Recent Posts

1

General Questions and Answers / Re: Implementing a new Reactive Forcefield

« Last post by Anders Blom on Yesterday at 20:19 »

I am trying to be constructive here, not criticize or downplay the problem, but why not fit an MTP for MoS2 instead, if this is urgent (and anyway)? I am sure it will be more accurate and perform similarly.

Even if that takes a week month to fit (which it doesn't, more like a day or two) it's faster than waiting for us to try to debug someone else's potential which may have some mistake in the numerical values, which is almost impossible to sort out; even if we see where the problem is we don't know the correct value. Or if there is a mistake in our ReaxFF model, it will take until September to release a new version...

So in any scenario you are probably much better off fitting a new MTP, and after that you can use the same procedure for any other 2D material (for which there are no ReaxFF potentials).

2

General Questions and Answers / Re: Explanation of optical spectrum

« Last post by Anders Blom on Yesterday at 20:14 »

Apart from numerical points like how many bands/levels you include, it's rather straightforward: the optical spectrum is computed from the difference of energy levels and the matrix elements between the eigenstates with the momentum operator. For two different molecules, obviously both will be quite distinct.

3

General Questions and Answers / Explanation of optical spectrum

« Last post by narin on May 31, 2024, 21:02 »

Hello

I have calculated the optical spectra of two similar molecules and obtained their susceptibility tensors. Their susceptibilities are different and I need to explain the reason of the difference. I checked the ATK manual (We're using v. 2020) and the Kubo-Greenwood formula is given. Which terms in the KG formula affects the value of susceptibility? How can I explain the difference of susceptibilities using KG formula (perhaps accessing the terms in ATK that affect the susceptibility values)? I have checked the references given in the manual and couldn't find the same formula in those references.

Thanks.

4

General Questions and Answers / Re: Implementing a new Reactive Forcefield

« Last post by AsifShah on May 31, 2024, 08:46 »

Dear Admin,
Is there any update? It is urgent.

5

General Questions and Answers / Re: Information and Capabilities of Pretrained MTPs in Force Field Library for MD

« Last post by Anders Blom on May 30, 2024, 19:43 »

Yeah MTP can be particularly sensitive to this, forces can diverge in such geometries. We have been experimenting with adding a short-range repulsive potential (ZBL) but it doesn't always work as well as desired. Good that you solved it!

6

General Questions and Answers / (Edited) ChargedPointDefect: interstitial doesn't work / substitutional is fine

« Last post by beomjin on May 30, 2024, 17:35 »

(Final revision: May 31, 2024, 10:30)

Q-ATK Version: V-2023.12-SP1
HPC OS: Rocky Linux 8.7
User: Non-sudoer

Hello, this is my first post on the Q-ATK forum. There might be mistakes in my post, so I appreciate your understanding and any feedback.

I am currently working on the ChargedPointDefect (CPD) module to calculate the charge transition level of defects. I followed the CPD tutorial (https://docs.quantumatk.com/tutorials/charged_point_defect_study_object/charged_point_defect_study_object.html), using Workflows instead of Script Generator as Q-ATK2023 does not support Script Generator.
Also, there was a previous post about Charged defects in the Q-ATK forum, but it's a different problem.
(https://forum.quantumatk.com/index.php?topic=11055.msg37116#msg37116)

I successfully obtained results for diamond with a boron substitutional defect (see attached image). However, the ChargedPointDefect module does not work for an interstitial defect. The two .py scripts for substitutional boron and interstitial hydrogen are attached.
Fortunately, I can export data from ChargedPointDefect .hdf5 file at Nanolab and it gives me formation energy for each charge state (See attached image). So only the GUI function that makes the charge transition plot doesn't work.

Error: Missing 2 required positional arguments: 'supercell_repetitions' and 'charge_state'    (The full error code is provided at the end of this post.)
In the attached .py scripts, 'supercell_repetitions' defaults to (1x1x1). The 'charge_state' parameter is correctly set in the CPD block, and it works for substitutional boron. However, using the same input scripts for interstitial hydrogen results in an input argument error.

It seems the ChargedPointDefect module works for substitutional defects but not for interstitial defects.

ChatGPT Suggestions:

1. Function Definition and Call Issue: The 'update' method or another method within the ChargedPointDefect class might be calling '_defectSymmetryGroups' without properly passing the required arguments.
2. Incorrect Function Call: Another part of the code might be calling '_defectSymmetryGroups' and missing the necessary arguments.
The 'ChargedPointDefect' library in the QATK.zip file is in .pye format, not .py, so I cannot access its content.

Can someone help me with this error?

Side Question: Does anyone know where the .vnl directory is? I couldn't find it. Some suggest that GUI issues can be solved by removing the ".hdf" file in the ".vnl" directory (https://forum.quantumatk.com/index.php?topic=6335.0).

Thank you in advance.

======================================================================================================
Error message when I try to open CPD .hdf5 result file of interstitial hydrogen from Nanolab GUI as belows:
Exporting CPD .hdf5 file seems to be okay as I mentioned.

Traceback (most recent call last):
  File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 844, in _onDoubleClicked
  File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 945, in open
  File "/tmp/tmp_xh4zvsfAddOns/ChargedPointDefectAnalyzer/ChargedPointDefectAnalyzerPlugin.py", line 112, in createWidget
  File "/tmp/tmp_xh4zvsfAddOns/ChargedPointDefectAnalyzer/ChargedPointDefectAnalyzerWidget.py", line 91, in __init__
  File "/tmp/tmp_xh4zvsfAddOns/ChargedPointDefectAnalyzer/DefectCollection.py", line 196, in addDefectCalculations
  File "zipdir/NL/Defects/ChargedPointDefects/DefectResultsSummary.py", line 138, in __init__
  File "zipdir/NL/Defects/ChargedPointDefects/DefectResultsSummary.py", line 1234, in loadData
  File "zipdir/NL/Defects/ChargedPointDefects/DefectResultsSummary.py", line 1268, in loadDataStudy
TypeError: ChargedPointDefect._defectSymmetryGroups() missing 2 required positional arguments: 'supercell_repetitions' and 'charge_state'

7

General Questions and Answers / Re: Information and Capabilities of Pretrained MTPs in Force Field Library for MD

« Last post by msingh96 on May 29, 2024, 17:35 »

Hello. I think I figured it out. the distance between surfaces in the initial geometry was too close, causing large forces to explode and break most structures.

8

General Questions and Answers / Re: Information and Capabilities of Pretrained MTPs in Force Field Library for MD

« Last post by msingh96 on May 27, 2024, 22:56 »

Hi Anders, I've been trying to figure this out on my own before posting again.

I am trying to use the Si/TiSi₂ potential for MD simulations. I have had modest success with small structures, but the most frequent error is atoms leaving the simulation cell. this error causes the MD simulation to stall and get stuck. my instinct is an issue with the structures I provided, I used the interface builder to make an initial structure with Si [100] surface and TiSi[001] surface but I have to manually modify the distance between the surfaces using shift surface. I want to equilibrate the surface distance suing NPT but that's not working either.

Are there any example geometries from the training data for this potential to see where I'm going wrong?

9

Installation and License Questions / Re: Is there any limitation for number of execution of Simulation?

« Last post by Anders Blom on May 24, 2024, 18:30 »

Could be. Finished just means the job is not running any more, but the Job Manager does not know anything about possible errors that arose.

10

Installation and License Questions / Re: Is there any limitation for number of execution of Simulation?

« Last post by techenthusiast on May 24, 2024, 08:55 »

Also there is a small doubt: Sometimes its showing Job status as "finished" even ongoing execution for example ("Executing task - 7/20")  . Without throwing any error. Its similar to this?