Sunday, September 27, 2015

Automatic data extraction from multiple GAMESS output files: an example

Jimmy ran many PM6-D3H+ geometry optimizations using different starting geometries.  Typing "grep EQUILIBRIUM *.log" showed that they had all converged, but how to extract the heat of formation on the optimized geometry?  This python program does the trick.  It finds the last heat of formation in each file or, more precisely, it finds the second to last "word" in the last line where the first word is HEAT.

Update 2015.10.03.
1. Apologies to +Jimmy Charnley Kromann  for the poor formulation.  Jimmy ran the calculations, I wrote the script. After the post came online he was immediately teased mercilessly by his so-called friends for writing such crappy code. That's on me.

2. As +Anders Steen Christensen pointed out in the comments this can be done in one line using Bash: "for f in *.log; do tac $f | grep -m1 HEAT; done"

3. If you want to do it in Fortran +Lars Bratholm suggested the following code

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Tuesday, September 1, 2015

Computational Chemistry Highlights: August issue

The August issue of Computational Chemistry Highlights is out.

CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here.

Table of content for this issue features contributions from CCH editors Steven Bachrach and Jan Jensen:

AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

Benzene-Fused Azacorannulene Bearing an Internal Nitrogen Atom

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This work is licensed under a Creative Commons Attribution 4.0