Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.

Messages - jalmeida

Pages: [1] 2


I don't have this option in the interface but I discovered that I can do <HybridSGGA.HSE06>. However, after a few hours I had this problem:

atkpython: /slowfs/qatkdev2/bamboo/de02vlbamboo13/bamboo-agent-home/xml-data/build-dir/QL-Q2-BLD/c++/src/physics/blocksparseatompairmatrix.cpp:361: BlockSparseAtomPairMatrix& BlockSparseAtomPairMatrix::operator+=(const BlockSparseAtomPairMatrix&): Assertion `spin_type_ == source.spinType()' failed.


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?

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

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 <>. 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?


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  :)

General Questions and Answers / Adaptive grid
« on: February 6, 2024, 12:10 »

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.


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

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

kpoints = AdaptiveGrid(
    kA_range=[-0.5, 0.5],
    kB_range=[-0.5, 0.5],

transmission_spectrum = TransmissionSpectrum(
    energies=numpy.linspace(-1.0, 1.0, 800)*eV,
nlsave('device.hdf5', transmission_spectrum)

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

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

Dear Anders Blom  :) ,

There is a rather old explanation on how to at least project the transmission onto the MPSH states here:
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 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 (, 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?

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!

Okay, thank you

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.

General Questions and Answers / Re: optimize_cell flag Error
« on: December 15, 2023, 11:38 »

Okay, thank you!


I got it, Thank you!


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

Pages: [1] 2