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Motivation for Post: I saw a question about how to plot a .cube file recently on the Mathematica & Wolfram Language Stack Exchange. It was marked "off-topic," so I am asking a different (but related) question in the hopes it is on-topic here. Please refer me to the answer if it has already been solved. I have volumetric data I would like to plot in a custom manner (either in Mathematica, but preferably Python). But I have had issues up to this point. I am new to coding, and to Quantum-ESPRESSO (QE) which is how I produced my .cube file. I am not an expert in anything, merely a student trying to simulate some things.


Goals: Either with Python or Mathematica, (1) Generate a 3D plot of my volumetric data. (2) Be able to "slice" through that 3D graph with a user-defined plane to view a 2D cross-section. I would love to be able to create something inspired by VESTA's ability to do goals (1) and (2), but in a more customizable, flexible way to suit my needs. (I want to customize color mapping especially.)

Produced by VESTA:

STMsimScanRepeated

sTMsimScanSingle


Attempts: Lots of failed attempts here. I even enlisted the help of a professional programmer who could not discern how the data was meant to be read, plotted, and/or modified. In one case, the voxels are not cubic; I would also like to be able to specify the voxel dimensions/spanning vectors. VESTA seems to be able to do this, but I want to do it from scratch so I can map the colors myself for figure-making and whatnot. Here is a failed attempt example. I will not include most here, as I wrote them on another computer.

fail01 fail02 fail03

Knowns:

This is how the data is listed: NX = 30, NY= 30, and NZ = 90. The output file has 6 columns (13,500 rows). (See https://gaussian.com/cubegen/) And each element corresponds to a 3D pixel (a voxel) and this volumetric data can be plotted in 3D. Then, I eventually need to take a slice/cross section of that. I am coming up with wacky plots.

Details for a specific case:

  Bias in eV =    -4.0817 # states  14
    2    0.000000    0.000000    0.000000
   30    0.155100    0.000000    0.000000
   30   -0.077550    0.134321    0.000000
   90    0.000000    0.000000    0.155133
    6    6.000000   -0.000000    2.686415   13.962000
    6    6.000000    2.326504    1.343207   13.962000
  0.55588E-05  0.34988E-04  0.11861E-03  0.24345E-03  0.39097E-03  0.54096E-03
  0.67531E-03  0.78084E-03  0.85041E-03  0.88243E-03  0.87942E-03  0.84643E-03
  0.78998E-03  0.71727E-03  0.63564E-03  0.55189E-03  0.47148E-03  0.39794E-03
  0.33282E-03  0.27609E-03  0.22697E-03  0.18457E-03  0.14835E-03  0.11800E-03
  0.93204E-04  0.73420E-04  0.57812E-04  0.45437E-04  0.35477E-04  0.27382E-04
  0.20868E-04  0.15779E-04  0.11943E-04  0.91091E-05  0.69791E-05  0.52905E-05
  0.38834E-05  0.27135E-05  0.18011E-05  0.11554E-05  0.73628E-06  0.46992E-06
  0.28540E-06  0.14217E-06  0.39326E-07  0.34955E-09  0.39326E-07  0.14217E-06
  0.28540E-06  0.46992E-06  0.73628E-06  0.11554E-05  0.18011E-05  0.27135E-05
  0.38834E-05  0.52905E-05  0.69791E-05  0.91091E-05  0.11943E-04  0.15779E-04
  0.20868E-04  0.27382E-04  0.35477E-04  0.45437E-04  0.57812E-04  0.73420E-04
  0.93204E-04  0.11800E-03  0.14835E-03  0.18457E-03  0.22697E-03  0.27609E-03
  0.33282E-03  0.39794E-03  0.47148E-03  0.55189E-03  0.63564E-03  0.71727E-03
  0.78998E-03  0.84643E-03  0.87942E-03  0.88243E-03  0.85041E-03  0.78084E-03
  0.67531E-03  0.54096E-03  0.39097E-03  0.24345E-03  0.11861E-03  0.34988E-04
  0.11671E-04  0.44003E-04  0.13569E-03  0.27204E-03  0.43228E-03  0.59398E-03
  0.73734E-03  0.84821E-03  0.91925E-03  0.94930E-03  0.94177E-03  0.90273E-03
  0.83954E-03  0.75996E-03  0.67161E-03  0.58146E-03  0.49513E-03  0.41637E-03
  0.34692E-03  0.28681E-03  0.23517E-03  0.19094E-03  0.15333E-03  0.12184E-03
  0.96098E-04  0.75528E-04  0.59316E-04  0.46516E-04  0.36275E-04  0.27993E-04
... etc

Question: Can someone please help me accomplish the two goals I laid out? It need only work for the specific case. If this specific case can work, I am hoping I can generalize it to other cases. Thank you so much in advance for any feedback, guidance, answers, or advice. I would love clarity on this issue and the file format.

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  • $\begingroup$ You are trying to get an STM plot from the .cube file. In this case, critic2 might be helpful. It can generate colorful plots from .cube files (but it's not Python as you requested). $\endgroup$ Sep 5, 2023 at 4:47
  • $\begingroup$ I think that the SISL package (in Python) can manipulate cube files. $\endgroup$
    – Camps
    Sep 5, 2023 at 10:47
  • $\begingroup$ During my Ph.D., for scanning tunneling spectroscopy simulations I landed on creating individual images with matplotlib and compiling them into a movie, so you could use time to "slide through" the 3rd dimension github.com/ltalirz/asetk/blob/master/scripts/cube-movie.py $\endgroup$ Oct 15, 2023 at 20:56

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