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)
atoms, qm_spacing, gpts = poissonsolver.cut_cell(atoms, vacuum=2.50)
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]]
# 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',
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(
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},
# Permittivity of Gold
# J. Chem. Phys. 135, 084121 (2011); http://dx.doi.org/10.1063/1.3626549
eps_gold = 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]])
# 1) Nanosphere only
classical_material = PolarizableMaterial()
classical_material.add_component(PolarizableSphere(center=sphere_center,
radius=radius,
permittivity=eps_gold))
qsfdtd = QSFDTD(classical_material=classical_material,
atoms=None,
cells=simulation_cell,
spacings=[2.0, 0.5],
remove_moments=(1, 1))
energy = qsfdtd.ground_state('gs.gpw',
nbands=1)
qsfdtd.time_propagation('gs.gpw',
kick_strength=[0.001, 0.000, 0.000],
time_step=10,
iterations=1500,
# 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())
qsfdtd.time_propagation('gs.gpw', kick_strength=[0.000, 0.000, 0.001], time_step=10, iterations=5, dipole_moment_file='dm.dat', restart_file='td.gpw')
qsfdtd.time_propagation('td.gpw', kick_strength=None, time_step=10, iterations=5, dipole_moment_file='dm.dat')
atoms = Atoms('Na2',
atom_center + np.array([[-1.5, 0.0, 0.0], [1.5, 0.0, 0.0]]))
# Permittivity of Gold
# J. Chem. Phys. 135, 084121 (2011); http://dx.doi.org/10.1063/1.3626549
eps_gold = 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]])
# 3) Nanosphere + Na2
classical_material = PolarizableMaterial()
classical_material.add_component(
PolarizableSphere(center=sphere_center,
radius=radius,
permittivity=eps_gold))
# Combined Poisson solver
poissonsolver = FDTDPoissonSolver(classical_material=classical_material,
qm_spacing=0.5,
cl_spacing=2.0,
cell=simulation_cell,
communicator=world,
remove_moments=(1, 1))
poissonsolver.set_calculation_mode('iterate')
# Combined system
atoms.set_cell(simulation_cell)
atoms, qm_spacing, gpts = poissonsolver.cut_cell(atoms, vacuum=4.0)