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serial.py
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serial.py
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# 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"
class GenericOutput(OrderedDict):
def __init__(self):
super(GenericOutput, self).__init__()
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 is not None:
return self._start_job.structure
else:
return None
@structure.setter
def structure(self, basis):
if self.start_job is not None:
self._start_job.structure = basis
else:
raise ValueError(
"A structure can only be set after a start job has been assinged."
)
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