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

Parameters

  • iteration_step (int) – Step for which the structure is requested

  • wrap_atoms (bool) – True if the atoms are to be wrapped back into the unit cell

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(master)[source]

Bases: pyiron_base.master.parallel.JobGenerator

modify_job(job, parameter)[source]

Modify next job with the parameter object. job is already the newly created job object cloned from the template job, so this function has to return the same instance, but may (and should) modify it.

Parameters
Returns

must be the given job

Return type

GenericJob

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, delete_existing_job=False)[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