Obtaining Geometries from a Gaussian09 optimization

When you are planning to start a computational investigation of an interesting molecular system, one of the very first information needed is its minimum energy geometries. This kind of procedure can be easily found in Quantum Chemistry packages, like the popular Gaussian09, for example.

Sometimes, the atomic coordinates related to the optimization steps, as well the desired one in which represents the stationary point of the Potential Energy Surface (PES), are not easily found in the output files. To help in this procedure, I write a useful Python3 script which can help the extraction of the cartesian coordinates from Gaussian09 log files. The script get_g09_geom.py can be found at my GitHub repository (together whit lots of other codes that also can be useful to you!).

Usage of get_g09_geom.py

You can just copy the script file to a directory found in your Terminal’s $PATH variable. A standard execution demands only the Gaussian09 log filename as an argument and gets the optimized geometry in the same orientation of the input file.

~ $ get_g09_geom.py <Gaussian09 Log Filename>

To obtain the geometry from a specific step of the optimization process, you can choose this using the option -n and inserting the integer number related to the cycle. You can also input a negative integer number, which means that the optimization steps count backward. 

Three geometries formats are also available using the option -f, according to the data found in the log file: the input orientation (input), the standard orientation done by Gaussian09 (standard) and also the Z-matrix orientation (zmat), available if Opt=Z-Mat was chosen in the optimization job.

~ $ get_g09_geom.py <Gaussian09 Log Filename> -n <Step> -f <Input Format>

The output is created in XYZ standard format and also contains the step number chosen in the last characters filename, to turn easy the tracking. Then, the atomic coordinates can be easily copied to another Gaussian09 input file or to a visualization software!

I hope you enjoy it! If you like it, give a star to the CompChemTools project!

Best regards!