Extxyz Reader

The features in the extxyz format are defined in the properties on the comment lines of a concatenated XYZ file. Each structure starts with the number of atoms, followed by the comment line and then the elements, positions, and forces as specified in the properties.

Multiple structures are concatenated together, hence the whole set of training structures can be in just one file, the validation structures in another, and the test structures in a third file.

Here’s a shortened example of the training data in the extxyz format:

21
Properties=species:S:1:pos:R:3:forces:R:3 energy=-17617.63598758549 pbc="F F F"
C  2.03112297  -1.10783801  -0.35158800   2.72979276  -1.55877755  -0.63202814
C  0.68817554   0.94896126  -1.72487641  -0.92555477  -0.52119051   2.26082812
C  2.47575017  -0.65064361  -1.63039847   1.67313734  -3.78441218   1.72467687
...

For loading the extxyz file, we internally use ase.io.read from the ASE library.

See below for the API reference to the associated loader class.

class mlip.data.chemical_systems_readers.extxyz_reader.ExtxyzReader(filepaths: str | PathLike | list[str | PathLike], data_download_fun: Callable[[str | PathLike, str | PathLike], None] | None = None, num_to_load: int | None = None, property_name_mapping: dict[str, str] | None = None)

Implementation of a chemical systems reader that loads data from extxyz format via the ase library.

__init__(filepaths: str | PathLike | list[str | PathLike], data_download_fun: Callable[[str | PathLike, str | PathLike], None] | None = None, num_to_load: int | None = None, property_name_mapping: dict[str, str] | None = None)

Constructor.

Parameters:

  • filepaths – Path or paths to file from which ChemicalSystem objects will be read.

  • data_download_fun – Optional function to download the data from filepath (source) to a local target path.

  • num_to_load – Optional limit on the number of systems to load per file. If None, all systems are loaded.

  • property_name_mapping – Optional mapping from canonical names ("forces", "energy", "stress") to the keys used in the data files. By default, it will be mapped to the same names. Any entries provided will override the corresponding defaults.

load() → list[ChemicalSystem]

Load chemical systems from all extxyz filepaths.