AtomicSystem.neutralize_charge

AtomicSystem.neutralize_charge(atom_types=None, tol=1e-08)

Neutralize the system by spreading its excess charge over atom types.

The current total_charge is subtracted back into the system as a per-atom offset, split across the given atom types. The offset for a type is added to every atom of that type, so any charge variation between individual atoms of the same type (e.g. per-atom ReaxFF/EEM charges) is preserved rather than overwritten.

Parameters:

atom_types

Mapping from atom type to a relative per-atom weight: every atom of type t receives the offset -excess * w_t / sum(w_i * n_i), where n_i is the number of atoms of type i. Equal weights therefore give the same offset to every atom of the listed types, whatever their number (only the ratio between weights matters, they need not sum to 1). Types absent from the mapping are left untouched. If omitted, the excess is divided uniformly over every atom in the system.

tol

Below this absolute total charge, the system is already considered neutral and nothing is done.