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:
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.
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.
