Source code for aiida_gulp.calculations.gulp_optimize

#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2019 Chris Sewell
#
# This file is part of aiida-gulp.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms and conditions
# of version 3 of the GNU Lesser General Public License.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Lesser General Public License for more details.
import six
from aiida.plugins import DataFactory
from aiida_gulp.calculations.gulp_abstract import GulpAbstractCalculation
from aiida_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("gulp.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,
        ]