Messages

1

General Questions and Answers / Re: Constrain angle metal/molecule in optimization geometry

« on: August 13, 2024, 15:25 »

Do you mean run the optimization in different angles? I would like to optimize the scattering region as usual but keeping a specific angle (the same from experiment).

 

2

General Questions and Answers / Re: Transmission pathway per kpoint

« on: August 13, 2024, 15:00 »

Great! Thank you.

Best,
Joseane

3

General Questions and Answers / Re: Interface dipole metal-molecule

« on: August 13, 2024, 14:57 »

All right, Thank you. Until now I am calculating the electronic density difference (fulll system density - gold density - molecule density) so I can know the reorganization of density around the surface. Then, I expand the density in multipoles and I take the dipole contribution using the script already provided in the documentation: (https://docs.quantumatk.com/manual/Types/ElectronDensity/ElectronDensity.html#electrondensity)

Is that a good way?

4

General Questions and Answers / Constrain angle metal/molecule in optimization geometry

« on: July 26, 2024, 11:05 »

Hello 

Please, I would like to optimize a system surface + molecule while maintaining the angle that the molecule makes with the surface. Is there a way to do it in QuantumATK?

I just found the class BondConstrain, but in that case I also have to constrain the bond length.

Best,
Joseane

5

General Questions and Answers / Interface dipole metal-molecule

« on: July 19, 2024, 18:09 »

Dear 

Please, How should I calculate the interface dipole? My system is a gold 111 surface + molecule.

I saw some tutorials which talk about interface dipole calculation from ElectronDifferenceDensity but without too much discussion (e.g. https://docs.quantumatk.com/tutorials/nisi2-si/nisi2-si.html).

Is this the best way to calculate it? Is there another way? How can I get the interface dipole value?

Best
Joseane

6

General Questions and Answers / Transmission pathway per kpoint

« on: July 18, 2024, 16:02 »

Dear 

Please, is there a way to calculate the transmission pathway for a specific kpoint? I saw the documentation, but the "kpoints" flag only accepts intergers, so maybe we can just set the number of points in A and B direction.

Joseane

7

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

« on: February 21, 2024, 10:19 »

Hello,

Thanks.

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.

8

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?

9

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.

10

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?

11

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 

12

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)

13

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!

14

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

15

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?