pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive module

Job class to run a reference jobs on all structures in a given container via an interactive job.

class pyiron_contrib.atomistics.atomistics.job.structurelistmasterinteractive.StructureMasterInt(project=None, job_name=None)[source]

Bases: GenericMaster

Runs given structures with given reference job.

This example shows how to run a simple energy vs distance calculation for a dimer.

>>> from pyiron_atomistics import Project
>>> from pyiron_contrib.atomistics.atomistics.job.structurestorage import StructureStorage
>>> pr = Project("container")
>>> container = StructureStorage()
>>> for d in [0.7, 0.8, 0.9, 1, 1.1, 1.2]:
...     container.add_structure(pr.create.structure.atoms(["Fe", "Fe"], positions=[[0,0,0], [0,0,d]], cell=[10,10,10])
>>> ref = pr.create.job.Lammps("ref")
>>> ref.structure = container.get_structure()
>>> ref.calc_static()
>>> master = pr.create.job.StructureContainerInteractive("master")
>>> master.container = container
>>> master.ref_job = ref
>>> master.run()
add_structure(structure)[source]

Add a structure to the StructureStorage to calculate. If no container set yet, create an empty one.

Parameters

structure (Atoms) – structure to add to calculation

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 hamiltonians.

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

Restore the GenericMaster from an HDF5 file

Parameters
  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

run_static()[source]

The run static function is called by run to execute the simulation.

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

Store the GenericMaster in an HDF5 file

Parameters
  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

validate_ready_to_run()[source]

Validate that the calculation is ready to be executed. By default no generic checks are performed, but one could check that the input information is complete or validate the consistency of the input at this point.

Raises

ValueError – if ready check is unsuccessful

write_input()[source]

Write the input files for the external executable. This method has to be implemented in the individual hamiltonians.