# -*- coding: utf-8 -*-
"""Contains a class for using the bond length between two atoms as a CV."""
import numpy as np
from .. import constants as c
from . import cvfunctions as cvf
from .cv import cv
[docs]class cv_bond(cv):
"""
Bond length between two 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 two atom indices for the calculation of the bond length
"""
def __init__(self, idx, symbols, **kwargs):
"""Construct bond length CV object."""
cv.__init__(self, idx, symbols, **kwargs)
self.atoms = self.get_kwargs("atoms")
self.x = np.linspace(0.5, 2.5, 200)
self.ticks = None
self.au2unit = c.a0
self.reset_width()
[docs] def set_s_and_ds(self, coords):
"""
Calculate bond length 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]
bond = cvf.bond(coord)
dbond = np.zeros(coords.shape)
dbond[self.atoms] = cvf.dbond(coord)
self.s = bond
self.ds_dr = dbond