[CP2K-user] [CP2K:13532] G3X3 and VIRTUAL_SITES

[Pierre Cazade]

Hi Matt,

I have just realized going through the source code that shake is only 
used with MD.

Thanks,
Pierre

On 17/06/2020 15:44, Matt W wrote:
> Constraints only work with MD not geo or cell opt.
>
> On Wednesday, June 17, 2020 at 1:13:01 PM UTC+1, Pierre-André Cazade 
> wrote:
>
>     Hi Alin,
>
>     Thanks for the example. I checked some of the regtest but not the
>     one you mentioned. This quite helpful. Yet, if you check my input
>     file, this exactly what I am doing, so I am puzzled as for why it
>     seems the constraints (at least g3x3) are not enforced. This leads
>     to distorted water molecules (I checked the restart file) and then
>     to the bad contacts causing cp2k to crash.
>
>     Regards,
>     Pierre
>
>     On Wednesday, June 17, 2020 at 1:02:19 PM UTC+1, Alin Marin Elena
>     wrote:
>
>         Hi Pierre,
>
>         there are some example in
>         tests/Fist/regtest-1-3/h2o-32-g3x3-mult.inp
>
>
>         Regards,
>         Alin
>
>         Without Questions there are no Answers!
>         ______________________________________________________________________
>
>         Dr. Alin Marin ELENA
>         http://alin.elena.space/
>         ______________________________________________________________________
>
>
>         On Wed, 17 Jun 2020 at 12:54, Pierre-André Cazade
>         <pie... at gmail.com> wrote:
>         >
>         > Hi Azade,
>         >
>         > Thanks for your answer. The molname is defined in the PSF
>         file, in the topology section. The molname seems to be
>         identified correctly as it is present in the output file
>         (attached) in the description of the topology.
>         >
>         > Regards,
>         > Pierre
>         >
>         > On Wednesday, June 17, 2020 at 12:20:32 PM UTC+1, Azade
>         Yazdan Yar wrote:
>         >>
>         >> Hi Pierre,
>         >> I know some of the answers to your first question.
>         >> What you use in the ATOMS should be the index of atoms
>         within that molecule. Constraints will be applied to all
>         molecules with the same MOLNAME or MOLECULE number.
>         >> From your input file, I cannot see how the SWM4 molecules
>         are defined in the coordinates section. You have to define the
>         MOLNAME in that part as below (what I have as H2O, or MOLECULE
>         1). Note that if you use MOLECULE, it is the 'molecule kind
>         number' and not molecule number.
>         >>
>         >> Hope this helps,
>         >> Azade
>         >>
>         >> &G3X3
>         >>        MOLECULE  1
>         >>        ATOMS  1..3
>         >>        DISTANCES     a b c
>         >>  &END G3X3
>         >>
>         >> O    5.1692824047308950E+00  5.3185376653354242E+00  
>          2.1483827179189252E+01 H2O 1
>         >>
>         >> On Wed, Jun 17, 2020 at 12:41 PM Pierre-André Cazade
>         <pie... at gmail.com> wrote:
>         >>>
>         >>> Dear CP2K users,
>         >>>
>         >>> I am trying to use G3X3 constraints on my water molecules
>         during a CELL_OPT motion. Needless to say, that it does not
>         work. The "manual" is not very clear about the indexes that
>         need to be provided. Should I use the index of the atoms in
>         the coordinate file, for example 15761 15762 15763, or the
>         indexes within the water molecule itself: 1 2 3. Does such
>         constraint apply to all my water molecules provided they have
>         the same molname "SWM4" or do I need an entry for each water
>         molecule?
>         >>>
>         >>> What about VIRTUAL_SITES?
>         >>>
>         >>> Finally, the "CONTRAINT_INFO ON" section does not print a
>         single information in the output to help me out.
>         >>>
>         >>> I attached my input file for clarity.
>         >>>
>         >>> Regards,
>         >>> Pierre
>         >>>
>         >>>
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-- 
Dr Pierre Cazade, PhD
AD3-023, Bernal Institute,
University of Limerick,
Plassey Park Road,
Castletroy, co. Limerick,
Ireland

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