RandomizedStructure

class autoplex.data.rss.jobs.RandomizedStructure(name='build_random_cells', struct_number=20, tag='Si', output_file_name='random_structs.extxyz', remove_tmp_files=True, buildcell_option=None, cell_seed_path=None, num_processes=32, fragment_file=None, fragment_numbers=None)

Bases: Maker

Maker to create random structures using the ‘buildcell’ tool.

Parameters:

• name (str) – Name of the flows produced by this maker.

• struct_number (int) – Expected number of generated randomized unit cells.

• tag (str) – Tag of systems. It can also be used for setting up elements and stoichiometry. For example, the tag of ‘SiO2’ will be recognized as a 1:2 ratio of Si to O and passed into the parameters of buildcell. However, note that this will be overwritten if the stoichiometric ratio of elements is defined in the ‘cell_seed_paths’ or ‘buildcell_options’.

• output_file_name (str) – Name of the file to store all generated structures.

• remove_tmp_files (bool) – Remove all temporary files raised by buildcell to save memory.

• buildcell_option (dict) – Customized parameters for buildcell.

• cell_seed_path (str) – Path to the custom buildcell control file, which ends with ‘.cell’. If this file exists, the buildcell_option argument will no longer take effect.

• num_processes (int) – Number of processes to use for parallel computation.

• fragment (Atoms | list[Atoms] (optional)) – Fragment(s) for random structures, e.g. molecules, to be placed indivudally intact. atoms.arrays should have a ‘fragment_id’ key with unique identifiers for each fragment if in same Atoms. atoms.cell must be defined (e.g. Atoms.cell = np.eye(3)*20).

• fragment_numbers (list[str] (optional)) – Numbers of each fragment to be included in the random structures. Defaults to 1 for all specified.

• fragment_file (str | None)

make()

Maker to create random structures by buildcell.