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#!/usr/bin/env python3
#***********************************************************************
# This file is part of OpenMolcas. *
# *
# OpenMolcas is free software; you can redistribute it and/or modify *
# it under the terms of the GNU Lesser General Public License, v. 2.1. *
# OpenMolcas is distributed in the hope that it will be useful, but it *
# is provided "as is" and without any express or implied warranties. *
# For more details see the full text of the license in the file *
# LICENSE or in <http://www.gnu.org/licenses/>. *
# *
# Copyright (C) 2019,2020, Oskar Weser *
#***********************************************************************
"""Script to automatically generate grid files from Orbfiles.
"""
import sys
import os
from os import remove
from os.path import join, basename, splitext, relpath
from pathlib import Path
import subprocess
from subprocess import run
import click
MIN_PYTHON = (3, 6)
if sys.version_info < MIN_PYTHON:
raise RuntimeError('F strings and ordered kwargs required. '
'This requires at least python 3.6.')
def create_module_input(module_name, **kwargs):
indentstep = 2
indentation = indentstep * ' '
out = f'&{module_name.upper()}\n'
for keyword, value in kwargs.items():
out += f'{1 * indentation}{keyword}\n'
if value:
out += f'{2 * indentation}{value}\n'
out += 'End of Input\n'
return out
def emil_cmd(cmd, *args):
return f'> {cmd} ' + ' '.join(args) + '\n'
def get_currdir_path(path):
return join('$CurrDir', relpath(path, os.getcwd()))
def create_input(coord, basis, inporb, density='sparse', group=None,
select=None, total=False):
inp = create_module_input(
'GATEWAY',
coord=get_currdir_path(coord),
basis=basis, group='full' if group is None else group)
inp += emil_cmd('COPY', get_currdir_path(inporb), 'INPORB')
gridit = {'NOLUSCUS': '', 'ASCII': '', density: ''}
if select:
gridit['select'] = select
if total:
gridit['total'] = ''
inp += create_module_input('GRIDIT', **gridit)
return inp
def start_calc(input_str, inp_path='make_grid.inp', molcas_exe='pymolcas'):
with open(inp_path, 'w') as f:
f.write(input_str)
run([molcas_exe, '-f', basename(inp_path)], stdout=subprocess.PIPE,
check=True)
def get_project_name(inporb):
return splitext(basename(inporb))[0]
def cleanup(project):
remove(f'{project}.inp')
remove(f'{project}.log')
remove(f'{project}.status')
remove(f'{project}.err')
remove('xmldump')
@click.command(context_settings={'help_option_names': ['-h', '--help']})
@click.option('--coord', '-c', required=True, type=str,
help='Filepath to xyz-file.')
@click.option('--basis', '-b', required=True, type=str,
help='Basisset to use in Molcas nomenclature.')
@click.option('--inporb', '-i', required=True, type=str,
help='Filepath to Molcas orbital file.')
@click.option('--density', '-d', default='sparse', type=str, show_default=True,
help='Gridit keyword. One of {sparse, normal, dense}.')
@click.option('--group', '-g', default='full', type=str, show_default=True,
help='Symmetry group in Molcas nomenclature.')
@click.option('--select', '-s', default=None, type=str, show_default=True,
help=('Gridit keyword to select certain orbitals. '
'The default depends on the Molcas implementation. '
'Usually the active space is used.'))
@click.option('--total/--no-total', '-t',default=False,
help='Total density computed from contributions of all orbitals.')
@click.option('--molcas_exe', '-m', default='pymolcas', type=str,
show_default=True,
help='Filepath of the Molcas driver script.')
@click.option('--clean/--no-clean', default=True,
help='Clean temporary files after calculation.')
def main(coord, basis, inporb, density, group, select, total, molcas_exe, clean):
project = 'make_grid'
start_calc(
create_input(coord, basis, inporb, density, group, select, total),
f'{project}.inp', molcas_exe)
if clean:
cleanup(project)
Path('make_grid.grid').rename(Path(inporb).stem + '.grid')
if __name__ == '__main__':
main()
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