# -*- coding: utf-8 -*-
"""Contains a class for using the angle between three atoms as a CV."""
import numpy as np
from . import cvfunctions as cvf
from .cv import cv
[docs]class cv_angle(cv):
"""
Angle between three atoms as collective variable, inherits from `metafalcon.cvs.cv.cv`.
Parameters
----------
idx : int
index of collective variable in the input file
symbols : list of str
atomic symbols of the molecule
**kwargs :
See below
Keyword Arguments
-----------------
atoms : list of int
list of three atom indices for the calculation of the angle
"""
def __init__(self, idx, symbols, **kwargs):
"""Construct angle CV object."""
cv.__init__(self, idx, symbols, **kwargs)
self.atoms = self.get_kwargs("atoms")
self.x = np.linspace(0., 180., 200)
self.ticks = 30.
[docs] def set_s_and_ds(self, coords):
"""
Calculate angle and its gradient for the current set of coordinates.
Parameters
----------
coords : np.2darray
cartesian coordinates of the molecule (shape: (N, 3))
"""
coord = [coords[i] for i in self.atoms]
angle = cvf.angle(coord)
dangle = np.zeros(coords.shape)
dangle[self.atoms] = cvf.dangle(coord)
self.s = angle
self.ds_dr = dangle