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Re: [lammps-users] trouble using rigid bodies in simulation (lost atoms)
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Re: [lammps-users] trouble using rigid bodies in simulation (lost atoms)

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 28 Jul 2017 09:30:11 -0400

On Fri, Jul 28, 2017 at 8:02 AM, surendra jain <jainsk.iitkgp@...24...> wrote:
Dear Lammps users,

  I am studying the diffusion of CO2 molecules in a carbon model. In
my simulation I fix the carbon atoms (setforce 0.0 ..) and make the
CO2 molecules as a rigid body molecule (having 3 atoms). However I get
the following error : "lost atoms:". After debugging I found that one
of the atoms of CO2 molecule is very close to a carbon atom (rsq = 0.5
Angsgtrom). This causes huge force and hence huge velocity on the
atom. I have the following question :

(1) Does the rigid body moves as a whole  or the coordinates of the
atoms are updated individually.

​this question is answered in the documentation ​
(2) If one atom faces huge force then the whole rigid body also
experiene the huge force.

​see (1)
(3) Since the molecule is rigid, is it possible for one of the atoms
to be detached from the molecule.


I ran a simulation of timestep 0.5fs and got the lost atoms error.
Should I use a smaller timestep. Can you please suggest me a suitable
timestep for rigid body simulations.

​please make tests to find what works for your simulation conditions and force field. there is no "the one right value(tm)".
please also note, that the situation you describe may as well be cause by unsuitable or incorrectly entered force field parameters.​



Best Regards,

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Dr. Axel Kohlmeyer  akohlmey@...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.