# -*- coding: utf-8 -*-
"""Contains a class for using Cremer Pople total amplitude Q as a CV."""
import numpy as np
from .cv import cv
from . import cremerpople
from .. import constants as c
[docs]class cv_cremerpople_q(cv):
"""
Cremer-Pople total ampltiude Q 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 ring atoms to be used for the Cremer-Pople calculation in correct ordering
"""
def __init__(self, idx, symbols, **kwargs):
"""Construct Cremer-Pople Q CV object."""
cv.__init__(self, idx, symbols, **kwargs)
# standard plotting options
self.x = np.linspace(0.5, 2.5, 200)
self.ticks = None
# unit conversion
self.au2unit = c.a0
self.reset_width()
# arguments should be saved in the following way
self.atoms = self.get_kwargs("atoms")
[docs] def set_s_and_ds(self, coords):
"""
Calculate Q and its gradient for the current set of coordinates.
Parameters
----------
coords : np.2darray
cartesian coordinates of the molecule (shape: (N, 3))
"""
coords_atoms = coords[self.atoms]
Q = cremerpople.find_Q(coords_atoms)
with open('Q.dat','a') as f:
f.write(str(Q)+'\n')
self.s = Q
dQ = np.zeros_like(coords)
dQ[self.atoms] = cremerpople.dQ(coords_atoms)
self.ds_dr = dQ