Topics

1

General Questions and Answers / problems with Hgga_hse06 and MGGA calculation to transmission spectrum

« on: January 17, 2024, 02:55 »

Hello, everyone

Recently I got some serious problems with calculating transmission with mgga.

I calculated transmission for Si in 110 direction by following the example on the quantumATK webpage(https://docs.quantumatk.com/tutorials/transmission_gr_mos2/transmission_gr_mos2.html#mos2).

I expected that the transmission should be 0 for the band gap.
However, I got a non-zero transmission for the energy in the band gap as seen in the attached Transmission vs. Energy plot.
I also calculated the band structure which is also attached in this post. And I could see the band structure calculation shows a clear band gap.
I attached the code that I used.

Please take a look and give me any advices to solve this problem.

Thank you

2

General Questions and Answers / Questions about nlread

« on: January 1, 2024, 05:17 »

Hello, and happy new year everyone.

Recently, I had a Deviceconfiguration that successfully converged with PLDOS. It took more than 10 hours

I wanted to reuse it with transmission spectrum, but since it consumed a lot of time, I was planning to redo it with 'nlread function'.

Here is my code

# DeviceConfiguration
Device_configuration = nlread('Si80_111_5e19_4040.hdf5',DeviceConfiguration_0)[0]

#Choose the first configuration in the list
Device_configuration = Device_configuration_list[0]

# %% Set Calculator

Device_configuration.setCalculator(calculator)

Device_configuration.update()

nlsave('Si80_111_5e19_5050trans.hdf5', Device_configuration)

# %% TransmissionSpectrum

kpoints = MonkhorstPackGrid(
    na=50,
    nb=50,
    nc=1,
    symmetries=[
        ([[ 1., 0., 0.],
          [ 0., 1., 0.],
          [ 0., 0., 1.]], [ 0., 0., 0.]),
        ([[-1., 0., 0.],
          [ 0.,-1., 0.],
          [ 0., 0.,-1.]], [ 0., 0., 0.]),
    ],
    force_timereversal=True,
    k_point_shift=None,
    shift_to_gamma=[True, True, True]
)

self_energy_calculator = RecursionSelfEnergy(
    storage_strategy=NoStorage()
)

device_transmission_method = GreensFunction(
    processes_per_contour_point=1,
    )

transmission_spectrum = TransmissionSpectrum(
    configuration=Device_configuration,
    energies=numpy.linspace(0.0, 0.0, 1)*eV,
    kpoints=kpoints,
    kpoints_weights=None,
    self_energy_calculator=self_energy_calculator,
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    device_transmission_method=device_transmission_method,
    enforce_zero_in_band_gap=True
)
nlsave('Si80_111_5e19_5050trans.hdf5', transmission_spectrum)

However when I ran the calculation nothing appeared on the log file, and the calculation did not run.

Could somebody please help me with how to use 'nlread' properly?

Thank you.

3

General Questions and Answers / mpirun hostfile rank allocate error

« on: December 11, 2023, 03:20 »

Dear Expert
Hello, I am currently having some problems when running mpi.

My hostfile is dirac1, dirac2... dirac8 and each one contains max. 20 mpi nodes.

I named each hostfile as dirac1=hf1, dirac2=hf2, dirac3+dirac4=hf34

I works well when I run just one hostfile, the calculation runs properly.

However, when the I run hostfiles more than 2 (for example, hf34=dirac3 and 4) the log file only shows blank space, although the terminal, shows that the process is working properly.

Also while allocating mpi, I make hostfile through terminal

vi hf34
dirac3:15
dirac4:15
:wq

and when I run the calculation
mpirun -n hf34 -p 30 home/edrl_04/Desktop/quantum23ver/quantumatk/V-2023.09/bin/atkpython opt_device_conf_110_5e20.py > opt_device_conf_110_5e20.log &

the process allocate as dirac3:20 and dirac4:10 although I already set their process as 15 each. And the log file shows nothing.

I am using 23.9 version of quantum atk and my intel mpi verison is 21.10 version

Is there anything that I can do to fix this 2 major problems?
Thank you for reading the questions.

4

General Questions and Answers / Device calculation error at 2022.12-U-atk

« on: November 8, 2023, 02:51 »

Hello, my name is changmin Lim and I am currently using Quantum-atk 2022.12-U version

Recently when I was calculating device I ran into unknown error.

Traceback (most recent call last):
  File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 793, in _onDoubleClicked
  File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 896, in open
  File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 896, in <listcomp>
  File "zipdir/NL/GUI/Tools/Data/ToolAnalysisPlugins.py", line 214, in createWidget
  File "zipdir/NL/GUI/Tools/Tool.py", line 960, in dropEvent
  File "zipdir/NL/GUI/DnD/DropExtractor.py", line 618, in extract
  File "zipdir/NL/GUI/DnD/DropExtractor.py", line 248, in mimeDataTextsFromInstances
  File "zipdir/NL/IO/NLPrint.py", line 70, in nlprint
  File "zipdir/NL/Study/Study.py", line 939, in nlprint
  File "zipdir/NL/Study/OptimizeDeviceConfiguration.py", line 514, in _nlprint
  File "zipdir/NL/Study/OptimizeDeviceConfiguration.py", line 463, in result
  File "zipdir/NL/Study/Study.py", line 620, in _results
  File "zipdir/NL/Study/Study.py", line 587, in _tasks
  File "zipdir/NL/Study/Study.py", line 510, in _workflow
NL.ComputerScienceUtilities.Exceptions.NLValueError: The study object workflow not available on a lightweight instance. To access the workflow read the study object as a heavyweight instance.


I tried to search heavyweight and lightweight on qna, but nothing was found.

also, I tried to find txt files that showed on error, but I could not find the error line as well.

Can anyone help me with this error?
Thank you