com_distance_sum#
- mbgdml.descriptors.com_distance_sum(Z, R, entity_ids)[source]#
The sum of pairwise distances from each entity’s center of mass to the total structure center of mass.
This descriptor, \(L\), is defined as
\[L = \sum_i^N l_i = \sum_i^N \Vert \mathbf{CM}_{i} - \mathbf{CM} \Vert_2\]where \(\mathbf{CM}\) is the center of mass of the structure and \(\mathbf{CM}_i\) is the center of mass of monomer \(i\).
- Parameters:
Z (
numpy.ndarray, ndim:1) – Atomic numbers of all atoms in the system.R (
numpy.ndarray, ndim:3) – Cartesian coordinates.entity_ids (
numpy.ndarray, ndim:1) – A uniquely identifying integer specifying what atoms belong to which entities. Entities can be a related set of atoms, molecules, or functional group. For example, a water and methanol molecule could be[0, 0, 0, 1, 1, 1, 1, 1, 1].
- Returns:
(ndim:
1) Calculated distance metric.- Return type: