pyiron_contrib.atomistics.atomicrex.base module

Pyiron interface to atomicrex

class pyiron_contrib.atomistics.atomicrex.base.AtomicrexBase(project, job_name)

Bases: GenericJob, PotentialFit

collect_output(cwd=None)

Internal function that parses the output of an atomicrex job

Parameters

cwd (str, optional) – Working directory. Defaults to None.

compress(files_to_compress=None)

Compress the output files of a job object.

Parameters

files_to_compress (list) – A list of files to compress (optional)

convergence_check()

Internal function, TODO find something to reasonably judge convegence

from_hdf(hdf=None, group_name=None)

Internal function to reload the job object from hdf5

get_lammps_potential() → DataFrame

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

property lammps_potential

plot_final_potential()

Plot the fitted potential. Returns the matplotlib objects to change the look of the plot.

Returns

[description]

Return type

[matplotlib figure, axis]

potential_as_pd_df()

Return the fitted potential as a pandas dataframe, which can be used for lammps calculations.

property publication

to_hdf(hdf=None, group_name=None)

Internal function to store the job in hdf5 format

write_input(directory=None)

Internal function that writes input files

Parameters

directory ([string], optional) – Working directory. Defaults to None.

class pyiron_contrib.atomistics.atomicrex.base.Factories

Bases: object

Provides conventient acces to other factory classes. Functionality to set up an atomicrex job can be found here.