"""This module implements a class for (true) time-dependent density
functional theory calculations.
"""
import time
import warnings
from math import log
import numpy as np
from gpaw.calculator import GPAW
from gpaw.mixer import DummyMixer
from gpaw.preconditioner import Preconditioner
from gpaw.tddft.units import (attosec_to_autime, autime_to_attosec,
aufrequency_to_eV)
from gpaw.tddft.utils import MultiBlas
from gpaw.tddft.solvers import create_solver
from gpaw.tddft.propagators import \
create_propagator, \
AbsorptionKick
from gpaw.tddft.tdopers import \
TimeDependentHamiltonian, \
TimeDependentOverlap, \
TimeDependentWaveFunctions, \
TimeDependentDensity, \
AbsorptionKickHamiltonian
from gpaw.wavefunctions.fd import FD
from gpaw.tddft.spectrum import photoabsorption_spectrum
from gpaw.lcaotddft.dipolemomentwriter import DipoleMomentWriter
from gpaw.lcaotddft.magneticmomentwriter import MagneticMomentWriter
from gpaw.lcaotddft.restartfilewriter import RestartFileWriter
__all__ = ['TDDFT', 'photoabsorption_spectrum',
'DipoleMomentWriter', 'MagneticMomentWriter',
'RestartFileWriter']
# T^-1
# Bad preconditioner
class KineticEnergyPreconditioner:
def __init__(self, gd, kin, dtype):
self.preconditioner = Preconditioner(gd, kin, dtype)
self.preconditioner.allocate()
def apply(self, kpt, psi, psin):
for i in range(len(psi)):
psin[i][:] = self.preconditioner(psi[i], kpt.phase_cd, None, None)
# S^-1
class InverseOverlapPreconditioner:
"""Preconditioner for TDDFT."""
def __init__(self, overlap):
self.overlap = overlap
def apply(self, kpt, psi, psin):
self.overlap.apply_inverse(psi, psin, kpt)
# ^^^^^^^^^^
class FDTDDFTMode(FD):
def __call__(self, *args, **kwargs):
reuse_wfs_method = kwargs.pop('reuse_wfs_method', None)
assert reuse_wfs_method is None
return TimeDependentWaveFunctions(self.nn, *args, **kwargs)
[docs]class TDDFT(GPAW):
"""Time-dependent density functional theory calculation based on GPAW.
This class is the core class of the time-dependent density functional
theory implementation and is the only class which a user has to use.
"""
def __init__(self, filename: str, *,
td_potential: object = None,
calculate_energy: bool = True,
propagator: dict = None,
solver: dict = None,
tolerance: float = None, # deprecated
parallel: dict = None,
communicator: object = None,
txt: str = '-'):
"""
Parameters
----------
filename
File containing ground state or time-dependent state to propagate.
td_potential
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.
calculate_energy
Whether to calculate energy during propagation.
propagator
Time propagator for the Kohn-Sham wavefunctions.
solver
The iterative linear equations solver for propagator.
tolerance
Deprecated. Do not use this, but use solver dictionary instead.
Tolerance for the linear solver.
parallel
Parallelization options
communicator
MPI communicator
txt
Text output
"""
# Default values
if propagator is None:
propagator = dict(name='SICN')
if solver is None:
solver = dict(name='CSCG', tolerance=1e-8)
assert filename is not None
# For communicating with observers
self.action = ''
self.time = 0.0
self.kick_strength = np.array([0.0, 0.0, 0.0], dtype=float)
self.niter = 0
self.dm_file = None # XXX remove and use observer instead
# Parallelization dictionary should default to strided bands
# but it does not work XXX
# self.default_parallel = GPAW.default_parallel.copy()
# self.default_parallel['stridebands'] = True
self.default_parameters = GPAW.default_parameters.copy()
self.default_parameters['mixer'] = DummyMixer()
self.default_parameters['symmetry'] = {'point_group': False}
self.default_parameters['experimental']['reuse_wfs_method'] = None
# NB: TDDFT restart files contain additional information which
# will override the initial settings for time/kick/niter.
GPAW.__init__(self, filename, parallel=parallel,
communicator=communicator, txt=txt)
assert isinstance(self.wfs, TimeDependentWaveFunctions)
assert isinstance(self.wfs.overlap, TimeDependentOverlap)
self.set_positions()
# Don't be too strict
self.density.charge_eps = 1e-5
self.rank = self.wfs.world.rank
self.calculate_energy = calculate_energy
if self.hamiltonian.xc.name.startswith('GLLB'):
self.log('GLLB model potential. Not updating energy.')
self.calculate_energy = False
# Time-dependent variables and operators
self.td_hamiltonian = TimeDependentHamiltonian(self.wfs, self.spos_ac,
self.hamiltonian,
td_potential)
self.td_density = TimeDependentDensity(self)
# Solver for linear equations
if isinstance(solver, str):
solver = dict(name=solver)
if tolerance is not None:
warnings.warn(
"Please specify the solver tolerance using dictionary "
"solver={'name': name, 'tolerance': tolerance}. "
"Confirm the used tolerance from the output file. "
"The old syntax will throw an error in the future.",
FutureWarning)
solver.update(tolerance=tolerance)
self.solver = create_solver(solver)
# Preconditioner
# No preconditioner as none good found
self.preconditioner = None # TODO! check out SSOR preconditioning
# self.preconditioner = InverseOverlapPreconditioner(self.overlap)
# self.preconditioner = KineticEnergyPreconditioner(
# self.wfs.gd, self.td_hamiltonian.hamiltonian.kin, complex)
# Time propagator
if isinstance(propagator, str):
propagator = dict(name=propagator)
self.propagator = create_propagator(propagator)
self.hpsit = None
self.eps_tmp = None
self.mblas = MultiBlas(self.wfs.gd)
self.tddft_initialized = False
def tddft_init(self):
if self.tddft_initialized:
return
self.log('')
self.log('')
self.log('------------------------------------------')
self.log(' Time-propagation TDDFT ')
self.log('------------------------------------------')
self.log('')
self.log('Charge epsilon:', self.density.charge_eps)
# Density mixer
self.td_density.density.set_mixer(DummyMixer())
# Solver
self.solver.initialize(self.wfs.gd, self.timer)
self.log('Solver:', self.solver.todict())
# Preconditioner
self.log('Preconditioner:', self.preconditioner)
# Propagator
self.propagator.initialize(self.td_density, self.td_hamiltonian,
self.wfs.overlap, self.solver,
self.preconditioner,
self.wfs.gd, self.timer)
self.log('Propagator:', self.propagator.todict())
# Parallelization
wfs = self.wfs
if self.rank == 0:
if wfs.kd.comm.size > 1:
if wfs.nspins == 2:
self.log('Parallelization Over Spin')
if wfs.gd.comm.size > 1:
self.log('Using Domain Decomposition: %d x %d x %d' %
tuple(wfs.gd.parsize_c))
if wfs.bd.comm.size > 1:
self.log('Parallelization Over bands on %d Processors' %
wfs.bd.comm.size)
self.log('States per processor =', wfs.bd.mynbands)
# 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.hamiltonian.poisson.set_density(self.density)
self.hamiltonian.poisson.print_messages(self.log)
self.log.flush()
# Update density and Hamiltonian
self.propagator.update_time_dependent_operators(self.time)
# XXX remove dipole moment handling and use observer instead
self._dm_args0 = (self.density.finegd.integrate(self.density.rhot_g),
self.calculate_dipole_moment())
# Call observers
self.action = 'init'
self.call_observers(self.niter)
self.tddft_initialized = True
def create_wave_functions(self, mode, *args, **kwargs):
mode = FDTDDFTMode(mode.nn, mode.interpolation, True)
GPAW.create_wave_functions(self, mode, *args, **kwargs)
def read(self, filename):
reader = GPAW.read(self, filename)
if 'tddft' in reader:
r = reader.tddft
self.time = r.time
self.niter = r.niter
self.kick_strength = r.kick_strength
def _write(self, writer, mode):
GPAW._write(self, writer, mode)
w = writer.child('tddft')
w.write(time=self.time,
niter=self.niter,
kick_strength=self.kick_strength)
[docs] def propagate(self, time_step: float, iterations: int,
dipole_moment_file: str = None, # deprecated
restart_file: str = None, # deprecated
dump_interval: int = None, # deprecated
):
"""Propagates wavefunctions.
Parameters
----------
time_step
Time step in attoseconds (10^-18 s).
iterations
Number of iterations.
dipole_moment_file
Deprecated. Do not use this.
Name of the data file where to the time-dependent dipole
moment is saved.
restart_file
Deprecated. Do not use this.
Name of the restart file.
dump_interval
Deprecated. Do not use this.
After how many iterations restart data is dumped.
"""
self.tddft_init()
if self.propagator.todict()['name'] in ['EFSICN', 'EFSICN_HGH']:
msg = ("You are using propagator for Ehrenfest dynamics. "
"Please use regular propagator.")
raise RuntimeError(msg)
def warn_deprecated(parameter, observer):
warnings.warn(
f"The {parameter} parameter is deprecated. "
f"Please use {observer} observer instead. "
"The old syntax will throw an error in the future.",
FutureWarning)
if dipole_moment_file is not None:
warn_deprecated('dipole_moment_file', 'DipoleMomentWriter')
if restart_file is not None:
warn_deprecated('restart_file', 'RestartFileWriter')
if dump_interval is not None:
warn_deprecated('dump_interval', 'RestartFileWriter')
else:
dump_interval = 100
if self.rank == 0:
self.log()
self.log('Starting time: %7.2f as'
% (self.time * autime_to_attosec))
self.log('Time step: %7.2f as' % time_step)
header = """\
Simulation Total log10 Iterations:
Time time Energy (eV) Norm Propagator"""
self.log()
self.log(header)
# Convert to atomic units
time_step = time_step * attosec_to_autime
if dipole_moment_file is not None:
self.initialize_dipole_moment_file(dipole_moment_file)
# Set these as class properties for use of observers
self.time_step = time_step
self.dump_interval = dump_interval # XXX remove, deprecated
self.restart_file = restart_file # XXX remove, deprecated
niterpropagator = 0
self.maxiter = self.niter + iterations
# FDTD requires extra care
if self.hamiltonian.poisson.get_description() == 'FDTD+TDDFT':
self.hamiltonian.poisson.set_time(self.time)
self.hamiltonian.poisson.set_time_step(self.time_step)
# The propagate calculation_mode causes classical part to evolve
# in time when self.hamiltonian.poisson.solve(...) is called
self.hamiltonian.poisson.set_calculation_mode('propagate')
# During each time step, self.hamiltonian.poisson.solve may be
# called several times (depending on the used propagator).
# Using the attached observer one ensures that actual propagation
# takes place only once. This is because the FDTDPoissonSolver
# changes the calculation_mode from propagate to
# something else when the propagation is finished.
self.attach(self.hamiltonian.poisson.set_calculation_mode, 1,
'propagate')
self.timer.start('Propagate')
while self.niter < self.maxiter:
norm = self.density.finegd.integrate(self.density.rhot_g)
# Write dipole moment at every iteration
if dipole_moment_file is not None:
if self._dm_args0 is not None:
self.update_dipole_moment_file(*self._dm_args0)
self._dm_args0 = None
else:
dm = self.calculate_dipole_moment()
self.update_dipole_moment_file(norm, dm)
# Propagate the Kohn-Shame wavefunctions a single timestep
niterpropagator = self.propagator.propagate(self.time, time_step)
self.time += time_step
self.niter += 1
# print output (energy etc.) every 10th iteration
if self.niter % 10 == 0:
self.get_td_energy()
T = time.localtime()
if self.rank == 0:
iter_text = 'iter: %3d %02d:%02d:%02d %11.2f' \
' %13.6f %9.1f %10d'
self.log(iter_text %
(self.niter, T[3], T[4], T[5],
self.time * autime_to_attosec,
self.Etot * aufrequency_to_eV,
log(abs(norm) + 1e-16) / log(10),
niterpropagator))
self.log.flush()
# Call registered callback functions
self.action = 'propagate'
self.call_observers(self.niter)
# Write restart data
if restart_file is not None and self.niter % dump_interval == 0:
self.write(restart_file, 'all')
if self.rank == 0:
print('Wrote restart file.')
print(self.niter, ' iterations done. Current time is ',
self.time * autime_to_attosec, ' as.')
self.timer.stop('Propagate')
# Write final results and close dipole moment file
if dipole_moment_file is not None:
# TODO final iteration is propagated, but nothing is updated
# norm = self.density.finegd.integrate(self.density.rhot_g)
# self.finalize_dipole_moment_file(norm)
self.finalize_dipole_moment_file()
# Finalize FDTDPoissonSolver
if self.hamiltonian.poisson.get_description() == 'FDTD+TDDFT':
self.hamiltonian.poisson.finalize_propagation()
if restart_file is not None:
self.write(restart_file, 'all')
def initialize_dipole_moment_file(self, dipole_moment_file):
if self.rank == 0:
if self.dm_file is not None and not self.dm_file.closed:
raise RuntimeError('Dipole moment file is already open')
if self.time == 0.0:
mode = 'w'
else:
# We probably continue from restart
mode = 'a'
self.dm_file = open(dipole_moment_file, mode)
# If the dipole moment file is empty, add a header
if self.dm_file.tell() == 0:
header = '# Kick = [%22.12le, %22.12le, %22.12le]\n' \
% (self.kick_strength[0], self.kick_strength[1],
self.kick_strength[2])
header += '# %15s %15s %22s %22s %22s\n' \
% ('time', 'norm', 'dmx', 'dmy', 'dmz')
self.dm_file.write(header)
self.dm_file.flush()
def calculate_dipole_moment(self):
dm = self.density.finegd.calculate_dipole_moment(self.density.rhot_g)
if self.hamiltonian.poisson.get_description() == 'FDTD+TDDFT':
dm += self.hamiltonian.poisson.get_classical_dipole_moment()
return dm
def update_dipole_moment_file(self, norm, dm):
if self.rank == 0:
line = '%20.8lf %20.8le %22.12le %22.12le %22.12le\n' \
% (self.time, norm, dm[0], dm[1], dm[2])
self.dm_file.write(line)
self.dm_file.flush()
def finalize_dipole_moment_file(self, norm=None):
if norm is not None:
dm = self.calculate_dipole_moment()
self.update_dipole_moment_file(norm, dm)
if self.rank == 0:
self.dm_file.close()
self.dm_file = None
def update_eigenvalues(self):
kpt_u = self.wfs.kpt_u
if self.hpsit is None:
self.hpsit = self.wfs.gd.zeros(len(kpt_u[0].psit_nG),
dtype=complex)
if self.eps_tmp is None:
self.eps_tmp = np.zeros(len(kpt_u[0].eps_n),
dtype=complex)
# self.Eband = sum_i <psi_i|H|psi_j>
for kpt in kpt_u:
self.td_hamiltonian.apply(kpt, kpt.psit_nG, self.hpsit,
calculate_P_ani=False)
self.mblas.multi_zdotc(self.eps_tmp, kpt.psit_nG,
self.hpsit, len(kpt_u[0].psit_nG))
self.eps_tmp *= self.wfs.gd.dv
kpt.eps_n[:] = self.eps_tmp.real
H = self.td_hamiltonian.hamiltonian
# Nonlocal
self.Enlkin = H.xc.get_kinetic_energy_correction()
# PAW
e_band = self.wfs.calculate_band_energy()
self.Ekin = H.e_kinetic0 + e_band + self.Enlkin
self.e_coulomb = H.e_coulomb
self.Eext = H.e_external
self.Ebar = H.e_zero
self.Exc = H.e_xc
self.Etot = self.Ekin + self.e_coulomb + self.Ebar + self.Exc
[docs] def get_td_energy(self):
"""Calculate the time-dependent total energy"""
self.tddft_init()
if not self.calculate_energy:
self.Etot = 0.0
return 0.0
self.wfs.overlap.update(self.wfs)
self.td_density.update()
self.td_hamiltonian.update(self.td_density.get_density(),
self.time)
self.update_eigenvalues()
return self.Etot
def set_absorbing_boundary(self, absorbing_boundary):
self.td_hamiltonian.set_absorbing_boundary(absorbing_boundary)
# exp(ip.r) psi
[docs] def absorption_kick(self, kick_strength):
"""Delta absorption kick for photoabsorption spectrum.
Parameters
----------
kick_strength
Strength of the kick in atomic units
"""
self.tddft_init()
if self.rank == 0:
self.log('Delta kick =', kick_strength)
self.kick_strength = np.array(kick_strength)
abs_kick_hamiltonian = AbsorptionKickHamiltonian(
self.wfs, self.spos_ac,
np.array(kick_strength, float))
abs_kick = AbsorptionKick(self.wfs, abs_kick_hamiltonian,
self.wfs.overlap, self.solver,
self.preconditioner, self.wfs.gd, self.timer)
abs_kick.kick()
# Kick the classical part, if it is present
if self.hamiltonian.poisson.get_description() == 'FDTD+TDDFT':
self.hamiltonian.poisson.set_kick(kick=self.kick_strength)
# Update density and Hamiltonian
self.propagator.update_time_dependent_operators(self.time)
# Call observers after kick
self.action = 'kick'
self.call_observers(self.niter)