get_atoms

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

Build an ASE structure from stored coordinates and fixed-atom flags.

Parameters:

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

  • stateID (int) – State identifier in /States.

  • 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:

ase.Atoms – Structure with cell, atomic numbers, and fixed-atom constraints.