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')