Source code for pyiron_atomistics.atomistics.master.sqsmaster

# 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 numpy as np
from pyiron_base import JobGenerator

from pyiron_atomistics.atomistics.master.parallel import AtomisticParallelMaster

__author__ = "Jan Janssen"
__copyright__ = (
    "Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
    "Computational Materials Design (CM) Department"
)
__version__ = "0.0.1"
__maintainer__ = "Jan Janssen"
__email__ = "janssen@mpie.de"
__status__ = "development"
__date__ = "Oct 29, 2020"



[docs]
class SQSMaster(AtomisticParallelMaster):
    """
    Master job to compute SQS structures for a list of concentrations.

    The input keys "species_one", "species_two" and "fraction_lst" are combined into dictionaries that are then passed
    to the input "mole_fractions" as defined on :class:`.SQSJob` according to the pseudo code

    >>> for f in fraction_lst:
    ...     {species_one: f, species_two: 1-f}

    The other options to :class:`.SQSJob` must be set on the reference job.
    """


[docs]
    def __init__(self, project, job_name):
        super(SQSMaster, self).__init__(project, job_name)

        self.__version__ = "0.0.1"
        self.input["fraction_lst"] = []
        self.input["species_one"] = ""
        self.input["species_two"] = ""
        self._job_generator = SQSJobGenerator(self)



[docs]
    def collect_output(self):
        pass


    @property
    def list_of_structures(self):
        """
        list: `len(self.input["fraction_lst"])` with the top-scoring structure from each sub job
        """
        return [
            self.project_hdf5.load(job_id).list_of_structures[0]
            for job_id in self.child_ids
        ]


[docs]
    def list_structures(self):
        """
        List of top-scoring structures from each sub job.

        Returns:
            list: value of :attribute:`.list_of_structures`
        """
        return self.list_of_structures





[docs]
class SQSJobGenerator(JobGenerator):
    @property
    def parameter_list(self):
        """

        Returns:
            (list)
        """
        return [
            [
                "sqs_" + str(np.round(f, 4)).replace(".", "_"),
                {
                    self._master.input["species_one"]: f,
                    self._master.input["species_two"]: 1 - f,
                },
            ]
            for f in self._master.input["fraction_lst"]
        ]


[docs]
    @staticmethod
    def job_name(parameter):
        return parameter[0]



[docs]
    def modify_job(self, job, parameter):
        job.input["mole_fractions"] = parameter[1]
        return job