dynsight.data_processing.createreferencesfromtrajectory

dynsight.data_processing.createreferencesfromtrajectory(h5soapdataset, addresses, lmax, nmax, donormalize=True)[source]

Generate a SOAPReferences object.

by storing the data found from h5SOAPDataSet. The atoms are selected trough the addresses dictionary.

  • Original author: Daniele Rapetti

Parameters:

  • h5soapdataset (h5py.Dataset) – the dataset with the SOAP fingerprints

  • addresses (dict) – the dictionary with the names and addresses of the fingerprints. The keys will be used as the names of the references and the values assigned to the keys must be tuples or similar with the number of the chosen frame and the atom number (for example dict(exaple=(framenum, atomID)))

  • lmax (int) – To be done.

  • nmax (int) – To be done.

  • donormalize (bool) – If True normalizes the SOAP vector before storing them. Defaults to True.

  • settingsUsedInDscribe – If none the SOAP vector are not preprocessed, if not none the SOAP vectors are decompressed, as dscribe omits the symmetric part of the spectra. Defaults to None.

Returns:

the container with the selected references

Return type:

SOAPReferences