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Messages - Anders Blom

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Sorry for not catching these basic things, I should have checked more carefully Volt of course, and thank Filip for the plotting part - I thought we converted the unit once only.

Questions and Answers / Re: How to get figure of merit.
« on: July 29, 2021, 23:59 »
It's not that you should change those lines, but they show how to calculate the quantities you need. You will need to create a whole standalone Python script to do this, but that code can serve as guidance, was my point.

If you don't have a spin-polarized calculation, I think you can just do it for one spin channel.

Otherwise the really simplest way to do this is to enter different temperature values in the widget in the GUI and write down the ZT for each temperature and plot it separately. Might even be faster ;)

Questions and Answers / Re: How to get figure of merit.
« on: July 29, 2021, 09:19 »
Sure, it's relatively straightforward in a Python script.

The best approach for you is to check out the code for the Thermoelectric plugin, which is available in open source in lib/site-packages/AddOns/TransportCoefficients in the installation tree.

The file contains a function that computes the moments, and then you can see in (line 386-389) how these are used to compute the Seebeck coefficient. Now you just need to do this as a function of temperature which is a parameter to the moments function, extract the values and plot them.

Note however that this will just capture the electron temperature dependence. If you also want to include the ionic temperature (specifically, how the transmission spectrum and the thermal conductances depend on temperature), you need much more work, e.g. using our SpecialThermalDisplacement method.

Sorry about the typo. Since the tutorial was published we changed the definition of the ElectrostaticDifferencePotential class to be specified in V, not eV, as is appropriate for a "potential".

Thus, all you need to do is change line 51 (which the error message complains about) to

vv = -v_z[index].inUnitsOf(V)

There was also a sign change involved, I recall, hence the leading minus sign.

This is not my area of expertise and it's quite complex, but since a lot of our support staff is on summer vacation I figured I at least answer what I can.

I think you are both right and wrong :-) You can certainly have more than 2 tags on atoms, in fact it's often necessary for polymers. The error message is just written like this to be as informative as possible. However, a particular atom cannot belong to more than one potential set, I believe. Otherwise we don't know which one to use to compute the forces on it...

Can't the potential terms be combined to a single parameter set? Maybe if the dummy atom is not H but, say He?

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

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.

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

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

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

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.

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.

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 ( is exactly the same as in other planewave codes, and explained in many places like

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

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).

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