Source code for gpaw.tddft

"""This module implements a class for (true) time-dependent density
functional theory calculations.

"""
import time
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.bicgstab import BiCGStab
from gpaw.tddft.cscg import CSCG
from gpaw.tddft.propagators import \
    ExplicitCrankNicolson, \
    SemiImplicitCrankNicolson, \
    EhrenfestPAWSICN,\
    EhrenfestHGHSICN,\
    EnforcedTimeReversalSymmetryCrankNicolson, \
    SemiImplicitTaylorExponential, \
    SemiImplicitKrylovExponential, \
    AbsorptionKick
from gpaw.tddft.tdopers import \
    TimeDependentHamiltonian, \
    TimeDependentOverlap, \
    TimeDependentWaveFunctions, \
    TimeDependentDensity, \
    AbsorptionKickHamiltonian
from gpaw.wavefunctions.fd import FD

from gpaw.tddft.spectrum import photoabsorption_spectrum

photoabsorption_spectrum = photoabsorption_spectrum


# 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, 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 # Parallelization dictionary should default to strided bands 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} # 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) if not self.initialized: self.initialize() 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.log 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.spos_ac, 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.bd.comm.size > 1: self.text('Parallelization Over bands on %d Processors' % wfs.bd.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.log.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 def create_wave_functions(self, mode, *args, **kwargs): mode = FDTDDFTMode(mode.nn, mode.interpolation, True) GPAW.create_wave_functions(self, mode, *args, **kwargs)
[docs] def read(self, filename): reader = GPAW.read(self, filename) if 'tddft' in reader: self.time = reader.tddft.time self.niter = reader.tddft.niter self.kick_strength = reader.tddft.kick_strength
[docs] def initialize(self, reading=False): self.parameters.mixer = DummyMixer() self.parameters.experimental['reuse_wfs_method'] = None GPAW.initialize(self, reading=reading)
def _write(self, writer, mode): GPAW._write(self, writer, mode) writer.child('tddft').write(time=self.time, niter=self.niter, kick_strength=self.kick_strength) # Electrodynamics requires extra care def initialize_FDTD(self): # Sanity check assert(self.hamiltonian.poisson.get_description() == 'FDTD+TDDFT') self.hamiltonian.poisson.set_density(self.density) # 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')
[docs] def propagate(self, time_step, iterations, dipole_moment_file=None, restart_file=None, dump_interval=100): """Propagates wavefunctions. Parameters: time_step: float Time step in attoseconds (10^-18 s), e.g., 4.0 or 8.0 iterations: integer Iterations, e.g., 20 000 as / 4.0 as = 5000 dipole_moment_file: string, optional Name of the data file where to the time-dependent dipole moment is saved restart_file: string, optional Name of the restart file dump_interval: integer After how many iterations restart data is dumped """ if self.rank == 0: self.text() self.text('Starting time: %7.2f as' % (self.time * autime_to_attosec)) self.text('Time step: %7.2f as' % time_step) header = """\ Simulation Total log10 Iterations: Time time Energy (eV) Norm Propagator""" self.text() self.text(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 niterpropagator = 0 self.maxiter = self.niter + iterations # Let FDTD part know the time step if self.hamiltonian.poisson.get_description() == 'FDTD+TDDFT': self.hamiltonian.poisson.set_time(self.time) self.hamiltonian.poisson.set_time_step(self.time_step) 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: self.update_dipole_moment_file(norm) # 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.text(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() # Propagate the Kohn-Shame wavefunctions a single timestep niterpropagator = self.propagator.propagate(self.time, time_step) self.time += time_step # Call registered callback functions self.call_observers(self.niter) self.niter += 1 # 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() # Call registered callback functions self.call_observers(self.niter, final=True) 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 update_dipole_moment_file(self, norm): 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() 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: self.update_dipole_moment_file(norm) 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""" if not self.calculate_energy: self.Etot = 0.0 return 0.0 self.td_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: [float, float, float] Strength of the kick, e.g., [0.0, 0.0, 1e-3] """ if self.rank == 0: self.text('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.td_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)