Misc utils

ase_grain.util.water_charge(ian)

Calculate charge for a water cluster’s fragment. Assign +1 for H and -2 for O.

Parameters:ian (ndarray[(N,), int]) – Atomic numbers Returns:charge in int

ase_grain.util.center_of_mass(acoords, ian)

Calculate the center of mass for a group of atoms.

Parameters:

• acoords (ndarray[(N,3), float]) – Atoms’ coordinates
• ian (ndarray[(N,), int]) – Atomic numbers

Returns:

coordinate for the center of mass (ndarray[(3,), float])

This library represents all atoms in atomic numbers. You may find ASE’s conversion utils helpful.

>>> from ase.symbols import symbols2numbers
>>> symbols2numbers(['H','O','H'])
[1, 8, 1]
>>> symbols2numbers("HOH")
[1, 8, 1]
>>> from ase.data import atomic_numbers
>>> atomic_numbers['O']
8