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.

Molekel

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!

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

pdf2ps file.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 file.ps file-bw.ps

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.

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 β_zzz. 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:  PUT TRIPLE: ZDIPLEN  ZDIPLEN  ZDIPLEN ON THE LIST. 
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.

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.

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 "test.ps"
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.ps test.png (and next rotated):

Vim/Vi Cheat Sheet and Tutorial

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

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}'

CESTC 2006

It's quite hard to find any info about Central European Symposium on Theoretical Chemistry 2006. So I'm adding link to the website: http://tiger.chem.uw.edu.pl/cestc/.

Great site about Gnuplot

Gnuplot is very good data and function plotting utility. There are a lot of demos what can you do with in at official website. But advises prepared by Toshihiko Kawano from Los Alamos National Laboratory are amazing. Check this link and learn what you can do with gnuplot!

exit code 139 [Dalton & Bash]

After building dalton program, you should test it. If something is going wrong you'll get Exit Codes. Quite often it is code 139, what means Invalid memory reference (signal SIGSEGV 11 = 139- 128 ).

Orbiton - gallery of orbitals

I've just found Orbitron . It is a gallery of atomic orbitals and molecular orbitals on the WWW. The pictures are really nice, but animation of creating of molecular orbitals are great.

New icons in OO2 [not only in Crux]

I was quite upset because standard Crux OpenOffice2 (and 1) port provide default, not so nice, icons. I prefer Ximian ones included i.e. in Debian and Ubuntu. Quite long I tried to find how to change my icons. Finally I did this! I took images_industrial.zip, from /usr/lib/openoffice/lib/config/ (from debian machine). Of course you can choose another one, there are images_crystal.zip (KDE) and images_hicolor.zip. Transfer into me Crux machine and copy on default OO icons set /usr/lib/openoffice/lib/config/images.zip.

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).

Benchmarking Filesystems - part I

In the 122nd number of Linux Gazette Justin Piszcz presented second part of his article about Benchmarking Filesystems. Author suggested the XFS is the best choice, however, briefly analysis of results exhibited that JFS could be even better.

Another site about Free Chemistry Software

I found another interesting website about chemistry software. There is only disadvantage of Tom's Free Chemistry Software, it was stop to maintain some time ago... Anyway you can check it, there are still a lof of working links.

Energy converter for chemists

I found a nice Energy Converter which can be useful for chemists.

My ports for Crux

You can find the list my ports hear. There are some programs which can be helpful for chemists: OpenBabel, EasyChem, Molden, ViewMol, ChemTool, gChemPaint and Povray. The last one can be also useful for others. I also added Polish dictionary for aspell, it have alt(ernative) in the name, but it is the official dictionary now. There are also my version of Gajim (with speller), Mutt with sidebr patch and WmCalClock (fixed problems with download). Recently, I added nice tool to creating static html image galleries - igal.