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
- 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