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1

General Questions and Answers / localized charge setting in complex vdW stacking supercells

« on: May 2, 2023, 06:26 »

Dear all, I need to applied nonzero charge on the sublayer in a vdW stacking supercell. Is it possible to do this operation in QuantumATK 2018.06? Or is there any script to achieve this?

2

General Questions and Answers / Difficult to converge in spin-polarized two-probe system

« on: December 13, 2022, 13:32 »

Hi all,

I am calculating the zero-bias transmission spectra of two-probe MBHT system. It is very difficult to converge and very low-efficient, even though I have set many computational parameters higher than the guide in https://docs.quantumatk.com/manual/technicalnotes/spin_polarized_negf_convergence_guide/spin_polarized_negf_convergence_guide.html. To make it converge more quick, I have even reduced the convergence criteria, but still failed to accelerate the calculation. The attachment is my script.
Is there any method for me to achieve a faster and more reliable convergence? It seems that SGGA calculation spends too much time. If I choose LSDA, is there any method to achiev a faster and more reliable convergence.

3

General Questions and Answers / error in PDOS calculation

« on: December 8, 2022, 13:11 »

Dear all,

I built a script to customize the PDOS of a spin-polarized nanoribbon. But an error occurs.
How can I modify the PDOS script to make it run correctly.
The error information is as follows:

Traceback (most recent call last):
File "/public/home/heyy/ATKJOBS/221208-LGvHMutP/pdos-z-GN-1.py", line 126, in <module>
Traceback (most recent call last):
File "/public/home/heyy/ATKJOBS/221208-LGvHMutP/pdos-z-GN-1.py", line 126, in <module>
Traceback (most recent call last):
File "/public/home/heyy/ATKJOBS/221208-LGvHMutP/pdos-z-GN-1.py", line 126, in <module>
projection_list = Projection(atom=[Carbon], l_quantum_numbers=[1], m_quantum_numbers=[-1, 0, 1], spin=Spin.up)
AttributeError: 'module' object has no attribute 'up'
projection_list = Projection(atom=[Carbon], l_quantum_numbers=[1], m_quantum_numbers=[-1, 0, 1], spin=Spin.up)
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2

4

General Questions and Answers / LDOS calculation of a spin-polarized bulk in older version

« on: November 30, 2022, 15:45 »

Hi all,

I have read the tutorial:
http://docs.quantumatk.com/tutorials/tamr_ldos/tamr_ldos.html#stm-simulations-of-tunneling-anisotropic-magneto-resistance-tamr. This is new for QuantumATK S-2021.06.

The script W8_Fe2_Co.py in the tutorial can not run in 2018 version. Is it possible to modify the script to run in 2018 version? If possible, how can I modify it?

The original script of W8_Fe2_Co.py in 2021 version is:
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------

angles = [(0,0), (90, 150)]

for (theta, phi) in angles:
filename = 'W8-Fe2-Co-2x2-theta_{}-phi_{}.hdf5'.format(theta, phi)

# Set up lattice
vector_a = [5.482287216117011, 0.0, 0.0]*Angstrom
vector_b = [-1.827429072039004, 5.168749955904878, 0.0]*Angstrom
vector_c = [0.0, 0.0, 44.9670510707337]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Tungsten, Tungsten, Tungsten, Tungsten, Tungsten, Tungsten,
Tungsten, Tungsten, Tungsten, Tungsten, Tungsten, Tungsten,
Tungsten, Tungsten, Tungsten, Tungsten, Tungsten, Tungsten,
Tungsten, Tungsten, Tungsten, Tungsten, Tungsten, Tungsten,
Tungsten, Tungsten, Tungsten, Tungsten, Tungsten, Tungsten,
Tungsten, Tungsten, Iron, Iron, Iron, Iron, Iron, Iron, Iron, Iron,
Cobalt]

# Define coordinates
fractional_coordinates = [[ 0.25 , 0.25 , 0.30118631364 ],
[ 0.25 , 0.75 , 0.301186278457],
[ 0.75 , 0.25 , 0.301186278457],
[ 0.75 , 0.75 , 0.301186242332],
[-0.000000998907, -0.000000998907, 0.350454016187],
[-0.000000503015, 0.500000503015, 0.350454015157],
[ 0.500000503015, -0.000000503015, 0.350454015157],
[ 0.500000998907, 0.500000998907, 0.350454016187],
[ 0.25 , 0.25 , 0.400260701577],
[ 0.25 , 0.75 , 0.400261649879],
[ 0.75 , 0.25 , 0.400261649879],
[ 0.75 , 0.75 , 0.400262571411],
[ 0.000013667016, 0.000013667016, 0.450062461809],
[ 0.000006758676, 0.499993241324, 0.450062741191],
[ 0.499993241324, 0.000006758676, 0.450062741191],
[ 0.499986332984, 0.499986332984, 0.450062461809],
[ 0.25 , 0.25 , 0.499890596355],
[ 0.25 , 0.75 , 0.49988412114 ],
[ 0.75 , 0.25 , 0.49988412114 ],
[ 0.75 , 0.75 , 0.499873815331],
[-0.000133552734, -0.000133552734, 0.54969793658 ],
[-0.000065862576, 0.500065862576, 0.549705930495],
[ 0.500065862576, -0.000065862576, 0.549705930495],
[ 0.500133552734, 0.500133552734, 0.54969793658 ],
[ 0.25 , 0.25 , 0.599373131644],
[ 0.25 , 0.75 , 0.599538357583],
[ 0.75 , 0.25 , 0.599538357583],
[ 0.75 , 0.75 , 0.599633530735],
[ 0.003412645763, 0.003412645763, 0.649063001825],
[-0.000133957938, 0.500133957938, 0.649263802117],
[ 0.500133957938, -0.000133957938, 0.649263802117],
[ 0.496587354237, 0.496587354237, 0.649063001825],
[ 0.25 , 0.25 , 0.696649707841],
[ 0.25 , 0.75 , 0.694517503389],
[ 0.75 , 0.25 , 0.694517503389],
[ 0.75 , 0.75 , 0.691660105602],
[-0.043518053127, -0.043518053127, 0.734575517354],
[ 0.012602780483, 0.487397219517, 0.735779056149],
[ 0.487397219517, 0.012602780483, 0.735779056149],
[ 0.543518053127, 0.543518053127, 0.734575517354],
[ 0.25 , 0.25 , 0.763611260037]]

# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)

# Add tags
bulk_configuration.addTags('molecule0_Co', [40])
bulk_configuration.addTags('substrate', [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
39])

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
BasisGGAPseudoDojoSO.Iron_Medium,
BasisGGAPseudoDojoSO.Cobalt_Medium,
BasisGGAPseudoDojoSO.Tungsten_Medium,
]

#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = SOGGA.PBE

k_point_sampling = KpointDensity(
density_a=7.0*Angstrom,
density_c=0.0*Angstrom,
force_timereversal=False,
)
numerical_accuracy_parameters = NumericalAccuracyParameters(
density_mesh_cutoff=120.0*Hartree,
k_point_sampling=k_point_sampling,
)

calculator = LCAOCalculator(
basis_set=basis_set,
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=numerical_accuracy_parameters,
)

bulk_configuration.setCalculator(calculator)

# -------------------------------------------------------------
# Initial State
# -------------------------------------------------------------
scaled_spins = [(i, 1.0, theta*Degrees, phi*Degrees) for i in range(len(bulk_configuration))]

initial_spin = InitialSpin(scaled_spins=scaled_spins)

bulk_configuration.setCalculator(
calculator,
initial_spin=initial_spin,
)
bulk_configuration.update()
nlsave(filename, bulk_configuration)
nlprint(bulk_configuration)

# -------------------------------------------------------------
# Local Density Of States
# -------------------------------------------------------------
kpoints = KpointDensity(
density_a=17.0*Angstrom,
density_c=0.0*Angstrom,
force_timereversal=False,
)

local_density_of_states = LocalDensityOfStates(
configuration=bulk_configuration,
kpoints=kpoints,
energies=numpy.linspace(-0.2, 0.8, 41)*eV,
band_indices=All,
energy_zero_parameter=FermiLevel,
spectrum_method=GaussianBroadening(0.025*eV),
density_mesh_cutoff=30*Hartree,
)
nlsave(filename, local_density_of_states)

# -------------------------------------------------------------
# Mulliken Population
# -------------------------------------------------------------
mulliken_population = MullikenPopulation(bulk_configuration)
nlsave(filename, mulliken_population)
nlprint(mulliken_population)

5

Installation and License Questions / Job manager failed on Win10

« on: September 9, 2022, 06:01 »

I installed QuantumATK 2018.06 on Win10 professional. All structures can not be shown in Builder and Viewer. They can only be shown in low-performance mode. When I enlarged the GUI, the buttons on the top were out of the screen and thus hard to be rescaled. The largest problen is: When I opened Job manager, the software quited immediately. On Win7, everything goes well. What is the problem? How can I deal with it?

6

General Questions and Answers / Is it possible to calculate the PLDOS at a definite bias from the I-V curve?

« on: October 21, 2021, 06:50 »

In the calculation of Ids-Vg curve, I forgot to analyze the PLDOS. Can I get the PLDOS at a definite Vg from the Ids-Vg curve results? If possible, how can I do that? Is there any guideline?

7

General Questions and Answers / the physical definition of the Fermi level in band structure calculation

« on: May 21, 2020, 13:46 »

What is the physical definition of the Fermi level in band structure calculation? Can I use the relative distance from CBM and VBM to the Fermi level to estimate the conduction type or doping type ?

8

General Questions and Answers / phosphorene nanotube optimization

« on: May 13, 2016, 06:49 »

Dear sir,
I built a phosphorene nanotube and optimized it. But during the optimization process, the structure was difficult to converge and all the P atoms were discreted from the bulk. T The .py file is attached as following. What's wrong with my optimization parameter?

# -------------------------------------------------------------
# Bulk configuration
# -------------------------------------------------------------

# Set up lattice
vector_a = [44.2622, 0.0, 0.0]*Angstrom
vector_b = [0.0, 44.2622, 0.0]*Angstrom
vector_c = [0.0, 0.0, 3.31586338739]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Phosphorus, Phosphorus, Phosphorus, Phosphorus, Phosphorus,
Phosphorus, Phosphorus, Phosphorus, Phosphorus, Phosphorus,
Phosphorus, Phosphorus, Phosphorus, Phosphorus, Phosphorus,
Phosphorus, Phosphorus, Phosphorus, Phosphorus, Phosphorus,
Phosphorus, Phosphorus, Phosphorus, Phosphorus, Phosphorus,
Phosphorus, Phosphorus, Phosphorus, Phosphorus, Phosphorus,
Phosphorus, Phosphorus, Phosphorus, Phosphorus, Phosphorus,
Phosphorus, Phosphorus, Phosphorus, Phosphorus, Phosphorus]

# Define coordinates
fractional_coordinates = [[ 0.36582515, 0.48499453, 0.25000081],
[ 0.47283227, 0.3677228 , 0.25000081],
[ 0.61743134, 0.43325366, 0.25000081],
[ 0.59979135, 0.5910257 , 0.25000081],
[ 0.44429017, 0.62300331, 0.25000081],
[ 0.44429017, 0.37699669, 0.74999917],
[ 0.59979135, 0.4089743 , 0.74999917],
[ 0.61743134, 0.56674634, 0.74999917],
[ 0.47283227, 0.6322772 , 0.74999917],
[ 0.36582515, 0.51500547, 0.74999917],
[ 0.40783012, 0.34090592, 0.74999943],
[ 0.62284893, 0.36314607, 0.74999943],
[ 0.66814176, 0.57451369, 0.74999943],
[ 0.48111546, 0.68290592, 0.74999943],
[ 0.32023402, 0.53852838, 0.74999943],
[ 0.37712092, 0.36338569, 0.24999903],
[ 0.59197975, 0.34088652, 0.24999903],
[ 0.67977275, 0.53827678, 0.24999903],
[ 0.51917299, 0.68276983, 0.24999903],
[ 0.33212387, 0.57468119, 0.24999903],
[ 0.40044368, 0.40909823, 0.24999996],
[ 0.55571165, 0.37719373, 0.24999996],
[ 0.63403508, 0.51500332, 0.24999996],
[ 0.52717365, 0.63207883, 0.24999996],
[ 0.38280622, 0.56662589, 0.24999996],
[ 0.38280623, 0.43337411, 0.75000002],
[ 0.52717365, 0.36792117, 0.75000002],
[ 0.63403508, 0.48499668, 0.75000002],
[ 0.55571165, 0.62280626, 0.75000002],
[ 0.40044368, 0.59090176, 0.75000002],
[ 0.33212387, 0.42531881, 0.75000097],
[ 0.51917299, 0.31723017, 0.75000097],
[ 0.67977275, 0.46172322, 0.75000097],
[ 0.59197974, 0.65911348, 0.75000097],
[ 0.37712092, 0.63661431, 0.75000097],
[ 0.32023402, 0.46147161, 0.25000057],
[ 0.48111546, 0.31709408, 0.25000057],
[ 0.66814176, 0.42548631, 0.25000057],
[ 0.62284892, 0.63685393, 0.25000057],
[ 0.40783012, 0.65909408, 0.25000057]]

# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = DFTBDirectory("dftb/mio/")

#----------------------------------------
# Pair Potentials
#----------------------------------------
pair_potentials = DFTBDirectory("dftb/mio/")

numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling=(1, 1, 10),
density_mesh_cutoff=200.0*Hartree,
)

iteration_control_parameters = IterationControlParameters()

poisson_solver = MultigridSolver(
boundary_conditions=[[NeumannBoundaryCondition,NeumannBoundaryCondition],
[NeumannBoundaryCondition,NeumannBoundaryCondition],
[PeriodicBoundaryCondition,PeriodicBoundaryCondition]]
)

calculator = SlaterKosterCalculator(
basis_set=basis_set,
pair_potentials=pair_potentials,
numerical_accuracy_parameters=numerical_accuracy_parameters,
iteration_control_parameters=iteration_control_parameters,
poisson_solver=poisson_solver,
)

bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('F:/P/P-AsP/bs-P-tube-40-dftb-0.2.nc', bulk_configuration)

bulk_configuration = OptimizeGeometry(
bulk_configuration,
max_forces=0.2*eV/Ang,
max_stress=0.2*eV/Ang**3,
max_steps=200,
max_step_length=0.2*Ang,
trajectory_filename=None,
optimizer_method=QuasiNewton(),
)
nlsave('F:/P/P-AsP/bs-P-tube-40-dftb-0.2.nc', bulk_configuration)
nlprint(bulk_configuration)

9

General Questions and Answers / eliminate dangling bond

« on: December 24, 2015, 04:48 »

How can I eliminate the dangling bond at the surface of ZnO sheet?
I mean the method except passivating dangling bond by H atoms, or the other atoms.

10

General Questions and Answers / transmission eigenstate of AsP nanoribbon

« on: November 27, 2015, 03:45 »

Hi, all!
I calculated the current of AsP nanoribbon under different directions. The current curves show that the zigzag current is higher than that in armchair direction. But the transmission eigenstate shows an opposite trend. Can anyone interpret it for me ? The energy is 0 eV, quantum number is 2, and ka, kb are 0.5 for the calculation of transmission eigenstate.

11

General Questions and Answers / phonon bandstructure of phosphorene with ATK-Classical method

« on: August 27, 2015, 07:01 »

Dear sir,
I tried to calculate the phonon bandstructure of monolayer phosphorene with ATK-Classical method, but there were negative bands. The bulk had been optimized to Max force less than 0.001 eV/A and Max stress less than 0.001 eV/A. How can I eliminate the negative bands?
# -------------------------------------------------------------
# Bulk configuration
# -------------------------------------------------------------

# Set up lattice
vector_a = [6.68209223283, 0.0, 0.0]*Angstrom
vector_b = [0.0, 9.16633794912, 0.0]*Angstrom
vector_c = [0.0, 0.0, 40.0]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Phosphorus, Phosphorus, Phosphorus, Phosphorus, Phosphorus,
Phosphorus, Phosphorus, Phosphorus, Phosphorus, Phosphorus,
Phosphorus, Phosphorus, Phosphorus, Phosphorus, Phosphorus,
Phosphorus]

# Define coordinates
fractional_coordinates = [[ 0.24999996, 0.25000008, 0.44609425],
[ 0. , 0.41331253, 0.44609424],
[ 0.50000005, 0.4133125 , 0.44609424],
[ 0.24999996, 0.74999997, 0.44609422],
[ 0.75 , 0.74999994, 0.44609423],
[ 0.00000001, 0.91331268, 0.44609425],
[ 0.50000005, 0.91331264, 0.44609424],
[ 0.74999999, 0.25000003, 0.44609426],
[ 0. , 0. , 0.5 ],
[ 0.50000005, 0.00000003, 0.5 ],
[ 0.24999996, 0.16331255, 0.49999999],
[ 0.74999999, 0.1633126 , 0.49999998],
[ 0.00000001, 0.49999985, 0.49999999],
[ 0.50000005, 0.49999989, 0.5 ],
[ 0.24999996, 0.66331266, 0.50000002],
[ 0.75 , 0.66331269, 0.50000001]]

# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------

potentialSet = EAMFS_FeP_2004()
calculator = TremoloXCalculator(parameters=potentialSet)

bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('F:/P-As/pb-P.nc', bulk_configuration)

bulk_configuration = OptimizeGeometry(
bulk_configuration,
max_forces=0.001*eV/Ang,
max_stress=0.001*eV/Ang**3,
max_steps=200,
max_step_length=0.2*Ang,
trajectory_filename=None,
optimizer_method=LBFGS(),
)
nlsave('F:/P-As/pb-P.nc', bulk_configuration)
nlprint(bulk_configuration)

# -------------------------------------------------------------
# Phonon bandstructure
# -------------------------------------------------------------
phonon_bandstructure = PhononBandstructure(
configuration=bulk_configuration,
route=['G', 'X', 'Y', 'Z', 'G'],
points_per_segment=100,
number_of_bands=20
)
nlsave('F:/P-As/pb-P.nc', bulk_configuration)
nlsave('F:/P-As/pb-P.nc', phonon_bandstructure)

12

General Questions and Answers / Calculation of phonon bandstructure of 2D materials

« on: July 30, 2015, 05:35 »

Dear sir,
I am calculating the phonon bandstricture of 2D materials with ATK 13.8.1. It spends too much time for calculating it by ATK-DFT. Do you have any method to save the time? What is the accurancy difference between ATK-DFT and ATK-classical in calculating phonon bandstructure?

13

General Questions and Answers / Optimization of c-parameter in MGGA

« on: July 24, 2015, 12:41 »

Dear sir,
How can I optimize c-parameter in MGGA when the experimental or HSE06 values of bandgap are unavailable?

14

General Questions and Answers / optomization of monolayer silicene device

« on: July 7, 2015, 03:00 »

Dear sir,
I have built the bulk of monolayer silicene and optimized it according to http://www.quantumwise.com/publications/tutorials/item/512-opening-a-band-gap-in-silicene-and-bilayer-graphene-with-an-electric-field. But the devices built from the optimized bulk is difficult to SCF. What is wrong with my device structure and the device optimization?
The attached file is the script for device optimization.

15

General Questions and Answers / Scritp for HSE06 in GGA

« on: June 29, 2015, 14:42 »

Dear sir,
I am using ATK 2014.2 to calculate the bandstructure of 2D materials. In order to get a more accurate result, I have to use HSE06 in GGA, but there is no option in software. Would you give me any script to define HSE06 ?

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