Messages

1

General Questions and Answers / Re: how to generate a file *.nc from hdf5 or py

« on: April 15, 2024, 19:23 »

Any tutorial which mentions NC files is just old. We use HDF5 files now for all data. So your previous step should have written an HDF5 file with the optimized structure, and you just read that same file in the next step.

2

General Questions and Answers / Re: How is Defect Diffusivity Calculated with calculateDiffusivity method?

« on: April 12, 2024, 23:51 »

https://docs.quantumatk.com/manual/technicalnotes/charged_point_defects/charged_point_defects.html#diffusivity-of-defects

3

General Questions and Answers / Re: LDA+U in noncollinear spin

« on: April 12, 2024, 23:46 »

Should be possible for Normconserving LCAO, yes.

4

General Questions and Answers / Re: Constraints_data parameter in function "writePOSCAR"

« on: April 12, 2024, 23:44 »

It requires 2 steps.

1) Define constraints via tags. Supported tags are "constrain" and "constrain_x" (y, z) in order to constrain each atom fully or only in x/y/z
2) Use a few lines of code

Code: python

from AddOns.VASPPlugins.Scripter.VASPConstraintsWidget import extractConstraintsFromTags
from AddOns.VASPPlugins.IO import writePOSCAR
vasp_constraints = extractConstraintsFromTags(configuration)
writePOSCAR(configuration, "POSCAR", vasp_constraints)

Example config attached, with the resulting POSCAR.

Note that you can also do this directly from the Builder, using Export and choosing the VASP format.

5

General Questions and Answers / Re: how to generate a file *.nc from hdf5 or py

« on: April 12, 2024, 23:17 »

Why do you need to do that? In general I would say it's not possible, these are not standard file formats you can just convert between.

6

General Questions and Answers / Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?

« on: April 12, 2024, 23:15 »

From these files it is at least clear that the self-consistent loops proceeds very differently in the two cases for some displacements (but not all), and in the end of course this makes a big difference for the dynamical matrix.

Now, when I submit this to our bug fixing team, the first thing they will ask is if it was tested in the latest version. I personally don't have a machine with 168 cores at hand to test on, but you do, so it would be really helpful if you could rerun this with V-2023.12-SP1 (which has many new features compared to U anyway), since in theory it could have been fixed since the version you used. This should only take you 7-8 hours :-)

Second, I find your choice of processes_per_displacement=28 odd when you run on 24-core machines. This gives at the very least odd load-balancing and unnecessary network communications.

So, please check using processes_per_displacement=24 instead. One can argue that any value should work numerically, so we might still look into it, but only if it appears in V-version also.

The nice news, once we resolve this, is that the speedup using a large processes_per_displacement is substantial, basically linear!

7

General Questions and Answers / Re: Bandstructure of B-P nanosheet not calculated correctly

« on: April 6, 2024, 20:23 »

The paper you refer to is done with DFT, but your model in the script is using an extended Huckel model. That might work, sometimes, and would save a lot of time, however as your test shows, for this system the Huckel parameters do not give the correct band structure etc for B-P, thus it cannot be used.

You might try other parameters such as the Muller or Hoffmann models, and also it will be important to perform the calculations self-consistently since there will be significant charge transfer between B and P atoms (might try that with Cerda parameters too but I doubt it will work, as the two parameter sets you are trying to mix come from fits to AlP and BN).

I think your main option will be DFT in this case.

8

General Questions and Answers / Re: Add dielectric to the electrode region

« on: April 6, 2024, 00:54 »

Add the dielectric region, going all the way out to the edges of the system in C (Z), before creating the device. Then when you use Device from Bulk, the regions will automatically be copied into the electrodes.

9

Installation and License Questions / Re: Error while opening Quantumatk

« on: April 6, 2024, 00:51 »

Looks like the main.ini file was corrupted, try rename it to main-backup.ini and try again. The file is in C:\Users\username\.quantumatk or .vnl for old versions.

10

General Questions and Answers / Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?

« on: April 6, 2024, 00:43 »

These are for 28 processes, right? The point will be to compare with the run using 4, so please upload those too.

11

General Questions and Answers / Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?

« on: April 1, 2024, 20:10 »

Could you zip the log files too, might help to look at them before rerunning, the HDF5 files don't tell us much how the problem arises

12

General Questions and Answers / Re: How to calculate the current after introducing spin-orbit coupling?

« on: March 27, 2024, 22:38 »

I don't think you need a script, actually. If you open the IV curve in the GUI (NanoLab) you should be able to change the curves to show any spin component.

13

General Questions and Answers / Re: Phonon dispersion is senstitive to "processes_per_displacement" paramter of DM?

« on: March 27, 2024, 22:36 »

I think we need to look at the exact scripts and output. If you don't want to share them publicly, you can email then.

14

General Questions and Answers / Re: questions about surface green's function(SGF)

« on: March 26, 2024, 23:39 »

All doable, yes

15

General Questions and Answers / Re: mean free path of electrons in metal

« on: March 26, 2024, 23:37 »

The script is rather specific to the calculation done with an explicit defect. In your case, you should go back to definitions in the theory section; looking at the line which actually defines the MFP, you can evaluate all quantities for your system and extract the MFP as

(R(L)/Rc-1) = L/MFP

(all depending on energy).

Here Rc is the conductance of the perfect system, and R(L) = 1/T(L) is computed for a device where L is the length of the part that has been thermally perturbed. A better option might even be to plot R(L) as a function of L, which should be a linear relation and you can get MFP from the slope.