get_species_list

soda_analyzer.get_species_list(h5_lib, stateID=0, procID=0, rsp=0, delta=True)

Read atomic numbers for the selected structure.

Parameters:

• h5_lib (h5py.File) – Open SODA HDF5 file. Keep it open while using views derived from it.

• stateID (int, optional) – State identifier in /States. Default: 0.

• procID (int, optional) – Process identifier within the selected state. Default: 0.

• rsp (int, optional) – Structure selector: 0 for reactant, 1 for saddle, 2 for product. Default: 0.

• delta (bool, optional) – Read the process delta representation when true; read the base state when false. Default: True.

Returns:

numpy.ndarray – One atomic number per atom, after reconstructing process deltas when requested.