Messages

1

General Questions and Answers / Re: Shielding tensors on dummy atoms

« on: June 26, 2023, 10:57 »

Dear Filip,
as you wrote, the basis set is a combination of planar waves and localized atom-centered orbitals. Perhaps if one could use a zero-charge atom and manually set the localized part of the basis to a very small spherical function, that would be a way to go. But I see that this might be challenging and no guarantee for success.

Let me think about it for a while, maybe I'll come up with an alternative solution.

Thanks for your help! V.

2

General Questions and Answers / Re: Shielding tensors on dummy atoms

« on: June 23, 2023, 12:48 »

Dear Filip,
thanks a lot for your help.

Perhaps I should better clarify what is the intention of the calculation. I would like to calculate the Nucleus Independent Chemical Shifts (NICS) which is a measure of induced ring currents in the material. My background is mostly calculations of large molecules in Gaussian, where this can be easily calculated using GIAO NMR. The dummy atoms serve as probes for measuring the induced magnetic fields - the shielding tensors on these atoms basically describe the induced fields without the influence of the nucleus, that's why they should have no charge. They should have no basis because otherwise, in the vicinity of other atoms (which is my case), there could be an unrealistic interaction with the dummy atoms.

Now the question is how to do this in ATK.
- One option would be to do it in the LCAO method, where the ghost atoms are defined and calculate the shielding tensors manually in the script. One problem is how to define the ghost atoms without the basis fcs, another one is that the calculation of the shielding tensor might be quite a challenge.
-Another one would be to use the GIPAW method and define the ghost atom with zero charge and no (or very small) localized basis
Let me know what you think is the best approach and I am definitely willing to try it out.
Thanks, Vaclav

3

General Questions and Answers / Shielding tensors on dummy atoms

« on: June 21, 2023, 16:42 »

Dear all,
I need to calculate NMR shielding tensors on dummy atoms (no nucleus and no basis functions, serve only as passive observers). Is there a way to do this in ATK?
- I found that the plane wave calculator can be used to calculate the shielding tensors but it does not seem to support the ghost atoms.
- Is there any way around such as defining my own atoms with no charge and no basis functions?

Thanks for help
Vaclav

4

Installation and License Questions / Error on Windows 10

« on: December 27, 2020, 11:51 »

Hello,
I installed the 2020 QuantumATK version on Windows10. After launching the program, I got a window with the error shown in the attached text file. The 2019 verison worked fine. I would appreciate any help to solve this problem. Thanks a lot, Vaclav

5

General Questions and Answers / Re: TremoloXCalculator: Cart_create with procs 1 1 1 and periods 1 1 1 failed

« on: November 25, 2020, 10:21 »

Hi Julian,
thanks a lot for your help. It took me some time to get to it so sorry for a late reply. I used 2019.03 version but I tried it also with the new 2020.09 version and unfortunately I got the same type of error:

TremoloXCalculator: Cart_create with procs 1 1 1 and periods 1 1 1 failed
Traceback (most recent call last):
  File "traj_generator.py", line 215, in <module>
    optimizer_method=LBFGS(),
  File "zipdir/NL/Dynamics/Optimization/OptimizeGeometry.py", line 377, in OptimizeGeometry
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 1790, in update
  File "build/lib/python3.6/site-packages/tremolox/TremoloBaseCalculator.py", line 417, in _update
  File "build/lib/python3.6/site-packages/tremolox/TremoloBaseCalculator.py", line 965, in _configure_tremolo_data
tremolox.RuntimeError: SomeError: Error in file ../../../../src/comm.c, line 238 (0): SomeError: StartParallel: Cart_create failed

Would you have any further suggestions what to do?

Thank you, Vaclav

6

General Questions and Answers / TremoloXCalculator: Cart_create with procs 1 1 1 and periods 1 1 1 failed

« on: November 9, 2020, 18:18 »

Hello,
I wrote a script which shifts a molecule on a graphene sheet surface and calculates Total energy. Everything seemed to work fine when just a few thousands of points are calculated but with a large number of calculated points I got this error message:

TremoloXCalculator: Cart_create with procs 1 1 1 and periods 1 1 1 failed
Traceback (most recent call last):
  File "traj_generator.py", line 222, in <module>
    total_energy = TotalEnergy(bulk_configuration)
  File "zipdir/NL/Analysis/TotalEnergy.py", line 35, in __init__
  File "zipdir/NL/ComputerScienceUtilities/Timer.py", line 145, in __call__
  File "zipdir/NL/Analysis/TotalEnergy.py", line 35, in <lambda>
  File "build/lib/python3.6/site-packages/tremolox/TremoloBaseCalculator.py", line 746, in _calculateTotalEnergy
  File "build/lib/python3.6/site-packages/tremolox/TremoloBaseCalculator.py", line 762, in _simplifiedCalculateTotalEnergy
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 1790, in update
  File "build/lib/python3.6/site-packages/tremolox/TremoloBaseCalculator.py", line 417, in _update
  File "build/lib/python3.6/site-packages/tremolox/TremoloBaseCalculator.py", line 965, in _configure_tremolo_data
tremolox.RuntimeError: SomeError: Error in file ../../../../src/comm.c, line 238 (0): SomeError: StartParallel: Cart_create failed

I am new to programming so I admit there might be an error in my script but I could not figure out what could be the source of this error message. Could anyone please explain this error message and direct me how to avoid it? I attached the full script.

Thanks a lot for any advice.