Source code for aiida_mlip.calculations.md

"""Class to run md calculations."""

from aiida.common import datastructures
import aiida.common.folders
from aiida.engine import CalcJobProcessSpec
import aiida.engine.processes
from aiida.orm import Dict, SinglefileData, Str, StructureData, TrajectoryData

from aiida_mlip.calculations.base import BaseJanus




class MD(BaseJanus):  # numpydoc ignore=PR01
    """
    Calcjob implementation to run geometry MD calculations using mlips.

    Methods
    -------
    define(spec: CalcJobProcessSpec) -> None:
        Define the process specification, its inputs, outputs and exit codes.
    prepare_for_submission(folder: Folder) -> CalcInfo:
        Create the input files for the `CalcJob`.
    """

    DEFAULT_TRAJ_FILE = "aiida-traj.xyz"
    DEFAULT_STATS_FILE = "aiida-stats.dat"
    DEFAULT_SUMMARY_FILE = "md_summary.yml"



    @classmethod
    def define(cls, spec: CalcJobProcessSpec) -> None:
        """
        Define the process specification, its inputs, outputs and exit codes.

        Parameters
        ----------
        spec : `aiida.engine.CalcJobProcessSpec`
            The calculation job process spec to define.
        """
        super().define(spec)

        # Additional inputs for molecular dynamics
        spec.input(
            "ensemble",
            valid_type=Str,
            required=False,
            help="Name for thermodynamic ensemble",
        )

        spec.input(
            "md_kwargs",
            valid_type=Dict,
            required=False,
            default=lambda: Dict(
                {
                    "traj-file": cls.DEFAULT_TRAJ_FILE,
                    "stats-file": cls.DEFAULT_STATS_FILE,
                    "summary": cls.DEFAULT_SUMMARY_FILE,
                }
            ),
            help="Keywords for molecular dynamics",
        )

        spec.inputs["metadata"]["options"]["parser_name"].default = "mlip.md_parser"

        spec.output(
            "results_dict",
            valid_type=Dict,
            help="The `results_dict` output node of the successful calculation.",
        )
        spec.output("summary", valid_type=SinglefileData)
        spec.output("stats_file", valid_type=SinglefileData)
        spec.output("traj_file", valid_type=SinglefileData)
        spec.output("traj_output", valid_type=TrajectoryData)
        spec.output("final_structure", valid_type=StructureData)

        spec.default_output_node = "results_dict"




    def prepare_for_submission(
        self, folder: aiida.common.folders.Folder
    ) -> datastructures.CalcInfo:
        """
        Create the input files for the `Calcjob`.

        Parameters
        ----------
        folder : aiida.common.folders.Folder
            Folder where the calculation is run.

        Returns
        -------
        aiida.common.datastructures.CalcInfo
            An instance of `aiida.common.datastructures.CalcInfo`.
        """
        # Call the parent class method to prepare common inputs
        calcinfo = super().prepare_for_submission(folder)
        codeinfo = calcinfo.codes_info[0]

        md_dictionary = self.inputs.md_kwargs.get_dict()

        md_dictionary.setdefault("traj-file", str(self.DEFAULT_TRAJ_FILE))
        md_dictionary.setdefault("stats-file", str(self.DEFAULT_STATS_FILE))
        md_dictionary.setdefault("summary", str(self.DEFAULT_SUMMARY_FILE))

        if "ensemble" in self.inputs:
            ensemble = self.inputs.ensemble.value.lower()
        elif "config" in self.inputs and "ensemble" in self.inputs.config.as_dictionary:
            ensemble = self.inputs.config.as_dictionary["ensemble"]
        else:
            raise ValueError("'ensemble' not provided.")

        # md is overwriting the placeholder "calculation" from the base.py file
        codeinfo.cmdline_params[0] = "md"

        codeinfo.cmdline_params += ["--ensemble", ensemble]

        for flag, value in md_dictionary.items():
            # Add boolean flags without value if True
            if isinstance(value, bool) and value:
                codeinfo.cmdline_params.append(f"--{flag}")
            else:
                codeinfo.cmdline_params += [f"--{flag}", value]

        calcinfo.retrieve_list.append(md_dictionary["traj-file"])
        calcinfo.retrieve_list.append(md_dictionary["stats-file"])
        calcinfo.retrieve_list.append(md_dictionary["summary"])

        return calcinfo