Révision 46
| database/import_gaussian_calc (revision 46) | ||
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| 2 | 2 |
# $Id$ |
| 3 | 3 |
import os, sys, argparse |
| 4 | 4 |
from ase import Atoms |
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from ase.io import read
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from ase.io.gaussian import read_gaussian_out
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| 6 | 6 |
from ase.db import connect |
| 7 | 7 |
from ase.calculators.gaussian import Gaussian |
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from ase.calculators.emt import EMT |
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| 8 | 9 |
from ase.constraints import FixAtoms |
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from numpy.linalg import norm |
| 10 | 11 |
from bz2 import BZ2File |
| ... | ... | |
| 35 | 36 |
# It was fine, give a normal answer |
| 36 | 37 |
return result |
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|
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def import_gaussian_calculations(path,db,include_dir=[],exclude_dir=[],use_input=False,creator=os.environ['USER'], nproc=8):
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def import_gaussian_calculations(path,db,include_dir=[],exclude_dir=[],use_input=False,project='gaussian',user=os.environ['USER'], nproc=8):
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| 39 | 40 |
#log = open('scan.log','w')
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| 40 | 41 |
_all = os.walk(os.path.abspath(path)) |
| 41 | 42 |
calculator=None |
| ... | ... | |
| 44 | 45 |
filenames = [] |
| 45 | 46 |
if os.path.exists(db): |
| 46 | 47 |
con = connect(db) |
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for row in con.select(code='GAUSSIAN'):
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for row in con.select(project='test'):
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filenames.append(row.filename) |
| 49 | 50 |
else: |
| 50 | 51 |
con = connect(db) |
| ... | ... | |
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condition1 = (read_all_dir or a[0].split('/')[-1] in include_dir)
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| 58 | 59 |
#condition2 = not files[0].split('/')[-1] in exclude_dir
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| 59 | 60 |
condition3 = [ i for i, x in enumerate(exclude_dir) if x in a[0] ] |
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_gass_out = [i for i in range(len(a[2])) if ('.log' in a[2][i] and a[2][i][-4:]=='.log')]
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_gass_out = [i for i in range(len(a[2])) if ('.log' in a[2][i])]
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if condition1 and not condition3: |
| 62 | 63 |
for f in _gass_out: |
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filetoread = a[2][f] |
|
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path = a[0] |
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filetoread = path +'/'+ a[2][f] |
|
| 65 | 66 |
if not filetoread in filenames: |
| 66 | 67 |
all_files.append(filetoread) |
| 67 | 68 |
paths.append(path) |
| ... | ... | |
| 69 | 70 |
multiprocessing.log_to_stderr() |
| 70 | 71 |
print 'using '+str(nproc)+' threads' |
| 71 | 72 |
pool = multiprocessing.Pool(nproc) |
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results = [] |
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for filetoread,path in zip(all_files, paths): |
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#result = pool.apply_async(LogExceptions(mp_worker), args=(con,files,use_input,filenames,xc_dict), callback=log_result) |
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pool.apply_async(LogExceptions(mp_worker), args=(con,filetoread,path,use_input,filenames,xc_dict), callback=log_result) |
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#def callback(result, func=LogExceptions(mp_worker)): |
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# results[func] = result |
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result = pool.apply_async(LogExceptions(mp_worker), args=(con,files,use_input,filenames,xc_dict), callback=log_result) |
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pool.close() |
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pool.join() |
| 78 | 79 |
t3 = time() |
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con = connect(db) |
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print 'total time used: ', t3-t2, ' seconds' |
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|
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def log_result(log): |
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logfile = open('scan.log','a')
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print >> logfile, log |
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return log |
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def mp_worker(con, filetoread, path, use_input,filenames,xc_dict):
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def mp_worker(con, filetoread, path, use_input,filenames, user, project):
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try: |
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t1 = time() |
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filetoread = path +'/'+ filetoread |
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Atoms = read(filetoread) |
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Atoms, data = read_gaussian_out(filetoread,quantity='all') |
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t2 = time() |
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print 'timing: ', t2-t1 |
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if use_input: |
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pass |
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#constraints = read(path+'/input').constraints |
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#Atoms.set_constraint(constraints) |
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#print 'get constraint from input', filetoread |
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else: |
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Atoms0 = read(filetoread, index=0) |
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pos0 = Atoms0.positions |
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pos = Atoms.positions |
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diff = pos - pos0 |
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disp = norm(diff, axis=1) |
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if disp.sum() > 0: |
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print 'find constraint from outcar' |
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mask = [_disp == 0 for _disp in disp] |
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constraints = FixAtoms(mask=mask) |
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Atoms.set_constraint(constraints) |
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else: |
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print 'no constraint' |
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constraints = None |
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#read version number, XC, ENCUT etc. |
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if filetoread[-4:] == '.bz2': |
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fobj = BZ2File(filetoread) |
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elif filetoread[-3:] == '.gz': |
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fobj = GzipFile(filetoread) |
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else: |
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fobj = open(filetoread) |
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with fobj as outcar: |
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version = outcar.readline() |
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line = outcar.readline() |
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read_para = 0 |
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lsol = False |
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ldipol = False |
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while line != '': |
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if line.startswith(' INCAR:'):
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line = outcar.readline().split() |
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if line[1] == 'PAW_PBE': |
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pot = 'PAW' |
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else: |
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pot = line[1] |
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elif line.startswith(' Dimension of arrays'):
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#if line.startswith(' Dimension of arrays'):
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read_para = 1 |
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elif read_para: |
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if 'LEXCH' in line: |
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xc_flag = line.split()[2].upper() |
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if xc_flag not in xc_dict.keys(): |
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raise ValueError('Unknown xc-functional flag found in POTCAR,'
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' LEXCH=%s' % xc_flag) |
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xc = xc_dict[xc_flag] |
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elif 'NKPTS' in line: |
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#if 'NKPTS' in line: |
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nkpts = int(line.split()[3]) |
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elif 'ENCUT' in line: |
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encut = float(line.split()[2]) |
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elif 'ENAUG' in line: |
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enaug = float(line.split()[2]) |
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elif 'NBANDS' in line: |
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nbands = int(line.split()[-1]) |
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elif 'EDIFFG' in line: |
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f_limit = -float(line.split()[2]) |
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elif 'LSOL' in line: |
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if line.split()[2] == 'T': |
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lsol = True |
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elif 'LDIPOL' in line: |
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if line.split()[2] == 'T': |
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ldipol = True |
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elif '-'*104 in line: |
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break |
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line = outcar.readline() |
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if constraints is not None: |
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fmax = ((Atoms.get_forces()) ** 2).sum(1).max()**0.5 |
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if fmax < f_limit: |
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#print >> log, 'updating the database with minimized calculation from file: ', fmax, files[2][f] |
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_log = 'archived_a: '+filetoread+' '+str(fmax) |
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#if use_input: |
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#print os.getenv('USER')
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id = con.reserve(filename=filetoread) |
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con.write(Atoms,functional = xc,path=path,code='GAUSSIAN',filename=filetoread, version=version, potential=pot, encut=encut, enaug=enaug, lsol=lsol, ldipol=ldipol, nkpts=nkpts, constraint=True) |
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del con[id] |
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else: |
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#print >> log, 'not updating the database as fmax is too big for file: ', fmax, files[2][f] |
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_log = 'skipped: '+filetoread+' '+str(fmax) |
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else: |
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#print >> log, 'updating the database with calculation', files[2][f] |
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_log = 'archived_b: '+filetoread |
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id = con.reserve(filename=filetoread) |
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con.write(Atoms,functional = xc,creator=creator,path=path,code='GAUSSIAN',filename=filetoread, version=version, potential=pot, encut=encut, enaug=enaug, lsol=lsol, ldipol=ldipol, nkpts=nkpts, constraint=False) |
|
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del con[id] |
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_log = 'archived_a: '+filetoread |
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id = con.reserve(filename=filetoread) |
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con.write(Atoms,functional = data['Method'],charge=data['Charge'],basis_set=data['Basis_set'],path=path,filename=filetoread, version=data['Version'],project='test') |
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del con[id] |
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record = con.select(filename=filetoread) |
|
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#================================== |
|
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#This part will only exist temporarily, it is for importing other people's calculation |
|
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#For update the user and calculator keys, tjiang's hacked copy of ase is needed, |
|
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#as these two are reserved keys that are not allowed to be updated manually |
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id = next(record)['id'] |
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con.update(id,user='edumont') |
|
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#================================== |
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con.update(id,calculator='gaussian') |
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print _log |
|
| 181 | 109 |
except (IndexError, ValueError): |
| 182 | 110 |
_log = 'failed: '+filetoread |
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print _log |
|
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#_log.flush() |
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print _log
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##_log.flush()
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| 185 | 113 |
return |
| 186 | 114 |
|
| 187 | 115 |
if __name__ == '__main__': |
| ... | ... | |
| 192 | 120 |
parser.add_argument("-e", "--exclude_dir",help="Directory to be excluded in the scanning")
|
| 193 | 121 |
parser.add_argument("-d", help="Name of the database file to store the scanned calculations")
|
| 194 | 122 |
parser.add_argument("-n", help="Number of processers")
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parser.add_argument("-j", help="Project name")
|
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| 195 | 124 |
args = parser.parse_args() |
| 196 | 125 |
if args.path is None: |
| 197 | 126 |
path = '.' |
| ... | ... | |
| 217 | 146 |
nproc = 8 |
| 218 | 147 |
else: |
| 219 | 148 |
nproc = int(args.n) |
| 149 |
if args.j is None: |
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project = 'gaussian' |
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else: |
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project = int(args.j) |
|
| 220 | 153 |
|
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import_gaussian_calculations(path, db, use_input=use_input, include_dir=include_dir, exclude_dir=exclude_dir, nproc=nproc) |
|
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import_gaussian_calculations(path, db, use_input=use_input, include_dir=include_dir, exclude_dir=exclude_dir, project=project, nproc=nproc) |
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Formats disponibles : Unified diff