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:

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.

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

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