cp2k and Bader analysis

Axel Kohlmeyer akoh... at gmail.com
Fri Sep 18 15:49:06 CEST 2009


On Sep 18, 9:16 am, Jörg Saßmannshausen
<jorg.sassm... at strath.ac.uk> wrote:
> Dear Axel and Ondrej,
>
> thanks for your feedbacks, much appreciated.
>
> I actually tried the Bader code from the group in Texas once and after a long
> calculation it segfaulted. So I gave up on that and went back to the AIM2000
> program.

the Utexas code is the fastest and best bader code, that i have
ever come across. same as cp2k, it puts some demands on the compiler,
so if it crashed for you, most likely it was miscompiled or you fed
it bad data. i have been using it several times and it was always
working well, fast, and efficient.

cheers,
   axel.



>
> So the bottom line is that it is not a straightforward task. I was somehow
> afraid of that.
>
> The reason behind my question was, I am trying to tackle a rather difficult
> system right now and I was hoping to overcome some of the problems with a
> plane wave code, rather then using programs uitilizing GTO (like GAMESS,
> Gaussian etc.).
>
> Thanks for your help!
>
> Jörg
>
> On Friday 18 September 2009 14:03:07 Axel Kohlmeyer wrote:
>
>
>
> > On Sep 18, 5:59 am, Ondrej Marsalek <ondrej.... at gmail.com> wrote:
>
> > dear ondrej,
>
> > > Dear Jörg,
>
> > > the implementation of Bader analysis that you can find here:
>
> > >http://theory.cm.utexas.edu/bader/
>
> > > can use Cube files as input. You can save volumetric data (for example
> > > the density and KS orbitals) from CP2K into Cube files, so you should
> > > be fine. The density is straightforward, if you want to do something
>
> > not quite. for AIM you need the _complete_ wavefunction, whereas
> > cp2k usually only outputs the valence part (even with *PAW) and
> > that can have a significant impact on the validity and accuracy
> > of the results. so you have to first add the core wavefunction
> > part back that is subtracted out during pseudopotential generation
> > or through the PAW procedure.
>
> > matthias krack once implemented a feature that you can do this
> > from GPAW, but it turned out to be extremely slow and had artefacts
> > that threw the bader code from the group in texas off.
>
> > i have been toying with the idea of constructing density files
> > to add to the existing valence density after the fact, by taking
> > the difference from a single atoms all-electron and pseudopotential
> > calculation, and then adding them to the valence density cube.
> > but that scheme only worked for me to some degree for s-electrons.
>
> > > with orbitals, you would perhaps need to use some Cube file
> > > manipulation program to obtain the densities from individual KS
> > > obrbitals first.
>
> > why the individual KS orbitals? AIM only works on the total density,
> > IIRC.
>
> > cheers,
> >     axel.
>
> > > Best regards from Prague,
> > > Ondrej
>
> > > On Fri, Sep 18, 2009 at 11:15, Jörg Saßmannshausen
>
> > > <jorg.sassm... at strath.ac.uk> wrote:
> > > > Dear all
>
> > > > I was wondering whether it is possible (at least in theory) to use cp2k
> > > > to generate the wavefunktion-file for Bader's AIM analysis.
> > > > So basically I would need an ASCII file, similar to the uploaded file
> > > > (which is the file for propene). Is that possible at all with cp2k or
> > > > as we are using plane waves here not possible?
>
> > > > The file location is:
> > > >http://groups.google.com/group/cp2k/web/bader-aim-file.wfn
>
> > > > All the best from Glasgow!
>
> > > > Jörg
>
> > > > --
> > > > *************************************************************
> > > > Jörg Saßmannshausen
> > > > Research Fellow
> > > > University of Strathclyde
> > > > Department of Pure and Applied Chemistry
> > > > 295 Cathedral St.
> > > > Glasgow
> > > > G1 1XL
>
> > > > email: jorg.sassm... at strath.ac.uk
> > > > web:http://sassy.formativ.net
>
> > > > Please avoid sending me Word or PowerPoint attachments.
> > > > Seehttp://www.gnu.org/philosophy/no-word-attachments.html
>
> --
> *************************************************************
> Jörg Saßmannshausen
> Research Fellow
> University of Strathclyde
> Department of Pure and Applied Chemistry
> 295 Cathedral St.
> Glasgow
> G1 1XL
>
> email: jorg.sassm... at strath.ac.uk
> web:http://sassy.formativ.net
>
> Please avoid sending me Word or PowerPoint attachments.
> Seehttp://www.gnu.org/philosophy/no-word-attachments.html


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