matmacore.utilities module
- matmacore.utilities.get_distance(at1, at2)[source]
Finds the distance between two atoms :param at1: (list) a list of xyz coordinates of atom1 :param at2: (list) a list of xyz coordinates of atom2 :return: (float) the distance between 2 atoms
- matmacore.utilities.proper_minus(value)[source]
Replaces the default minus (-) with an actual minus sign instead of a dash
- matmacore.utilities.read_coordinates(xyz_file, atom_list)[source]
Extracts collective variables from an xyz file containing an MD trajectory (CP2K). :param xyz_file: (string) The xyz file containing your MD trajectory. :param atom_list: (list) a list of atoms that defines your collective variable. :return: (list) Distances / Angles / Dihedrals, corresponding with your specified colvar.