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All functionals supporting escf in bash script

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Simple, but sometimes can help. If you are going to prepare the Turbomole control
files with all functionals supporting electronic excited state calculation – use sed tool in bash script.
It is assumed that control.template file contains the pbe0 functional. In the 5th line there is a submission to the queuing system realized by other scripts (TMOLE_submit and TMOLE_commands).

#!/bin/bash
for func in b3-lyp b3-lyp_Gaussian bh-lyp b-lyp pbe s-vwn s-vwn_Gaussian
do
sed 's/pbe0/'$func'/g' control.template > control
./TMOLE_submit 6AC_$func TMOLE_commands
done

Hevea

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Recently I had to convert piece of LaTeX document into HTML form. There are quite a few tools that are capable of doing it. Among them one can find, for instance: latex2html, tth. I have not gone through these tools, so feel free to check them out. Instead I got encouraged by Hevea.

An installation of this tool is pretty straightforward can be done via mac port (just port install hevea). Is is required to install OCaml (if not already installed), but it is worth of doing it. An installation via port takes care of all required dependencies. For me it was essential to translate single equations from Latex into HTML language. For instance, the following equation (Boys function)

(1)    \begin{align*} F_{m}(t)=\int\limits_{0}^{1}\exp(-tx^{2})x^{2m}dx \end{align*}

can easily be transformed into

Fm(t)=
1
0
exp(−tx2)x2mdx

The HTML code looks like the following:

</pre>
<table class="display dcenter">
<tbody>
<tr style="vertical-align: middle;">
<td class="dcell"><span style="font-style: italic;">F</span><sub><span style="font-style: italic;">m</span></sub>(<span style="font-style: italic;">t</span>)=</td>
<td class="dcell">
<table class="display">
<tbody>
<tr>
<td class="dcell" style="text-align: center;">1</td>
</tr>
<tr>
<td class="dcell" style="text-align: center;"></td>
</tr>
<tr>
<td class="dcell" style="text-align: center;">0</td>
</tr>
</tbody>
</table>
</td>
<td class="dcell">exp(<span style="font-style: italic;">tx</span><sup>2</sup>)<span style="font-style: italic;">x</span><sup>2<span style="font-style: italic;">m</span></sup><span style="font-style: italic;">dx</span></td>
</tr>
</tbody>
</table>

Calculations with Turbomole 1

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Below I want to show short guide related to the usage of  quantum chemistry package: Turbomole.

First thing is to appropriately set up environmental variables. To do this just go to your Turbomole directory and type:

$ source Config_turbo_env

Now you are ready to execute any of Turbomole programs/scripts. You can easily check it by typing:

$ which ridft
_some_path_/ridft

In the Turbomole package handling of input data is slightly different than in the case of many other quantum chemistry packages. Instead of one input file (like in the case of Gaussian) there are few other files that contain entire information about considered system. From the point of view of the user it is important to prepare the geometry of molecule, for example in the xyz format (using e.g. Molden program). The rest can be generated with the define program (a part of Turbomole package). However, Turbomole has its own format in which the geometry is expressed. To obtain this file you should use script x2t in the following way:

$ x2t geometry_in_the_xyz_format &gt; coord

Now your geometry is ready to go and define program should be used. In principle define is an interactive program that takes the user through couple of screens where one can load the geometry, set up the basis set and so on. It is a good idea to get familiar with define, but going through it routinely is a bit slow and a good idea is to write a short input to define. This input should contain all information which normally would be entered interactively. Below and exaple of such a input file:

$ cat define.inp
a coord
ired
*
b all def2-SV(P)
*
eht
0
ri
jbas
*
on
*
dft
on
*
*

Starting from the beginnig we have the following commands:
a coord – get the geometry from the coord file
ired – impose the internal redundant coordinates (for geometry optimization)
b all def2-SV(P) – choose the def2-SV(P) as the orbital basis set
eht – compute the initial Huckel guess for the molecular orbitals
0 – here we want to have the neutral molecule (charge=0)
ri – use the resolution-of-the-identity for Coulomb integrals (calles sometimes the density fitting)
jbas – take the auxiliary basis set which is adequate to orbital basis (with the same name, but this is completely different basis set)
dft – turn on the dft mode (the SCF procedure will be calculating the DFT rather than Hartree-Fock energy)