Source code for pyiron.atomistics.master.structure

# 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.

from pyiron.atomistics.structure.atoms import Atoms
from pyiron.atomistics.master.parallel import ParallelMaster
from pyiron_base import JobGenerator

"""
The StructureListMaster class is a parallel master consisting of a list of structures which are executed in parallel.
"""

__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"


[docs]class StructureJobGenerator(JobGenerator): """ JobGenerator for the StructureListMaster - this class implements the functions to generate the parameter list, modify the individual jobs according to the parameter list and generate the new job names according to the parameter list. """ @property def parameter_list(self): """ Returns: (list): [[index(int), pyiron.atomistics.structure.atoms.Atoms], ...] """ return list(enumerate(self._job.structure_lst))
[docs] @staticmethod def job_name(parameter): """ Generate job name for a give set of parameters Args: parameter: For the StructureListMaster the structures are simply numbered - struct_0, struct_1, ... Returns: str: job name for the next job """ return "struct_" + str(parameter[0])
[docs] def modify_job(self, job, parameter): """ Modify the next job by setting the structure for the specific parameter Args: job (GenericJob): next job object to be executed parameter: includes the atomistic structure Returns: GenericJob: """ job.structure = parameter[1] return job
[docs]class StructureListMaster(ParallelMaster): """ The GenericMaster is the template class for all meta jobs - meaning all jobs which contain multiple other jobs. It defines the shared functionality of the different kind of job series. Args: project (ProjectHDFio): ProjectHDFio instance which points to the HDF5 file the job is stored in job_name (str): name of the job, which has to be unique within the project Attributes: .. attribute:: job_name name of the job, which has to be unique within the project .. attribute:: status execution status of the job, can be one of the following [initialized, appended, created, submitted, running, aborted, collect, suspended, refresh, busy, finished] .. attribute:: job_id unique id to identify the job in the pyiron database .. attribute:: parent_id job id of the predecessor job - the job which was executed before the current one in the current job series .. attribute:: master_id job id of the master job - a meta job which groups a series of jobs, which are executed either in parallel or in serial. .. attribute:: child_ids list of child job ids - only meta jobs have child jobs - jobs which list the meta job as their master .. attribute:: project Project instance the jobs is located in .. attribute:: project_hdf5 ProjectHDFio instance which points to the HDF5 file the job is stored in .. attribute:: job_info_str short string to describe the job by it is job_name and job ID - mainly used for logging .. attribute:: working_directory working directory of the job is executed in - outside the HDF5 file .. attribute:: path path to the job as a combination of absolute file system path and path within the HDF5 file. .. attribute:: version Version of the hamiltonian, which is also the version of the executable unless a custom executable is used. .. attribute:: executable Executable used to run the job - usually the path to an external executable. .. attribute:: library_activated For job types which offer a Python library pyiron can use the python library instead of an external executable. .. attribute:: server Server object to handle the execution environment for the job. .. attribute:: queue_id the ID returned from the queuing system - it is most likely not the same as the job ID. .. attribute:: logger logger object to monitor the external execution and internal pyiron warnings. .. attribute:: restart_file_list list of files which are used to restart the calculation from these files. .. attribute:: job_type Job type object with all the available job types: ['ExampleJob', 'SerialMaster', 'ParallelMaster', 'ScriptJob', 'ListMaster'] .. attribute:: child_names Dictionary matching the child ID to the child job name. """ def __init__(self, project, job_name): super(StructureListMaster, self).__init__(project, job_name) self.__name__ = "StructureListMaster" self.__version__ = "0.0.1" self._job_generator = StructureJobGenerator(self) self._structure_lst = [] @property def structure_lst(self): return self._structure_lst @structure_lst.setter def structure_lst(self, structure_lst): self._structure_lst = structure_lst
[docs] def to_hdf(self, hdf=None, group_name=None): """ Store the StructureListMaster object in the HDF5 File Args: hdf (ProjectHDFio): HDF5 group object - optional group_name (str): HDF5 subgroup name - optional """ super(StructureListMaster, self).to_hdf(hdf=hdf, group_name=group_name) with self.project_hdf5.open("input/structures") as hdf5_input: for ind, struct in enumerate(self.structure_lst): struct.to_hdf(hdf=hdf5_input, group_name="s_" + str(ind))
[docs] def from_hdf(self, hdf=None, group_name=None): """ Restore the StructureListMaster object in the HDF5 File Args: hdf (ProjectHDFio): HDF5 group object - optional group_name (str): HDF5 subgroup name - optional """ super(StructureListMaster, self).from_hdf(hdf=hdf, group_name=group_name) with self.project_hdf5.open("input/structures") as hdf5_input: self._structure_lst = [ Atoms().from_hdf(hdf5_input, group_name) for group_name in sorted(hdf5_input.list_groups()) ]
[docs] def collect_output(self): """ Implemented for compatibilty """ pass
[docs] def run_if_interactive_non_modal(self): """ Implemented for compatibilty """ raise TypeError
def _run_if_busy(self): """ Implemented for compatibilty """ pass