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Messages - sukhito teh

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1
Dear developers and users,
Does the function calculatePlasmaFrequency returns plasma frequency or square of plasma frequency? The formula in documentation https://docs.quantumatk.com/manual/Types/OpticalSpectrum/OpticalSpectrum.html#opticalspectrum-c uses ω2, but the return value has unit of energy. Thank you for your attention.

2
1. Yes, memory, and you found the right solution - more threads rather than more MPIs per node reduces memory usage but keep the speed roughly the same, in many cases.
2. There are two guides in the manual around performance/parallelization and memory usage:
https://docs.quantumatk.com/manual/technicalnotes/parallelization/parallelization.html
https://docs.quantumatk.com/manual/technicalnotes/advanced_performance/advanced_performance.html
It's hard to give a single advice that works for all systems, but QuantumATK speeds up very well to high count of cores, and the more memory you need, the more you should rely on threading rather than MPI.
3. To me this is a very natural part of the projection algorithm, not least considering the way QuantumATK uses atomic orbitals as basis. It also provides a logical way to interpret the results. If your larger system is not really an extension of something with a smaller periodicity, the effective band structure may not be the best tool to analyze the results. The band gap for any system can always be inferred from the density of states, and the curvature is the same as the effective mass basically, which can also be computed directly for the supercell system.

Thank you for your reply.
1. You are right, the effective bandstructure that I had obtained is indeed very disordered due to poor symmetry.
2. Thanks, I would look into the effective mass module.

3
From what I know, the dipole moment can be approximated using equation 7 in this paper https://journals.aps.org/prb/abstract/10.1103/PhysRevB.68.195408 . Another method  is to build a 3D configuration with "2D polarization configuration" (I don't know how to put in words, but you can check the supplementary information in this paper https://iopscience.iop.org/article/10.1088/1361-648X/ab1d0f )

4
Point 2 is probably not a way forward, you'd just end up reimplementing the feature we have.

What did you try so far? The whole point of the effective band structure is that the supercell has a lot more atoms than the original primitive cell, so that is not a fundamental limitation.

Do you have any reference publication for the plot you want to make? I am not sure this is a clearcut application of the effective band structure method. What information will you gain from the effective band structure which is not seen from just doing the corresponding calculation of the supercell (which you need to do anyway)?
Thank you for your reply. In general, I plot effective bandstructure to see the change in curvature of bandstructure, direct/indirect bandgap.

The initial error message I receive when performing the calculation are as below:
===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 274903 RUNNING AT node05
=   EXIT CODE: 9
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Terminated (signal 15)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions


The above issue was resolved by setting processes_per_kpoint to 2 increasing the threads per process. This leads me to the following questions:
1. Memory Issues? Does this observation suggest that the original error was due to insufficient memory allocation?
2. Optimizing Parallelization: What are the best practices for determining the optimal processes_per_kpoint value and the corresponding number of nodes to use for maximum computational efficiency? Are these parameters related to the k-points of the bulk configuration, the k-points used for the effective band structure calculation, or both?
3. Effective Band Structure Limitations: The effectivebandstructure module has a specific requirement: the 'configuration' must be divisible into an integer number of smaller unit cells, each identical in size and number of basis functions, as defined by the 'primitive_configuration'. This limitation is not present when plotting effective band structures derived from standard Plane-Wave DFT band structure calculations (e.g., VASP). Could you briefly explain the reason for this limitation within the effectivebandstructure module?"

5
I never use the Slater Koster Model, so I can only provide limited suggestion. As the other comment had pointed out, you may need to increase vector_a and vector_b to reduce interaction between neighboring cells. I also don't see any calculation regarding the device hamiltonian, so it is hard to tell whether convergence happens.

6
Dear developers and users,
I am trying to plot the effective bandstructure of a MoS2 Moire Superlattice. Unfortunately the number of atoms in a "unit cell" of Moire Superlattice is not always equal to that of primitive cell, thus I am unable to use the built in EffectiveBandstructure analysis. I humbly ask if any of you can answer the following questions:
1. Is there any workaround to plot the effective bandstructure using quantumatk?
2. Is this limitation inherent from the atomic basis? Is it possible for me to extract internal variable of quantumatk and write my own code (for example using method in this paper https://iopscience.iop.org/article/10.1088/0953-8984/25/34/345501)to plot the effective bandstructure. I suppose I need the overlap matrix and Hamiltonian (which can be assessed through function calculateHamiltonianAndOverlap() )to plot the effective bandstructure. I also hope developers can shed some insights if there's some inherent difficulty in implementing such method, so that I can assess the feasibility of writing the codes. 
Thank you for your attention.
 
Update: the issue was resolved when I set the processes_per_kpoint to 2 increase the threads per process. So I think the error happens due to insufficient memory, contrary to my initial assumption.     

7
Dear users and staffs,
May I know how parallelization works in ProjectedDensityOfStates ? Lets say I have 4 kpoints, does that mean I should use not more than 4 processes in calculation? And how can I know what is the reduced number of kpoints?
Thank you for your attention.

best regars,
sukhito

8
Thanks for your reply.

9
Dear developers and users,
I am using QATK Version: T-2022.03 . May I know how can I pass information to parameter 'constrained_data' within the 'writePOSCAR' function? Thanks for your attention.

best regards
Sukhito Teh

10
You can read more about it here: https://docs.quantumatk.com/tutorials/dft_half_pps/dft_half_pps.html. In short, it's an attempt to bring some aspect of empirical pseudopotentials into DFT, but instead of a scissor operator acting on the final band structure (which wouldn't work in Ge for instance) there are shifts being applied within the self-consistent cycle. It does require empirical tuning, i.e. you should know the band gap from experiments to tune the parameters.

We implemented this method quite a long time ago, and honestly have not found much use for it. Since then, we have added DFT+1/2 which seems to be a more robust and general scheme, where the same parameters seem to work for many different systems, although you can fine tune them if you do know the band gap. And of course HSE06 and other hybrid functionals which perform really well in LCAO, and which can be truly predictive of the band gaps of unknown materials.

Thank you, I would look into DFT-1/2; HSE06 is good, I have found good results with them,  the ADMM can even speed up HSE calculation so the efficiency is comparable to regular DFT. However ADMM is not compatible to NEGF, so I am looking for alternatives.

11
General Questions and Answers / Papers related to DFT-PPS method
« on: December 18, 2023, 13:56 »
Dear developers and users,

Do you know any paper that explain how DFT-PPS method works or use the method to correct electronic bandgap? I tried but unable to find any related paper.  Or is there a general guide on how to optimize the parameters?

Thank you for your time.

Best regards,
Sukhito

12
Future Releases / Re: Dielectric Constant with Local Field Effect
« on: December 14, 2023, 12:33 »
Thank you for the reply! I am looking forward to the new feature!

13
Dear developers and users,
I am reaching out to seek assistance in reproducing the results presented in a paper titled "Theory of atomic-scale dielectric permittivity at insulator interfaces" https://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.144104.

I am particularly interested in the calculation of the local dielectric constant. For ionic part, the class 'BornEffectiveCharge' can return values for individual atoms, render the calculation of local dielectric constant feasible. However I can't specify which orbitals to be included in OpticalSpectrum class for calculation of electronic dielectric constant, so I wonder if I can use the derivative functions from Class 'BlochState' to calculate the momentum of individual orbital and thus the local dielectric constant. Could you please provide guidance on whether this approach is viable? Additionally, if there exists a more efficient method for performing the calculations, I would greatly appreciate your insights.

Thank you for your time.

Best regards,
Sukhito Teh

14
Future Releases / Dielectric Constant with Local Field Effect
« on: December 8, 2023, 05:31 »
Dear developers,
From what I understand, the dielectric constant obtained from OpticalSpectrum currently does not account for local field effects, rendering it unsuitable for calculating the dielectric properties of 2D materials. I have observed that QATK now offers GW calculations, and I am curious whether the dielectric tensor involved in GW calculation takes local field effects into consideration. If so, is it possible to save these values for further use?

Thank you for your attention to this matter.

Best Regards,
Sukhito Teh

15
Great.
How many cores you are using & how many atoms?
ranging from 100 to 500 atoms. Using 2-4 process/ 2-4 nodes per k point

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