Introductions not only to Quantum Chemistry

Supercomputer Institute at University of Minnesota presents set of PDF files being nice introduction to resources available there. Most of them are related to Quantum Chemistry, but there is also CSD System and Material Studio. If you are interested please check the link.

Two chemical links

This time two links to websites related to chemistry.

• The Supercomputing Institute from University of Minnesota prepared kit of Tutorials for Computational Chemistry and Physics Sciences.
• Vitalii Vanovschi created the website with many important chemical informations.

Geometries from Gaussian Scan

Reading geometries from Gaussian file storing information about Potential Energy Scan (PES) isn't easy. I was sure that there were some tools to do this, but I cannot find any yesterday, so I prepared my own. It is writing in python, of course ;). Right now have very basic features. It reads input file and created output xyz files (as many as stationary points was found). You are using it simply writing in command line:

scaner-0.1.py inputfile

Greping excitation energy from Gaussian output

I've already written about CIS energies, but my suggestion is more general. You can use that command also for TDDFT calculations. But if you need energies from perturbative correction of CIS method (CIS(D) method) you have to use this:

 grep "CIS(D) Exc\. E" *.log

CCLib

The new version (0.5) of CCLib has been release. CCLib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, GAMESS (US), Gaussian, and PC GAMESS.

gaussfield.sh v0.1

It can be very useful to obtain value of some molecular properties in electric field. I.e. you can get dipole moment of excited states from energies in fields F and -F, hyperpolarizability from analytic polarizability etc. But it's quite annoying to create many very similar Gaussian input files, so I wrote short script to created this files:

#!/usr/bin/env bash
for i in $*
do
        name=`basename $i .com`
        sed -e '/^%/d; /^#/s/$/ Field=X-10/' $i > ${name}-x.com
        sed -e "/^%/d; /^#/s/$/ Field=X+10/" $i > ${name}+x.com
done

No CIS(D) in solvent [Gaussian]

I tried to calculate excitation energy with CIS(D) method in solvent (PCM method). I found that the CIS resalts from CIS and CIS(D) outout are different. I checked and CIS with Direct and without this option gave another results. I wrote to Gaussian Help and got replay: Yes, there are differences and the CIS=Direct results are correct.The non-direct methods, both CIS and CIS(D) use MO integrals where the solvent effects are not present and thus neither of them will give the correct results. Starting with G03 Rev. D the program correctly forces the use of CIS=Direct when combined with solvation. There is no option for doing CIS(D) with solvent and I don't expect this to change. Sorry for any confusion.

Massive changes in input files

Imagine, you have to change basis set in 10 files. It is a lot of work. Not really, sed will be your friend. For example, I would like to change 6-31+G(d) into 6-311++G(2d,p) basis set in Gaussian, so I did:

sed -i.bak *.com -e " s/6-31+G(d)/6-311++G(2d,p)/"

. This command created backup of my file. If you would like to change the level of theory in gamess you should write:

sed scf.inp =e "s/scftyp=rhf/scftyp=rhf mplevl=2/" > mp2.inp

Of course you can change much more thinks in any of quantum chemical program.

NLO in Gaussian 98/03

Sometime ago Damian Gregory published very nice article about NonLinear Optical (NLO) properties in Gaussian. Later he moved his website into wordress and forgot to transfer this article. Right now "Gaussian98/03 Nonlinear Optical (NLO) Response" is back. BTW. Damian's blog is very nice place for all interesting in so called NanoThechnology. His Nanotechnology Gallery is beautiful.

Dipole moment in excited state [Gaussian]

To get values of dipole moment obtain with CIS method using Gaussian program you can use this bash command:

egrep "Tot*=|Population" *.log

From all of line you need only the line after Population analysis using the CI density. You can automate it. For example to get the total value of dipole moment use this script (you can write it in one line):

grep "Tot*=" *.log|
 gawk '  BEGIN { currline = 1 }
  {if (currline%3==0){print $9}
  currline = currline + 1}'

Excited state parameters in Gaussian

You can get excited state parameters from gaussian log/out file using one bash command:

grep "Excited State *1" *.log

Of course you can change state number (1) and file(s) name (*.log).

Massive jobs starting in queue system

Quite often we need to start many jobs in a supercomputer center. In this example I have to submit Gaussian files with com extension. All of them are in one directory. (I have my own script g03-test to start Gaussian). We can do it in a one line:

for i in *.com ; do g03-test "$i"; done