[CPMD-list] Density Cubefile

[Ari P Seitsonen]

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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