light_pfp_data.sample.custom.atoms_to_dataset(atoms: Atoms, dataset: Union[str, Path, H5DatasetWriter, File], model_version: str = ”, calc_mode: str = ”, extra_info: Optional[Dict[str, Any]] = None) → None#

Save one ASE atoms into the dataset.

Parameters

  • atoms (Atoms) – The input ASE atoms.

  • model_version (str) – The PFP version to get the potential energy.

  • calc_mode (str) – The PFP calculation mode to to get the potential energy.

  • dataset (Union[str, pathlib.Path, H5DatasetWriter, File]) – The dataset.

  • extra_info (Optional[Dict[str, Any]], optional) – Extra information to be saved into the dataset. Defaults to None.

Raises

TypeError –

light_pfp_data.sample.custom.traj_to_dataset(traj: Union[str, Trajectory, List[Atoms]], dataset: Union[str, Path, H5DatasetWriter, File], model_version: str = ”, calc_mode: str = ”, start: int = 0, end: Optional[int] = None, step: int = 1, show_progress_bar: bool = False) → None#

Save an ase trajectory or a list of ase atoms into the dataset.

Parameters

  • traj (Union[str, Trajectory, List[Atoms]]) – ASE trajectory or a list of ASE atoms.

  • model_version (str) – The PFP version to generate the trajectory.

  • calc_mode (str) – The PFP calculation mode to generate the trajectory.

  • dataset (Union[str, pathlib.Path, H5DatasetWriter, File]) – The dataset.

  • start (int, optional) – The starting index. Defaults to 0.

  • end (int, optional) – The stopping index. If None, the last element. Defaults to None.

  • step (int, optional) – The select every “step” structures and save to dataset. Defaults to 1.

  • show_progress_bar (bool, optional) – When True, show the progress bar. Defaults to False.