[CPMD-list] Density Cubefile

[Dr. Balasubramanian Sundaram]

dear Apsi,
   Yes, they and everything else (including the grid size) are in a.u. 
I will now try the cubecenter=0 option mentioned by Axel. 

Regards,
Bala

Ari P Seitsonen wrote:
> 
> Dear Bala,
> 
>   'cpmd2cube' does NOT force using HALFMESH (does it even work in the old
> version?). The final atomic coordinates are listed in the beginning of the
> cube file, there you can check that you are using the correct, consistent
> coordinates (I think that they are in Bohr, can someone confirm?).
> 
>     Greetings,
> 
>        apsi
> 
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>  Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>  Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35
>  Anschrift: Physikalisch Chemisches Institut (PCI), Universität Zürich (UniZh)
>  Indirizzo: Winterthurerstraße 190, CH-8057 Zürich
>  Address:   Schweiz / Svizzera / Suisse / Svizra / Switzerland
> 
> On Mon, 9 Feb 2004, Dr. Balasubramanian Sundaram wrote:
> 
> > Axel Kohlmeyer wrote:
> > >
> > > >>> "BS" == Balasubramanian Sundaram <Dr.> writes:
> > >
> > > BS> Dear All,
> > > BS>    I am getting the RHO_TOT.cube file for a bulk system (with 3-d PBC)
> > > BS> in liquid state through the PROP keyword. I am able to understand the
> > > BS> header portion of this file, as containing the origin (lowerleft corner
> > > BS> in the source code), the grid spacing, the ion coordinates, followed by
> > > BS> the density values in 2-column format. (z is the innermost loop, y is
> > > BS> the middle one, and x is the outermost loop).
> > >
> >
> > Hi Axel,
> >
> > Thanks for your prompt reply.
> >
> > > to get those you only need to fgure out the x-, y-, and z counting index
> > > for each point and then multiply with the respective grid vectors (lines
> > > 4-6) and finally add those three vectors. this is the standard gaussian
> > > style cube file format (although it looks a bit different). the version
> > > of the code in cpmd 3.7 has some problems on some machines. you may want
> > > to try using RHOOUT and cpmd2cube (which has other problems) as an
> > > alternative route to get to the same result.
> > >
> > > both problems mentioned have been fixed in the current development
> > > versions, which are scheduled to be relased in the near future.
> >
> > We found RHOOUT (through cpmd.x itself) to be easier to use than
> > cpmd2cube,
> > as we can avoid using the HALFMESH (I suppose cpmd2cube cumpulsorily
> > writes
> > the density in the HALFMESH).
> >
> > For the records: We use v3.7.2 on an IBM-SP-SMP.
> >
> > We do obtain the coordinates of the grid points in the way you describe.
> > Our
> > simulation cell is cubic.  So, the grid goes from 0 to L in each of the
> > 3 directions. However, the ion coordinates, after performing a PBC on
> > the
> > molecular centre of mass, lie between -L/2 to +L/2. How does one
> > position
> > the density grid on top of the ion positons?
> >
> > > BS>    Specifically I am trying to reproduce the result of Laasonen, Sprik
> > > BS> and
> > > BS> Parrinello, JCP (1993) to obtain the molecular dipole moment of water
> > > BS> molecules
> > > BS> in liquid water, as a learning exercise. I realize that it is possible
> > >
> > > if i am not totally mistaken, this has also been implemented in the
> > > development version of cpmd. so you will have a nice opportunity to
> > > cross-check your results.
> >
> > sorry, what feature has also been implemented in the development
> > version?
> >
> > Thanks again for the help,
> >
> > Regards,
> > Bala
> >
> >
> >
> >
> >
> >
> > > take care,
> > >      axel.
> > > BS> to
> > > BS> get this information from the Wannier+Ion centers as well, but I need to
> > > BS> obtain
> > > BS> it from the charge density+Ion Centers.
> > >
> > > BS> Thanks!
> > >
> > > BS> Best Regards,
> > > BS> Bala
> > > BS> _______________________________________________
> > > BS> CPMD-list mailing list
> > > BS> CPMD-list at cpmd.org
> > > BS> http://www.cpmd.org/mailman/listinfo/cpmd-list
> > >
> > > --
> > >
> > > =======================================================================
> > > Axel Kohlmeyer       e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de
> > > Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
> > > Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
> > > D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> > > =======================================================================
> > > If you make something idiot-proof, the universe creates a better idiot.
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