Recent Posts

71

General Questions and Answers / M3GNet energies

« Last post by AsifShah on March 16, 2024, 08:08 »

Dear Admin,
When using M3GNet to calculate the total energy of a system the output shows nothing. Is it due to some bug?

Thanks
Here is the code:
# %% MoSe2

# Set up lattice
lattice = Hexagonal(3.288*Angstrom, 40.0*Angstrom)

# Define elements
elements = [Molybdenum, Selenium, Selenium]

# Define coordinates
fractional_coordinates = [[ 0.333333333333,  0.666666666667,  0.5           ],
                          [ 0.666666666667,  0.333333333333,  0.4583975     ],
                          [ 0.666666666667,  0.333333333333,  0.5416025     ]]

# Set up configuration
mose2 = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )
mose2_name = "mose2"


# %% Set LCAOCalculator

from tremolox.neighborlistcalculator.M3GNetCalculator import TremoloXM3GNetDirectPESCalculator
calculator = TremoloXM3GNetDirectPESCalculator(device='cpu')


# %% Set Calculator

mose2.setCalculator(calculator)

mose2.update()

nlsave('TE.hdf5', mose2)


# %% TotalEnergy

total_energy = TotalEnergy(
    configuration=mose2
)
nlsave('TE.hdf5', total_energy)

72

General Questions and Answers / Re: Extract 3D/2D potential profile as a text file

« Last post by filipr on March 13, 2024, 14:52 »

The columns in the text representation have no meaning - it's just a way to visually "compress" the output. It is just one long list of numbers, 111x111x431 = 5,310,351 numbers to be exact. So you can just take the "matrix" of numbers and split at whitespace and you get a 1-dimensional array of numbers. This is the potential. To convert a 3D index (i, j, k) into a 1D index n in this list you use: n = k + Nk * j + Nj * Nk * i as is somewhat documented at the top of of the text representation (outer loop: x, middle loop: y, inner loop: z)

If you know Python you can also more conveniently get the binary exact numbers as a numpy array by using the QuantumATK python API, see https://docs.quantumatk.com/manual/Python.html and https://docs.quantumatk.com/manual/Types/ElectrostaticDifferencePotential/ElectrostaticDifferencePotential.html This allows you to directly extract the data, do post-processing and plotting in the same Python script.

73

General Questions and Answers / Re: Zero bias transmission

« Last post by AsifShah on March 13, 2024, 14:36 »

Thanks

74

General Questions and Answers / Re: Extract 3D/2D potential profile as a text file

« Last post by maheswari on March 13, 2024, 12:47 »

Hi, Is there any response to my earlier query? Thanks!

75

Plugin Development / ATK to calculate superconducting Tc and device

« Last post by Roc2019 on March 13, 2024, 02:37 »

Dear Developers,

Does ATK have a plan to add some function to calculate the superconducting Tc and devices (e.g., superconducting diode or Josephson junction) in the future?

Some references and codes could be helpful, i.e.,

PHYSICAL REVIEW B 95, 054506 (2017)  https://doi.org/10.1103/PhysRevB.95.054506
SCTK code:  https://github.com/mitsuaki1987/sctk/tree/develop

Thanks.

Roc

76

General Questions and Answers / Re: Zero bias transmission

« Last post by Anders Blom on March 11, 2024, 19:57 »

No, all transport we compute is elastic by default. Otherwise you would have to introduce extra effects that take/give the energy the electron loses/gains in the process. This could be phonons, and QuantumATK can handle inelastic phonon scattering, see corresponding tutorials on that, like https://docs.quantumatk.com/tutorials/inelastic_current_in_si_pn_junction/inelastic_current_in_si_pn_junction.html.

77

General Questions and Answers / Extract 3D/2D potential profile as a text file

« Last post by maheswari on March 11, 2024, 11:34 »

Hi, I am interested in getting the raw data (in txt or excel) of the 3D or 2D potential profile of across the device. I could see the 2D image using Viewer, but I don't see an option to extract the raw data. Alternatively, when I tried the "Text Representation" tool, it was hard to read the file since there was no label. It seems to have 6 columns. Is this (x,y,z, potential)? If all the data is just potential, where do I get the (x,y,z) information? Where do I find the information related to sampling? I have attached the snapshot of the output file for your reference.

Thanks!

78

General Questions and Answers / Re: Zero bias transmission

« Last post by AsifShah on March 9, 2024, 10:55 »

Dear Ander Bloms,

Thanks for your response. I still have a doubt, when you say QATK includes the effects of all atoms, "Does that mean it takes account of an electron scattering from energy E1 to E2? In other words, if an electron is traveling with energy E1 from the electrode and encounters a scatterer in the central region taking it to energy E2, will such an event be included in the transmission calculated from QATK?"

79

General Questions and Answers / Re: What is the current option for the previous "Analysis from File"?

« Last post by Anders Blom on March 9, 2024, 00:54 »

Good question, happy that we get a chance to answer it here for the benefit of all users.

• Start we a fresh empty workflow in the Workflow Builder
• Insert a "Load from file" block from the Algorithms group and double-click the inserted block to open it
• Click the button "Load from file" and select the file and object in the file that you want to read in
• Close the "Load from file" widget
• Now you can add any analysis you want to the script. Usually it's automatically connected to the loaded object, if not (some analysis takes multiple input configurations) you can connect them manually by clicking the little colorful icons on the right (next to the red warning badge that appears in these situations).

I didn't make screenshots as I hope it's clear already but let me know if you need more guidance.

80

General Questions and Answers / Re: Zero bias transmission

« Last post by Anders Blom on March 9, 2024, 00:37 »

The term "ballistic" is somewhat ambiguous. In our NEGF mode it's taken to mean the opposite of diffusive (as in "ballistic transport", below the mean free path, i.e. no energy relaxation from phonon scattering), since we include scattering of interfaces, defects, surface roughness, etc as created by any atom not in a perfectly periodic arrangement. In some other models i's defined it as "no scattering at all", which would only be possible in a perfect crystal, and thus is rather uninteresting in an atomistic picture, but makes sense in higher-level models when you only use the mobility or set transmission to 1 to model a ballistic conductor.

No matter the bias, the transmission spectrum is computed including the effects of all atoms present in the system.