[0.4411, 0.1480, -12.55],
[0.7603, 1.946, -40.89],
[1.161, 1.396, 17.22],
[2.946, 1.183, 15.76],
[4.161, 1.964, 36.63],
[5.747, 1.958, 22.55],
[7.912, 1.361, 81.04]]
# Initialize classical material
classical_material = PolarizableMaterial()
# Classical nanosphere
classical_material.add_component(
PolarizableSphere(center=0.5 * large_cell,
radius=radius,
permittivity=PermittivityPlus(data=gold)))
# Quasistatic FDTD
qsfdtd = QSFDTD(classical_material=classical_material,
atoms=None,
cells=large_cell,
spacings=[8.0, 1.0],
communicator=world,
remove_moments=(4, 1))
# Run ground state
energy = qsfdtd.ground_state('gs.gpw', nbands=-1)
# Run time evolution
qsfdtd.time_propagation('gs.gpw',
time_step=10,
atom_center = np.array([10.0, 10.0, 20.0])
atoms = Atoms(
'Na2', [atom_center + [0.0, 0.0, -1.50], atom_center + [0.0, 0.0, +1.50]])
# Permittivity file
if world.rank == 0:
fo = open('ed.txt', 'w')
fo.writelines(['1.20 0.20 25.0'])
fo.close()
world.barrier()
# Classical subsystem
classical_material = PolarizableMaterial()
sphere_center = np.array([10.0, 10.0, 10.0])
classical_material.add_component(
PolarizableSphere(permittivity=PermittivityPlus('ed.txt'),
center=sphere_center,
radius=5.0))
# Combined Poisson solver
poissonsolver = FDTDPoissonSolver(classical_material=classical_material,
qm_spacing=0.40,
cl_spacing=0.40 * 4,
cell=large_cell,
remove_moments=(1, 4),
communicator=world,
potential_coupler='Refiner')
poissonsolver.set_calculation_mode('iterate')
# Combined system
atoms.set_cell(large_cell)
import pylab as plt
from ase.units import Hartree, Bohr
from gpaw.fdtd.polarizable_material import PermittivityPlus, _eps0_au
# Nanosphere radius (Angstroms)
radius = 50.0
# Permittivity of Gold
# J. Chem. Phys. 135, 084121 (2011); http://dx.doi.org/10.1063/1.3626549
gold = [[0.2350, 0.1551, 95.62], [0.4411, 0.1480, -12.55],
[0.7603, 1.946, -40.89], [1.161, 1.396, 17.22], [2.946, 1.183, 15.76],
[4.161, 1.964, 36.63], [5.747, 1.958, 22.55], [7.912, 1.361, 81.04]]
# Plot calculated spectrum and compare with Mie theory
spec = np.loadtxt('spec.dat')
perm = PermittivityPlus(data=gold).value(spec[:, 0] / Hartree)
plt.figure()
plt.plot(spec[:, 0], spec[:, 1], 'r', label='QSFDTD')
plt.plot(spec[:, 0],
3. * (4. / 3. * np.pi * (radius / Bohr)**3) * (spec[:, 0] / Hartree) /
(2. * np.pi**2) / Hartree * np.imag(
(perm - _eps0_au) / (perm + 2. * _eps0_au)),
'b',
label='Mie theory')
plt.legend(loc=2)
plt.xlabel('Energy [eV]', fontsize=12)
plt.ylabel('Dipole strength [1/eV]', fontsize=12)
plt.xlim((0, 5.0))
plt.ylim((-1, 3500))
plt.savefig('qsfdtd_vs_mie.png')
plt.subplot(1, 2, 2)
plt.plot(energy_j, eps_j.imag, 'bv')
plt.plot(energy_e, fiteps_e.imag, 'b-')
plt.xlim(energy_e.min(), energy_e.max())
# plt.ylim(fiteps_e.imag.min(), fiteps_e.imag.max())
plt.ylim(0, 7)
plt.xlabel('Energy (eV)')
plt.ylabel('Imaginary($\epsilon$)')
plt.tight_layout()
plt.savefig('%s.png' % fname)
# Permittivity of Gold
# Source:
# http://refractiveindex.info/?shelf=main&book=Au&page=Johnson
# Direct download link:
# wget http://refractiveindex.info/database/main/Au/Johnson.yml -O Au.yml
ymlfname = 'Au.yml'
# Fit to the permittivity
# J. Chem. Phys. 135, 084121 (2011); http://dx.doi.org/10.1063/1.3626549
fiteps = PermittivityPlus(data=[[0.2350, 0.1551, 95.62],
[0.4411, 0.1480, -12.55],
[0.7603, 1.946, -40.89],
[1.161, 1.396, 17.22],
[2.946, 1.183, 15.76],
[4.161, 1.964, 36.63],
[5.747, 1.958, 22.55],
[7.912, 1.361, 81.04]])
plot(ymlfname, fiteps)
from gpaw.fdtd.poisson_fdtd import QSFDTD
from gpaw.fdtd.polarizable_material import PermittivityPlus, PolarizableMaterial, \
PolarizableSphere, PolarizableBox, \
PolarizableEllipsoid, PolarizableRod, \
PolarizableTetrahedron
from gpaw.test import equal
# Whole simulation cell (Angstroms)
cell = [40, 40, 20]
# Classical subsystem
classical_material = PolarizableMaterial()
classical_material.add_component(
PolarizableSphere(permittivity=PermittivityPlus(data=[[1.20, 0.20, 25.0]]),
center=[10, 10, 10],
radius=4.5))
classical_material.add_component(
PolarizableBox(permittivity=PermittivityPlus(data=[[1.40, 0.20, 25.0]]),
corner1=[18.1, 5.1, 5.1],
corner2=[22.9, 14.9, 14.9]))
classical_material.add_component(
PolarizableEllipsoid(
permittivity=PermittivityPlus(data=[[1.60, 0.20, 25.0]]),
center=[30.0, 10.0, 10.0],
radii=[3.9, 5.9, 4.9]))
classical_material.add_component(
PolarizableRod(permittivity=PermittivityPlus(data=[[1.80, 0.20, 25.0]]),
corners=[[10.0, 21.5, 10.0], [10.0, 33.5, 10.0]],
round_corners=True,
radius=3.9))
classical_material.add_component(
# Accuracy
energy_eps = 0.0005
# Whole simulation cell (Angstroms)
cell = [20, 20, 30]
# Quantum subsystem
atom_center = np.array([10.0, 10.0, 20.0])
atoms = Atoms(
'Na2', [atom_center + [0.0, 0.0, -1.50], atom_center + [0.0, 0.0, +1.50]])
# Classical subsystem
sphere_center = np.array([10.0, 10.0, 10.0])
classical_material = PolarizableMaterial()
classical_material.add_component(
PolarizableSphere(permittivity=PermittivityPlus(data=[[1.20, 0.20, 25.0]]),
center=sphere_center,
radius=5.0))
# Wrap calculators
qsfdtd = QSFDTD(classical_material=classical_material,
atoms=atoms,
cells=(cell, 2.50),
spacings=[1.60, 0.40],
remove_moments=(1, 4),
communicator=world)
# Run
qsfdtd.ground_state('gs.gpw',
eigensolver='cg',
nbands=-1,
# Accuracy
energy_eps = 0.0005
# Whole simulation cell (Angstroms)
cell = [20, 20, 30];
# Quantum subsystem
atom_center = np.array([10.0, 10.0, 20.0])
atoms = Atoms('Na2', [atom_center + [0.0, 0.0, -1.50],
atom_center + [0.0, 0.0, +1.50]])
# Classical subsystem
sphere_center = np.array([10.0, 10.0, 10.0])
classical_material = PolarizableMaterial()
classical_material.add_component(PolarizableSphere(permittivity = PermittivityPlus(data = [[1.20, 0.20, 25.0]]),
center = sphere_center,
radius = 5.0
))
# Wrap calculators
qsfdtd = QSFDTD(classical_material = classical_material,
atoms = atoms,
cells = (cell, 2.50),
spacings = [1.60, 0.40],
remove_moments = (1, 4),
communicator = world)
# Run
qsfdtd.ground_state('gs.gpw', eigensolver='cg', nbands=-1, convergence={'energy': energy_eps})
equal(qsfdtd.energy, -0.631881, energy_eps * qsfdtd.gs_calc.get_number_of_electrons())
from gpaw.fdtd.poisson_fdtd import QSFDTD
from gpaw.fdtd.polarizable_material import PermittivityPlus, PolarizableMaterial, \
PolarizableSphere, PolarizableBox, \
PolarizableEllipsoid, PolarizableRod, \
PolarizableTetrahedron
from gpaw.mpi import world
from gpaw.tddft import photoabsorption_spectrum, units
from gpaw.test import equal
import numpy as np
# Whole simulation cell (Angstroms)
cell = [40, 40, 20];
# Classical subsystem
classical_material = PolarizableMaterial()
classical_material.add_component(PolarizableSphere(permittivity = PermittivityPlus(data = [[1.20, 0.20, 25.0]]),
center = [10, 10, 10],
radius = 4.5))
classical_material.add_component(PolarizableBox(permittivity = PermittivityPlus(data = [[1.40, 0.20, 25.0]]),
corner1 = [18.1, 5.1, 5.1],
corner2 = [22.9, 14.9, 14.9]))
classical_material.add_component(PolarizableEllipsoid(permittivity = PermittivityPlus(data = [[1.60, 0.20, 25.0]]),
center = [30.0, 10.0, 10.0],
radii = [ 3.9, 5.9, 4.9]))
classical_material.add_component(PolarizableRod(permittivity = PermittivityPlus(data = [[1.80, 0.20, 25.0]]),
corners = [[10.0, 21.5, 10.0], [10.0, 33.5, 10.0]],
round_corners = True,
radius = 3.9))
classical_material.add_component(PolarizableRod(permittivity = PermittivityPlus(data = [[1.00, 0.20, 25.0]]),
corners = [[20.0, 21.5, 10.0], [25.0, 33.5, 10.0]],
round_corners = False,