Source code for aiida_crystal17.gulp.calculations.gulp_optimize

import six
from aiida.plugins import DataFactory
from aiida_crystal17.gulp.calculations.gulp_abstract import GulpAbstractCalculation
from aiida_crystal17.gulp.parsers.raw.write_input import InputCreationOpt


class GulpOptCalculation(GulpAbstractCalculation):
    """
    AiiDA calculation plugin to run the gulp executable,
    for single point energy calculations
    """

    @classmethod
    def define(cls, spec):

        super(GulpOptCalculation, cls).define(spec)

        spec.input('metadata.options.parser_name',
                   valid_type=six.string_types, default='gulp.optimize')

        spec.input('metadata.options.out_cif_file_name',
                   valid_type=six.string_types, default='output.cif',
                   help="name of the cif file to output with final geometry")
        spec.input('metadata.options.use_input_kinds',
                   valid_type=bool, default=True,
                   help=(
                       "if True, use the atoms kinds from the input structure, "
                       "when creating the output structure"))
        # spec.input('metadata.options.out_str_file_name',
        #            valid_type=six.string_types, default='output.str',
        #            help="name of the str file (i.e. a CRYSTAL98 .gui file)")

        spec.input(
            'symmetry', valid_type=DataFactory('crystal17.symmetry'),
            required=False,
            help=('parameters to create the symmetry section of the '
                  '.gin file content (for constrained optimisation).'))

        spec.exit_code(
            250, 'ERROR_CIF_FILE_MISSING',
            message='the output cif file was not found')
        spec.exit_code(
            251, 'ERROR_MISSING_INPUT_STRUCTURE',
            message='an input structure is required to create the output structure of an optimisation')
        spec.exit_code(
            252, 'ERROR_CIF_INCONSISTENT',
            message='the output cif file was not consistent with the input structure')
        spec.exit_code(
            253, 'ERROR_STRUCTURE_PARSING',
            message='The final structure coordinates were not parsed from the output file')

        spec.output(cls.link_output_structure,
                    valid_type=DataFactory('structure'),
                    required=True,
                    help='the optimized structure output from the calculation')

    def create_input(self,
                     structure, potential,
                     parameters=None, symmetry=None):
        input_creation = InputCreationOpt(
            outputs={"cif": self.metadata.options.out_cif_file_name}
        )
        # TODO assert potential species contains at least one from structure
        input_creation.create_content(structure, potential.get_input_lines(), parameters, symmetry)
        return input_creation.get_content()

    def get_retrieve_list(self):
        """ should return the files to be retrieved """
        return [
            self.metadata.options.output_main_file_name,
            self.metadata.options.output_stderr_file_name,
            self.metadata.options.out_cif_file_name
        ]