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Re: [lammps-users] Reaxc computing bonds
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Re: [lammps-users] Reaxc computing bonds


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 1 May 2018 17:32:01 -0400

On Tue, May 1, 2018 at 4:13 PM, Faure Quentin
<quentin.faure.30@...24...> wrote:
> Hi all,
>
> I have created a prism of cement and surrounded by water and I am using reax/c with it. I would like to compute the number of dissociation of water per angstrom square for each surface at the interface cement/water. I looked in the manual how to do it and did not find any commands that can do it directly. So my plan is to compute the bond informations of a small region of water at the interface (thin rectangular shape region). I also determine the number of H and O in this region. From that I can have the number of water molecules that have been “broken”. For that I use the command fix reax/c/bonds. However in the file that is created, there is the information for all the bonds in the entire system (around 130 000 bonds). >From the manual it seems that the bond informations are only computed for the group ID specified (I created a group from the region). But it does not seems to be the case for me (there is only 140 atoms in the group I specified). Does anyone know why the bond information of the entire system are computed and not the one of the group I specified in the command line?

the group information is ignored by fix reax/c/bonds. the
documentation doesn't mention it, so this needs to be corrected.
to have the group honored, some additional programming would be
required. not extremely difficult to do, but also not trivial.

axel.

>
> Quentin
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.