Source code for pyiron_contrib.atomistics.mlip.mlipselect

# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.

import os
from pyiron_contrib.atomistics.mlip.mlip import Mlip, read_cgfs

__author__ = "Jan Janssen"
__copyright__ = "Copyright 2020, Max-Planck-Institut für Eisenforschung GmbH - " \
                "Computational Materials Design (CM) Department"
__version__ = "1.0"
__maintainer__ = "Jan Janssen"
__email__ = "janssen@mpie.de"
__status__ = "development"
__date__ = "Sep 1, 2018"


class MlipSelect(Mlip):
    def __init__(self, project, job_name):
        super(MlipSelect, self).__init__(project, job_name)
        self.__version__ = None
        self.__name__ = "MlipSelect"
        self._executable_activate()
        del self.input['min_dist']
        del self.input['max_dist']
        del self.input['iteration']
        del self.input['energy-weight']
        del self.input['force-weight']
        del self.input['stress-weight']
        self._command_line._delete_line(0)
        self._command_line._delete_line(0)

    def validate_ready_to_run(self):
        if len(self.restart_file_list) == 0:
            raise ValueError()

    def write_input(self):
        species_count = self._write_test_set(file_name='testing.cfg', cwd=self.working_directory)
        self._copy_potential(species_count, file_name='start.mtp', cwd=self.working_directory)
        self._command_line[0] = self._command_line[0].replace('Trained.mtp_', 'start.mtp')
        self._command_line.write_file(file_name='mlip.sh', cwd=self.working_directory)

    def collect_output(self):
        file_name = os.path.join(self.working_directory, 'diff.cfg')
        cell, positions, forces, stress, energy, indicies, grades, jobids, timesteps = read_cgfs(file_name=file_name)
        with self.project_hdf5.open('output') as hdf5_output:
            hdf5_output['forces'] = forces
            hdf5_output['energy_tot'] = energy
            hdf5_output['pressures'] = stress
            hdf5_output['cells'] = cell
            hdf5_output['positions'] = positions
            hdf5_output['indicies'] = indicies