Recent Posts

21

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

« Last post by Anders Blom on April 24, 2024, 19:29 »

Thanks for trying 2023, it is certainly concerning that you still see the problem. However, we have also run multiple versions of this calculation with the current version and cannot reproduce it. In theory there could be unusual connection to your hardware or MPI libraries etc, but would you also mind running it with 24 and not 28 processes?

22

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

« Last post by krabidix on April 24, 2024, 13:17 »

Here are the bulk_configuration and other script files if the QuantumATK team wants to investigate the issue.

23

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

« Last post by krabidix on April 24, 2024, 13:15 »

Hi,
The latest version does not make any difference.
The question remains why "process_per_displacement" parameter is so sensitive to phonon calculations ?

24

General Questions and Answers / Regarding one existed .py file from software tutorial itself. Opening at builder

« Last post by techenthusiast on April 23, 2024, 11:52 »

Good evening,
Hope this text finds you well.
This text is mainly to clarifying one doubt. Regarding one existed .py file(https://docs.quantumatk.com/_downloads/c344073d8389b8850d8b352ffed2f855/cnt-gaa-pin.py) from software tutorial itself. Though, Opening at builder.


Is that possible to characterize the same device for the same ? 

Thank You.

25

General Questions and Answers / Building type 1, 2, 3 quaternary heusler alloy

« Last post by physics on April 22, 2024, 17:00 »

Hi everyone,

How to build type 1, 2, 3 quaternary heusler alloy with varying composition?

Thanks

26

General Questions and Answers / Half integer transmission in hdf5 file

« Last post by kaihuang on April 21, 2024, 06:55 »

Hello,

I conducted the transmission calculation for a bulk system and attempted to plot the transmission concerning k by parsing the hdf5 file. In this instance, I initiated the DFT calculation, incorporating Spin-Orbit Coupling and noncollinear magnetic moments. GGA method and SG15-SO pseudopotential. Subsequently, the transmission was calculated. Within the output hdf5 file, I observed that the transmission is delineated in the data tree as follows:

- TransmissionSpectrum_0
    - transmission
        - 0
            - data
        - 1
            - data
        - 2
            - data
        - 3
            - data

For each 'data,' there is a 2D array. Two indices represent k points and energy, respectively.

However, two questions arise:

1. Is it correct that 0, 1, 2, 3 above represent the transmission of spin all, x, y, and z, respectively? Or do they represent spin all, y, z, and x? Or something else?
2. In the transmission->0->data, I noticed that the transmission plot matches the electron band structure well, which implies the validity of the result. However, I saw many half-integer transmissions, like 0.5, 1.5, 2.5, etc. It seems that each band only contributes 0.5 transmission channel rather than 1. So, I would like to inquire about the meaning of this dataset. Can I multiply it by 2 to get the right result?

Additionally, I attempted the transmission calculation without SOC, i.e., choosing just spin polarized. The transmission output in the hdf5 file is as follows:

- TransmissionSpectrum_0
    - transmission
        -0
            - data

This time, there's no spin projection. But again, each band contributes only 1 transmission channel rather than 2 (for the two spin eigenstates). Again, what's the meaning of this data in hdf5, and can I just multiply by 2?

Thanks,
Kai

 

27

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

« Last post by AsifShah on April 21, 2024, 03:11 »

Dear Admin,
Sure. Looking forward to your response.

28

General Questions and Answers / M3GNet error

« Last post by AsifShah on April 20, 2024, 21:21 »

Dear Admin,

When running M3GNet based molecular dynamics alongwith DZ3 correction as:

from tremolox.neighborlistcalculator.M3GNetCalculator import TremoloXM3GNetDirectPESCalculator
calculator_m3gnet = TremoloXM3GNetDirectPESCalculator(device='cpu')
calculator_d3 = TremoloXCalculator(parameters=DispersionD3Z(xc='PBE'))
calculator = CombinedCalculator([calculator_m3gnet,calculator_d3])

The simulations runs for sometime (few picoseconds) and then I get the following error:

TremoloXCalculator: Cart_create with procs 1 1 1 and periods 1 1 1 failed
Traceback (most recent call last):
  File "/home/Asif/QATK_V2023_12/quantumatk/V-2023.12/atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 780, in __run_atkpython
  File "VF_Multilayer_MoS2.py", line 406, in <module>
    md_trajectory = MolecularDynamics(
                    ^^^^^^^^^^^^^^^^^^
  File "zipdir/NL/Dynamics/MolecularDynamics/MolecularDynamics.py", line 1073, in MolecularDynamics
  File "zipdir/NL/Dynamics/MolecularDynamics/DynamicsEnergyForcesStress.py", line 30, in wrapped_analysis
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 46, in forcesFunction
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 72, in _checkAndUpdate
  File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/Analysis/FastEnergyForcesStress.py", line 100, in _update
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 3080, in update
  File "zipdir/NL/Calculators/CombinedCalculator.py", line 373, in _update
  File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 3080, in update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/neighborlistcalculator/neighborlistcalculator.py", line 467, in _update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/TremoloBaseCalculator.py", line 501, in _update
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 311, in __init__
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 251, in wrapper
  File "build/atkpython/lib/python3.11/site-packages/tremolox/calculation/calculation.py", line 540, in _setSystem
  File "build/atkpython/lib/python3.11/site-packages/tremolox/pymolo_avx.py", line 813, in conf_data_domain
tremolox.RuntimeError: SomeError: Error in file /slowfs/qatkdev2/users/qatktest/de02vlbamboo06/exlibs/.conan/data/tremolox/2023.08/quantumatk/stable/build/0bd0f4ede5a9e99cf053738a382952d716d95ea1/src/comm.cpp, line 234 (0): SomeError: StartParallel: Cart_create failed

Kindly help in this regard.

29

General Questions and Answers / Re: Local energy in MTP calculation

« Last post by nils.holle on April 16, 2024, 18:14 »

Hi Julian,

Thank you for your reply. We would like to observe local relaxation events in glasses, which should become a much easier tasks if local atomic energies are known.
I think this alone is a very general idea, but I could also imagine many other use cases.

Best regards,
Nils

30

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

« Last post by Anders Blom 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.