Extracting xyz geometries from Gaussian output files (cclib)

Turns out my G09 geometry optimization output files are split between listing the optimized coordinates (if the calc began with a z-matrix) and the xyz coordinates. The above split makes it difficult to extract geometries in an automated fashion. Several tools came up during a Google search, but these only work to pull out the xyz coordinates if G09 lists the final geometry in the cartesian format.

Surprisingly, cclib was nowhere near the top of my search results after multiple different sets of search terms, though it eventually came up and it looked like a perfect solutions. My initial stab at installing it using:

$ sudo apt-get install python3-numpy cclib python3-cclib

was not met with resounding success as the former did not really give much of anything useful (no ccget or ccwrite), and the latter still lacked ccwrite. Moreover, the current Ubuntu 18.04 package is a rather ancient 1.3 (perhaps this explains the lack of ccwrite).

My next step was finding the source for 1.6.2 and attempting to install that (which worked, but ccwrite barfed on itself when I tried the xyz option). This made me think it was not quite ready, and some Ubuntu pages listed 1.6-1 as the most current stable branch, so I started over with this slightly older version. Instead of manually installing, I thought it might be useful to try pip3 (my pip instance links to python 2, so I had to be careful to tack 3s on the end of most of these).

$ sudo apt-get install python3-setuptools python3-pip
$ tar xzvf cclib-1.6.tar.gz
$ cd cclib-1.6
$ pip3 install .

This worked like a charm (using -t to install cclib in a different location did not, and browsing cclib bug reports makes me think this feature is not currently working), and I now had ccget, cda, ccwrite, etc in ~/.local/bin.

$ ~/.local/bin/ccwrite xyz test.log

produced a decent xyz file at test.xyz. Success!