Messages

1

Scripts, Tutorials and Applications / Exporting COSMO solvent surface

« on: August 26, 2026, 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:

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

2

General Questions and Answers / Re: Transmission with Different electrodes

« on: January 25, 2024, 10:29 »

I would second that!

3

General Questions and Answers / Re: Error message for HybridGGA with non-collinear spin-resolved bulk calculation

« on: November 9, 2023, 14:22 »

Alright, that is good to know. Many thanks for your reply!

4

General Questions and Answers / Error message for HybridGGA with non-collinear spin-resolved bulk calculation

« on: November 1, 2023, 15:57 »

Dear all,

I want to carry out a non-collinear spin-resolved bulk calculation with a HybridGGA exchange correlation functional, but when selecting HybridGGA I encounter the following error:

Traceback (most recent call last):
  File "zipdir/NL/GUI/ModelViewControl/QtControls.py", line 1120, in updateModel
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 798, in __setitem__
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 471, in __newState
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 495, in _processKey
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 187, in emit
  File "zipdir/NL/GUI/Tools/ScriptGenerator/ScriptBlocks/NewCalculatorWidgets/ExchangeCorrelation/ExchangeCorrelationWidget.py", line 430, in _onModelTypeChanged
  File "zipdir/NL/GUI/Store/Store.py", line 678, in __setitem__
  File "zipdir/NL/GUI/Store/Store.py", line 638, in _set
  File "build/atkpython/lib/python3.8/contextlib.py", line 120, in __exit__
  File "zipdir/NL/GUI/Store/Store.py", line 722, in batch
  File "zipdir/NL/GUI/Store/Store.py", line 781, in _closeTransaction
  File "zipdir/NL/GUI/Store/Signal.py", line 133, in emit
  File "zipdir/NL/GUI/Tools/ScriptGenerator/ScriptBlocks/NewCalculatorWidgets/ExchangeCorrelation/ExchangeCorrelationWidget.py", line 562, in _onXCStoreChanged
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 798, in __setitem__
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 464, in __newState
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 495, in _processKey
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 187, in emit
  File "zipdir/NL/GUI/Tools/ScriptGenerator/ScriptBlocks/NewCalculatorWidgets/ExchangeCorrelation/ExchangeCorrelationWidget.py", line 546, in _onModelFunctionalChanged
  File "zipdir/NL/GUI/Tools/ScriptGenerator/ScriptBlocks/NewCalculatorWidgets/ExchangeCorrelation/ExchangeCorrelationWidget.py", line 505, in updateModelType
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 798, in __setitem__
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 464, in __newState
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 495, in _processKey
  File "zipdir/NL/GUI/ModelViewControl/Model.py", line 187, in emit
  File "zipdir/NL/GUI/Tools/ScriptGenerator/ScriptBlocks/NewCalculatorWidgets/LCAOBasisSet/BasisSetWidget.py", line 285, in exchangeCorrelationTypeChanged
  File "zipdir/NL/GUI/Tools/ScriptGenerator/ScriptBlocks/NewCalculatorWidgets/LCAOBasisSet/BasisSetWidget.py", line 527, in admmFunctionalChanged
  File "zipdir/NL/GUI/Store/Store.py", line 678, in __setitem__
  File "zipdir/NL/GUI/Store/ResetStore.py", line 345, in _set
  File "build/atkpython/lib/python3.8/contextlib.py", line 120, in __exit__
  File "zipdir/NL/GUI/Store/Store.py", line 722, in batch
  File "zipdir/NL/GUI/Store/Store.py", line 777, in _closeTransaction
  File "zipdir/NL/GUI/Store/Store.py", line 577, in emit
  File "zipdir/NL/GUI/Store/Views/Bindings.py", line 386, in updateView
  File "zipdir/NL/GUI/Store/ResetFields.py", line 92, in errorMessage
IndexError: list index out of range

If I dismiss the error and choose HybridGGA anyway, there will simply be SOGGA.PBE in the input file.

Why does this error occur and what can I do? I'm using the QuantumATK version 2022.12.

Many thanks in advance!

All the best,
Ulrich