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Messages - narin

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1
Thanks, I will try by changing the width and report here.

2
Hello

i have checked the tutorial given on the following page: https://docs.quantumatk.com/tutorials/graphene_nanoribbon_device/graphene_nanoribbon_device.html#graphene-nanoribbon-device

the conductance obtained in the given example changes about 20 times for the gate voltages of 0V and -2V. however, the reference paper given here: https://doi.org/10.1021/nl070133j shows that the conductance changes 2000 times for the gate voltages of 0V and -2V.

What is the source of the big difference between the results given in the reference paper and the tutorial?

thanks.

3
General Questions and Answers / IV-curve question
« on: January 14, 2024, 11:26 »
Here's the example of the quantumatk website for the IV-curve calculation. My question is: do we need to do
Quote
device_configuration.update()
before the IVcurve command or does the IV curve command already do
Quote
device_configuration.update()
inside?

Quote
# -------------------------------------------------------------
# Two-probe Configuration
# -------------------------------------------------------------

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

# Set up lattice
vector_a = [5.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 5.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 9.0]*Angstrom
left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

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

# Define coordinates
left_electrode_coordinates = [[ 2.5,  2.5,  1.5],
                              [ 2.5,  2.5,  4.5],
                              [ 2.5,  2.5,  7.5]]*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 = [5.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 5.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 9.0]*Angstrom
right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

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

# Define coordinates
right_electrode_coordinates = [[ 2.5,  2.5,  1.5],
                               [ 2.5,  2.5,  4.5],
                               [ 2.5,  2.5,  7.5]]*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 = [5.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 5.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 22.0]*Angstrom
central_region_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
central_region_elements = [Lithium, Lithium, Lithium, Hydrogen, Hydrogen, Lithium, Lithium,
                           Lithium]

# Define coordinates
central_region_coordinates = [[  2.5,   2.5,   1.5],
                              [  2.5,   2.5,   4.5],
                              [  2.5,   2.5,   7.5],
                              [  2.5,   2.5,  10.5],
                              [  2.5,   2.5,  11.5],
                              [  2.5,   2.5,  14.5],
                              [  2.5,   2.5,  17.5],
                              [  2.5,   2.5,  20.5]]*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]
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
left_electrode_k_point_sampling = MonkhorstPackGrid(
    na=1,
    nb=1,
    nc=100,
    )
left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=left_electrode_k_point_sampling,
    )

right_electrode_k_point_sampling = MonkhorstPackGrid(
    na=1,
    nb=1,
    nc=100,
    )
right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=right_electrode_k_point_sampling,
    )

#----------------------------------------
# Poisson Solver Settings
#----------------------------------------
left_electrode_poisson_solver = FastFourier2DSolver(
    boundary_conditions=[[PeriodicBoundaryCondition(),PeriodicBoundaryCondition()],
                         [PeriodicBoundaryCondition(),PeriodicBoundaryCondition()],
                         [PeriodicBoundaryCondition(),PeriodicBoundaryCondition()]]
    )

right_electrode_poisson_solver = FastFourier2DSolver(
    boundary_conditions=[[PeriodicBoundaryCondition(),PeriodicBoundaryCondition()],
                         [PeriodicBoundaryCondition(),PeriodicBoundaryCondition()],
                         [PeriodicBoundaryCondition(),PeriodicBoundaryCondition()]]
    )

#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = HuckelCalculator(
    numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters,
    poisson_solver=left_electrode_poisson_solver,
    )

right_electrode_calculator = HuckelCalculator(
    numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters,
    poisson_solver=right_electrode_poisson_solver,
    )

#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceHuckelCalculator(
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    )

device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration.update()
nlsave('ivcurve.nc', 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

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

4
Thanks for the reply.

5
Dear sirs,

Is it possible to simulate the water radiolysis in Quantumatk such as in this paper: https://pubs.acs.org/doi/abs/10.1021/acs.jpca.8b01259

Thanks
Narin

6
General Questions and Answers / OS choice for QuantumATK
« on: May 31, 2023, 19:24 »
Dear sirs,

We have an active license for Quantumatk and we will install on a new machine. Is there a performance difference between Windows and Linux versions? I mean does QuantumATK perform faster in Windows or Linux?

Also which OS do you recommend for Linux, Ubuntu, RHEL, etc?

If there is not a performance difference between Windows and Linux versions, I'll just install on a Windows PC.

Best regards,
Narin

7
Thanks a lot for your replies.

8
Dear Sirs,

How does QuantumATK calculate the kinetic energy? I looked the help page and the manual but couldn't find any formula.

Thanks.

9
Is the DFTB simulation valid when done with the no SCF option?

10
General Questions and Answers / Meaning of no SCF iterations
« on: September 29, 2020, 20:23 »
Hello

What is the usage of non-scf iterations in a DFT calculation in ATK? What is the difference of results (electron density, potential) when using SCF or noSCF iterations.

Any help will be apreciated alot.

11
Hi all,

I'm using PyMol to calculate the electrostatic potential of molecules using APBS (Adaptive Poisson Boltzmann Solver). Its results show the electrostatic potential of the surface of a molecule. What is the equivalent analysis  to use in ATK? I checked the manual and there are several alternatives such as  ElectrostaticDifferencePotential(), EffectivePotential() and ChemicalPotential(), etc. Which of these analysis in ATK is the equivalent of the result of APBS (elecrostatic potential)?

Additional question: Is there an analysis in ATK to calculate the strength of atomic bond between two atoms in a molecule?

Thanks.
Narin

12
Dear users,

I'm a newcomer to ATK and trying to optimize an arsenene structure in ATK-VNL. I placed an Optimize Geometry block and let the default values as shown in the attached figure 1. Then, I run the simulation without any errors. I checked the resulting geometry (trajectory) as shown in attached figure 2 but the optimization did not change the z-positions of (so called buckling) of atoms. What can I do to geometrically optimze this structure so that I can see the buckling after optimization?

Thanks a lot.
Narin :

13
I tried to calculate the Fermi velocity of the 6 atoms wide graphene nanoribbon structure using the calculateVelocity function as given in the attached file. The velocity is calculated as 136361 m/s as given in the log file. I selected the 10th band with k=[0.475, 0.475, 0.475] looking at at the bandstructure given in the figure attached. I just wanted to know if these band and k-point selection is correct or would you recommend to use another band and k-point?

Thanks a lot.
Narin

14
Dear Sir/Madam

I'm trying to build the buckled arsenene structure as attached. The atom-atom distance is 2.50A while the interlayer distance is 1.35A. I tried to build it using the crystal builder tutorial but no success. Is there another way to build it?

Thanks in advance...
Narin

15
Hi,

I tried the attached script for calculating the inelastic transmission spectrum of a very short graphene nanoribbon and it seems to take hundreds of hours. Is there a problem with my script or does the inelastic transmission spectrum takes hunderds of hours in ATK?

Thanks...

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