Species index function
Moved and slightly changed two functions, _get_number_in_species
and _get_absolute_number
, from the CASTEP calculator to the main Atoms object, as they were labelled in comments as such and could indeed work well. Now renamed:
get_index_in_species
accepts an index of an atom and returns the index of that atom in an array composed only of the other atoms of the same species. For example:
a = Atoms(['H', 'H', 'C', 'H'])
print(a.get_index_in_species(3))
prints 2. Raises a ValueError
for invalid indices.
get_global_index
takes a species symbol and an integer and works in reverse, finding the global index. Raises a RuntimeError
if no fitting atom is found.