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.
"""


import argparse
import logging
import multiprocessing
import os
import re

from tabulate import tabulate

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

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() logging.info("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(e.energy), "{:.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, instead of reusing gaussian_analyzer_data.gz.", ) args = parser.parse_args() for d in args.directories: get_energies(d, args.reanalyze, args.verbose)
if __name__ == "__main__": main()