Chimie Théorique » scripts_chimie4psmn » DockOnSurf

"""Functions to deal with DockOnSurf input files.

str2lst: Converts a string of integers, and groups of them, to a list of lists.

check_expect_val: Checks whether the value of an option has an adequate value.

get_run_type: Gets 'run_type' value and checks that its value is acceptable.

get_code: Gets 'code' value and checks that its value is acceptable.

get_batch_q_sys: Gets 'batch_q_sys' value and checks that its value is

get_relaunch_err: Gets 'relaunch_err' value and checks that its value is

get_max_jobs: Gets 'max_jobs' value and checks that its value is acceptable.

get_special_atoms: Gets 'special_atoms' value and checks that its value is

get_isol_inp_file: Gets 'isol_inp_file' value and checks that its value is

get_num_conformers: Gets 'num_conformers' value and checks that its value is

get_pre_opt: Gets 'pre_opt' value and checks that its value is acceptable.

get_screen_inp_file: Gets 'screen_inp_file' value and checks that its value is

get_sites: Gets 'sites' value and checks that its value is acceptable.

get_pts_per_angle: Gets 'pts_per_angle' value and checks that its value is

get_coll_thrsld: Gets 'coll_thrsld' value and checks that its value is

get_refine_inp_file: Gets 'refine_inp_file' value and checks that its value is

get_energy_cutoff: Gets 'energy_cutoff' value and checks that its value is

"""

import os.path

import logging

dos_inp = ConfigParser(inline_comment_prefixes='#',

                       empty_lines_in_values=False)

new_answers = {'n': False, 'none': False, 'nay': False,

               'y': True, 'sí': True, 'aye': True, 'sure': True}

for answer, val in new_answers.items():

turn_true_answers = [answer for answer in dos_inp.BOOLEAN_STATES

                     if dos_inp.BOOLEAN_STATES[answer]]

no_sect_err = "Section '%s' not found on input file"

no_opt_err = "Option '%s' not found on section '%s'"

num_error = "'%s' value must be a %s"

def str2lst(cmplx_str, func=int):  # TODO: enable deeper level of nested lists

    # TODO Treat all-enclosing parenthesis as a list instead of list of lists.

    Keyword arguments:

    @param cmplx_str: str, string of integers (or floats) and groups of them

    return True

    if code == 'cp2k':

        from pycp2k import CP2K

        if not isinstance(inp_files, str):

                               "also enabled via the 'potcar_dir' keyword. The "

                               "POTCAR specified as input_file will be used "

                               "instead of the auto-generated one.")

        if not isinstance(inp_files, list) and all(isinstance(inp_file, str)

                                                   for inp_file in inp_files):

            err_msg = "'inp_files' should be a list of file names/paths"

def get_relaunch_err():

    relaunch_err_vals = ['geo_not_conv']

    relaunch_err = dos_inp.get('Global', 'relaunch_err',

                               fallback="False")

# Read input parameters

def read_input(in_file):

    from modules.formats import adapt_format

    err_msg = False

    try:

        dos_inp.read(in_file)

            logger.error(no_opt_err % (opt, 'Global'))

            raise NoOptionError(opt, 'Global')

    isolated, screening, refinement = get_run_type()

    inp_vars['isolated'] = isolated

    inp_vars['screening'] = screening

            logger.error(no_sect_err % 'Isolated')

            raise NoSectionError('Isolated')

        # Mandatory options

        iso_mand_opts = ['isol_inp_file', 'molec_file']

        for opt in iso_mand_opts:

            if not dos_inp.has_option('Isolated', opt):

            raise NoSectionError('Screening')

        # Mandatory options:

        # Checks whether the mandatory options are present.

        screen_mand_opts = ['screen_inp_file', 'surf_file', 'sites',

                            'molec_ctrs']

        for opt in screen_mand_opts:

        inp_vars['molec_ctrs'] = get_molec_ctrs()

        # Checks for PBC

        atms = adapt_format('ase', inp_vars['surf_file'],

                            inp_vars['special_atoms'])

        if inp_vars['code'] == 'vasp' and np.linalg.det(atms.cell) == 0.0 \