solver='BiCGStab',
txt=strbody + '_td.txt',
parallel=parallel)
proj_idx = 50 # atomic index of the projectile
delta_stop = 5.0 / Bohr # stop condition when ion is within 5 A of boundary.
# Setting the initial velocity according to the kinetic energy.
amu_to_aumass = _amu / _me
Mproj = tdcalc.atoms.get_masses()[proj_idx] * amu_to_aumass
Ekin *= 1 / Hartree
v = np.zeros((proj_idx + 1, 3))
v[proj_idx, 2] = -np.sqrt((2 * Ekin) / Mproj) * Bohr / AUT
tdcalc.atoms.set_velocities(v)
evv = EhrenfestVelocityVerlet(tdcalc)
traj = Trajectory(traj_file, 'w', tdcalc.get_atoms())
trajdiv = 1 # number of timesteps between trajectory images
densdiv = 10 # number of timesteps between saved electron densities
niters = 100 # total number of timesteps to propagate
for i in range(niters):
# Stopping condition when projectile z coordinate passes threshold
if evv.x[proj_idx, 2] < delta_stop:
tdcalc.write(strbody + '_end.gpw', mode='all')
break
# Saving trajectory file every trajdiv timesteps
if i % trajdiv == 0:
F_av = evv.F * Hartree / Bohr # forces converted from atomic units
d = 4.0
atoms = Atoms('NaCl', [(0, 0, 0), (0, 0, d)])
atoms.center(vacuum=4.5)
gs_calc = GPAW(nbands=4,
eigensolver='cg',
gpts=(32, 32, 44),
xc='LDA',
setups={'Na': '1'})
atoms.set_calculator(gs_calc)
atoms.get_potential_energy()
gs_calc.write('nacl_gs.gpw', 'all')
td_calc = TDDFT('nacl_gs.gpw', propagator='EFSICN')
evv = EhrenfestVelocityVerlet(td_calc, 0.001)
i = 0
evv.get_energy()
r = evv.x[1][2] - evv.x[0][2]
# print 'E = ', [i, r, evv.Etot, evv.Ekin, evv.e_coulomb]
for i in range(5):
evv.propagate(1.0)
evv.get_energy()
r = evv.x[1][2] - evv.x[0][2]
print('E = ', [i + 1, r, evv.Etot, evv.Ekin, evv.e_coulomb])
equal(r, 7.558883144, 1e-6)
equal(evv.Etot, -0.1036763317, 1e-7)
N_c = 8 * np.round(cell_c / (0.2 * 8))
calc = GPAW(gpts=N_c, nbands=5, basis='dzp', txt=name + '_gs.txt',
eigensolver='rmm-diis')
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write(name + '_gs.gpw', mode='all')
del atoms, calc
time.sleep(10)
while not os.path.isfile(name + '_gs.gpw'):
print('Node %d waiting for file...' % world.rank)
time.sleep(10)
world.barrier()
tdcalc = TDDFT(name + '_gs.gpw', txt=name + '_td.txt', propagator='EFSICN')
ehrenfest = EhrenfestVelocityVerlet(tdcalc)
traj = PickleTrajectory(name + '_td.traj', 'w', tdcalc.get_atoms())
t0 = time.time()
f = paropen(name + '_td.log', 'w')
for i in range(1, niter+1):
ehrenfest.propagate(timestep)
if i % ndiv == 0:
rate = 60 * ndiv / (time.time()-t0)
ekin = tdcalc.atoms.get_kinetic_energy()
epot = tdcalc.get_td_energy() * Hartree
F_av = ehrenfest.F * Hartree / Bohr
print('i=%06d (%6.2f min^-1), ekin=%13.9f, epot=%13.9f, etot=%13.9f' % (i, rate, ekin, epot, ekin+epot), file=f)
t0 = time.time()
from gpaw.tddft.ehrenfest import EhrenfestVelocityVerlet
from gpaw.test import equal
d = 4.0
atoms = Atoms('NaCl', [(0,0,0),(0,0,d)])
atoms.center(vacuum=4.5)
gs_calc = GPAW(nbands=4, eigensolver='cg', gpts=(32, 32, 44), xc='LDA',
setups={'Na': '1'})
atoms.set_calculator(gs_calc)
atoms.get_potential_energy()
gs_calc.write('nacl_gs.gpw', 'all')
td_calc = TDDFT('nacl_gs.gpw', propagator='EFSICN')
evv = EhrenfestVelocityVerlet(td_calc, 0.001)
i=0
evv.get_energy()
r = evv.x[1][2] - evv.x[0][2]
# print 'E = ', [i, r, evv.Etot, evv.Ekin, evv.Epot]
for i in range(5):
evv.propagate(1.0)
evv.get_energy()
r = evv.x[1][2] - evv.x[0][2]
print 'E = ', [i+1, r, evv.Etot, evv.Ekin, evv.Epot]
equal(r, 7.558883144, 1e-7)
equal(evv.Etot, -0.1036763317, 1e-7)
