Generating Electrostatic Potential Maps

Woody Wilson

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Oct 11, 2022, 5:29:16 PM10/11/22

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Hello everyone,

I am trying to make an electrostatic potential map of a molecule. After obtaining the electrostatic potential and electron density CUBE files from CP2K, and after processing the cube files with

" $ cubecruncher.x -i cp2k-ELECTRON_DENSITY-2.cube -espot_cube cp2k-v_hartree-2.cube -espot -o edensity_pot.cube ", the resulting cube file is not the electrostatic potential map that I was expecting. I've attached the CP2K input file I was using as well as a screenshot of me trying to visualize the cube file generated by cubecruncher in VESTA. Is there something I am doing wrong or do I need additional information? Any help would be much appreciated. Thanks!

Sincerely,

Woody

Screen Shot 2022-10-11 at 4.25.29 PM.png

cp2k.inp

Marcella Iannuzzi

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Oct 12, 2022, 2:56:21 AM10/12/22

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Hallo Woody

The argument -espot of cubecruncher is something very specialised for getting an electrostatic potential map on top of a STM 2D topography.

It is not generalised for a 3D map. If you want to generalise to 3D you should introduce a new feature in cubecruncher.

Kind regards

Marcella

Woody Wilson

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Oct 12, 2022, 11:31:53 AM10/12/22

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Hi Dr. Iannuzzi,

Thank you so much for the reply and for clearing up my confusion. That would be a very nice feature indeed I may work on that! Thanks again and have a great day!