Hi,
I am currently working on calculating the phonon band structure for a particular system. However, I encountered a discrepancy between the results obtained using ATK (QuantumATK) and VASP:
ATK Calculation: The phonon band structure shows negative frequencies, suggesting dynamic instability.
VASP Calculation: The phonon band structure does not exhibit these negative frequencies.
For your reference, I have attached the phonon band structures generated by both ATK and VASP. Additionally, I have included the input script used for the ATK calculations below:
-------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------
# Set up lattice
lattice = Hexagonal(6.53017*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]
# Define coordinates
fractional_coordinates = [[ 0. , 0. , 0.420238],
[ 0.095238, 0.47619 , 0.420238],
[ 0.285714, 0.428571, 0.420238],
[ 0.523809, 0.619047, 0.420238],
[ 0.142857, 0.714286, 0.420238],
[ 0.380952, 0.904761, 0.420238],
[ 0.571429, 0.857143, 0.420238],
[ 0.809524, 1.047619, 0.420238],
[ 0.238095, 1.190476, 0.420238],
[ 0.428571, 1.142857, 0.420238],
[ 0.666667, 1.333334, 0.420238],
[ 0.857143, 1.285714, 0.420238],
[ 0.714286, 1.571429, 0.420238],
[ 0.952381, 1.761905, 0.420238],
[ 0. , 0. , 0.579762],
[ 0.190476, 0.238095, 0.579762],
[ 0.142857, 0.428571, 0.579762],
[ 0.333333, 0.666666, 0.579762],
[ 0.571429, 0.714286, 0.579762],
[ 0.761905, 0.952381, 0.579762],
[ 0.047619, 0.809524, 0.579762],
[ 0.285714, 0.857143, 0.579762],
[ 0.47619 , 1.095238, 0.579762],
[ 0.714286, 1.142857, 0.579762],
[ 0.904762, 1.380953, 0.579762],
[ 0.428571, 1.285714, 0.579762],
[ 0.619048, 1.52381 , 0.579762],
[ 0.857143, 1.571429, 0.579762]]
# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
k_point_sampling = MonkhorstPackGrid(
na=7,
nb=7,
)
numerical_accuracy_parameters = NumericalAccuracyParameters(
density_mesh_cutoff=50.0*Hartree,
k_point_sampling=k_point_sampling,
occupation_method=MethfesselPaxton(1000.0*Kelvin*boltzmann_constant, 1),
)
algorithm = PulayMixer(
restart_strategy=AdaptiveHistoryRestart(
effective_rank_fraction=0.0,
),
)
iteration_control_parameters = IterationControlParameters(
tolerance=1e-06,
algorithm=algorithm,
)
#----------------------------------------
# Grimme DFTD3
#----------------------------------------
correction_extension = GrimmeDFTD3(
exchange_correlation=GGA.PBE,
maximum_neighbour_distance=30.0*Ang,
include_three_body_term=False,
)
calculator = LCAOCalculator(
numerical_accuracy_parameters=numerical_accuracy_parameters,
iteration_control_parameters=iteration_control_parameters,
correction_extension=correction_extension,
)
bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('TBG-21-relax.hdf5', bulk_configuration)
# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------
constraints = [FixStrain(x=False, y=False, z=True)]
bulk_configuration = OptimizeGeometry(
bulk_configuration,
max_forces=0.001*eV/Ang,
max_stress=0.1*GPa,
max_steps=200,
max_step_length=0.2*Ang,
constraints=constraints,
trajectory_filename='TBG-21-relax_trajectory.hdf5',
trajectory_interval=5.0*Minute,
restart_strategy=RestartFromTrajectory(),
optimizer_method=LBFGS(),
enable_optimization_stop_file=True,
)
nlsave('TBG-21-relax.hdf5', bulk_configuration)
nlprint(bulk_configuration)
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Analysis from File
# -------------------------------------------------------------
path = '/home/energy/zhenlan/ATK/TBG/21/TBG-21-relax.hdf5'
configuration = nlread(path, object_id='BulkConfiguration_1')[0]
# -------------------------------------------------------------
# Dynamical Matrix
# -------------------------------------------------------------
dynamical_matrix = DynamicalMatrix(
configuration,
filename='TBG-21-dynmat.hdf5',
object_id='dynamical_matrix',
repetitions=(3, 3, 1),
use_symmetry=False,
atomic_displacement=0.01*Angstrom,
acoustic_sum_rule=True,
finite_difference_method=Central,
force_tolerance=1e-08*Hartree/Bohr**2,
processes_per_displacement=4,
log_filename_prefix='forces_displacement_',
use_wigner_seitz_scheme=False,
)
dynamical_matrix.update()
# -------------------------------------------------------------
# Phonon Bandstructure
# -------------------------------------------------------------
phonon_bandstructure = PhononBandstructure(
configuration=configuration,
dynamical_matrix=dynamical_matrix,
route=['G', 'M', 'K', 'G'],
points_per_segment=100,
number_of_bands=All
)
nlsave('TBG-21-dynmat.hdf5', phonon_bandstructure)
If anyone has encountered similar issues or has insights on how to align the settings between ATK and VASP more closely, I would greatly appreciate your input.
Best regards,
ZY
