def __init__(self, symbol, f_sln, h=0.05, rcut=10.0, **kwargs):
assert len(f_sln) in [1, 2]
self.symbol = symbol
gd = AtomGridDescriptor(h, rcut)
GPAW.__init__(self,
mode=MakeWaveFunctions(gd),
eigensolver=AtomEigensolver(gd, f_sln),
poissonsolver=AtomPoissonSolver(),
stencils=(1, 9),
nbands=sum([(2 * l + 1) * len(f_n)
for l, f_n in enumerate(f_sln[0])]),
communicator=mpi.serial_comm,
**kwargs)
self.occupations = AtomOccupations(f_sln)
self.initialize(Atoms(symbol, calculator=self))
self.calculate(converge=True)
def __init__(self, symbol, f_sln, h=0.05, rcut=10.0, **kwargs):
assert len(f_sln) in [1, 2]
self.symbol = symbol
gd = AtomGridDescriptor(h, rcut)
GPAW.__init__(self,
mode=MakeWaveFunctions(gd),
eigensolver=AtomEigensolver(gd, f_sln),
poissonsolver=AtomPoissonSolver(),
stencils=(1, 9),
nbands=sum([(2 * l + 1) * len(f_n)
for l, f_n in enumerate(f_sln[0])]),
communicator=mpi.serial_comm,
**kwargs)
self.occupations = AtomOccupations(f_sln)
self.initialize(Atoms(symbol, calculator=self))
self.calculate(converge=True)
def __init__(self, filename, td_potential=None, propagator='SICN',
propagator_kwargs=None, solver='CSCG', tolerance=1e-8,
**kwargs):
"""Create TDDFT-object.
Parameters:
-----------
filename: string
File containing ground state or time-dependent state to propagate
td_potential: class, optional
Function class for the time-dependent potential. Must have a method
'strength(time)' which returns the strength of the linear potential
to each direction as a vector of three floats.
propagator: {'SICN','ETRSCN','ECN','SITE','SIKE4','SIKE5','SIKE6'}
Name of the time propagator for the Kohn-Sham wavefunctions
solver: {'CSCG','BiCGStab'}
Name of the iterative linear equations solver for time propagation
tolerance: float
Tolerance for the linear solver
The following parameters can be used: `txt`, `parallel`, `communicator`
`mixer` and `dtype`. The internal parameters `mixer` and `dtype` are
strictly used to specify a dummy mixer and complex type respectively.
"""
# Set initial time
self.time = 0.0
# Set initial kick strength
self.kick_strength = np.array([0.0, 0.0, 0.0], dtype=float)
# Set initial value of iteration counter
self.niter = 0
# Override default `mixer` and `dtype` given in InputParameters
kwargs.setdefault('mixer', DummyMixer())
kwargs.setdefault('dtype', complex)
# Parallelization dictionary should also default to strided bands
parallel = kwargs.setdefault('parallel', {})
parallel.setdefault('stridebands', True)
# Initialize paw-object without density mixing
# NB: TDDFT restart files contain additional information which
# will override the initial settings for time/kick/niter.
GPAW.__init__(self, filename, **kwargs)
assert isinstance(self.wfs, TimeDependentWaveFunctions)
assert isinstance(self.wfs.overlap, TimeDependentOverlap)
# Prepare for dipole moment file handle
self.dm_file = None
# Initialize wavefunctions and density
# (necessary after restarting from file)
self.set_positions()
# Don't be too strict
self.density.charge_eps = 1e-5
wfs = self.wfs
self.rank = wfs.world.rank
self.text('')
self.text('')
self.text('------------------------------------------')
self.text(' Time-propagation TDDFT ')
self.text('------------------------------------------')
self.text('')
self.text('Charge epsilon: ', self.density.charge_eps)
# Time-dependent variables and operators
self.td_potential = td_potential
self.td_hamiltonian = TimeDependentHamiltonian(self.wfs, self.atoms,
self.hamiltonian, td_potential)
self.td_overlap = self.wfs.overlap #TODO remove this property
self.td_density = TimeDependentDensity(self)
# Solver for linear equations
self.text('Solver: ', solver)
if solver == 'BiCGStab':
self.solver = BiCGStab(gd=wfs.gd, timer=self.timer,
tolerance=tolerance)
elif solver == 'CSCG':
self.solver = CSCG(gd=wfs.gd, timer=self.timer,
tolerance=tolerance)
else:
raise RuntimeError('Solver %s not supported.' % solver)
# Preconditioner
# No preconditioner as none good found
self.text('Preconditioner: ', 'None')
self.preconditioner = None #TODO! check out SSOR preconditioning
#self.preconditioner = InverseOverlapPreconditioner(self.overlap)
#self.preconditioner = KineticEnergyPreconditioner(wfs.gd, self.td_hamiltonian.hamiltonian.kin, np.complex)
# Time propagator
self.text('Propagator: ', propagator)
if propagator_kwargs is None:
propagator_kwargs = {}
if propagator == 'ECN':
self.propagator = ExplicitCrankNicolson(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer, **propagator_kwargs)
elif propagator == 'SICN':
self.propagator = SemiImplicitCrankNicolson(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer, **propagator_kwargs)
elif propagator == 'EFSICN':
self.propagator = EhrenfestPAWSICN(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer, **propagator_kwargs)
elif propagator == 'EFSICN_HGH':
self.propagator = EhrenfestHGHSICN(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer, **propagator_kwargs)
elif propagator == 'ETRSCN':
self.propagator = EnforcedTimeReversalSymmetryCrankNicolson(
self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer, **propagator_kwargs)
elif propagator == 'SITE':
self.propagator = SemiImplicitTaylorExponential(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer, **propagator_kwargs)
elif propagator == 'SIKE':
self.propagator = SemiImplicitKrylovExponential(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer, **propagator_kwargs)
elif propagator.startswith('SITE') or propagator.startswith('SIKE'):
raise DeprecationWarning('Use propagator_kwargs to specify degree.')
else:
raise RuntimeError('Time propagator %s not supported.' % propagator)
if self.rank == 0:
if wfs.kpt_comm.size > 1:
if wfs.nspins == 2:
self.text('Parallelization Over Spin')
if wfs.gd.comm.size > 1:
self.text('Using Domain Decomposition: %d x %d x %d' %
tuple(wfs.gd.parsize_c))
if wfs.band_comm.size > 1:
self.text('Parallelization Over bands on %d Processors' %
wfs.band_comm.size)
self.text('States per processor = ', wfs.bd.mynbands)
self.hpsit = None
self.eps_tmp = None
self.mblas = MultiBlas(wfs.gd)
def __init__(self, *args, **kwargs):
sys.stderr.write('Please start using GPAW instead of Calculator!\n')
GPAW.__init__(self, *args, **kwargs)
def __init__(self, *args, **kwargs):
sys.stderr.write('Please start using GPAW instead of Calculator!\n')
GPAW.__init__(self, *args, **kwargs)
def __init__(self, ground_state_file=None, txt='-', td_potential=None,
propagator='SICN', solver='CSCG', tolerance=1e-8,
parsize=None, parsize_bands=1, parstride_bands=True,
communicator=None):
"""Create TDDFT-object.
Parameters:
-----------
ground_state_file: string
File name for the ground state data
td_potential: class, optional
Function class for the time-dependent potential. Must have a method
'strength(time)' which returns the strength of the linear potential
to each direction as a vector of three floats.
propagator: {'SICN','ETRSCN','ECN','SITE','SIKE4','SIKE5','SIKE6'}
Name of the time propagator for the Kohn-Sham wavefunctions
solver: {'CSCG','BiCGStab'}
Name of the iterative linear equations solver for time propagation
tolerance: float
Tolerance for the linear solver
"""
if ground_state_file is None:
raise RuntimeError('TDDFT calculation has to start from converged '
'ground or excited state restart file')
# Set initial time
self.time = 0.0
# Set initial kick strength
self.kick_strength = np.array([0.0, 0.0, 0.0], dtype=float)
# Set initial value of iteration counter
self.niter = 0
# Initialize paw-object without density mixing
# NB: TDDFT restart files contain additional information which
# will override the initial settings for time/kick/niter.
GPAW.__init__(self, ground_state_file, txt=txt, mixer=DummyMixer(),
parallel={'domain': parsize, 'band': parsize_bands,
'stridebands': parstride_bands},
communicator=communicator, dtype=complex)
# Prepare for dipole moment file handle
self.dm_file = None
# Initialize wavefunctions and density
# (necessary after restarting from file)
self.set_positions()
# Don't be too strict
self.density.charge_eps = 1e-5
wfs = self.wfs
self.rank = wfs.world.rank
# Convert PAW-object to complex
if wfs.dtype == float:
raise DeprecationWarning('This should not happen.')
wfs.dtype = complex
from gpaw.fd_operators import Laplace
nn = self.input_parameters.stencils[0]
wfs.kin = Laplace(wfs.gd, -0.5, nn, complex)
wfs.pt = LFC(wfs.gd, [setup.pt_j for setup in wfs.setups],
self.kpt_comm, dtype=complex)
for kpt in wfs.kpt_u:
for a,P_ni in kpt.P_ani.items():
assert not np.isnan(P_ni).any()
kpt.P_ani[a] = np.array(P_ni, complex)
self.set_positions()
# Wave functions
for kpt in wfs.kpt_u:
kpt.psit_nG = np.array(kpt.psit_nG[:], complex)
self.text('')
self.text('')
self.text('------------------------------------------')
self.text(' Time-propagation TDDFT ')
self.text('------------------------------------------')
self.text('')
self.text('Charge epsilon: ', self.density.charge_eps)
# Time-dependent variables and operators
self.td_potential = td_potential
self.td_hamiltonian = TimeDependentHamiltonian(self.wfs, self.atoms,
self.hamiltonian, td_potential)
self.td_overlap = TimeDependentOverlap(self.wfs)
self.td_density = TimeDependentDensity(self)
# Solver for linear equations
self.text('Solver: ', solver)
if solver is 'BiCGStab':
self.solver = BiCGStab(gd=wfs.gd, timer=self.timer,
tolerance=tolerance)
elif solver is 'CSCG':
self.solver = CSCG(gd=wfs.gd, timer=self.timer,
tolerance=tolerance)
else:
raise RuntimeError('Solver %s not supported.' % solver)
# Preconditioner
# No preconditioner as none good found
self.text('Preconditioner: ', 'None')
self.preconditioner = None #TODO! check out SSOR preconditioning
#self.preconditioner = InverseOverlapPreconditioner(self.overlap)
#self.preconditioner = KineticEnergyPreconditioner(wfs.gd, self.td_hamiltonian.hamiltonian.kin, np.complex)
# Time propagator
self.text('Propagator: ', propagator)
if propagator is 'ECN':
self.propagator = ExplicitCrankNicolson(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer)
elif propagator is 'SICN':
self.propagator = SemiImplicitCrankNicolson(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer)
elif propagator is 'ETRSCN':
self.propagator = EnforcedTimeReversalSymmetryCrankNicolson(
self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer)
elif propagator in ['SITE4', 'SITE']:
self.propagator = SemiImplicitTaylorExponential(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer, degree = 4)
elif propagator in ['SIKE4', 'SIKE']:
self.propagator = SemiImplicitKrylovExponential(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer, degree = 4)
elif propagator is 'SIKE5':
self.propagator = SemiImplicitKrylovExponential(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer, degree = 5)
elif propagator is 'SIKE6':
self.propagator = SemiImplicitKrylovExponential(self.td_density,
self.td_hamiltonian, self.td_overlap, self.solver,
self.preconditioner, wfs.gd, self.timer, degree = 6)
else:
raise RuntimeError('Time propagator %s not supported.' % propagator)
if self.rank == 0:
if wfs.kpt_comm.size > 1:
if wfs.nspins == 2:
self.text('Parallelization Over Spin')
if wfs.gd.comm.size > 1:
self.text('Using Domain Decomposition: %d x %d x %d' %
tuple(wfs.gd.parsize_c))
if wfs.band_comm.size > 1:
self.text('Parallelization Over bands on %d Processors' %
wfs.band_comm.size)
self.text('States per processor = ', wfs.mynbands)
self.hpsit = None
self.eps_tmp = None
self.mblas = MultiBlas(wfs.gd)
def __init__(self,
filename,
td_potential=None,
propagator='SICN',
calculate_energy=True,
propagator_kwargs=None,
solver='CSCG',
tolerance=1e-8,
**kwargs):
"""Create TDDFT-object.
Parameters:
filename: string
File containing ground state or time-dependent state to propagate
td_potential: class, optional
Function class for the time-dependent potential. Must have a method
'strength(time)' which returns the strength of the linear potential
to each direction as a vector of three floats.
propagator: {'SICN','ETRSCN','ECN','SITE','SIKE4','SIKE5','SIKE6'}
Name of the time propagator for the Kohn-Sham wavefunctions
solver: {'CSCG','BiCGStab'}
Name of the iterative linear equations solver for time propagation
tolerance: float
Tolerance for the linear solver
The following parameters can be used: `txt`, `parallel`, `communicator`
`mixer` and `dtype`. The internal parameters `mixer` and `dtype` are
strictly used to specify a dummy mixer and complex type respectively.
"""
# Set initial time
self.time = 0.0
# Set initial kick strength
self.kick_strength = np.array([0.0, 0.0, 0.0], dtype=float)
# Set initial value of iteration counter
self.niter = 0
# Override default `mixer` and `dtype` given in InputParameters
kwargs.setdefault('mixer', DummyMixer())
kwargs.setdefault('dtype', complex)
# Parallelization dictionary should also default to strided bands
parallel = kwargs.setdefault('parallel', {})
parallel.setdefault('stridebands', True)
# Initialize paw-object without density mixing
# NB: TDDFT restart files contain additional information which
# will override the initial settings for time/kick/niter.
GPAW.__init__(self, filename, **kwargs)
assert isinstance(self.wfs, TimeDependentWaveFunctions)
assert isinstance(self.wfs.overlap, TimeDependentOverlap)
# Prepare for dipole moment file handle
self.dm_file = None
# Initialize wavefunctions and density
# (necessary after restarting from file)
self.set_positions()
# Don't be too strict
self.density.charge_eps = 1e-5
wfs = self.wfs
self.rank = wfs.world.rank
self.text('')
self.text('')
self.text('------------------------------------------')
self.text(' Time-propagation TDDFT ')
self.text('------------------------------------------')
self.text('')
self.text('Charge epsilon: ', self.density.charge_eps)
# Time-dependent variables and operators
self.td_potential = td_potential
self.td_hamiltonian = TimeDependentHamiltonian(self.wfs, self.atoms,
self.hamiltonian,
td_potential)
self.td_overlap = self.wfs.overlap #TODO remove this property
self.td_density = TimeDependentDensity(self)
# Solver for linear equations
self.text('Solver: ', solver)
if solver == 'BiCGStab':
self.solver = BiCGStab(gd=wfs.gd,
timer=self.timer,
tolerance=tolerance)
elif solver == 'CSCG':
self.solver = CSCG(gd=wfs.gd,
timer=self.timer,
tolerance=tolerance)
else:
raise RuntimeError('Solver %s not supported.' % solver)
# Preconditioner
# No preconditioner as none good found
self.text('Preconditioner: ', 'None')
self.preconditioner = None #TODO! check out SSOR preconditioning
#self.preconditioner = InverseOverlapPreconditioner(self.overlap)
#self.preconditioner = KineticEnergyPreconditioner(wfs.gd, self.td_hamiltonian.hamiltonian.kin, np.complex)
# Time propagator
self.text('Propagator: ', propagator)
if propagator_kwargs is None:
propagator_kwargs = {}
if propagator == 'ECN':
self.propagator = ExplicitCrankNicolson(
self.td_density, self.td_hamiltonian, self.td_overlap,
self.solver, self.preconditioner, wfs.gd, self.timer,
**propagator_kwargs)
elif propagator == 'SICN':
self.propagator = SemiImplicitCrankNicolson(
self.td_density, self.td_hamiltonian, self.td_overlap,
self.solver, self.preconditioner, wfs.gd, self.timer,
**propagator_kwargs)
elif propagator == 'EFSICN':
self.propagator = EhrenfestPAWSICN(self.td_density,
self.td_hamiltonian,
self.td_overlap, self.solver,
self.preconditioner, wfs.gd,
self.timer, **propagator_kwargs)
elif propagator == 'EFSICN_HGH':
self.propagator = EhrenfestHGHSICN(self.td_density,
self.td_hamiltonian,
self.td_overlap, self.solver,
self.preconditioner, wfs.gd,
self.timer, **propagator_kwargs)
elif propagator == 'ETRSCN':
self.propagator = EnforcedTimeReversalSymmetryCrankNicolson(
self.td_density, self.td_hamiltonian, self.td_overlap,
self.solver, self.preconditioner, wfs.gd, self.timer,
**propagator_kwargs)
elif propagator == 'SITE':
self.propagator = SemiImplicitTaylorExponential(
self.td_density, self.td_hamiltonian, self.td_overlap,
self.solver, self.preconditioner, wfs.gd, self.timer,
**propagator_kwargs)
elif propagator == 'SIKE':
self.propagator = SemiImplicitKrylovExponential(
self.td_density, self.td_hamiltonian, self.td_overlap,
self.solver, self.preconditioner, wfs.gd, self.timer,
**propagator_kwargs)
elif propagator.startswith('SITE') or propagator.startswith('SIKE'):
raise DeprecationWarning(
'Use propagator_kwargs to specify degree.')
else:
raise RuntimeError('Time propagator %s not supported.' %
propagator)
if self.rank == 0:
if wfs.kd.comm.size > 1:
if wfs.nspins == 2:
self.text('Parallelization Over Spin')
if wfs.gd.comm.size > 1:
self.text('Using Domain Decomposition: %d x %d x %d' %
tuple(wfs.gd.parsize_c))
if wfs.band_comm.size > 1:
self.text('Parallelization Over bands on %d Processors' %
wfs.band_comm.size)
self.text('States per processor = ', wfs.bd.mynbands)
self.hpsit = None
self.eps_tmp = None
self.mblas = MultiBlas(wfs.gd)
# Restarting an FDTD run generates hamiltonian.fdtd_poisson, which now overwrites hamiltonian.poisson
if hasattr(self.hamiltonian, 'fdtd_poisson'):
self.hamiltonian.poisson = self.hamiltonian.fdtd_poisson
self.hamiltonian.poisson.set_grid_descriptor(self.density.finegd)
# For electrodynamics mode
if self.hamiltonian.poisson.get_description() == 'FDTD+TDDFT':
self.initialize_FDTD()
self.hamiltonian.poisson.print_messages(self.text)
self.txt.flush()
self.calculate_energy = calculate_energy
if self.hamiltonian.xc.name.startswith('GLLB'):
self.text("GLLB model potential. Not updating energy.")
self.calculate_energy = False
