Isotopic dilution study

[Eric Shamay]

One last issue on this - When the trajectories are printed (i.e. when
doing geo_opt or MD) the output XYZ file contains the name of the
element H again. I.e. my input coordinates specify that the atom name
is 'D', but then the output, instead of printing 'D' for each atom, it
prints out 'H' as if I had never changed the KIND. Is the output based
on the 'ELEMENT' parameter? Is there a way to force it to output the
name associated with the 'KIND' and not the 'ELEMENT' of each atom?



On Nov 28, 12:45 pm, Laino Teodoro <teodor... at gmail.com> wrote:
> here's the way to fix this problem:
>
> &KI ND D
>        BASIS_SET TZV2P-GTH
>        POTENTIAL GTH-BLYP-q1
>        MASS 2.0
>        ELEMENT H
> &END KIND
>
> teo
>
> On 28 Nov 2008, at 21:43, Eric Shamay wrote:
>
>
>
> > Here's the error I receive when trying the following:
>
> >  ***  Unknown element for KIND <D>. This problem can be fixed
> > specifying  ***
> >  *** properly elements in PDB or specifying a KIND section or getting
> > in  ***
> >  *** touch with one of  the
> > developers!                                   ***
>
> > My KIND section is as follows:
>
> >     &KIND H
> >       BASIS_SET TZV2P-GTH
> >       POTENTIAL GTH-BLYP-q1
> >     &END KIND
> >     &KIND D
> >       BASIS_SET TZV2P-GTH
> >       POTENTIAL GTH-BLYP-q1
> >       MASS 2.0
> >     &END KIND
> >     &KIND O
> >       BASIS_SET TZV2P-GTH
> >       POTENTIAL GTH-BLYP-q6
> >     &END KIND
> >     &KIND N
> >       BASIS_SET TZV2P-GTH
> >       POTENTIAL GTH-BLYP-q5
> >     &END KIND
>
> > It's the error I received when trying that out before, but forgot what
> > the problem was. Any insight on this?
>
> > ~Eric
>
> > On Nov 21, 2:52 pm, Laino Teodoro <teodor... at gmail.com> wrote:
> >> Ciao Erick,
>
> >> sure it is possible. Please, follow this pseudo-input..
>
> >> &COORD
> >>    D  x y z
> >>    D  x y z
> >>    O  x y z
> >>    H x y z
> >>    H x y z
> >>    O x y z
> >> &END
>
> >> &KIND H
> >>     BASIS_SET ..
> >>     POTENTIAL ..
> >> &END
>
> >> &KIND D
> >>     BASIS_SET ..
> >>     POTENTIAL ..
> >>     MASS 2.0
> >> &END
>
> >> ...etc..
>
> >> ciao,
> >> Teo
>
> >> On 21 Nov 2008, at 23:46, Eric Shamay wrote:
>
> >>> Does anyone know of how I would specify this in my input file for
> >>> cp2k? Is this possible to do?