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2

Using ORCA and reverse engineering the calculation provided in the question (HF/STO-3G at a $\ce{H}$-$\ce{F}$ distance of 0.955464 Angstroem), I obtained the following output, to which I added the matrix product of the density and overlap matrices, dubbed the Mulliken Population Matrix. By comparing to the output of other programs, the reader can follow the ...

5

This is actually a lot simpler than I initially thought. I'll be using the same example as previously explained in How to obtain the radial probability distribution function from a quantum chemical calculation? My test setup has slightly changed since then, i.e. I've tried it with Gaussian 16 B.01 and Multiwfn 3.6.0 and it worked the same. We start the same ...

2

OK, in between I found it, it is the GEO_DAT keyword, for example, reading in previously converged PM7 geometry of methane: AUX LARGE CHARGE=0 SINGLET GEO_DAT="metan_geomopt_pm7.arc" THERMO(298,298) PM7

3

These notations signify someone performed calculations in Visual MINTEQ accounting for dissolved organic matter (DOM) using a NICA-Donnan modeling method. From the manual nicadonnan.pdf bundled with the installer: In Visual MINTEQ, a “D” suffix is used to identify a diffuse-layer species such as a Donnan species. […] The numbers 6, 7, 8 and 9 ...

2

Some examples are: MOLDEN, Avogadro, JMol and VMD. But there is a very thorough list (along with comparisons) here: https://en.m.wikipedia.org/wiki/List_of_molecular_graphics_systems.

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