Source code for aiida_gromacs.calculations.editconf

"""
Calculations provided by aiida_gromacs.

This calculation configures the ability to use the 'gmx editconf' 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

EditconfParameters = DataFactory("gromacs.editconf")




class EditconfCalculation(CalcJob):
    """
    AiiDA calculation plugin wrapping the 'gmx editconf' executable.

    AiiDA plugin wrapper for adding a simulation box to structure file.
    """



    @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,
        }

        # Requied inputs.
        spec.inputs['metadata']['options']['parser_name'].default = 'gromacs.editconf'
        spec.input('metadata.options.output_filename', valid_type=str, default='editconf.out')
        spec.input('grofile', valid_type=SinglefileData, help='Input structure file.')
        spec.input('parameters', valid_type=EditconfParameters, help='Command line parameters for gmx editconf.')
        spec.input('metadata.options.output_dir', valid_type=str, default=os.getcwd(),
                help='Directory where output files will be saved when parsed.')

        # Optional inputs.
        spec.input('n_file', required=False, valid_type=SinglefileData, help='Index file.')
        spec.input('bf_file', required=False, valid_type=SinglefileData, help='Generic data file.')

        # Default outputs.
        spec.output('stdout', valid_type=SinglefileData, help='stdout')
        spec.output('grofile', valid_type=SinglefileData, help='Output file containing simulation box.')

        # Optional outputs.
        spec.output('mead_file', required=False, valid_type=SinglefileData, help='Coordination file for MEAD')

        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()

        # Setup data structures for files.
        input_options = ["grofile", "n_file", "bf_file"]
        output_options = ["o", "mead"] 
        cmdline_input_files = {}
        input_files = []
        output_files = []

        # Map input files to AiiDA plugin data types.
        for item in input_options:
            if item in self.inputs:
                cmdline_input_files[item] = self.inputs[item].filename
                input_files.append((
                        self.inputs[item].uuid,
                        self.inputs[item].filename,
                        self.inputs[item].filename,
                    ))
                    
        # Add output files to retrieve list.
        output_files.append(self.metadata.options.output_filename)
        for item in output_options:
            if item in self.inputs.parameters:
                output_files.append(self.inputs.parameters[item])

        # Form the commandline.
        codeinfo.cmdline_params = self.inputs.parameters.cmdline_params(cmdline_input_files)

        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 = input_files
        calcinfo.retrieve_list = output_files

        return calcinfo