BuildMultiRandomizedStructure

BuildMultiRandomizedStructure#

class autoplex.data.rss.flows.BuildMultiRandomizedStructure(tag, generated_struct_numbers, builder='buildcell', custom_builder_cmd=None, custom_builder_args=None, pass_index_to_builder=False, cell_seed_paths=None, buildcell_options=None, fragment_file=None, fragment_numbers=None, remove_tmp_files=True, initial_selection_enabled=False, selected_struct_numbers=None, bcur_params=None, random_seed=None, num_processes=1, name='do_randomized_structure_generation', jobprefix='')[source]#

Bases: Maker

Maker to create random structures by ‘buildcell’, or a user-defined third party package.

Parameters:

  • 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’.

  • generated_struct_numbers (list[int]) – Expected number of generated randomized unit cells.

  • builder (str | None) – Builder to be used for generating random structures. Currently only accepts ‘buildcell’ or ‘custom’. Default is buildcell.

  • custom_builder_cmd (str | None) – Command to be called when using ‘custom’ option for builder. Must be either an absolute path to executable, or accessible via $PATH. Default is None.

  • custom_builder_args (str | dict[str, str] | None) – Arguments to be passed to the custom builder command. Default is None.

  • pass_index_to_builder (bool) – Whether the process index should be included in the final argument string for the custom builder command (the index will always be appended as the last argument). Default is False.

  • cell_seed_paths (list[str]) – A list of paths to the custom buildcell control files, which ends with ‘.cell’. If these files exist, the buildcell_options argument will no longer take effect.

  • buildcell_options (list[dict]) – A list of customized buildcell parameters.

  • fragment_file (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.

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

  • initial_selection_enabled (bool) – If true, sample structures using CUR.

  • selected_struct_numbers (list) – Number of structures to be sampled.

  • bcur_params (dict) – Parameters for Boltzmann CUR selection.

  • random_seed (int) – A seed to ensure reproducibility of CUR selection.

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

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

  • jobprefix (str) – Prefix that precedes the jobname.

make()[source]#

Maker to create random structures by buildcell.