Messages

16

General Questions and Answers / Spin-polarized calculation with Hybrid Functional

« on: February 19, 2024, 17:49 »

Hello,

I am trying to use the hybrid functional HSE06 to calculate the electronic structure of a spin-polarized molecular junction. The ATK version is 2021.06. However, I do not know how to give this in the input and I did not find in the documentation. Please, Could you help me?

17

General Questions and Answers / Re: Molecular Dynamics for Devices and Boundary Conditions

« on: February 13, 2024, 11:47 »

Thank you! I will do both ensembles and see how the structure evolves.

18

General Questions and Answers / Re: Molecular Dynamics for Devices and Boundary Conditions

« on: February 12, 2024, 14:52 »

Thank you very much for your reply!

So, if I understand correctly, if I want to perform the transmission spectrum for some MD configurations, it is better to do it already in the device configuration to maintain the correspondence between my scattering region and the electrode extension. And NPT is not recommended because it can also cause mismatch, right?

It seems to me that the best way to perform molecular dynamics in devices is to use the NVT ensemble in different calculations with different sizes only in the z direction of the scattering region, as described in this tutorial <https://docs.quantumatk.com/casestudies/md_landauer/md_landauer.html>. In my case, the system is a single-molecule junction, so the correct way to increase the cell size (like in the tutorial) is to increase the number of gold layers in the scattering region?

19

General Questions and Answers / Molecular Dynamics for Devices and Boundary Conditions

« on: February 9, 2024, 15:09 »

Dear,

It is my first time trying to do Molecular Dynamics (MD) simulation and I have some questions that I did not find in details in the documentation and in the forum.

Please, Does ATK use always periodic boundary conditions in MD simulations, even for finite systems, e.g. molecules?

I tried to use MD for a device, so the electrodes and electrode repetitions are fixed automatically, right? Some atoms is going outside of the cell!

Is it better keep just the scattering region in a bulk configuration? Does cell size change in MD?

How can I choose a suitable unit cell? Should I increase the cell and keep the scattering region centralized or use a supercelll with the ATK tool "repeat cell" in all directions?

Thanks in advance 

20

General Questions and Answers / Adaptive grid

« on: February 6, 2024, 12:10 »

Dear,

I am simulating an electronic transmission function for a single molecular junction and part of the k-points used are not contributing well for the transmission values in some energies. So now I am trying to use the AdaptiveGrid that it takes much more time than the Monkhorst-Pack scheme. I decrease the maximum number of refinement steps (=7 now) to see if can be faster. How can I use the flag << function_values >> in this case if the transmission value for each k-point depends on the energy? The list of k-points for this function values is given in the flag << kpoints >>, right? How does it affect the kpoints chosen to construct the triangles? 

My initial code is below.

Code

device_configuration=nlread('/path/device.hdf5', DeviceConfiguration)[0]

# -------------------------------------------------------------
# Transmission Spectrum
# -------------------------------------------------------------

kpoints = AdaptiveGrid(
    kA_range=[-0.5, 0.5],
    kB_range=[-0.5, 0.5],
    tolerance=1e-3,
    error_measure=Absolute,
    number_of_initial_levels=3,
    maximum_number_of_levels=20,
    kpoints=None,
    intervals=None,
    triangles=None,
    function_values=None,
    )

transmission_spectrum = TransmissionSpectrum(
    configuration=device_configuration,
    energies=numpy.linspace(-1.0, 1.0, 800)*eV,
    kpoints=kpoints,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=RecursionSelfEnergy(),
    )
nlsave('device.hdf5', transmission_spectrum)
nlprint(transmission_spectrum)

21

General Questions and Answers / Re: Phase/Magnitude of Transmission through Molecular Orbitals

« on: January 26, 2024, 14:14 »

Please, Could you help me with this? Thanks in advance!

22

General Questions and Answers / Re: Mulliken Charge for each optimization step

« on: January 26, 2024, 14:10 »

Dear AsifShah,

It's good advice! I'm not going to use the variation itself, it's just to better understand what's going on with my system that it's difficult to maintain the correct magnetic moment when I optimize it. Thanks for your collaboration.

Best regards

23

General Questions and Answers / Re: Phase/Magnitude of Transmission through Molecular Orbitals

« on: January 18, 2024, 15:17 »

Dear Anders Blom  ,

There is a rather old explanation on how to at least project the transmission onto the MPSH states here:
https://docs.quantumatk.com/tutorials/low_level_entities/low_level_entities.html
I hope it still works, but perhaps some small changes in the code lately will require the utility script at least to be updated...

You will have to loop over the energy and record the contribution to the transmission from each MPSH state to make the plot.

1) I projected the transmission onto the MPSH states using the files on the link you sent to me. Which kind of required updates you were talking about? I am working with single molecular junctions. First, I did a MPSH calculation to take the index of the molecular orbitals (MO) that I want to work with. Since my system is open shell, I just change in the inputs the spin for up/down if I want MO up/down.

2) And if I want to make this for a specific k-point (ka, kb), I just need to change the k-point in the python functions vectorToGrid() and scatteringStates() in the utilities.py file, right?

The phase is defined the paper through the ratio of the real and imaginary parts of the projected transmission eigenvalues, as I understand it. By default, the transmission eigenvalues computed by QuantumATK are expressed in the basis of the original basis set orbitals (https://docs.quantumatk.com/manual/Types/TransmissionEigenvalues/TransmissionEigenvalues.html), so again one would need to perform a unitary transformation to the space spanned by the MPSH states. I'll check on the best way to do that.

3) Please, How can I do this?

24

General Questions and Answers / Re: Mulliken Charge for each optimization step

« on: January 16, 2024, 11:45 »

Yeah, I am trying to see how the Mulliken charge is changing with the steps and this could be important on my case.

Thank you all for the reply!

25

General Questions and Answers / Re: wide-band limit in molecular junctions

« on: January 16, 2024, 11:38 »

Okay, thank you

26

General Questions and Answers / wide-band limit in molecular junctions

« on: December 19, 2023, 11:52 »

Hello 

Please, is it possible uses wide-band limit approximation to calculate electronic and phonon transport in ATK for molecular junctions? I found just an example with cnt but it uses semi-empirical model.

27

General Questions and Answers / Re: optimize_cell flag Error

« on: December 15, 2023, 11:38 »

Okay, thank you!

28

General Questions and Answers / Re: Optimization in OneProbe Configuration

« on: December 15, 2023, 11:36 »

I got it, Thank you!

29

General Questions and Answers / Mulliken Charge for each optimization step

« on: December 14, 2023, 16:04 »

Hello,

Please, is it possible calculate automatically the Mulliken charge for each optimization step in QuantumATK?

30

General Questions and Answers / Re: Phase/Magnitude of Transmission through Molecular Orbitals

« on: December 11, 2023, 14:55 »

Thank you very much, I understood the idea. I will do the loop and I am looking forward for the phase information. Here is my email if you need << [email protected] >>