Source code for gpaw.tddft

"""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,
from gpaw.tddft.utils import MultiBlas
from gpaw.tddft.solvers import create_solver
from gpaw.tddft.propagators import \
    create_propagator, \
from gpaw.tddft.tdopers import \
    TimeDependentHamiltonian, \
    TimeDependentOverlap, \
    TimeDependentWaveFunctions, \
    TimeDependentDensity, \
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',

# T^-1
# Bad preconditioner
class KineticEnergyPreconditioner:
    def __init__(self, gd, kin, dtype):
        self.preconditioner = Preconditioner(gd, kin, dtype)

    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.calculate_energy = calculate_energy if'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.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.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.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.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 > 1: self.log('Using Domain Decomposition: %d x %d x %d' % tuple( if > 1: self.log('Parallelization Over bands on %d Processors' % self.log('States per processor =', # 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 =, 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 =[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 *= 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.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)