Exporting COSMO solvent surface

[ulrich_poto]

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

[yuby]

Yes. The traceback indicates that the visualization step, rather than necessarily the COSMO calculation itself, which is what is exhausting memory. QuantumATK is trying to construct an intermediate array of roughly 740 GiB.

There may be a way to work around this by accessing the COSMO surface/tessera data directly from the QuantumATK Python API and writing it to a more suitable format, but the exact approach depends on your QuantumATK version and on which COSMO object/calculator produced the surface.