Messages

1

General Questions and Answers / Plumed Issue in QATK 2024.09

« on: January 4, 2025, 17:00 »

Hi, I try to run the "Metadynamics Simulation of Cu Vacancy Diffusion on Cu(111) - Using PLUMED" using QATK 2024.09, It always gives the error message:

Traceback (most recent call last):
  File "/home/ubuntu/synopsys/quantumatk/W-2024.09/bin/../atkpython/bin/atkpython", line 8, in <module>
    sys.exit(__run_atkpython())
             ^^^^^^^^^^^^^^^^^
  File "zipdir/ATKExecutables/atkwrappers/__init__.py", line 803, in __run_atkpython
  File "device.py", line 208, in <module>
    nlsave('Copper_111_results.hdf5', hook_functions)
  File "zipdir/NL/IO/NLSaveUtilities.py", line 314, in nlsave
  File "zipdir/NL/IO/HDF5.py", line 964, in writeHDF5Group
  File "zipdir/NL/IO/HDF5.py", line 821, in writeHDF5GroupFromSerializable
  File "zipdir/NL/IO/Serializable.py", line 283, in _getVersionedData
  File "zipdir/NL/Dynamics/MolecularDynamics/HookFunctions.py", line 79, in __versionedData
  File "zipdir/NL/Dynamics/MolecularDynamics/HookFunctions.py", line 523, in _functions
TypeError: cannot pickle 'SwigPyObject' object
Abort(1) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

How can I fix this issue? Thank you for the help!

2

General Questions and Answers / HSE-LCAO gives wrong bandgap evolution?

« on: June 22, 2021, 12:04 »

Hi, I'm using QATK 2020 to perform an LCAO-HSE06 calculation of Ga2O3. However, the bandgap reduced when the alpha (HF part) was increasing, which is incorrect.
the results are listed as bandgap(alpha) : 3.84 eV(0.20),  2.75 eV(0.25), 2.38 eV(0.30).
Both SG15 and PseduoDojo basis were tested, and they gave the same wrong bandgap evolution.
Please find the attached *py file for more detail.

3

General Questions and Answers / Re: How to extract the core level in the LCAO calculations?

« on: March 10, 2021, 03:54 »

Thank you. As the band alignment derived from PBE calculation can suffer the issue of the underestimated bandgap, I want to correct it with the HSE-LCAO result. But the alignment usually needs a potential or the core level (the very deep orbitals, not the valence states).  It seems that the electrostatic potential (not the difference electrostatic potential ) can not be obtained from the two-probe devices, I wonder if the core level can be extracted.

4

General Questions and Answers / How to extract the core level in the LCAO calculations?

« on: March 9, 2021, 08:22 »

Hello,  I am doing a band alignment calculation based on a combination of the two-probe device model and HSE.
I want to obtain the core levels in the two-probe device, and then use the core level and band edges from HSE-LCAO to align the band offset.
So my question is how to extract the core level in the two-probe device model and HSE-LCAO results?
Thank you!

5

General Questions and Answers / Re: Ghost atom in NEGF surface simulation with regarding surface reconstructions?

« on: October 24, 2019, 09:06 »

Thank you. Slab model usually presents strong quantum confinement effect, so we prefer NEGF method.
 I still have 2 questions.
1. Does only workfunction depend on ghost atom?  How about electronic structure (surface states, band structure, etc)?
2. Supposing the surface is a heterostrcuture, is band alignment, which usually correlates to the electrostatic potential, at interfacial region sensitive to the ghost atom?

6

General Questions and Answers / Ghost atom in NEGF surface simulation with regarding surface reconstructions?

« on: October 19, 2019, 11:56 »

Hi, I am facing an issue when dealing with NEGF surface simulations. There are many surface reconstructions for semiconductors, especially for III-V, how to determine the ghost atoms?

For example, GaN 0001 surface has a stable configuration that a Ga atom absorbed at the ideal  surface. If we followed the tutorial, the outmost Ga atom should be set as ghost atom, however, this seems to be completely unphysical, as the the adatom is part of surface reconstruction. 

Thank you for the response!