1
General Questions and Answers / Re: procedure to change bond lengths
« on: August 8, 2022, 11:44 »
2013.8 version is not supported any longer.
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.
2
General Questions and Answers / Re: Including the gravity effect in MD simulations!
« on: May 5, 2022, 14:24 »
I believe you can neglect a gravity effect, given it is much smaller compared, e.g., with dispersion (van der Waals) interaction, unless this simulation is meant to describe this process on a surface of a neutron star.
3
General Questions and Answers / Re: Convergence issues
« on: May 5, 2022, 14:19 »
You might take a look at this technical notes on device calculation convergence https://docs.quantumatk.com/technicalnotes/negf_convergence_guide/negf_convergence_guide.html.
Having flat LDOS in the electrode extension region ensures that the device central region is large enough, compared to the screening length of the system.
I guess adding more surface layers might serve the same purpose or have a different one, e.g., to check if the subsequent geometry relaxation of the near surface region capture the local strain accurately; note that electrode extension regions are fixed (not allowed to relax by construction). Probably, one should consider every specific case to understand the actual purpose.
Having flat LDOS in the electrode extension region ensures that the device central region is large enough, compared to the screening length of the system.
I guess adding more surface layers might serve the same purpose or have a different one, e.g., to check if the subsequent geometry relaxation of the near surface region capture the local strain accurately; note that electrode extension regions are fixed (not allowed to relax by construction). Probably, one should consider every specific case to understand the actual purpose.
4
General Questions and Answers / Re: Transport calculation for a Triclinic crystal
« on: March 4, 2022, 10:57 »
You have to cleave your crystal in the way that makes the A and B vectors orthogonal to the C-transport direction. There is no way of doing transport calculations without having the transport direction perpendicular to cross section area; this is not QuantumATK specific, but rather general.
5
General Questions and Answers / Re: Charge transfer
« on: November 25, 2021, 15:42 »
You might consider using the Bader analysis instead of Mulliken population, see https://docs.quantumatk.com/manual/Types/BaderCharges/BaderCharges.html and reference therein.
Another way is based on the electron density analysis, as described, e.g., in this paper First-principles study of the dipole layer formation at metal-organic interfaces, Paul C. Rusu, Gianluca Giovannetti, Christ Weijtens, Reinder Coehoorn, and Geert Brocks
Phys. Rev. B 81, 125403 – Published 3 March 2010.
Another way is based on the electron density analysis, as described, e.g., in this paper First-principles study of the dipole layer formation at metal-organic interfaces, Paul C. Rusu, Gianluca Giovannetti, Christ Weijtens, Reinder Coehoorn, and Geert Brocks
Phys. Rev. B 81, 125403 – Published 3 March 2010.
6
General Questions and Answers / Re: Export data for Sentaurus Device
« on: November 8, 2021, 14:10 »
It is possible to calculate band velocity as discussed at https://docs.quantumatk.com/manual/Types/calculateVelocity/calculateVelocity.html, as well as density of states https://docs.quantumatk.com/manual/Types/DensityOfStates/DensityOfStates.html (old analysis object for DOS calculations - kept for legacy support) and https://docs.quantumatk.com/manual/Types/ProjectedDensityOfStates/ProjectedDensityOfStates.html (this is a new analysis object - recommended to use).
For carrier distribution analysis, you might consider using https://docs.quantumatk.com/manual/Types/PartialElectronDensity/PartialElectronDensity.html. Note that there is a GUI support for these features. Note that the Fermi-Dirac (equilibrium) distribution is assumed in all the calculations for bulk (not device) configurations. Also, note that this is all single particle distributions.
For carrier distribution analysis, you might consider using https://docs.quantumatk.com/manual/Types/PartialElectronDensity/PartialElectronDensity.html. Note that there is a GUI support for these features. Note that the Fermi-Dirac (equilibrium) distribution is assumed in all the calculations for bulk (not device) configurations. Also, note that this is all single particle distributions.
7
General Questions and Answers / Re: Is it possible to calculate the PLDOS at a definite bias from the I-V curve?
« on: November 8, 2021, 13:48 »
I think you should first read the Milliken population results from the IVCharacteristics study object as described in the following, and then the extracted data for further analysis:
Code
iv_characteristics = nlread('pldos-Sn4S8-1e19-n-Vds0.64V-Vg-1.0V.hdf5', IVCharacteristics)[-1]
mp = iv_characteristics.results(
-1.0*Volt,
0.64*Volt,
[MullikenPopulation])[-1]
nlsave('mp_results.hdf5', mp)
m = nlread('mp_results.hdf5', MullikenPopulation)[0]
print(m.atomicCharge().sum())
8
General Questions and Answers / Re: it is possible to calculate the electron transport under spin-orbit coupling
« on: November 8, 2021, 13:06 »
Could you attach the script file to your post?
9
General Questions and Answers / Re: How to share simulation results of hdf5 file?
« on: November 8, 2021, 13:06 »
Depending on the data type, you can save your data in text format, for example. One example would be optical spectrum, transmission spectrum, atomistic structure (which can be saved in multiple formats, including the ones used by other codes), and so on. You specify what type of data you want to store and share, we could tell you more about how that could be made available to the others.
10
General Questions and Answers / Re: Transmission spectrum calculation error
« on: November 8, 2021, 12:07 »
It is a memory issue when calculating transmission spectrum. The same could happen, for instance, when calculating DOS with too many k-points, provided not sufficient memory is available. Try to calculated transmission spectrum using analysis from file, i.e., using already SCF-calculated device configuration, but reduce the number of tasks per node by half or more.
11
General Questions and Answers / Re: Device Optimization
« on: November 8, 2021, 11:56 »
The issue is likely a recently-found bug with Parallel conjugate gradient and related type of the Poisson solvers - the corresponding fix will be available in Service Pack 2 (SP2) in about a month time. I think for your system (I see no continuum metal or dielectric regions in the script you have posted), you could use FFT2D type of the Poisson solver instead of PCG; the FFT2D is not affected by this bug.
12
General Questions and Answers / Re: 16 GB of memory not enough to plot a band structure from DFTB calculation!
« on: November 8, 2021, 11:35 »
You might try using threading as discussed in this post: https://forum.quantumatk.com/index.php?topic=7126.msg29011#msg29011.
13
General Questions and Answers / Re: Barrier height
« on: November 8, 2021, 11:32 »
You might take a look at the following paper on SB extraction for 2D material contacts.
Schottky barrier lowering due to interface states in 2D heterophase devices
By: Jelver, Line; Stradi, Daniele; Stokbro, Kurt; et al.
NANOSCALE ADVANCES Volume: 3 Issue: 2 Pages: 567-574 Published: JAN 21 2021
In principle, you might just do bulk calculation, obtaining LDOS across the contact, using a new PDOS analysis object projecting on Sites. Hartree Difference Potential can then be used as well, in combination with LDOS analysis. Note that one does not get any bias dependence in this calculation, for that one needs to do device calcualtions.
Schottky barrier lowering due to interface states in 2D heterophase devices
By: Jelver, Line; Stradi, Daniele; Stokbro, Kurt; et al.
NANOSCALE ADVANCES Volume: 3 Issue: 2 Pages: 567-574 Published: JAN 21 2021
In principle, you might just do bulk calculation, obtaining LDOS across the contact, using a new PDOS analysis object projecting on Sites. Hartree Difference Potential can then be used as well, in combination with LDOS analysis. Note that one does not get any bias dependence in this calculation, for that one needs to do device calcualtions.
14
General Questions and Answers / Re: out of memory error by allocating 8000 GB memory withing DFTB calculation!
« on: November 8, 2021, 11:14 »
Could you try using threading instead of increasing the number of nodes/cores, e.g., reducing the number of tasks per node to 12 and then setting cpus per task to 2, or even using less tasks if setting it to 12 does not work? I think it is not an issue with total memory, but rather not enough memory on a single compute node.
An ultimate test would be setting the number of tasks per node to 1 and cpus per task to 24. Having 20 fast communicating nodes would then sill allow you for 20 MPI processes to use for this job - I assume your nodes InfiniBand-type of communication, otherwise, using multiple nodes might be not really advantages, and even increase compute time due to slow communication.
An ultimate test would be setting the number of tasks per node to 1 and cpus per task to 24. Having 20 fast communicating nodes would then sill allow you for 20 MPI processes to use for this job - I assume your nodes InfiniBand-type of communication, otherwise, using multiple nodes might be not really advantages, and even increase compute time due to slow communication.
15
General Questions and Answers / Re: Can we mimic neutron stars?
« on: November 5, 2021, 01:05 »
What is a typical mass density of iron in an neutron star? It is likely to be so dense that nuclei are so close to each other that classical electrostatics might fail, requiring quantum electrodynamics corrections to the Coulomb law describing interaction between point charges assumed in all our calculations. I am not sure nuclei can be seen as point charges in neutron stars, maybe at the surface region.
Formally, one can indeed compress iron in atomistic, DFT calculations to any mass density, provided this does not cause numerical issues due to too close atoms. Also, what do those layered structures look like? I would guess a material under that enormous pressure would show a phase transition to some peculiar phase. In principle, that can be studied, provided the governing equations of DFT still hold true, and no numerical issues are encountered for a given, high mass density.
Formally, one can indeed compress iron in atomistic, DFT calculations to any mass density, provided this does not cause numerical issues due to too close atoms. Also, what do those layered structures look like? I would guess a material under that enormous pressure would show a phase transition to some peculiar phase. In principle, that can be studied, provided the governing equations of DFT still hold true, and no numerical issues are encountered for a given, high mass density.