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Gaussian has Orbital-by-Orbital Population Analysis.

From the manual:

# UHF/6-311+G(d) Pop=Orbitals=3
Here is the resulting output from a calculation on FeO+ quartet:

Atomic contributions to Alpha molecular orbitals:
Alpha occ 16 OE=-0.923 is Fe1-d=1.00
Alpha occ 17 OE=-0.699 is O2-p=0.88
Alpha occ 18 OE=-0.690 is O2-p=0.68 Fe1-s=0.21
Alpha vir 19 OE=-0.253 is Fe1-s=0.70 Fe1-p=0.27
Alpha vir 20 OE=-0.188 is Fe1-p=0.71 O2-p=0.29
Alpha vir 21 OE=-0.133 is Fe1-p=1.04

Atomic contributions to Beta  molecular orbitals:
Beta  occ 13 OE=-0.801 is O2-p=0.79
Beta  occ 14 OE=-0.783 is Fe1-d=1.00
Beta  occ 15 OE=-0.758 is O2-p=0.89
Beta  vir 16 OE=-0.241 is Fe1-s=0.81 Fe1-p=0.17
Beta  vir 17 OE=-0.139 is Fe1-p=0.91 Fe1-d=0.14

This can be used to provide a more quantitative characterization of the nature of canonical molecular orbitals.

Due to certain restrictions on the use of Gaussian (http://www.bannedbygaussian.org/), I am unable to use Gaussian. Are there other programs that can perform such a calculation? NBO only seems to provide such a breakdown in terms of NBOs, and I can't find the feature available in any other quantum chemistry program. I realize that I can do this myself by extracting the C matrix, figuring which coefficients go with which orbital, and summing up myself. However, this would probably take me a day to program.

Note: My calculations use B3LYP, ECPs, and the COSMO solvent model. So the program would need to be able to at least produce single points with such a method.

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    $\begingroup$ I'm sure, almost any program can do that. Since you mentioned some restrictions on the use of Gaussian, I suggest you try free programs, such as, GAMESS (US), NWChem, ORCA. I quickly checked their manuals, so I'm sure all three support everything you need (Population Analysis, B3LYP, ECPs, COSMO). And all these programs are gratis (freeware) for academics, NWChem being libre as well (free software). $\endgroup$ – Wildcat Oct 22 '15 at 9:07
  • $\begingroup$ Maybe it is not in the manual, but most programs put this info in the detailed output file. $\endgroup$ – Greg Mar 6 '17 at 2:02
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ORCA can perform population analysis for each individual molecular orbital. This is an excerpt from the output file:

-----------------------------------
MULLIKEN ORBITAL POPULATIONS PER MO
-----------------------------------
THRESHOLD FOR PRINTING IS 0.1%
SPIN UP
                      0         1         2         3         4         5
                 -177.49372 -100.54186 -100.54186 -100.54184 -100.54179 -100.54174
                   1.00000   1.00000   1.00000   1.00000   1.00000   1.00000
                  --------  --------  --------  --------  --------  --------
  0Ti  1s             99.6       0.0       0.0       0.0       0.0       0.0
  0Ti  2s              0.4      -0.0      -0.0      -0.0      -0.0      -0.0
  1Cl  1s             -0.0       4.5       3.8       0.0      48.9       0.4
  1Cl  2s              0.0       0.0       0.0       0.0       0.3       0.0
  2Cl  1s             -0.0       4.9       4.1       0.0      50.5       0.4
  2Cl  2s              0.0       0.0       0.0       0.0       0.3       0.0
  3Cl  1s             -0.0      69.2       3.8       0.0       0.0      23.3
  3Cl  2s              0.0       0.5       0.0       0.0       0.0       0.2
  4Cl  1s             -0.0       1.4      71.5       0.0       0.0      23.4
  4Cl  2s              0.0       0.0       0.5       0.0       0.0       0.2
  5Cl  1s             -0.0       8.9       7.5      50.7       0.0      26.2
  5Cl  2s              0.0       0.1       0.1       0.3       0.0       0.2
  6Cl  1s             -0.0      10.4       8.7      48.6       0.0      25.6
  6Cl  2s              0.0       0.1       0.1       0.3       0.0       0.2

The program supports all options that you listed, and this input file header should get you started:

! B3LYP def2-SVP ECP{def2-SVP} COSMO(water) LargePrint
*xyz charge multiplicity
coordinates go here
*

You can find more detailed information in the manual.

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    $\begingroup$ That's what I wanted, I looked through the ORCA manual and somehow could not find it, thanks! $\endgroup$ – Jonathon Oct 22 '15 at 11:02
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    $\begingroup$ @Jonathon If you just want to turn on this reporting, without all of the other extra output afforded by LargePrint, you can add %output Print[ OrbPopMO_M ] 1 end on its own line for the Mulliken populations. Replace _M with _L for Loewdin populations. $\endgroup$ – hBy2Py Oct 23 '15 at 17:04
  • $\begingroup$ I found those flags, but thanks. Also, as a note to other users, the program segfaults if you use ROKS, but only after printing all the necessary information (I think it has to do with the fact that there are no beta orbitals for high spin complexes). $\endgroup$ – Jonathon Oct 23 '15 at 19:23
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NBO's natural population analysis (NPA) may in fact be a better option since it lacks many deficiencies Mulliken population analysis has (e.g. non-orthogonality of the basis set, sensitivity to the basis set choice).

You may run a NPA analysis in the standalone executable GENNBO after obtaining a suitable input for it:

$ gennbo < water.gen > water.nboout

A proper input may be generated by NWChem by the use of the nbofile keyword:

property
 nbofile
end

NWChem has all the features you've cited.

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