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Messages - Anders Blom

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1
Questions and Answers / Re: ionic dielectric constant
« on: July 21, 2021, 08:28 »

2
Questions and Answers / Re: error
« on: July 16, 2021, 21:51 »
Looks to me like you are trying to run a counterpoise-corrected calculation, but you haven't actually specified which atoms belong to the two parts of the system. But it's hard to tell exactly without seeing the input file.

Also I find it odd that these error messages appear more than once, but maybe there is a good reason for it. Just make sure that when you run in parallel, you use the mpiexec that we ship with the software.

3
Questions and Answers / Re: Build silicene nanoribbons
« on: June 30, 2021, 22:09 »
Then there is no net spin polarization across the ribbon

4
Questions and Answers / Re: MD error
« on: June 29, 2021, 07:45 »
To start with, yes, but we are also planning a dedicated MTP webinar in August

5
Questions and Answers / Re: MD error
« on: June 29, 2021, 04:05 »
Hard to say but yes it's likely to be an issue with the parameters. Was this a published ReaxFF potential, or something you made yourself?

Perhaps you want to try your hand at using our Moment Tensor Potentials instead - you can see some details about this in the release webinar linked above

7
Questions and Answers / Re: MD error
« on: June 25, 2021, 09:03 »
I looks like the force and then the velocities of the atoms became ill defined, probably because the atoms ended up too close to each other. Some potentials cannot handle when atoms have high energy/temperature/velocity and does not reject them well enough when they come close. See if you can run with lower initial velocities, or at lower temperature. Also, try first to run the ReaxFF model on a more static problem to test it and see that it behaves correctly.

8
Thank you for already using S-2021.06!

Usually this error message means you have run out of memory. The model you run is fairly large and will require a serious machine to run.

9
Questions and Answers / Re: Energy Cut-off
« on: June 24, 2021, 06:22 »
QuantumATK has two different flavors of DFT: planewave and localized orbitals (LCAO), each with its own benefits.

The meaning of the energy cutoff in the planewave calculator settings (https://docs.quantumatk.com/manual/Types/PlaneWaveCalculator/PlaneWaveCalculator.html#planewavecalculator-c) is exactly the same as in other planewave codes, and explained in many places like https://www.researchgate.net/post/What-is-the-importance-of-cut-off-energy-in-Plane-Wave-DFT

10
Oh yes, sorry - I was misled by the long cell size in C, but of course a topological insulator needs that! (I have recently looked into 2D topological insulators, so I think that's where my mind went.)

Still, 5x5 or 7x7 will be significantly easier to run than 9x9!

To run on the HPC, you don't need to run the GUI (NanoLab) there, only  the calculations, and those do not require any GPU. The simplest approach is just to copy your input Python file to the cluster and run it manually from the command line, but you can also set up the Job Manager to submit jobs into the queue (if you have one) on the HPC directly from NanoLab running on your Windows machine. If you need help to set that up, let us know, but first see https://docs.quantumatk.com/tutorials/job_manager_remote/job_manager_remote.html

MTP for topological insulators would be so cool - we will also do a separate webinar on that in August (I mean MTP, not for topological insulators specifically).

11
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...!

12
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.

13
General Questions / Re: Zig-Zag CNT
« 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!

14
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

15
General Questions / Re: Zig-Zag CNT
« on: June 17, 2021, 22:06 »
Zigzag nanotubes are of the chiral index type (n,0) and armchair are (n,n).

A friendly suggestion is to catch up on the basic properties on nanotubes via some review article or the many, many resources you can easily find online. A Google search on "zigzag cnt" immediately shows pictures of the property I mentioned above, e.g. via http://www.photon.t.u-tokyo.ac.jp/~maruyama/kataura/chirality.html. That way it will be easier for you to successfully run the calculations you are interested in.

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