pyiron.atomistics.job.interactivewrapper module

class pyiron.atomistics.job.interactivewrapper.InteractiveWrapper(project, job_name)[source]

Bases: pyiron.base.master.generic.GenericMaster

check_setup()[source]

Checks whether certain parameters (such as plane wave cutoff radius in DFT) are changed from the pyiron standard values to allow for a physically meaningful results. This function is called manually or only when the job is submitted to the queueing system.

collect_logfiles()[source]

Collect the log files of the external executable and store the information in the HDF5 file. This method has to be implemented in the individual hamiltonians.

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.

db_entry()[source]

Generate the initial database entry

Returns

db_dict

Return type

(dict)

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

Restore the InteractiveWrapper from an HDF5 file

Parameters

  • hdf (ProjectHDFio) – HDF5 group object - optional

  • group_name (str) – HDF5 subgroup name - optional

get_final_structure()[source]

Returns:

property ref_job

Get the reference job template from which all jobs within the ParallelMaster are generated.

Returns

reference job

Return type

GenericJob

ref_job_initialize()[source]
set_input_to_read_only()[source]

This function enforces read-only mode for the input classes, but it has to be implement in the individual classes.

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

Store the InteractiveWrapper 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.

class pyiron.atomistics.job.interactivewrapper.ReferenceJobOutput(job)[source]

Bases: object

property cells
property energy_pot
property energy_tot
property forces
property indices
property positions
property pressures
property steps
property temperatures
property time
property unwrapped_positions
property volume