pyiron_contrib.atomistics.mlip.mlip module

class pyiron_contrib.atomistics.mlip.mlip.CommandLine(input_file_name=None, **qwargs)

Bases: GenericParameters

activate_postprocessing(file_content=None)

load_default(file_content=None)

Load defaults resets the dataset in the background to be empty

class pyiron_contrib.atomistics.mlip.mlip.Mlip(project, job_name)

Bases: GenericJob, PotentialFit

add_job_to_fitting(job_id, time_step_start=0, time_step_end=- 1, time_step_delta=10)

property calculation_dataframe

collect_logfiles()

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()

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.

from_hdf(hdf=None, group_name=None)

Restore the GenericJob from an HDF5 file

Parameters

• hdf (ProjectHDFio) – HDF5 group object - optional

• group_name (str) – HDF5 subgroup name - optional

get_lammps_potential()

Return a pyiron compatible dataframe that defines a potential to be used with a Lammps job (or subclass thereof).

Returns

contains potential information to be used with a Lammps job.

Return type

DataFrame

get_structure(iteration_step=- 1)

get_suggested_number_of_configuration(species_count=None, multiplication_factor=2.0)

property potential

potential_dataframe(elements=None)

pandas.DataFrame: potential dataframe for lammps jobs

Attention

The elements argument must be given for in any case for non-unary alloys, as the scrapping code from the training data is currently broken!

Parameters

elements (list of str, optional) – name of elements in this potential in the order of their indices in pyiron structures, if not given use elements seen in training data

property potential_files

set_input_to_read_only()

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

static stress_tensor_components(stresses)

to_hdf(hdf=None, group_name=None)

Store the GenericJob in an HDF5 file

Parameters

• hdf (ProjectHDFio) – HDF5 group object - optional

• group_name (str) – HDF5 subgroup name - optional

write_input()

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

class pyiron_contrib.atomistics.mlip.mlip.MlipParameter(separator_char=' ', comment_char='#', table_name='mlip_inp')

Bases: GenericParameters

load_default(file_content=None)

Load defaults resets the dataset in the background to be empty

pyiron_contrib.atomistics.mlip.mlip.read_cgfs(file_name)

pyiron_contrib.atomistics.mlip.mlip.write_cfg(file_name, indices_lst, position_lst, cell_lst, forces_lst=None, energy_lst=None, track_lst=None, stress_lst=None)