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Messages - jalmeida

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1
General Questions and Answers / Gold layers in central region
« on: February 4, 2025, 12:18 »
Hello  :D,

I work with molecular junctions using gold electrodes and I would like to know more about the increasing of gold layers in the central region for reability of optimized geometry and transmission function. What is the best approach:

1. Include gold layers in the electrode extension?
2. Include gold layers in the most inner part of central region (inside of "dashed lines")?

I believe if we do not optimize the junction the results will be the same. However, if we optimize, since the electrodes extension remains not relaxed, not gold layers enough in the most inner part could gives a geometry far from the reality. What is the case?

2
Hello,

Please, I would like to know if there are some analysis in the optimized junction to check its reliability. I know that we can perform a optimization using NEGF but it takes much longer. Do you know if there are some studies about the differences in the result from the two approaches, please?

For zero bias at least is enough to check if forces and total energy is going smoothly to the final geometry?

3
General Questions and Answers / IVCurve and IVCharacteristics
« on: February 3, 2025, 12:01 »
Hello,

I am using the IVCurve class for calculating an IV curve from -1 V to 1 V with step of 100 mV. I would like to understand how these calculations work. Here is what I believe is the step by step:

1. Do a self-consistent calculation for zero-bias
2. Do a self-consistent calculation at 100 mV reading the zero-bias
3. Do a self-consistent calculation at 200 mV reading the device configuration of 100 mV
4. And so on...
5. Do a transmission calculation for each self-consistent calculation already done.

However for negative bias I do not know if is the same procedure or for each negative bias, for example -100 mV, is reading the device configuration of the correspondent positive bias, i.e. 100 mV.

Is the procedure the same for IVCharacteristics class?

4
General Questions and Answers / Re: perform_device_optimization
« on: January 30, 2025, 16:49 »
Thank you  :D

5
General Questions and Answers / perform_device_optimization
« on: January 28, 2025, 14:49 »
Dear all,

Please, how exactly is done the optimization when I set "perform_device_optimization=True" in OptimizeDeviceConfiguration class? Is a full optimization with NEGF instead of bulk as it is previously? Is that too much longer?


6

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).

 

7

Great! Thank you.

Best,
Joseane

8
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?


9
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

10
Dear  :D

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


11
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

12
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:

Quote
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.

13
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?




14
Thank you! I will do both ensembles and see how the structure evolves.


15
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?

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