"""Helper classes for doing jellium calculations."""
from math import pi
import numpy as np
from ase.units import Bohr
def create_background_charge(**kwargs):
if 'z1' in kwargs:
return JelliumSlab(**kwargs)
return Jellium(**kwargs)
[docs]class Jellium():
""" The Jellium object """
def __init__(self, charge):
""" Initialize the Jellium object
Input: charge, the total Jellium background charge.
"""
self.charge = charge
self.rs = None # the Wigner-Seitz radius
self.volume = None
self.mask_g = None
self.gd = None
def todict(self):
return {'charge': self.charge}
[docs] def set_grid_descriptor(self, gd):
""" Set the grid descriptor for the Jellium background charge"""
self.gd = gd
self.mask_g = self.get_mask().astype(float)
self.volume = self.gd.comm.sum_scalar(self.mask_g.sum()) * self.gd.dv
if self.charge != 0.:
self.rs = (3 / pi / 4 * self.volume / abs(self.charge))**(1 / 3)
else:
self.rs = np.inf # Avoid having to see numpy's warning.
[docs] def get_mask(self):
"""Choose which grid points are inside the jellium.
gd: grid descriptor
Return ndarray of ones and zeros indicating where the jellium
is. This implementation will put the positive background in the
whole cell. Overwrite this method in subclasses."""
return self.gd.zeros() + 1.0
[docs] def add_charge_to(self, rhot_g):
""" Add Jellium background charge to pseudo charge density rhot_g"""
rhot_g -= self.mask_g * (self.charge / self.volume)
def add_fourier_space_charge_to(self, pd, rhot_q):
rhot_g = pd.gd.zeros()
self.add_charge_to(rhot_g)
rhot_q += pd.fft(rhot_g)
[docs]class JelliumSlab(Jellium):
""" The Jellium slab object """
def __init__(self, charge, z1, z2):
"""Put the positive background charge where z1 < z < z2.
z1: float
Position of lower surface in Angstrom units.
z2: float
Position of upper surface in Angstrom units."""
Jellium.__init__(self, charge)
self.z1 = (z1 - 0.0001) / Bohr
self.z2 = (z2 - 0.0001) / Bohr
def todict(self):
dct = Jellium.todict(self)
dct.update(z1=self.z1 * Bohr + 0.0001,
z2=self.z2 * Bohr + 0.0001)
return dct
[docs] def get_mask(self):
r_gv = self.gd.get_grid_point_coordinates().transpose((1, 2, 3, 0))
# r_gv: 4-dimensional ndarray
# positions of the grid points in Bohr units.
return np.logical_and(r_gv[:, :, :, 2] > self.z1,
r_gv[:, :, :, 2] < self.z2)