Source code for pyiron.atomistics.master.serial

# 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 __future__ import print_function
from collections import OrderedDict
from pyiron_base import SerialMasterBase
from pyiron.atomistics.job.atomistic import AtomisticGenericJob

__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__ = "production"
__date__ = "Sep 1, 2017"


[docs]class GenericOutput(OrderedDict): def __init__(self): super(GenericOutput, self).__init__()
[docs]class SerialMaster(SerialMasterBase, AtomisticGenericJob): """ The serial master class is a metajob consisting of a dynamic list of jobs which are executed in serial mode. The job is derived from the GenericMaster. 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. .. attribute:: start_job The first job of the series. .. attribute:: input The input of the start job - the first job of the series. """ def __init__(self, project, job_name): super(SerialMaster, self).__init__(project, job_name=job_name) @property def structure(self): if self.start_job: return self._start_job.structure else: return None @structure.setter def structure(self, basis): if self.start_job: self._start_job.structure = basis else: raise ValueError( "A structure can only be set after a start job has been assinged." )
[docs] def get_structure(self, iteration_step=-1): """ Returns: """ if len(self.child_ids) > 0: return self.project.load(self.child_ids[-1]).get_structure( iteration_step=iteration_step ) else: return None