Source code for aiida_gromacs.calculations.solvate

"""
Calculations provided by aiida_gromacs.

This calculation configures the ability to use the 'gmx solvate' executable.
"""
import os

from aiida.common import CalcInfo, CodeInfo
from aiida.engine import CalcJob
from aiida.orm import SinglefileData, Str
from aiida.plugins import DataFactory

SolvateParameters = DataFactory("gromacs.solvate")




class SolvateCalculation(CalcJob):
    """
    AiiDA calculation plugin wrapping the 'gmx solvate' executable.

    AiiDA plugin wrapper for solvating a molecular system.
    """



    @classmethod
    def define(cls, spec):
        """Define inputs and outputs of the calculation."""
        # yapf: disable
        super().define(spec)

        # Define inputs and outputs of the calculation.
        spec.input('command',
                valid_type=Str, required=False,
                help='The command used to execute the job.')

        # set default values for AiiDA options
        # TODO: something changed about withmpi in aiida-2.4.0, needs investigation.
        spec.inputs['metadata']['options']['withmpi'].default = False
        spec.inputs['metadata']['options']['resources'].default = {
            'num_machines': 1,
            'num_mpiprocs_per_machine': 1,
        }
        spec.inputs['metadata']['options']['parser_name'].default = 'gromacs.solvate'
        spec.input('metadata.options.output_filename', valid_type=str, default='solvate.out')
        spec.input('grofile', valid_type=SinglefileData, help='Input structure')
        spec.input('topfile', valid_type=SinglefileData, help='Input topology')
        spec.input('parameters', valid_type=SolvateParameters, help='Command line parameters for gmx solvate.')
        spec.input('metadata.options.output_dir', valid_type=str, default=os.getcwd(),
                help='Directory where output files will be saved when parsed.')

        spec.output('stdout', valid_type=SinglefileData, help='stdout')
        spec.output('grofile', valid_type=SinglefileData, help='Output solvated gro file.')
        spec.output('topfile', valid_type=SinglefileData, help='Output topology file.')

        spec.exit_code(300, 'ERROR_MISSING_OUTPUT_FILES', message='Calculation did not produce all expected output files.')




    def prepare_for_submission(self, folder):
        """
        Create input files.

        :param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files
            needed by the calculation.
        :return: `aiida.common.datastructures.CalcInfo` instance
        """
        codeinfo = CodeInfo()
        codeinfo.cmdline_params = self.inputs.parameters.cmdline_params(
            grofile=self.inputs.grofile.filename, topfile=self.inputs.topfile.filename
        )
        codeinfo.code_uuid = self.inputs.code.uuid
        codeinfo.stdout_name = self.metadata.options.output_filename
        codeinfo.withmpi = self.inputs.metadata.options.withmpi

        # Prepare a `CalcInfo` to be returned to the engine
        calcinfo = CalcInfo()
        calcinfo.codes_info = [codeinfo]
        calcinfo.local_copy_list = [
            (
                self.inputs.grofile.uuid,
                self.inputs.grofile.filename,
                self.inputs.grofile.filename,
            ),
            (
                self.inputs.topfile.uuid,
                self.inputs.topfile.filename,
                self.inputs.topfile.filename,
            ),
        ]
        calcinfo.retrieve_list = [
            self.metadata.options.output_filename,
            self.inputs.parameters["o"],
            self.inputs.topfile.filename,
        ]

        return calcinfo