def __init__(self,
nn=3,
relax='J',
eps=1e-24,
classical_material=None,
cell=None,
qm_spacing=0.30,
cl_spacing=1.20,
remove_moments=(1, 1),
potential_coupler='Refiner',
communicator=serial_comm):
self.rank = mpi.rank
self.messages = []
assert (potential_coupler in ['Multipoles', 'Refiner'])
self.potential_coupling_scheme = potential_coupler
if classical_material is None:
self.classical_material = PolarizableMaterial()
else:
self.classical_material = classical_material
self.set_calculation_mode('solve')
self.has_subsystems = False
self.remove_moment_cl = remove_moments[0]
self.remove_moment_qm = remove_moments[1]
self.time = 0.0
self.time_step = 0.0
self.kick = np.array([0.0, 0.0, 0.0], dtype=float)
self.maxiter = 2000
self.eps = eps
self.relax = relax
self.nn = nn
# Only handle the quantities via self.qm or self.cl
self.cl = PoissonOrganizer()
self.cl.spacing_def = cl_spacing * np.ones(3) / Bohr
self.cl.extrapolated_qm_phi = None
self.cl.dcomm = communicator
self.cl.dparsize = None
self.qm = PoissonOrganizer(FDPoissonSolver) # Default solver
self.qm.spacing_def = qm_spacing * np.ones(3) / Bohr
self.qm.cell = np.array(cell) / Bohr
# Classical spacing and simulation cell
_cell = np.array(cell) / Bohr
self.cl.spacing = self.cl.spacing_def
if np.size(_cell) == 3:
self.cl.cell = np.diag(_cell)
else:
self.cl.cell = _cell
# Generate classical grid descriptor
self.initialize_clgd()
# Whole simulation cell (Angstroms)
large_cell = np.array([3 * radius, 3 * radius, 3 * radius])
# 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]]
# 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))
def read(self, reader):
r = reader.hamiltonian.poisson
# FDTDPoissonSolver related data
self.description = r.description
self.time = r.time
self.time_step = r.time_step
# Try to read time-dependent information
self.kick = r.kick
self.maxiter = r.maxiter
# PoissonOrganizer: classical
self.cl = PoissonOrganizer()
self.cl.spacing_def = r.cl_spacing_def
self.cl.spacing = r.cl_spacing
self.cl.cell = np.diag(r.cl_cell)
self.cl.dparsize = None
# TODO: it should be possible to use different
# communicator after restart
if r.cl_world_comm:
self.cl.dcomm = world
else:
self.cl.dcomm = mpi.serial_comm
# Generate classical grid descriptor
self.initialize_clgd()
# Classical materials data
self.classical_material = PolarizableMaterial()
self.classical_material.read(r)
self.classical_material.initialize(self.cl.gd)
# PoissonOrganizer: quantum
self.qm = PoissonOrganizer()
self.qm.corner1 = r.qm_corner1
self.qm.corner2 = r.qm_corner2
self.given_corner_v1 = r.given_corner_1
self.given_corner_v2 = r.given_corner_2
self.given_cell = np.diag(r.given_cell)
self.hratios = r.hratios
self.shift_indices_1 = r.shift_indices_1.astype(int)
self.shift_indices_2 = r.shift_indices_2.astype(int)
self.num_indices = r.num_indices.astype(int)
self.num_refinements = int(r.num_refinements)
# Redefine atoms to suit the cut_cell routine
newatoms = read_atoms(reader.atoms)
newatoms.positions = newatoms.positions + self.qm.corner1 * Bohr
newatoms.set_cell(np.diag(self.given_cell))
self.create_subsystems(newatoms)
# Read self.classical_material.charge_density
if self.cl.gd.comm.rank == 0:
big_charge_density = \
np.array(r.get('classical_material_rho'), dtype=float)
else:
big_charge_density = None
self.cl.gd.distribute(big_charge_density,
self.classical_material.charge_density)
# Read self.classical_material.polarization_total
if self.cl.gd.comm.rank == 0:
big_polarization_total = \
np.array(r.get('polarization_total'), dtype=float)
else:
big_polarization_total = None
self.cl.gd.distribute(big_polarization_total,
self.classical_material.polarization_total)
# Read self.classical_material.polarizations
if self.cl.gd.comm.rank == 0:
big_polarizations = np.array(r.get('polarizations'), dtype=float)
else:
big_polarizations = None
self.cl.gd.distribute(big_polarizations,
self.classical_material.polarizations)
# Read self.classical_material.currents
if self.cl.gd.comm.rank == 0:
big_currents = np.array(r.get('currents'), dtype=float)
else:
big_currents = None
self.cl.gd.distribute(big_currents, self.classical_material.currents)
def read(self, paw, reader):
r = reader
version = r['version']
# Helper function
def read_vector(v):
return np.array([
float(x) for x in v.replace('[', '').replace(']', '').split()
])
# FDTDPoissonSolver related data
self.eps = r['fdtd.eps']
self.nn = r['fdtd.nn']
self.relax = r['fdtd.relax']
self.potential_coupling_scheme = r['fdtd.coupling_scheme']
self.description = r['fdtd.description']
self.remove_moment_qm = int(r['fdtd.remove_moment_qm'])
self.remove_moment_cl = int(r['fdtd.remove_moment_cl'])
self.time = float(r['fdtd.time'])
self.time_step = float(r['fdtd.time_step'])
# Try to read time-dependent information
self.kick = read_vector(r['fdtd.kick'])
self.maxiter = int(r['fdtd.maxiter'])
# PoissonOrganizer: classical
self.cl = PoissonOrganizer()
self.cl.spacing_def = read_vector(r['fdtd.cl_spacing_def'])
self.cl.spacing = read_vector(r['fdtd.cl_spacing'])
self.cl.cell = np.diag(read_vector(r['fdtd.cl_cell']))
self.cl.dparsize = None
# TODO: it should be possible to use different
# communicator after restart
if r['fdtd.cl_world_comm']:
self.cl.dcomm = world
else:
self.cl.dcomm = mpi.serial_comm
# Generate classical grid descriptor
self.initialize_clgd()
# Classical materials data
self.classical_material = PolarizableMaterial()
self.classical_material.read(r)
self.classical_material.initialize(self.cl.gd)
# PoissonOrganizer: quantum
self.qm = PoissonOrganizer()
self.qm.corner1 = read_vector(r['fdtd.qm_corner1'])
self.qm.corner2 = read_vector(r['fdtd.qm_corner2'])
self.given_corner_v1 = read_vector(r['fdtd.given_corner_1'])
self.given_corner_v2 = read_vector(r['fdtd.given_corner_2'])
self.given_cell = np.diag(read_vector(r['fdtd.given_cell']))
self.hratios = read_vector(r['fdtd.hratios'])
self.shift_indices_1 = read_vector(r['fdtd.shift_indices_1'])
self.shift_indices_2 = read_vector(r['fdtd.shift_indices_2'])
self.num_indices = read_vector(r['fdtd.num_indices'])
self.num_refinements = int(r['fdtd.num_refinements'])
# Redefine atoms to suit the cut_cell routine
newatoms = paw.atoms.copy()
newatoms.positions = newatoms.positions + self.qm.corner1 * Bohr
newatoms.set_cell(np.diag(self.given_cell))
self.create_subsystems(newatoms)
# Read self.classical_material.charge_density
if self.cl.gd.comm.rank == 0:
big_charge_density = np.array(r.get('classical_material_rho'),
dtype=float)
else:
big_charge_density = None
self.cl.gd.distribute(big_charge_density,
self.classical_material.charge_density)
# Read self.classical_material.polarization_total
if self.cl.gd.comm.rank == 0:
big_polarization_total = np.array(r.get('polarization_total'),
dtype=float)
else:
big_polarization_total = None
self.cl.gd.distribute(big_polarization_total,
self.classical_material.polarization_total)
# Read self.classical_material.polarizations
if self.cl.gd.comm.rank == 0:
big_polarizations = np.array(r.get('polarizations'), dtype=float)
else:
big_polarizations = None
self.cl.gd.distribute(big_polarizations,
self.classical_material.polarizations)
# Read self.classical_material.currents
if self.cl.gd.comm.rank == 0:
big_currents = np.array(r.get('currents'), dtype=float)
else:
big_currents = None
self.cl.gd.distribute(big_currents, self.classical_material.currents)