Getting Data out of Gaussian
As we noted earlier, some data formats are better than others. Gaussian, unfortunately, picks one of the worst possible ones for some of its data, and a workable, if clunky, one for the rest.
Let’s start with the workable one.
.chk and .fchk files
If you recall from the previous section, when you made your .gjf file you set an option called %Chk to indicate where to store the check-pointing data.
This file is in a totally inscrutable binary format, basically a dump of Gaussian’s internals as it goes.
On the other hand, bundled with Gaussian is a program called formcheck that we call like
formchk checkpoint_file.chk formatted_file.fchk
and which takes the inscrutable binary data and gives a file that looks something looking like
title
Freq UB2PLYPD3-FC CC-pVTZ
Number of atoms I 15
Info1-9 I N= 9
66 64 1002 0 0 100
6 2 6001
Full Title C N= 1
title
Route C N= 5
#p b2plypd3/cc-pvtz integral=...
Nuclear charges R N= 15
6.00000000E+00 6.00000000E+00 1.00000000E+00 1.00000000E+00 8.00000000E+00
8.00000000E+00 1.00000000E+00 6.00000000E+00 1.00000000E+00 1.00000000E+00
1.00000000E+00 6.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
Current cartesian coordinates R N= 45
7.04878179E-01 8.24102648E-03 1.33661317E-01 4.64699369E-01 -4.61527005E-01
2.89747925E+00 ...
Number of symbols in /Mol/ I 0
Force Field I 0
Atom Types C N= 15
Int Atom Types I N= 15
0 0 0 0 0 0
0 0 0 0 0 0
0 0 0
MM charges R N= 15
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
where we can see that there are successive named blocks of numbers, some cryptic I/R/C labels, etc.
At the very least, we can write a single class that will parse all of this data, since it’s all got a well-defined, regular structure.
This is very helpful, but unfortunately, being a check-point, is only a snapshot of a calculation.
The .log File
Usually we need a full potential energy surface, or dipole surface, or the like, which brings us to the much dirtier .log file.
As Gaussian runs, it prints all sorts of info out to the .log file. Some of it we find very useful, e.g. dipole moments, electronic energies, coordinates, and the like. Some of it, like orbital populations, isn’t all that useful.
If there were regularity to the way the data were stored, we could deal. Unfortunately we get stuff out like
Mulliken charges and spin densities with hydrogens summed into heavy atoms:
1 2
1 C 0.284937 -0.047805
2 C -0.084087 0.975289
5 O -0.198441 0.044417
6 O -0.009235 0.004233
8 C 0.009751 0.022752
12 C -0.002925 0.001113
Electronic spatial extent (au): <R**2>= 586.1312
Charge= 0.0000 electrons
Dipole moment (field-independent basis, Debye):
X= 0.8917 Y= -0.4708 Z= 1.6277 Tot= 1.9147
Quadrupole moment (field-independent basis, Debye-Ang):
XX= -37.2983 YY= -36.8835 ZZ= -38.3391
XY= 2.0489 XZ= -3.3046 YZ= -1.1258
Traceless Quadrupole moment (field-independent basis, Debye-Ang):
XX= 0.2087 YY= 0.6235 ZZ= -0.8321
XY= 2.0489 XZ= -3.3046 YZ= -1.1258
Octapole moment (field-independent basis, Debye-Ang**2):
XXX= -16.5453 YYY= -5.3136 ZZZ= -3.4279 XYY= -5.5706
XXY= -6.4237 XXZ= 3.4940 XZZ= -3.5574 YZZ= 0.7124
YYZ= 0.6046 XYZ= 1.7525
Hexadecapole moment (field-independent basis, Debye-Ang**3):
XXXX= -335.5914 YYYY= -215.5172 ZZZZ= -195.0758 XXXY= 20.4569
XXXZ= -9.7915 YYYX= 1.7567 YYYZ= -1.2146 ZZZX= -2.3024
ZZZY= 1.8767 XXYY= -89.8989 XXZZ= -95.5782 YYZZ= -67.4313
XXYZ= -0.8395 YYXZ= -0.0618 ZZXY= 1.2617
N-N= 2.598308771361D+02 E-N=-1.240434554405D+03 KE= 3.068245376935D+02
Exact polarizability: 62.069 -0.830 55.437 -2.686 -0.888 55.152
Approx polarizability: 66.871 -1.448 60.217 -2.414 0.418 61.197
Isotropic Fermi Contact Couplings
Atom a.u. MegaHertz Gauss 10(-4) cm-1
1 C(13) -0.01947 -21.88400 -7.80875 -7.29972
2 C(13) 0.04515 50.75819 18.11179 16.93111
3 H(1) -0.01412 -63.09256 -22.51300 -21.04541
4 H(1) -0.01377 -61.55167 -21.96317 -20.53143
5 O(17) 0.03457 -20.95714 -7.47803 -6.99055
6 O(17) 0.00489 -2.96727 -1.05880 -0.98978
7 H(1) -0.00009 -0.40514 -0.14456 -0.13514
8 C(13) 0.02456 27.61551 9.85390 9.21154
9 H(1) 0.00363 16.22441 5.78927 5.41188
10 H(1) -0.00047 -2.09733 -0.74838 -0.69960
11 H(1) 0.00051 2.25983 0.80636 0.75380
12 C(13) -0.00035 -0.39272 -0.14013 -0.13100
13 H(1) -0.00015 -0.65043 -0.23209 -0.21696
14 H(1) 0.00070 3.11829 1.11269 1.04015
15 H(1) -0.00019 -0.85732 -0.30591 -0.28597
which as we noted before is a pain to parse.
McUtils.GaussianInterface
Over the past ~2 years we’ve been slowly working on a package to make parsing these things nicer.
It’s part of a larger package of McCoy group utilities called McUtils.
We’re working on usage and documentation, but it allows you to pull dipole moments, energies, coordinates, optimization parameters, etc. from these files (it supports both .fchk and .log files) and is built so that it can be easily extended.
Let us know if you’d like to check it out and we’ll be happy to help.
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