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Scripts, Tutorials and Applications / Exporting COSMO solvent surface

« Last post by ulrich_poto on Yesterday at 11:55 »

Dear QuantumATK community,

I would like to visualize a COSMO solvent surface of a very large system but cannot do so within the GUI:

Quote

Traceback (most recent call last):
File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 846, in _onDoubleClicked
File "zipdir/NL/GUI/Tools/Data/DataCatalogWidget.py", line 947, in open
File "zipdir/NL/GUI/Tools/Data/ToolAnalysisPlugins.py", line 134, in createWidget
File "zipdir/NL/GUI/Tools/Viewer/Viewer.py", line 1023, in addObjects
File "zipdir/NL/GUI/Tools/Viewer/Viewer.py", line 1015, in createAndPopulateScene
File "zipdir/NL/GUI/Tools/Viewer/Viewer.py", line 413, in _addObjects
File "zipdir/NL/GUI/Graphics/GL/Scene/Scene.py", line 712, in addCosmoSurface
File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/SolvationModel/CosmoSolventSurface.py", line 526, in tesseraeChargeDensities
File "zipdir/NL/CommonConcepts/PhysicalQuantity.py", line 1337, in __sub__
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 740. GiB for an array with shape (918636, 36051, 3) and data type float64

While I am aware how ridiculously large this array is, I was wondering if there was any way how to export it in a (maybe even compressed) format so that it can be visualized using an alternative software? So far, I could not find any export options.

Many thanks in advance!

Kind regards,
Ulrich

General Questions and Answers / Different phase colors for different transmission eigenchannels

« Last post by Jahanzaib on August 24, 2026, 14:01 »

I'm plotting transmission eigenchannels in QuantumATK using isosurfaces with the BlueRed colormap, where color shows Phase (radians). When I plot two different eigenchannels at the same energy, they show different color/phase patterns even though they're in the same spot on the molecule. Is this normal, or does it mean something is wrong with my setup? Also, if I just want to compare how "big" or "spread out" the two channels are (not their phase), should I be plotting something else instead, like the magnitude/amplitude?

General Questions and Answers / Publication reference for the ML-DFT Density Predictor

« Last post by Lim changmin on August 11, 2026, 07:20 »

Hello,

I am currently using the ML-DFT DensityPredictor introduced in QuantumATK Y-2026.03.

The release notes explain that it uses a graph neural network to predict DFT-quality electron densities and can provide an initial density for SCF calculations. However, I could not find a publication reference describing the underlying methodology.

Is the Density Predictor based on any previously published method or research paper? If so, could you please provide the recommended reference(s)?

I would also like to know what reference would be most appropriate when mentioning the use of the QuantumATK Density Predictor in a research paper.

Thank you.

General Questions and Answers / error in running QATK

« Last post by Dr. Sabyasachi Sen on July 25, 2026, 14:29 »

getting the attached error while trying to open QATK

Cannot connect to license server system.
The license server manager (lmgrd) has not been started yet,
the wrong port@host or license file is being used, or the
port or hostname in the license file has been changed.
Feature: qatk_nanolab
Server name: 172.17.52.59
License path: [email protected];
FlexNet Licensing error:-15,10032

General Questions and Answers / HOMO LUMO

« Last post by Jahanzaib on July 18, 2026, 03:29 »

I have optimized the geometry of an isolated molecular system using DFT-LCAO in QuantumATK. For device calculations, I understand that the Molecular Projected Self-Consistent Hamiltonian (MPSH) is used to obtain the molecular energy levels in the presence of electrodes.

However, for a simple isolated molecule (MoleculeConfiguration) without any electrodes, what is the recommended way to calculate and visualize the HOMO and LUMO in QuantumATK?

General Questions and Answers / Mobility workflow completes Electron–Phonon Coupling but no mobility output

« Last post by Nemthianhoi Zou on July 6, 2026, 06:56 »

I am trying to calculate the carrier mobility of K₃BiI₉ using the Mobility (Full) workflow. Although most of the workflow appears to execute successfully, I am unable to obtain the final mobility results and would appreciate your guidance. The following intermediate calculations appear to be completed successfully:

✔ Self-consistent field (SCF)
✔ Band structure
✔ Dynamical Matrix
✔ Hamiltonian Derivatives
✔ Phonon Band Structure
✔ Electron–Phonon Coupling (at least up to lifetime calculation)

The only missing output is the final mobility result.
Is the Mobility (Full) workflow fully supported for Hybrid (HSE) + Noncollinear SOC calculations in QuantumATK X-2025.06?
Could the HDF5 file become corrupted even when the Job Manager reports that the task has finished successfully?
Is there any known issue in QuantumATK X-2025.06 that could prevent the mobility object from being written after the electron–phonon coupling calculation?
Is there any additional debug option or verbose logging that I can enable to determine where the workflow stops after the lifetime calculation?
Would you recommend performing the mobility calculation using PBE/PBE+SOC instead of HSE+SOC, or should the current setup work correctly?

General Questions and Answers / G0W0 - k-point related error message

« Last post by hagelberg on June 22, 2026, 15:41 »

Hello -
This is about a G0W0 calculation on a nanoribbon system. The job fails with the error message
"The k-point sampling needs to be a least '5' in each direction for metallic systems, if a Gamma-point correction is used."
Some comments:
(1) Even the minimal choice of 5x5x5 makes my system prohibitively large.
(2) As the system is one-dimensional, it should be possible to select k_x = k_y = 1 for the non-periodic directions.
(3) Since the system is an AFM zigzag nanoribbon, it should be semiconducting (the expected bandgap is around 0.8 eV), and so the metallicity assignment looks like a misdiagnosis.
(4) Setting 'include_gamma_point=False' does not seem to change anything.
My question, therefore: Is there any way around the k-points constraint for G0W0 calculations?

Please find the respective .py input file attached. I'm using QuantumATK-X-2025.6.
Thanks a lot,
Frank Hagelberg

General Questions and Answers / Re: Update - Stress outliers in TrainingSet

« Last post by AsifShah on June 16, 2026, 06:50 »

Dear all,

QuantumATK only allows setting the threshold for forces, not energies or stresses.
I have written a code that removes stress outliers from TrainingSet.

Link: https://github.com/AsifShah-19/QuantumATK-Scripts

Thankyou

General Questions and Answers / tutorial on using COSMO-RS with version 2024 or 2025

« Last post by KHipps on June 12, 2026, 22:50 »

I am looking for information on how to use Quantum ATK with COSMO-RS to calculate temperature dependent heats of solution. Are there tutorials anywhere? Can anyone provide a basic example?

General Questions and Answers / Update - Stress outliers in TrainingSet

« Last post by AsifShah on June 12, 2026, 02:41 »

Dear All,

I use an optimization trajectory to relax the interface between two materials, A-B, and then use it to fine-tune the MACE model.
However, there are some high-stress outliers in the optimization trajectory.
I would like to know how to delete such high-stress outlier images and save a new trajectory.

Thank you