Messages

1

General Questions and Answers / Re: Explanation of optical spectrum

« on: June 17, 2024, 21:51 »

Dr. Blom, thanks A LOT for your detailed reply...

2

General Questions and Answers / Re: Explanation of optical spectrum

« on: June 6, 2024, 12:15 »

Dear Dr. Anders Blom,

Thanks a lot for your reply. In this forum I have seen a post regarding the computation of the dielectric constant using a script here: https://forum.quantumatk.com/index.php?topic=318.msg1845#msg1845 but I guess that's now integrated into the ATK as the opticalSpectrum class.

So my question is how I can extract the values determining the susceptibility values? I have saved the self-consistent bulk configurations and I'll try to extract the "matrix elements between the eigenstates with the momentum operator" to explain the difference of the susceptibility values of the two different molecules. It is like going deeper to explain the difference of the susceptibility values.

In short: How can I extract the values shown inside ellipsoids from the converged bulk configuration:

3

General Questions and Answers / Explanation of optical spectrum

« on: May 31, 2024, 21:02 »

Hello

I have calculated the optical spectra of two similar molecules and obtained their susceptibility tensors. Their susceptibilities are different and I need to explain the reason of the difference. I checked the ATK manual (We're using v. 2020) and the Kubo-Greenwood formula is given. Which terms in the KG formula affects the value of susceptibility? How can I explain the difference of susceptibilities using KG formula (perhaps accessing the terms in ATK that affect the susceptibility values)? I have checked the references given in the manual and couldn't find the same formula in those references.

Thanks.

4

General Questions and Answers / Re: graphene nanoribbon transistor tutorial problem

« on: February 13, 2024, 12:39 »

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

5

General Questions and Answers / graphene nanoribbon transistor tutorial problem

« on: February 10, 2024, 14:46 »

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.

6

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

device_configuration.update()

before the IVcurve command or does the IV curve command already do

device_configuration.update()

inside?

# -------------------------------------------------------------
# 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)

7

General Questions and Answers / Re: Time-dependent DFT in Quantumatk

« on: January 10, 2024, 06:12 »

Thanks for the reply.

8

General Questions and Answers / Time-dependent DFT in Quantumatk

« on: January 1, 2024, 11:23 »

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

9

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

10

General Questions and Answers / Re: How does QuantumATK calculate the kinetic energy?

« on: August 16, 2022, 18:27 »

Thanks a lot for your replies.

11

General Questions and Answers / How does QuantumATK calculate the kinetic energy?

« on: August 15, 2022, 19:36 »

Dear Sirs,

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

Thanks.

12

General Questions and Answers / Re: SlaterKoster Parameters for Tungsten

« on: October 7, 2020, 03:01 »

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

13

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.

14

General Questions and Answers / How to calculate the electrostatic potential in ATK?

« on: August 31, 2020, 06:25 »

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

15

General Questions and Answers / Simple (?) optimization question

« on: June 12, 2020, 12:52 »

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 :