Dear all,
I am currently working on a phonon band structure calculation. Unfortunately, the process stopped before completion. I would like to restart it but couldn't find instructions on how to do so in the tutorial. Below is the script I am using.
# Set up lattice
lattice = Hexagonal(10.7585*Angstrom, 21.0*Angstrom)
# Define elements
elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon]
# Define coordinates
fractional_coordinates = [[ 0. , 0. , 0.42024],
[ 0.03509, 0.2807 , 0.42024],
[ 0.15789, 0.26315, 0.42024],
[ 0.29825, 0.38597, 0.42024],
[ 0.05263, 0.42105, 0.42024],
[ 0.19298, 0.54386, 0.42024],
[ 0.31579, 0.52632, 0.42024],
[ 0.45614, 0.64912, 0.42024],
[ 0.57895, 0.63158, 0.42024],
[ 0.7193 , 0.75439, 0.42024],
[ 0.08772, 0.70176, 0.42024],
[ 0.21053, 0.68421, 0.42024],
[ 0.35088, 0.80702, 0.42024],
[ 0.47368, 0.78947, 0.42024],
[ 0.61404, 0.91229, 0.42024],
[ 0.73684, 0.89473, 0.42024],
[ 0.87719, 1.01754, 0.42024],
[ 0.10526, 0.8421 , 0.42024],
[ 0.24561, 0.96491, 0.42024],
[ 0.36842, 0.94737, 0.42024],
[ 0.50877, 1.07017, 0.42024],
[ 0.63158, 1.05263, 0.42024],
[ 0.77193, 1.17544, 0.42024],
[ 0.89474, 1.1579 , 0.42024],
[ 0.14035, 1.12281, 0.42024],
[ 0.26316, 1.10527, 0.42024],
[ 0.40351, 1.22807, 0.42024],
[ 0.52632, 1.21053, 0.42024],
[ 0.66667, 1.33334, 0.42024],
[ 0.78947, 1.31579, 0.42024],
[ 0.92982, 1.43859, 0.42024],
[ 0.42105, 1.36842, 0.42024],
[ 0.5614 , 1.49122, 0.42024],
[ 0.68421, 1.47368, 0.42024],
[ 0.82456, 1.59649, 0.42024],
[ 0.94737, 1.57895, 0.42024],
[ 0.84211, 1.73685, 0.42024],
[ 0.98246, 1.85965, 0.42024],
[ 0. , 0. , 0.57976],
[ 0.12281, 0.14035, 0.57976],
[ 0.10526, 0.26315, 0.57976],
[ 0.22807, 0.40351, 0.57976],
[ 0.36842, 0.42105, 0.57976],
[ 0.49123, 0.56141, 0.57976],
[ 0.07018, 0.50878, 0.57976],
[ 0.21053, 0.52632, 0.57976],
[ 0.33333, 0.66666, 0.57976],
[ 0.47368, 0.68421, 0.57976],
[ 0.59649, 0.82456, 0.57976],
[ 0.73684, 0.8421 , 0.57976],
[ 0.85965, 0.98246, 0.57976],
[ 0.05263, 0.63158, 0.57976],
[ 0.17544, 0.77193, 0.57976],
[ 0.31579, 0.78947, 0.57976],
[ 0.4386 , 0.92983, 0.57976],
[ 0.57895, 0.94737, 0.57976],
[ 0.70175, 1.08771, 0.57976],
[ 0.84211, 1.10527, 0.57976],
[ 0.96491, 1.24561, 0.57976],
[ 0.01754, 0.87719, 0.57976],
[ 0.15789, 0.89473, 0.57976],
[ 0.2807 , 1.03509, 0.57976],
[ 0.42105, 1.05263, 0.57976],
[ 0.54386, 1.19298, 0.57976],
[ 0.68421, 1.21053, 0.57976],
[ 0.80702, 1.35088, 0.57976],
[ 0.94737, 1.36842, 0.57976],
[ 0.26316, 1.1579 , 0.57976],
[ 0.38596, 1.29824, 0.57976],
[ 0.52632, 1.31579, 0.57976],
[ 0.64912, 1.45614, 0.57976],
[ 0.78947, 1.47368, 0.57976],
[ 0.91228, 1.61403, 0.57976],
[ 0.63158, 1.57895, 0.57976],
[ 0.75439, 1.7193 , 0.57976],
[ 0.89474, 1.73685, 0.57976]]
# Set up configuration
tbg13cif = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)
tbg13cif_name = "tbg13cif"
# %% Set LCAOCalculator
# %% LCAOCalculator
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = GGA.PBE
correction_extension = GrimmeDFTD3(
exchange_correlation=exchange_correlation
)
k_point_sampling = MonkhorstPackGrid(
na=5,
nb=5,
nc=1
)
numerical_accuracy_parameters = NumericalAccuracyParameters(
density_mesh_cutoff=70.0*Hartree,
k_point_sampling=k_point_sampling
)
iteration_control_parameters = IterationControlParameters(
tolerance=1e-06
)
calculator = LCAOCalculator(
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=numerical_accuracy_parameters,
iteration_control_parameters=iteration_control_parameters,
checkpoint_handler=NoCheckpointHandler,
correction_extension=correction_extension
)
# %% Set Calculator
tbg13cif.setCalculator(calculator)
tbg13cif.update()
nlsave('TBG-13-ocu-relax-dyn.hdf5', tbg13cif)
# %% OptimizeGeometry
restart_strategy = RestartFromTrajectory(
trajectory_filename='TBG-13-ocu-relax-dyn.hdf5',
object_id='optimize_trajectory'
)
optimized_configuration = OptimizeGeometry(
configuration=tbg13cif,
max_forces=0.001*eV/Angstrom,
constraints=[
FixStrain(False, False, True)
],
trajectory_filename='TBG-13-ocu-relax-dyn.hdf5',
trajectory_object_id='optimize_trajectory',
optimize_cell=True,
restart_strategy=restart_strategy
)
nlsave('TBG-13-ocu-relax-dyn.hdf5', optimized_configuration)
# %% Bandstructure
bandstructure = Bandstructure(
configuration=optimized_configuration,
route=['G', 'M', 'K', 'G']
)
nlsave('TBG-13-ocu-relax-dyn.hdf5', bandstructure)
# %% DynamicalMatrix
dynamical_matrix = DynamicalMatrix(
configuration=optimized_configuration,
filename='TBG-13-ocu-relax-dyn.hdf5',
object_id='dm',
calculator=calculator,
repetitions=(3, 3, 1),
processes_per_displacement=8
)
dynamical_matrix.update()
# %% PhononBandstructure
phonon_bandstructure = PhononBandstructure(
dynamical_matrix=dynamical_matrix,
configuration=optimized_configuration,
route=['G', 'M', 'K', 'G'],
points_per_segment=100
)
nlsave('TBG-13-ocu-relax-dyn.hdf5', phonon_bandstructure)
Thank you for your assistance!
Best regards,
Zy
