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Messages - Petr Khomyakov

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Questions and Answers / Re: Doping in Device Simulations
« on: May 3, 2021, 12:59 »
It would instructive to see Hartree Difference Potential / PLDOS  for the device calculated using the tutorial vs. new doping level adopted in your calculation.

Note that for low-dimensional systems such as films and nanowires one should use charge per atom units when setting doping level, meaning that one should recalculated e/cm**3 for bulk system to e/atom for low dimensional. The doping assumed in your calculation seems to be significantly larger than that adopted in the tutorial.

If you refer to inset (a) in the figure, creating tags for top, middle and bottom layers and then doing projection on tags is the right thing to do.

Please could you explain what exactly failed in projecting on the tags - you may also post the corresponding picture of the band structure, script and log of the calculation for the sake of completeness?

Questions and Answers / Re: lattice parameters
« on: May 3, 2021, 12:38 »
There are typically 2 choice (not limited by no means so): measured value or equilibrium value calculated with a particular Calculator using OptimizeGeometry,, In the latter, the target stress should be set to zero to get an equilibrium lattice parameter.

In some cases, one may want to strain crystal structure to match it to another material, see

Note that using measured value would like to mean introducing some strain into the corresponding structure, unless the calculated one is exactly as  the measured one.

Questions and Answers / Re: Absorption coefficient
« on: March 24, 2021, 14:40 »
An additional comment is that the optical spectrum analysis object assumes an array of molecules, e.g., molecular crystal, rather than a single molecule. One can still do the calculation for a single molecule, but then there will be a dependence of the optical properties on the amount of vacuum around the molecular structure.

I do not see anything peculiar in your script. You may try calculating ElectrostaticDifferencePotential for epsilon=1 and epsilon>>1, and compare that for the 2 cases to see if there is any effect of changing epsilon on the electrostatic potential in your calculations. 

Please take a look at an example of H2 dissociation energy calculation in the manual Enclosed you may also find a script that does separation distance optimization in an automated manner, and H2 do not dissociate upon optimization (d_eq~0.76 Ang for the computational settings chosen).

So, these are 2 examples of successful optimization of H2.

If you do not see Counterpoise in the Calculator, see a png-image enclosed, it means you have to do it manually as described in the tutorial.

For DFT calculations, I would start with GGA-PBE. You may also need this correction,, this can now be set in the GUI. Also, you might consider including van der Waals interaction. But that needs to be checked.

General Questions / Re: single electron transistor
« on: January 12, 2021, 15:31 »
I have done that tutorial and the Quantum wise tutorial "Benzene Single-Electron Transistor".
Which tutorial are you referring to? Could you post a link?

Questions and Answers / Re: MemoryError
« on: January 12, 2021, 15:16 »
What is the QuantumATK version you are using? It would be helpful to see your script and log file, and know how you run this job, 48 Gb is it for a node or core (MPI process)? 

Device calculation means that you have a central region of whatever system sandwiched between two semi-infinite electrodes, this is why these layers are added, in fact, the represent semi-infinite graphite-like leads.

I am not sure SK would be work for this kind of problems. Did you see any example in literature? You may always verify that by benchmarking SK against DFT, e.g., calculating absorption energy or any physical quantity of interest, at least for some configuration, to see how that performs. 

For the second one, you may introduce a solvent dielectric constant in the Poisson solver for DFT as well. Also, did you do self-consistent calculation with SK (you would need to unselect "No SCF iteration" in the Calculator)?  Seeing your script might be helpful.

It is not really about running it with different codes; this matter is fully geometrical related Brillouin zone folding when enlarging unit cell size.

If 1x1 BN refers to 1x1 primitive cell (not some other unit cell) of hexagonal BN, then K-point of the primitive Brillouin zone folds onto the Gamma-point of the 6x6 hexagonal BN Brillouin zone.

For example, 2x2 BN would have K-point folded on K-point, the same as for graphene, but 3x3 BN would have it on Gamma-point, meaning that 6x6 BN also has it folded on the Gamma-point.

I am guessing that there must be some issue with interpretation of the VASP band structure data.

I do not think there is any magic vacuum thickness such as 15 Ang to assume that artifacts of using periodic boundary conditions are eliminated. One should always verify if the results are converged with respect to this parameter.

Note that the best way to avoid this issue is to use Dirichlet/Neumann boundary conditions  in left/right vacuum region for slab calculations, and Dirichlet and Neumann for the left electrode and right vacuum region for surface Green's function calculations, i.e., for one-probe device. One still has to choose vacuum regions carefully, checking that there exist sufficiently large, flat potential (e.g., HartreeDifferencePotential) regions in vacuum near the boundaries.

Questions and Answers / Re: Poisson Ratio nanotube
« on: January 8, 2021, 11:37 »
You can definitely calculate and print out total energy as given in the usage examples in the QuantumATK manual, You can print other quantities (strain value, radius and so on) in a similar manner. Plotting can be done, e.g., using pyplot,,, that requires some python scripting and then one can execute the script by sending it to the Job Manager,

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