pyiron.atomistics.master.parallel module

class pyiron.atomistics.master.parallel.AtomisticParallelMaster(project, job_name)[source]

Bases: pyiron.base.master.parallel.ParallelMaster, pyiron.atomistics.job.atomistic.AtomisticGenericJob

get_structure(iteration_step=- 1)[source]

Gets the structure from a given iteration step of the simulation (MD/ionic relaxation). For static calculations there is only one ionic iteration step :param iteration_step: Step for which the structure is requested :type iteration_step: int :param wrap_atoms: True if the atoms are to be wrapped back into the unit cell :type wrap_atoms: bool

Returns

The required structure

Return type

pyiron.atomistics.structure.atoms.Atoms

property structure

Returns:

class pyiron.atomistics.master.parallel.GenericOutput[source]

Bases: collections.OrderedDict

class pyiron.atomistics.master.parallel.MapJobGenerator(job, no_job_checks=False)[source]

Bases: pyiron.base.master.parallel.JobGenerator

modify_job(job, parameter)[source]
property parameter_list

Returns: (list)

class pyiron.atomistics.master.parallel.MapMaster(project, job_name)[source]

Bases: pyiron.atomistics.master.parallel.AtomisticParallelMaster

collect_output()[source]

Collect the output files of the external executable and store the information in the HDF5 file. This method has to be implemented in the individual meta jobs derived from the ParallelMaster.

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

Restore the ParameterMaster from an HDF5 file

Parameters

  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

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

Store the ParameterMaster in an HDF5 file

Parameters

  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

pyiron.atomistics.master.parallel.pipe(project, job, step_lst)[source]

Create a job pipeline

Parameters

  • project (pyiron.Project) – Project to calculate pipeline in

  • job (AtomisticGenericJob) – Template for the calculation

  • step_lst (list) – List of functions which create calculations

Returns

Return type

FlexibleMaster