Source code for pymatgen.cli.gaussian_analyzer

#!/usr/bin/env python
#  coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

A convenience script engine to read Gaussian output in a directory tree.

__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Shyue Ping Ong"
__email__ = ""
__date__ = "Jul 9, 2012"

import argparse
import os
import logging
import re

from pymatgen.apps.borg.hive import GaussianToComputedEntryDrone
from pymatgen.apps.borg.queen import BorgQueen
import multiprocessing
from tabulate import tabulate

save_file = "gau_data.gz"

[docs]def get_energies(rootdir, reanalyze, verbose): """ :param rootdir: :param reanalyze: :param verbose: :return: """ if verbose: FORMAT = "%(relativeCreated)d msecs : %(message)s" logging.basicConfig(level=logging.INFO, format=FORMAT) drone = GaussianToComputedEntryDrone(inc_structure=True, parameters=['filename']) ncpus = multiprocessing.cpu_count()'Detected {} cpus'.format(ncpus)) queen = BorgQueen(drone, number_of_drones=ncpus) if os.path.exists(save_file) and not reanalyze: msg = 'Using previously assimilated data from {}.'.format(save_file) + \ ' Use -f to force re-analysis.' queen.load_data(save_file) else: queen.parallel_assimilate(rootdir) msg = 'Results saved to {} for faster reloading.'.format(save_file) queen.save_data(save_file) entries = queen.get_data() entries = sorted(entries, key=lambda x: x.parameters['filename']) all_data = [(e.parameters['filename'].replace("./", ""), re.sub(r"\s+", "", e.composition.formula), "{}".format(e.parameters['charge']), "{}".format(e.parameters['spin_mult']), "{:.5f}".format(, "{:.5f}".format(e.energy_per_atom), ) for e in entries] headers = ("Directory", "Formula", "Charge", "Spin Mult.", "Energy", "E/Atom") print(tabulate(all_data, headers=headers)) print("") print(msg)
[docs]def main(): """ Main function """ desc = ''' Convenient Gaussian run analyzer which can recursively go into a directory to search results. Author: Shyue Ping Ong Version: 1.0 Last updated: Jul 6 2012''' parser = argparse.ArgumentParser(description=desc) parser.add_argument('directories', metavar='dir', default='.', type=str, nargs='*', help='directory to process') parser.add_argument('-v', '--verbose', dest="verbose", action='store_const', const=True, help='verbose mode. Provides detailed output ' + 'on progress.') parser.add_argument('-f', '--force', dest="reanalyze", action='store_const', const=True, help='force reanalysis. Typically, gaussian_analyzer' + ' will just reuse a gaussian_analyzer_data.gz if ' + 'present. This forces the analyzer to reanalyze.') args = parser.parse_args() for d in args.directories: get_energies(d, args.reanalyze, args.verbose)
if __name__ == "__main__": main()