def write(self, filename=None, indices=None, *args, **kwargs):
"""Write parsed attributes to a file.
Possible extensions:
.cjson or .json - output a chemical JSON file
.cml - output a chemical markup language (CML) file
.xyz - output a Cartesian XYZ file of the last coordinates available
"""
from cclib.io import ccwrite
outputstr = ccwrite(self, outputdest=filename, indices=indices,
*args, **kwargs)
return outputstr
def write(self, filename=None, indices=None, *args, **kwargs):
"""Write parsed attributes to a file.
Possible extensions:
.cjson or .json - output a chemical JSON file
.cml - output a chemical markup language (CML) file
.xyz - output a Cartesian XYZ file of the last coordinates available
"""
from cclib.io import ccwrite
outputstr = ccwrite(self, outputdest=filename, indices=indices,
*args, **kwargs)
return outputstr
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
'outputtype',
choices=('json', 'cjson', 'cml', 'xyz', 'molden', 'wfx'),
help='the output format to write (json/cjson are identical)')
parser.add_argument(
'compchemlogfile',
nargs='+',
help=
'one or more computational chemistry output files to parse and convert'
)
parser.add_argument(
'-v',
'--verbose',
action='store_true',
help='more verbose parsing output (only errors by default)')
parser.add_argument('-g',
'--ghost',
type=str,
default=None,
help='Symbol to use for ghost atoms')
parser.add_argument(
'-t',
'--terse',
action='store_true',
help=
'CJSON by default is not indented for readability, saves space (indented for readability\'s sake)'
)
parser.add_argument(
'-u',
'--future',
action='store_true',
help='use experimental features (currently optdone_as_list)')
parser.add_argument(
'-i',
'--index',
type=int,
default=None,
help='optional zero-based index for which structure to extract')
args = parser.parse_args()
outputtype = args.outputtype
filenames = args.compchemlogfile
verbose = args.verbose
terse = args.terse
future = args.future
index = args.index
ghost = args.ghost
for filename in filenames:
# We might want to use this option in the near future.
ccopen_kwargs = dict()
if future:
ccopen_kwargs['future'] = True
print("Attempting to parse {}".format(filename))
log = ccopen(filename, **ccopen_kwargs)
if not log:
print(
"Cannot figure out what type of computational chemistry output file '{}' is."
.format(filename))
print(
"Report this to the cclib development team if you think this is an error."
)
sys.exit()
if verbose:
log.logger.setLevel(logging.INFO)
else:
log.logger.setLevel(logging.ERROR)
data = log.parse()
print("cclib can parse the following attributes from {}:".format(
filename))
hasattrs = [
' {}'.format(attr) for attr in ccData._attrlist
if hasattr(data, attr)
]
print('\n'.join(hasattrs))
# Write out to disk.
outputdest = '.'.join(
[os.path.splitext(os.path.basename(filename))[0], outputtype])
ccwrite_kwargs = dict()
if future:
ccwrite_kwargs['future'] = True
if ghost:
ccwrite_kwargs['ghost'] = ghost
# For XYZ files, write the last geometry unless otherwise
# specified.
if not index:
index = -1
ccwrite_kwargs['jobfilename'] = filename
# The argument terse presently is only applicable to
# CJSON/JSON formats
ccwrite(data,
outputtype,
outputdest,
indices=index,
terse=terse,
**ccwrite_kwargs)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('outputtype',
choices=('json', 'cjson', 'cml', 'xyz', 'molden', 'wfx'),
help='the output format to write (json/cjson are identical)')
parser.add_argument('compchemlogfile',
nargs='+',
help='one or more computational chemistry output files to parse and convert')
parser.add_argument('-v', '--verbose',
action='store_true',
help='more verbose parsing output (only errors by default)')
parser.add_argument('-t', '--terse',
action='store_true',
help='CJSON by default is not indented for readability, saves space (indented for readability\'s sake)')
parser.add_argument('-u', '--future',
action='store_true',
help='use experimental features (currently optdone_as_list)')
parser.add_argument('-i', '--index',
type=int,
default=None,
help='optional zero-based index for which structure to extract')
args = parser.parse_args()
outputtype = args.outputtype
filenames = args.compchemlogfile
verbose = args.verbose
terse = args.terse
future = args.future
index = args.index
for filename in filenames:
# We might want to use this option in the near future.
ccopen_kwargs = dict()
if future:
ccopen_kwargs['future'] = True
print("Attempting to parse {}".format(filename))
log = ccopen(filename, **ccopen_kwargs)
if log == None:
print("Cannot figure out what type of computational chemistry output file '{}' is.".format(filename))
print("Report this to the cclib development team if you think this is an error.")
sys.exit()
if verbose:
log.logger.setLevel(logging.INFO)
else:
log.logger.setLevel(logging.ERROR)
data = log.parse()
print("cclib can parse the following attributes from {}:".format(filename))
hasattrs = [' {}'.format(attr) for attr in ccData._attrlist if hasattr(data, attr)]
print('\n'.join(hasattrs))
# Write out to disk.
outputdest = '.'.join([os.path.splitext(os.path.basename(filename))[0], outputtype])
ccwrite_kwargs = dict()
if future:
ccwrite_kwargs['future'] = True
# For XYZ files, write the last geometry unless otherwise
# specified.
if not index:
index = -1
ccwrite_kwargs['jobfilename'] = filename
# The argument terse presently is only applicable to
# CJSON/JSON formats
ccwrite(data, outputtype, outputdest, terse=terse, indices=index,
**ccwrite_kwargs)
help="""Extract all possible geometries into a trajectory-like file?"""
)
parser.add_argument('--suffix')
args = parser.parse_args()
return args
if __name__ == '__main__':
args = getargs()
for outputfilename in args.outputfilename:
data = ccread(outputfilename, loglevel=logging.ERROR)
converged_geoms = np.where(data.optstatus == 4)[0]
stub = os.path.splitext(outputfilename)[0]
if args.suffix:
xyzfilename_prefix = '{}.{}'.format([stub, args.suffix])
else:
xyzfilename_prefix = stub
for step, index in enumerate(converged_geoms):
xyzfilename = '{}_{}.xyz'.format(xyzfilename_prefix, step + 1)
ccwrite(data,
outputdest=xyzfilename,
indices=index,
outputtype='xyz')