
|
| 181 |
#elif 'NKPTS' in line:
|
|
| 182 |
if 'NKPTS' in line: |
|
| 153 | 183 |
nkpts = int(line.split()[3]) |
| 154 | 184 |
elif 'ENCUT' in line: |
| 155 | 185 |
encut = float(line.split()[2]) |
| ... | ... | |
| 194 | 224 |
#del con[id] |
| 195 | 225 |
record = con.select(filename=filetoread) |
| 196 | 226 |
if update_method: |
| 197 |
id = con.reserve(filename=filetoread) |
|
| 198 |
con.write(Atoms,functional = xc,path=path,code='VASP',filename=filetoread, version=version, potential=pot, encut=encut, enaug=enaug, lsol=lsol, ldipol=ldipol, nkpts=nkpts, constraint=False) |
|
| 199 |
del con[id] |
|
| 200 |
record = con.select(filename=filetoread) |
|
| 201 |
id = next(record)['id'] |
|
| 202 |
con.update(id,user=user) |
|
| 203 |
con.update(id,calculator='vasp') |
|
| 227 |
try: |
|
| 228 |
id = con.reserve(filename=filetoread) |
|
| 229 |
con.write(Atoms,functional = xc,path=path,code='VASP',filename=filetoread, version=version, potential=pot, encut=encut, enaug=enaug, lsol=lsol, ldipol=ldipol, nkpts=nkpts, constraint=False) |
|
| 230 |
del con[id] |
|
| 231 |
record = con.select(filename=filetoread) |
|
| 232 |
id = next(record)['id'] |
|
| 233 |
con.update(id,user=user) |
|
| 234 |
con.update(id,calculator='vasp') |
|
| 235 |
except UnboundLocalError: |
|
| 236 |
print 'err:',filetoread |
|
| 237 |
return |
|
| 204 | 238 |
|
| 205 | 239 |
except (IndexError, ValueError): |
| 206 | 240 |
_log = 'failed: '+filetoread |
| ... | ... | |
| 251 | 285 |
if args.j is None: |
| 252 | 286 |
project = 'gaussian' |
| 253 | 287 |
else: |
| 254 |
project = int(args.j)
|
|
| 288 |
project = args.j
|
|
| 255 | 289 |
|
| 256 | 290 |
#import_vasp_calculations('/data/users/tjiang/rkerber', con)
|
| 257 | 291 |
#import_vasp_calculations('.', con, include_dir=['<opt_dir>'], exclude_dir=['<to_exclude_dir1>', '<to_exclude_dir2>'])
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Formats disponibles : Unified diff