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I am busy trying to do density calculations in Gaussian16 as I need the .cube output for input to the PIXEL software. But my Gaussian output seems to be missing an entire chunk of data and I don't know why.

The output is supposed to look like: Sample out

However, my output is missing the entire chunk of electron density data, formatted as 6E13.5 (the block of floating point values indicating electron density at each point in the block).

My input in the route section is

#MP2/6-31G** guess=core NoSymm Pop=MK Density=MP2

And I use the following to generate the .cube file

Formchk NAME.chk NAME.fchk

Cubegen 0 NAME.fchk NAME.cube 0 h

Am I missing a keyword/command to include the electron density data?

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  • $\begingroup$ I haven't used it before, but you seem to have missed the kind keyword in your cubegen command @thalsit $\endgroup$ – Tyberius Mar 19 '19 at 18:50
  • $\begingroup$ Thanks @Tyberius. Since I included it in the input file to perform the calculation I thought it would be redundant also having it as part of the cubegen command, since I thought the cubegen utility would read from my checkpoint file that there is MP2 density data. But it seems I was wrong, adding the kind keyword solved the issue $\endgroup$ – thalsit Mar 20 '19 at 7:19
  • $\begingroup$ I think the reason they don't just scan for what kind you want is that there are different cubes you can generate besides the density, so its clearer to just let the user specify rather than just generating the first set or all of the cube data that it finds. $\endgroup$ – Tyberius Mar 20 '19 at 14:53
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    $\begingroup$ @Tyberius I completely agree, and would suggest you turning your two comments into an answer. (Also could you imagine it would produce all-the-cubes, that would produce awfully much data.) $\endgroup$ – Martin - マーチン♦ Mar 20 '19 at 17:23
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You aren't getting the density data in your cube file because you haven't specified the kind keyword in your cubegen command. Gaussian allows a variety of different types of cube files to be generated, including electronic densities/spin-densities/gradients, MOs, and electrostatic potential, along with magnetic current and shielding densities. Without specifying the type of cube file you want, the program doesn't know what to generate.

The reason it can't determine what you want by parsing the chk file is that the file in general will contain information that could be used for multiple types of cubes. The program could hypothetically use the first valid piece of information or some specific type of cube data by default, but this would often produce an undesired output. It could also make all valid cubes files, but these take up a lot of memory so this would be wasteful. They presumably decided the default case should be to do nothing if a type of cube file isn't specified so as not to produce unnecessary or incorrect output.

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