Monthly Archives: December 2017
Python scripts for calculating Fukui Indexes
One of the most popular posts in this blog has to do with calculating Fukui indexes, however, when dealing with a large number of molecules, our described methodology can become cumbersome since it requires to manually extract the population analysis from two or three different output files and then performing the arithmetic on them separately with a spreadsheet or something.
Our new team member Ricardo Loaiza has written a python script that takes the three aforementioned files and yields a .csv file with the calculated Fukui indexes, and it even points out which of the atoms exhibit the largest values so if you have a large molecule you don’t have to manually check for them. We have also a batch version which takes all the files in any given directory and performs the Fukui calculations for each, provided it can find file triads with the naming requirements described below.
Output files must be named filename.log (the N electrons reference state), filename_plus.log (the state with N+1 electrons) and filename_minus.log (the N-1 electrons state). Another restriction is that so far these scripts only work with NBO population analysis as provided by the NBO3.1 program available in the various versions of Gaussian. I imagine the listing is similar in NBO5.x and NBO6.x and so it should work if you do the population analysis with them.
The syntax for the single molecule version is:
python fukui.py filename.log filename_minus.log filename_plus.log
For the batch version is:
./fukuiPorLote.sh
(Por Lote means In Batch in Spanish.)
These scripts are available via GitHub. We hope you find them useful, and you do please let us know whether here at the comments section or at our GitHub site.
fchk file errors (Gaussian) Missing or bad Data: RBond
We’ve covered some common errors when dealing with formatted checkpoint files (*.fchk) generated from Gaussian, specially when analyzed with the associated GaussView program. (see here and here for previous posts on the matter.)
Prof. Neal Zondlo from the University of Delaware kindly shared this solution with us when the following message shows up:
CConnectionGFCHK::Parse_GFCHK() Missing or bad data: Rbond Line Number 1234
The Rbond label has to do with the connectivity displayed by the visualizer and can be overridden by close examination of the input file. In the example provided by Prof. Zondlo he found the following line in the connectivity matrix of the input file:
2 9 0.0
which indicates a zero bond order between atoms 2 and 9, possibly due to their proximity. He changed the line to simply
2
So editing the connectivity of your atoms in the input can help preventing the Rbond message.
I hope this helps someone else.