pyiron.atomistics.master.structure module

class pyiron.atomistics.master.structure.StructureJobGenerator(job, no_job_checks=False)[source]

Bases: pyiron.base.master.parallel.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.

static job_name(parameter)[source]

Generate job name for a give set of parameters

Parameters

parameter – For the StructureListMaster the structures are simply numbered - struct_0, struct_1, …

Returns

job name for the next job

Return type

str

modify_job(job, parameter)[source]

Modify the next job by setting the structure for the specific parameter

Parameters

  • job (GenericJob) – next job object to be executed

  • parameter – includes the atomistic structure

Returns

Return type

GenericJob

property parameter_list

Returns: (list): [[index(int), pyiron.atomistics.structure.atoms.Atoms], …]

class pyiron.atomistics.master.structure.StructureListMaster(project, job_name)[source]

Bases: pyiron.base.master.parallel.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.

Parameters

  • 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

.. 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.

collect_output()[source]

Implemented for compatibilty

from_hdf(hdf=None, group_name=None)[source]

Restore the StructureListMaster object in the HDF5 File

Parameters

  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

run_if_interactive_non_modal()[source]

Implemented for compatibilty

property structure_lst
to_hdf(hdf=None, group_name=None)[source]

Store the StructureListMaster object in the HDF5 File

Parameters

  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional