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Messages - korand

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Btw, there are forcefields for Bi2Te3, such as

Qiu, B.; Ruan, X. L. Molecular dynamics simulations of lattice thermal conductivity of bismuth telluride using two-body interatomic potentials Phys. Rev. B 2009, 80, 165203
Huang, B. L.; Kaviany, M. Ab initio and molecular dynamics predictions for electron and phonon transport in bismuth telluride Phys. Rev. B 2008, 77, 125209

But I could not find one for Bi2Se3... Maybe a case for our new machine-learned Moment Tensor Potentials...!

Dear Dr Blom

Bi2Se3 and Bi2Te3 have completely opposite feature in the terms of electrical behavior as far as I know.
That's true, I found that yours new machine-learned potentials would be useful in this case. However, I do not have access to this version.  I will ask my question about this issue in the webinar at Jun 22 from lecturers.

Thanks in advance

There are a few things here and there that could be finetuned, but the most important thing you should fix first is that the automatically detected repetitions for the system is 9x9x3. Since this is a 2D sheet, you really want this to be 9x9x1, or, to run a smaller test calculation, perhaps just 5x5x1 or 7x7x1. You could make the Automatic repetition return 1 in C by including more vacuum, but 28 Å is probably enough.

So, instead, simply set the repetitions manually instead of using the Automatic keyword, and the calculation will use much, much less memory. Since there are 15 atoms in the original cell, currently you are running calculations with 9*9*3*15=3645 atom, which is very heavy, and completely unnecessary, since it should just have been 9*9*15 in the most accurate case. Still 1200 atoms or so, but that is much more manageable. I would however suggest first running 5x5x1 (375 atoms) and then 7x7x1 (735 atoms). If these results are similar, that should be accurate enough.

And finally, you are running on a single machine, so yes, these calculations will take time. If you have any chance to run in parallel on multiple nodes, that will speed things up essentially linearly by the number of additional computers you use.

Dear Dr Blom

I appreciate the time you spent to help me.

I precisely follow the instruction and user manual of quantumATK and in the webinars I found that for 2D material I need one repetition. However, my configuration is not 2D and actually it is a bulk configuration. Therefore I should at least set 3 repetitions in C direction. In this example for next simulation I will test 5x5x3 repetitions in Dynamicalmatrix and also set potentials to lower levels of accuracy.

Dear Dr Blom, I had a hard work to install ATK2020 on the HPC server, since it needs GPU, just launch on the a normal windows 10, does not match with remote desktop. My personal 2Core server does not have GPU and other professional accessible HPC server does support batch and ATK is not compatible with its terminal environment. Thus, I installed this version on a workstation.

Questions and Answers / Dynamicalmatrix huge matrix size
« on: June 20, 2021, 08:56 »
   I am trying to calculate Bi2Se3 "dielectric tensor" with ATK2020.9. I have reviewed manuals and webinars precisely and I found that I should apply "Forcefield" calculator to evaluate "dynamicalmatrix", and "LCAO" to calculate other modules like "optical spectrum, Born charge effects and dielectric tensor".
I found that the reason for this setting might be due the huge computational work in "dynamical matrix". So, exerting "forcefield" calculation will reduce the amount of cpu and ram usage for such module. However, selected configuration of Bi2Se3 is not compatible with "forcefield and semiEmprical" calculators.
Instead of that using LCAO for dynamicalmatrix, after few hours, the simulation stops in the first force calculation because of matrix large size. I tried to set basis with low precision; however, the results does not have enough accuracy like what is mentioned in dynamicalmatrix manual documents.

In the following I have attached the log and the python code.
I will appreciate it if you give advice to solve this issue.

Best regards,

Hi dear friends,

I apply noncollinear spin orbit setting to evaluate dielectric tensor of topological insulator material like Bi2Se3. However, at the end of the simulation I encounter with the following note in log file:

NL.ComputerScienceUtilities.Exceptions.NLValueError: BornEffectiveCharge currently does not support calculators with spin type Noncollinear or SpinOrbit.

Similar to the tutorial I use two calculators, where the first one is used as initial spin for second one.

Best regards,

Dear Dr Blom and dear Dr Tue

Thanks for your time and guidance.
What Dr Tue says will solve my problem.

Best regard,

Yep, that's how you do it.

Now, searching for "plasma frequency" on our excellent documentation site brings you to which has an example on precisely this (

Note that this feature was added in a recent version only.

Dear Dr Blom

I want to thank you for taking the time to answer my question. I am sure that you are busy, and so I greatly appreciate your response.

I should clarify that I want to calculate plasma frequencies for every modes, in order to supply the Lorentz's formula summation (not Drude section). For instance, Bi2Se3 has 4 major phonon modes and each on them contributes in the permittivity. However, through the manner that described in documentation site that you mentioned, plasma freq for single resonance related to intraband in each direction will obtain.
Also, these phonon modes energy are far below the bandgap of Bi2Se3; therefore, my problem is not related to intraband contribution that appear in energies (freq) around energygap. My concern is belongs to interband counterpart.

I am looking forward to the hearing from you.

Best regard,

Hi dear friends

Earlier I have posted a question about the calculating optical properties at low frequencies. DFT does not give a reasonable answer, I found that this is possible by using Drude-lorentz model. In this model (attached figure), "wi" is natural frequency that will obtain from phonon band diagram or Raman. However, I dont know how to calculated  plasma frequencies in the numerator (here "fi*wi")!
I will appreciate it if you help me.

Best regard,

Hi dear friends,
Does photocurrent module just calculate based on sun flux spectrum. I mean both flux and spectrums can be selected in the module. However, the energy spectrum range limits in this function from 0.3 to 4.5 eV make misunderstanding about the application of this module that it may exclusively belongs to photodetector illuminated by sun.

I want to use that to evaluate my IR detector.

Thanks in advance

I checked it out for MoSe2 and it works. renormalization to the 2D material thickness works.

there is a same question here

See the below link:

More QuantumATK documents are in
Dear Mlee
thanks for your answer to this topic.
But still i didnt get an answer. I know how to work with optical spectrum section in ATK. Unlikely, this section is just available in bulk configuration.
Again I clarify my question. I want to change the fermi level (chemical potential) of graphene and this would be happen by change electrical potential, apply different voltage at both surfaces of the graphene layer. (like what you see in fig. 6 of this article
in other words, i want to put graphene as channel in a FET and set drain and source to ground and sweep the gate voltage and calculate the permittivity.
thanks in advance

I am looking forward to the hearing from you!

Hi there,

I want to calculate optical spectrum (permittivity) of stacks of graphene layers by changing the external field (EF). Like what we know as changing chemical potential by changing applied EF in articles. How it is possible?
In my calculation I use GGA.PBE function and bulk configuration as version 2016.4 supports Optical Spectrum in this configuration.
I have read topic but the first included link doesn't work properly.
I will appreciate it if you answer my question.

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