pyiron_contrib.atomistics.randspg.randspg module

class pyiron_contrib.atomistics.randspg.randspg.ExampleInput(input_file_name=None)

Bases: GenericParameters

load_default()

Loading the default settings for the input file.

write_file(file_name, cwd=None)

Write GenericParameters to input file

Parameters

• file_name (str) – name of the file, either absolute (then cwd must be None) or relative

• cwd (str) – path name (default: None)

class pyiron_contrib.atomistics.randspg.randspg.RandSpg(project, job_name)

Bases: GenericJob, HasStructure

RandSpg is a program that generates random crystals with specific space groups. The user inputs a specific composition and space group to be generated. The algorithm then proceeds by finding all combinations of Wyckoff positions that satisfy the composition. It then randomly selects a combination of Wyckoff positions for the space group, generates random coordinates for variables in the Wyckoff positions, and places atoms in those sites. It ensures that any constraints the user placed on the system (lattice constraints including min/max volume, minimum interatomic distances, specific Wyckoff positions for specific atoms, etc.) are satisfied. Code: https://github.com/xtalopt/randSpg Paper: https://www.sciencedirect.com/science/article/pii/S0010465516303848

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()

Parse the output files of the example job and store the results in the HDF5 File.

collect_output_log(dir_name='randSpgOut')

general purpose routine to extract output from logfile

Parameters

file_name (str) – output.log - optional

from_hdf(hdf=None, group_name=None)

Restore the ExampleJob object in the HDF5 File

Parameters

• hdf (ProjectHDFio) – HDF5 group object - optional

• group_name (str) – HDF5 subgroup name - optional

property list_of_structures

list_structures()

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.

to_hdf(hdf=None, group_name=None)

Store the ExampleJob object in the HDF5 File

Parameters

• hdf (ProjectHDFio) – HDF5 group object - optional

• group_name (str) – HDF5 subgroup name - optional

write_input()

Call routines that generate the codespecifc input files