Hi Axel,
Thanks for your reply.
I can run the system well with one cpu, so there should not have very
bad structure or high energy shoot in my system. I doubt it is the cpu
allocation problem. Because there is no pair interaction, hence no cut
off distance, the neighboring list cannot be built. I'm not sure about
this. If it's really the neighbouring list problem, what can I do?
Thanks!
Dongshan
On Tue, May 25, 2010 at 12:43 PM, Axel Kohlmeyer <akohlmey.gmail.com> wrote:
> On Tue, May 25, 2010 at 12:28 PM, Dongshan Wei <dswei0523.gmail.com> wrote:
>> Hi all,
>>
>> I'm simulating an artificial system in which there are only the bond,
>> angle and dihedral interactions, no pair interactions. When I begin
>> one cpu serial running, lammps can work well. But when I begin
>> parallel running, lammps will report an error as follows:
>>
>> 1 by 1 by 4 processor grid
>> 2000 atoms
>> 3000 bonds
>> 6000 angles
>> 12000 dihedrals
>> Finding 1-2 1-3 1-4 neighbors ...
>> 3 = max # of 1-2 neighbors
>> 6 = max # of 1-3 neighbors
>> 18 = max # of 1-4 neighbors
>> 18 = max # of special neighbors
>> Setting up run ...
>> ERROR on proc 0: Bond atoms 1 198 missing on proc 0 at step 0
>> ERROR on proc 3: Bond atoms 151 152 missing on proc 3 at step 0
>> ERROR on proc 1: Bond atoms 51 52 missing on proc 1 at step 0
>> ERROR on proc 2: Bond atoms 149 150 missing on proc 2 at step 0
>>
>>
>> Does anyone have some experience to deal with this parallel problem?
>
>
> many people have. check the mailing list archives.
>
> most likely your initial structure is very high in potential energy.
> you can run a minimization first before starting MD.
> there also is nve/limit and shorter timesteps, fix viscous
> and other tricks to bring down your system to a reasonable
> state near equilibrium where you can use "normal" parameters.
>
> cheers,
> axel.
>
>>
>> Thanks so much!
>>
>> Dongshan
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
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>> lammps-users.lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/lammps-users
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey.gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
--
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Received on Tue May 25 2010 - 10:30:04 PDT
