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Sunday, April 30, 2006

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.

Friday, April 28, 2006


I've just check the website of Molekel one of the most interesting program to visualization Quantum Chemistry date. An there are good news. Yes, they are working on the new version. And Yes, it is GPL program now!

Wednesday, April 26, 2006

How to convert color pdf (ps) to b&w file

I have a pdf file, where foreground color is blue. It is very nice when you look at it at your monitor, but no so nice when you have to print it on b&w printer. Today I found the way how to convert a color pdf (or rather ps) into a b&w file. First you have to convert a pdf into a ps
Printing into a file from Acrobat Reader doesn't work. Next you have to download this small perl script and use it
 bw_convert -b
Now you have file ready to print on your b&w printer.
I found link to bw_convert script on this FAQu. There are more interesting advices.

Wednesday, April 12, 2006

Regular expression [βzzz from Dalton]

Very often you need only one number from whole output. Going through all the file is boring, especially if you have more then one file. In these situation regular expression are a great help. For example: I needed to find out the value of βzzz. I figured out from an output file that I needed lines with 3 ZDIPLEN words. I prepared the command which should work:
grep "Z.*Z.*Z" *.out
But I got more than I wanted:
betaccs_rhb-631+gd.out: ZDIPLEN  (unrel.) 0.0000  ZDIPLEN (unrel.) 0.0000  ZDIPLEN (unrel.) 0.0000  -383.12517
So I modified my expression (brackets are only in wanted lines):
Z.*(.*Z.*Z" *.out
BTW. If you want to obtaine the correct value of β you'll have to multiply value from output file by -1.

rsp_zfs and gcc 3.4.x [Dalton]

In Dalton FAQ it is written that "g77-3.4.2 (Fedora Core 3) miscompiles DLAMC3 routine from gp_zlapack.F file leading to apparent hang in rsp_zfs test". I had the same problem (hangs of rsp_zfs) on my CRUX with gcc-3.4.4. Adding of -ffloat-store option helps. Moreover, after adding this option Dalton has been build without and failed tastes on Athlon.

Saturday, April 08, 2006

Points style in Gnuplot - part II

My friend Paweł Kędzierski showed me another (better?) way how to present points style in gnuplot. It is describe in docs. (Shame on me!) The ps_symbols.gpi script can be found in gnuplot docs directory or hear. Below you see output from it: BTW I would like to add link to another nice site with gnuplot images. It was created by Petr Mikulik.

Thursday, April 06, 2006

Points style in Gnuplot

It's quite annoying to find the best points styles for your postscript output from gnuplot. I tried to find the site with list of all points style, but I failed, so made my own:
set term postscript
set output ""
set xrange [0:30]
set yrange [0:30]
set key right bottom
plot   x+1   with linespoints pt 1 title "1",  
       x+2   with linespoints pt 2 title "2",
       x+3   with linespoints pt 3 title "3",
       x+4   with linespoints pt 4 title "4",
       x+5   with linespoints pt 5 title "5",
       x+6   with linespoints pt 6 title "6",
       x+7   with linespoints pt 7 title "7",
       x+8   with linespoints pt 8 title "8",
       x+9   with linespoints pt 9 title "9",
       x+10  with linespoints pt 10 title "10",
       x+11  with linespoints pt 11 title "11",
       x+12  with linespoints pt 12 title "12",
       x+13  with linespoints pt 13 title "13",
       x+14  with linespoints pt 14 title "14",
       x+15  with linespoints pt 15 title "15",
       x+16  with linespoints pt 16 title "16",
       x+17  with linespoints pt 17 title "17",
       x+18  with linespoints pt 18 title "18",
       x+19  with linespoints pt 19 title "19",
       x+20  with linespoints pt 20 title "20"
The result is below. It was obtained by: convert test.png (and next rotated):

Monday, April 03, 2006

Vim/Vi Cheat Sheet and Tutorial

Deelopers of ViEmu published very nice help for Vim. I've missed something like this.

Saturday, April 01, 2006

Medical Computing

Alex Amies is writing the blog about Medical Computing. It can be interesting for some people hitting my webpage.

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}'