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Friday, December 29, 2006

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: inputfile

Thursday, December 28, 2006

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

Thursday, December 14, 2006

'Symmetry' font in LaTeX

If you need nice font for symmetry group names use mathrsfs package and next (example for C2 group) $\mathscr{C}_2$ in the text. Of course you can use it for many other purpose.

Thursday, December 07, 2006

Hack a Rox

I like Rox, but it has some annoying small problems. One of them is that the program which open the file is running from home directory. Now I write short script which fix it for gvim and I'm thinking how to do global...
cd `dirname "$@"`
gvim `basename "$@"`

Wednesday, December 06, 2006

Vim's colorscheme

I've found nice site with sample of Vim's colorschemse. I miss only python samples.

Sunday, December 03, 2006

XymTeX: example

I'm using XymTeX to creating chemical structures in PhD thesis. I'm not fully satisfe, but it create structures' counter , which can be use for numbering and refering to structures. Recently I created Reichardt Betaine subtituted by eter crown. The command which create this picture is below. Is nice, isn't it ;) \begin{XyMcompd}(800,2000)(,-1400){zw:korona}{}
\sixheterov[ace]{4==\upnobond{N}{$\oplus$}} %
{1==Ph;3==Ph;5==Ph; %
4==\cyclohexanev[ace %
{c\sixfusev[ %
{c\sixfusev[ %
{d\sixfusev{2==O;5==\null}{}{A}[ef]} %
]{1==\null;4==\null}{}{F}[de]} %
]{3==O}{}{F}[cde]} %
{d\sixfusev[ %
{d\sixfusev[ %
{c\sixfusev{3==O;6==O}{}{F}[ab]} %
]{1==\null;4==\null}{}{A}[bc]} %
]{5==O}{}{A}[bcd]} %
] %
{4D=={\hspace*{-1.5mm}$| \underline{\mathrm{O}}|^{\ominus}$};1==(yl)}}
If you don't like XymTeX you can try konwerter very nice program by Piotr Wawrzyniak.