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Questions and Answers / Re: Dynamicalmatrix huge matrix size
« Last post by korand on Today at 11:02 »
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
Korand
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Questions and Answers / Re: Dynamicalmatrix huge matrix size
« Last post by korand on Today at 11:02 »
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.
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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...!
4
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.
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Questions and Answers / Dynamicalmatrix huge matrix size
« Last post by korand on Yesterday at 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,
Korand
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Dear experts,
I have performed an electron properties calculation. I have properly optimized the structure before running the calculations.
Upon analyzing the result, an extra band line(marked by red color) is observed in the conduction band region whereas in the dos plot there is no such states present.
I have attached the band and the dos plot.
Please suggest to me how to resolve this one.
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General Questions / Re: Zig-Zag CNT
« Last post by Anders Blom on June 18, 2021, 20:52 »
I always enjoy interacting with our users and one has to remember that we are all new to a subject at some point :) I also take it as feedback that perhaps it could make sense to use the labels zigzag/armchair even in the nanotube builder, as shortcuts. Note that we do have these in the graphene nanoribbon builder!
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General Questions / Re: Zig-Zag CNT
« Last post by bhanuCh on June 18, 2021, 10:34 »
Thank you very much for replying to such a basic question, sir. Surely, I will try to catch up with the basics.
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Questions and Answers / MoS2-Graphene Heterostructure
« Last post by Deep Singh on June 18, 2021, 09:53 »
I am trying to make  a heterostructure of Graphene-MoS2.
I am using 3x3 MoS2 and 4x4 Graphene.
The paramters and optimisation parameters value is taken from the
reference work
https://doi.org/10.1063/1.5144078

I am not getting the bandstructure correct.
Also, the total energy is -27919.79 eV, while in the paper it is -500 eV.

I have attached the python script with this post.

I would like to know where am I getting wrong in the simulation.
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This is not implemented, and I am not even sure it's possible to do so. It seems the common approach is to compute the Born charges without spin-orbit included, even for spin applications, the assumption being that the Born charges themselves are not strongly sensitive to the inclusion of spin or not. Of course that assumption is hard to prove, if you cannot compute the charges with spin-orbit and check, but it is a reasonable one plus the Born charges are extremely to compute accurately anyway, the error estimates are often 10-20%, thus a few extra percent do not really matter. See e.g. https://arxiv.org/pdf/1207.2916 and https://arxiv.org/pdf/0906.3803.pdf
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