pyiron_atomistics.lammps.output.remap_indices#
- pyiron_atomistics.lammps.output.remap_indices(lammps_indices: np.ndarray | List, potential_elements: np.ndarray | List, structure: Atoms) np.ndarray[source]#
Give the Lammps-dumped indices, re-maps these back onto the structure’s indices to preserve the species.
The issue is that for an N-element potential, Lammps dumps the chemical index from 1 to N based on the order that these species are written in the Lammps input file. But the indices for a given structure are based on the order in which chemical species were added to that structure, and run from 0 up to the number of species currently in that structure. Therefore we need to be a little careful with mapping.
- Parameters:
lammps_indices (numpy.ndarray/list) – The Lammps-dumped integers.
potential_elements (numpy.ndarray/list)
structure (pyiron_atomistics.atomistics.structure.Atoms)
- Returns:
Those integers mapped onto the structure.
- Return type:
numpy.ndarray