aimmd.coords.internal

This file is part of AIMMD.

AIMMD is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

AIMMD is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with AIMMD. If not, see <https://www.gnu.org/licenses/>.

Functions

generate_indices(topology, source_idx[, ...])	Generates the index pairs, triples and quadroples needed to calculate distances, angles and dihedrals for internal coordinate representation of a single molecule.
get_involved(idx, pairs, triples, quadruples)	For a given index to internal coordinates array return the atom indices of the involved atoms
ic(mdtra, pairs, triples, quadruples)	Calculates internal coordinate representation consisting of distances, angles and dihedrals given by pairs, triples and quadruples.
transform(mdtra, pairs, triples, quadruples)	Calculates internal coordinate representation consisting of distances, angles and dihedrals given by pairs, triples and quadruples.