# -*- coding: utf-8 -*-
"""Contains a class for using Cremer Pople angle phi as a CV."""
import numpy as np
from .cv import cv
from . import cremerpople
[docs]class cv_cremerpople_phi(cv):
"""
Cremer-Pople angle phi 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 phi 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 = 1.0
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 theta 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]
phi = cremerpople.find_phi(coords_atoms)
with open('phi.dat','a') as f:
f.write(str(phi)+'\n')
self.s = phi
dphi = np.zeros_like(coords)
dphi[self.atoms] = cremerpople.dphi(coords_atoms)
self.ds_dr = dphi