[CP2K:1589] Re: Isotopic dilution study
Laino Teodoro
teodor... at gmail.com
Tue Dec 2 06:54:49 UTC 2008
Hi Eric,
On 2 Dec 2008, at 01:46, Eric Shamay wrote:
>
> 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
of course you never changed the KIND, but the "standard" of XYZ is to
have:
ELEMENT X Y Z
and not
KIND x y z
If you want to be able to track the "D", then I suggest you to
exploit the
capabilities of VMD, first loading an XYZ with the names you like and
loading
on the top of that molecule the whole trajectory you like (since the
order of the atoms
in the trajectory is the same as the one in input).
Instead of the original XYZ, you can as well use PSF or PDB.
Teo
> 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?
> >
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