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31
General Questions and Answers / Bandstructure of B-P nanosheet not calculated correctly
« Last post by sguha on April 2, 2024, 08:48 »
I am trying to calculate the bandstructure of Boron phosphide nanosheet, however I am getting 0 ev direct bandgap which is not correct.
I am attaching the script file, can someone please help me?
Reference: H. Li, Y. Zhou, and J. Dong, ‘First-Principles Study of the Electron Transport Properties of Graphene-Like 2D Materials’, Nanoelectronics and Materials Development. InTech, Jul. 27, 2016. doi: 10.5772/64109.
32
Installation and License Questions / Error while opening Quantumatk
« Last post by maheswari on April 2, 2024, 05:32 »
Hi, I am encountering an error while opening Quantumatk software. It happens while loading preference as shown below.
"Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "zipdir\NL\GUI\Main\Main.py", line 244, in main
  File "zipdir\NL\GUI\Preferences\Preferences.py", line 158, in loadSettings
ValueError: invalid literal for int() with base 10: '\x00'
"
It was working perfectly fine until now in this workstation. I reinstalled the software, but couldn't resolve it. There is also enough space in the C (371 GB free) and D (116 GB free) drives. Kindly let me know how to debug this. Thanks!
33
General Questions and Answers / Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
« Last post by Anders Blom on April 1, 2024, 20:10 »
Could you zip the log files too, might help to look at them before rerunning, the HDF5 files don't tell us much how the problem arises
34
General Questions and Answers / Add dielectric to the electrode region
« Last post by dmicje12 on April 1, 2024, 16:04 »

Hello everyone,
I want to know how to add dielectric to the electrode region,
Because the dielectric of my structure must cover the entire component,
I don't understand why there is a warning "Spatial regions extending into the electrodes are ignored during the electrode calculation"
35
General Questions and Answers / Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
« Last post by krabidix on March 31, 2024, 00:28 »
Here are the output (in zip files) and script for the case in which I used a large value (28) for processes_per_displacement.
The attached image is for the case when I used the value of processes_per_displacement =4.

The only question is why the energies are that much off!
36
General Questions and Answers / Implementing a new Reactive Forcefield
« Last post by AsifShah on March 30, 2024, 03:40 »
Dear Admin,
I am trying to implement a new MoS2 reactive forcefield file into my simulation. The method I use is as follows:

1. I send the configuration to workflow and then choose the forcefield calculator. Then, I choose some inbuilt forcefield and add an optimization block.
2. Then send it to editor with all details present.
3. Then change reactive forcefield parameters with new parameters.

But it shows error. I have attached the python file and as well as the reactive forcefield parameter file. Kindly look into the matter why simulations shows error "Segmentation fault- core dumped"

Thanks
Regards
37
General Questions and Answers / Re: How to calculate the current after introducing spin-orbit coupling?
« Last post by Anders Blom on March 27, 2024, 22:38 »
I don't think you need a script, actually. If you open the IV curve in the GUI (NanoLab) you should be able to change the curves to show any spin component.
38
General Questions and Answers / Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
« Last post by Anders Blom on March 27, 2024, 22:36 »
I think we need to look at the exact scripts and output. If you don't want to share them publicly, you can email then.
39
General Questions and Answers / Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?
« Last post by krabidix on March 27, 2024, 10:39 »
Thank you for your input!

I understand that I may have overgeneralized regarding geometry optimization and script parameters.

My primary focus is on the unexpected behaviour of phonon energies when changing the "processes_per_displacement" parameter within my script.

Using a large value for "processes_per_displacement" (e.g., 26) results in unusually high phonon energies (~12000 meV), while a smaller value (e.g., 4) produces the expected range for graphene (~200 meV).

This discrepancy is puzzling and leads me to question the impact of this parameter.

I am using QuantumATK Version U-2022.12. 
I used the Wigner-Seitz scheme in both cases. I changed only "processes_per_displacement".
40
General Questions and Answers / Re: How to calculate the current after introducing spin-orbit coupling?
« Last post by guojunnan on March 27, 2024, 09:31 »
Sorry.This colour may not be clear as I've just set it.
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Two-probe Configuration
# -------------------------------------------------------------

# -------------------------------------------------------------
# Left Electrode
# -------------------------------------------------------------

# Set up lattice
vector_a = [15.0, 0.0, 0.0]*Angstrom
vector_b = [9.18485099360515e-16, 15.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 7.0637512743]*Angstrom
left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
left_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                           Gold]

# Define coordinates
left_electrode_coordinates = [[  7.1907375    ,   6.671025     ,   1.17729901125],
                              [ 10.0745025    ,   6.671025     ,   1.17729901125],
                              [  5.7488625    ,   9.168435     ,   1.17729901125],
                              [  8.6326275    ,   9.168435     ,   1.17729901125],
                              [  5.7488625    ,   7.503495     ,   3.5318775823 ],
                              [  8.6326125    ,   7.503495     ,   3.5318775823 ],
                              [  4.3069725    ,  10.000905     ,   3.5318775823 ],
                              [  7.1907375    ,  10.000905     ,   3.5318775823 ],
                              [  5.7488625    ,   5.838555     ,   5.88645226305],
                              [  8.6326125    ,   5.838555     ,   5.88645226305],
                              [  4.3069725    ,   8.335965     ,   5.88645226305],
                              [  7.1907375    ,   8.335965     ,   5.88645226305]]*Angstrom

# Set up configuration
left_electrode = BulkConfiguration(
    bravais_lattice=left_electrode_lattice,
    elements=left_electrode_elements,
    cartesian_coordinates=left_electrode_coordinates
    )

# -------------------------------------------------------------
# Right Electrode
# -------------------------------------------------------------

# Set up lattice
vector_a = [15.0, 0.0, 0.0]*Angstrom
vector_b = [9.18485099360515e-16, 15.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 7.063755164599996]*Angstrom
right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
right_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                            Gold]

# Define coordinates
right_electrode_coordinates = [[  6.662341185865,   6.369654444235,   1.17729901125 ],
                               [  9.546091185865,   6.369654444235,   1.17729901125 ],
                               [  5.220451185865,   8.867064444235,   1.17729901125 ],
                               [  8.104216185865,   8.867064444235,   1.17729901125 ],
                               [  6.662341185865,   8.034594444235,   3.53185813085 ],
                               [  9.546091185865,   8.034594444235,   3.53185813085 ],
                               [  5.220451185865,  10.532004444235,   3.53185813085 ],
                               [  8.104216185865,  10.532004444235,   3.53185813085 ],
                               [  8.104216185865,   7.202124444235,   5.88645615335 ],
                               [ 10.987981185865,   7.202124444235,   5.88645615335 ],
                               [  6.662341185865,   9.699534444235,   5.88645615335 ],
                               [  9.546091185865,   9.699534444235,   5.88645615335 ]]*Angstrom

# Set up configuration
right_electrode = BulkConfiguration(
    bravais_lattice=right_electrode_lattice,
    elements=right_electrode_elements,
    cartesian_coordinates=right_electrode_coordinates
    )

# -------------------------------------------------------------
# Central Region
# -------------------------------------------------------------

# Set up lattice
vector_a = [15.0, 0.0, 0.0]*Angstrom
vector_b = [9.18485099360515e-16, 15.0, 0.0]*Angstrom
vector_c = [3.061616997868383e-15, 3.061616997868383e-15, 38.454696774010465]*Angstrom
central_region_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
central_region_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                           Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                           Gold, Gold, Gold, Hydrogen, Carbon, Hydrogen, Carbon, Carbon,
                           Carbon, Carbon, Hydrogen, Carbon, Hydrogen, Hydrogen, Carbon,
                           Hydrogen, Nitrogen, Hydrogen, Hydrogen, Carbon, Hydrogen, Gold,
                           Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                           Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
                           Gold, Gold]

# Define coordinates
central_region_coordinates = [[  7.1907375     ,   6.671025      ,   1.17729901125 ],
                              [ 10.0745025     ,   6.671025      ,   1.17729901125 ],
                              [  5.7488625     ,   9.168435      ,   1.17729901125 ],
                              [  8.6326275     ,   9.168435      ,   1.17729901125 ],
                              [  5.7488625     ,   7.503495      ,   3.5318775823  ],
                              [  8.6326125     ,   7.503495      ,   3.5318775823  ],
                              [  4.3069725     ,  10.000905      ,   3.5318775823  ],
                              [  7.1907375     ,  10.000905      ,   3.5318775823  ],
                              [  5.7488625     ,   5.838555      ,   5.88645226305 ],
                              [  8.6326125     ,   5.838555      ,   5.88645226305 ],
                              [  4.3069725     ,   8.335965      ,   5.88645226305 ],
                              [  7.1907375     ,   8.335965      ,   5.88645226305 ],
                              [  7.1907375     ,   6.671025      ,   8.24105028555 ],
                              [ 10.0745025     ,   6.671025      ,   8.24105028555 ],
                              [  5.7488625     ,   9.168435      ,   8.24105028555 ],
                              [  8.6326275     ,   9.168435      ,   8.24105028555 ],
                              [  5.7488625     ,   7.503495      ,  10.59560940515 ],
                              [  8.6326125     ,   7.503495      ,  10.59560940515 ],
                              [  4.3069725     ,  10.000905      ,  10.59560940515 ],
                              [  7.1907375     ,  10.000905      ,  10.59560940515 ],
                              [  5.7488625     ,   5.838555      ,  12.95016852475 ],
                              [  8.6326125     ,   5.838555      ,  12.95016852475 ],
                              [  4.3069725     ,   8.335965      ,  12.95016852475 ],
                              [  7.1907375     ,   8.335965      ,  12.95016852475 ],
                              [  7.1907375     ,   6.671025      ,  14.66018439715 ],
                              [  7.5971775     ,   9.163875      ,  16.53717151635 ],
                              [  7.6306125     ,   7.07118       ,  16.62544219645 ],
                              [  7.7716125     ,   4.999095      ,  17.08099515545 ],
                              [  7.7615325     ,   8.356965      ,  17.14323979545 ],
                              [  7.8641325     ,   5.945415      ,  17.45500763605 ],
                              [  8.1154275     ,   8.5434        ,  18.49390958055 ],
                              [  8.2241325     ,   6.14085       ,  18.80163151955 ],
                              [  8.1996375     ,   9.502425      ,  18.84049551665 ],
                              [  8.3453025     ,   7.43991       ,  19.35090156465 ],
                              [  8.3952975     ,   5.313585      ,  19.37848372075 ],
                              [ 10.6930275     ,   7.5312        ,  20.46784272655 ],
                              [  8.6974575     ,   7.629105      ,  20.78906397185 ],
                              [  8.7963525     ,   8.69124       ,  21.03131233015 ],
                              [ 10.0186125     ,   7.044675      ,  21.06297929075 ],
                              [  6.6569775     ,   7.51299       ,  21.56377632245 ],
                              [  7.5273975     ,   5.97462       ,  21.64905147925 ],
                              [  7.6306125     ,   7.056435      ,  21.75506188175 ],
                              [ 10.2633675     ,   7.272105      ,  22.02944403545 ],
                              [  8.104216185865,   7.202124444235,  23.79450848656 ],
                              [  6.662341185865,   6.369654444235,  25.50452435896 ],
                              [  9.546091185865,   6.369654444235,  25.50452435896 ],
                              [  5.220451185865,   8.867064444235,  25.50452435896 ],
                              [  8.104216185865,   8.867064444235,  25.50452435896 ],
                              [  6.662341185865,   8.034594444235,  27.85908347856 ],
                              [  9.546091185865,   8.034594444235,  27.85908347856 ],
                              [  5.220451185865,  10.532004444235,  27.85908347856 ],
                              [  8.104216185865,  10.532004444235,  27.85908347856 ],
                              [  8.104216185865,   7.202124444235,  30.21364259816 ],
                              [ 10.987981185865,   7.202124444235,  30.21364259816 ],
                              [  6.662341185865,   9.699534444235,  30.21364259816 ],
                              [  9.546091185865,   9.699534444235,  30.21364259816 ],
                              [  6.662341185865,   6.369654444235,  32.56824062066 ],
                              [  9.546091185865,   6.369654444235,  32.56824062066 ],
                              [  5.220451185865,   8.867064444235,  32.56824062066 ],
                              [  8.104216185865,   8.867064444235,  32.56824062066 ],
                              [  6.662341185865,   8.034594444235,  34.92279974026 ],
                              [  9.546091185865,   8.034594444235,  34.92279974026 ],
                              [  5.220451185865,  10.532004444235,  34.92279974026 ],
                              [  8.104216185865,  10.532004444235,  34.92279974026 ],
                              [  8.104216185865,   7.202124444235,  37.27739776276 ],
                              [ 10.987981185865,   7.202124444235,  37.27739776276 ],
                              [  6.662341185865,   9.699534444235,  37.27739776276 ],
                              [  9.546091185865,   9.699534444235,  37.27739776276 ]]*Angstrom

# Set up configuration
central_region = BulkConfiguration(
    bravais_lattice=central_region_lattice,
    elements=central_region_elements,
    cartesian_coordinates=central_region_coordinates
    )

device_configuration = DeviceConfiguration(
    central_region,
    [left_electrode, right_electrode],
    equivalent_electrode_lengths=[7.0637512743, 7.0637551646]*Angstrom,
    transverse_electrode_repetitions=[[1, 1], [1, 1]],
    )

# Add tags
device_configuration.addTags('Selection 0', [ 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, 40, 41, 42])
device_configuration.addTags('Selection 1', [43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
                                             56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67])

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
HydrogenBasis = OpenMXBasisSet(
    element=PeriodicTable.Hydrogen,
    filename="openmx/pao/H5.0.pao.zip",
    atomic_species="s2p1",
    hubbard_u=[0.0, 0.0, 0.0]*eV,
    dft_half_parameters=Automatic,
    filling_method=SphericalSymmetric,
    onsite_spin_orbit_split=[0.0, 0.0, 0.0]*eV,
    pseudopotential=NormConservingPseudoPotential("normconserving/upf2/H_PBE13.upf.zip"),
    )

CarbonBasis = OpenMXBasisSet(
    element=PeriodicTable.Carbon,
    filename="openmx/pao/C6.0.pao.zip",
    atomic_species="s2p2d1",
    hubbard_u=[0.0, 0.0, 0.0, 0.0, 0.0]*eV,
    dft_half_parameters=Automatic,
    filling_method=SphericalSymmetric,
    onsite_spin_orbit_split=[0.0, 0.0, 0.0, 0.0, 0.0]*eV,
    pseudopotential=NormConservingPseudoPotential("normconserving/upf2/C_PBE13.upf.zip"),
    )

NitrogenBasis = OpenMXBasisSet(
    element=PeriodicTable.Nitrogen,
    filename="openmx/pao/N6.0.pao.zip",
    atomic_species="s2p2d1",
    hubbard_u=[0.0, 0.0, 0.0, 0.0, 0.0]*eV,
    dft_half_parameters=Automatic,
    filling_method=SphericalSymmetric,
    onsite_spin_orbit_split=[0.0, 0.0, 0.0, 0.0, 0.0]*eV,
    pseudopotential=NormConservingPseudoPotential("normconserving/upf2/N_PBE13.upf.zip"),
    )

basis_set = [
    HydrogenBasis,
    CarbonBasis,
    NitrogenBasis,
    BasisGGAPseudoDojoSO.Gold_Medium,
    ]

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

#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
device_k_point_sampling = MonkhorstPackGrid(
    nc=100,
    force_timereversal=False,
    )
device_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=device_k_point_sampling,
    exx_grid_cutoff=75.0*Hartree,
    density_mesh_cutoff=75.0*Hartree,
    )

#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=device_numerical_accuracy_parameters,
    )

device_configuration.setCalculator(calculator)

# -------------------------------------------------------------
# Initial State
# -------------------------------------------------------------
scaled_spins = [
    (0, 1.0, 0.0*Degrees, 0.0*Degrees),
    (1, 1.0, 0.0*Degrees, 0.0*Degrees),
    (2, 1.0, 0.0*Degrees, 0.0*Degrees),
    (3, 1.0, 0.0*Degrees, 0.0*Degrees),
    (4, 1.0, 0.0*Degrees, 0.0*Degrees),
    (5, 1.0, 0.0*Degrees, 0.0*Degrees),
    (6, 1.0, 0.0*Degrees, 0.0*Degrees),
    (7, 1.0, 0.0*Degrees, 0.0*Degrees),
    (8, 1.0, 0.0*Degrees, 0.0*Degrees),
    (9, 1.0, 0.0*Degrees, 0.0*Degrees),
    (10, 1.0, 0.0*Degrees, 0.0*Degrees),
    (11, 1.0, 0.0*Degrees, 0.0*Degrees),
    (12, 1.0, 0.0*Degrees, 0.0*Degrees),
    (13, 1.0, 0.0*Degrees, 0.0*Degrees),
    (14, 1.0, 0.0*Degrees, 0.0*Degrees),
    (15, 1.0, 0.0*Degrees, 0.0*Degrees),
    (16, 1.0, 0.0*Degrees, 0.0*Degrees),
    (17, 1.0, 0.0*Degrees, 0.0*Degrees),
    (18, 1.0, 0.0*Degrees, 0.0*Degrees),
    (19, 1.0, 0.0*Degrees, 0.0*Degrees),
    (20, 1.0, 0.0*Degrees, 0.0*Degrees),
    (21, 1.0, 0.0*Degrees, 0.0*Degrees),
    (22, 1.0, 0.0*Degrees, 0.0*Degrees),
    (23, 1.0, 0.0*Degrees, 0.0*Degrees),
    (24, 1.0, 0.0*Degrees, 0.0*Degrees),
    (25, 0.0, 0.0*Degrees, 0.0*Degrees),
    (26, 0.0, 0.0*Degrees, 0.0*Degrees),
    (27, 0.0, 0.0*Degrees, 0.0*Degrees),
    (28, 0.0, 0.0*Degrees, 0.0*Degrees),
    (29, 0.0, 0.0*Degrees, 0.0*Degrees),
    (30, 0.0, 0.0*Degrees, 0.0*Degrees),
    (31, 0.0, 0.0*Degrees, 0.0*Degrees),
    (32, 0.0, 0.0*Degrees, 0.0*Degrees),
    (33, 0.0, 0.0*Degrees, 0.0*Degrees),
    (34, 0.0, 0.0*Degrees, 0.0*Degrees),
    (35, 0.0, 0.0*Degrees, 0.0*Degrees),
    (36, 0.0, 0.0*Degrees, 0.0*Degrees),
    (37, 0.0, 0.0*Degrees, 0.0*Degrees),
    (38, 0.0, 0.0*Degrees, 0.0*Degrees),
    (39, 0.0, 0.0*Degrees, 0.0*Degrees),
    (40, 0.0, 0.0*Degrees, 0.0*Degrees),
    (41, 0.0, 0.0*Degrees, 0.0*Degrees),
    (42, 0.0, 0.0*Degrees, 0.0*Degrees),
    (43, 1.0, 0.0*Degrees, 0.0*Degrees),
    (44, 1.0, 0.0*Degrees, 0.0*Degrees),
    (45, 1.0, 0.0*Degrees, 0.0*Degrees),
    (46, 1.0, 0.0*Degrees, 0.0*Degrees),
    (47, 1.0, 0.0*Degrees, 0.0*Degrees),
    (48, 1.0, 0.0*Degrees, 0.0*Degrees),
    (49, 1.0, 0.0*Degrees, 0.0*Degrees),
    (50, 1.0, 0.0*Degrees, 0.0*Degrees),
    (51, 1.0, 0.0*Degrees, 0.0*Degrees),
    (52, 1.0, 0.0*Degrees, 0.0*Degrees),
    (53, 1.0, 0.0*Degrees, 0.0*Degrees),
    (54, 1.0, 0.0*Degrees, 0.0*Degrees),
    (55, 1.0, 0.0*Degrees, 0.0*Degrees),
    (56, 1.0, 0.0*Degrees, 0.0*Degrees),
    (57, 1.0, 0.0*Degrees, 0.0*Degrees),
    (58, 1.0, 0.0*Degrees, 0.0*Degrees),
    (59, 1.0, 0.0*Degrees, 0.0*Degrees),
    (60, 1.0, 0.0*Degrees, 0.0*Degrees),
    (61, 1.0, 0.0*Degrees, 0.0*Degrees),
    (62, 1.0, 0.0*Degrees, 0.0*Degrees),
    (63, 1.0, 0.0*Degrees, 0.0*Degrees),
    (64, 1.0, 0.0*Degrees, 0.0*Degrees),
    (65, 1.0, 0.0*Degrees, 0.0*Degrees),
    (66, 1.0, 0.0*Degrees, 0.0*Degrees),
    (67, 1.0, 0.0*Degrees, 0.0*Degrees),
]
initial_spin = InitialSpin(scaled_spins=scaled_spins)

device_configuration.setCalculator(
    calculator,
    initial_spin=initial_spin,
)
device_configuration.update()
nlsave('iv-SOGGA-p-1.hdf5', device_configuration)
nlprint(device_configuration)

# -------------------------------------------------------------
# IV Curve
# -------------------------------------------------------------
biases = [0.000000, 0.200000, 0.400000, 0.600000, 0.800000, 1.000000,
          1.200000, 1.400000, 1.600000, 1.800000, 2.000000]*Volt

kpoint_grid = KpointDensity(
    density_a=2.38732414638*Angstrom,
    density_c=0.0*Angstrom,
    force_timereversal=False,
    )

iv_curve = IVCurve(
    configuration=device_configuration,
    biases=biases,
    energies=numpy.linspace(-2,2,101)*eV,
    kpoints=kpoint_grid,
    self_energy_calculator=RecursionSelfEnergy(),
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    selfconsistent_configurations_filename_prefix="ivcurve_selfconsistent_configuration_",
    log_filename_prefix="ivcurve_"
    )
nlsave('iv-SOGGA-p-1.hdf5', iv_curve)
nlprint(iv_curve)
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