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Re: [lammps-users] Rigid bodies will slightly deform if a barostat is used
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Re: [lammps-users] Rigid bodies will slightly deform if a barostat is used


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 25 Aug 2017 09:25:09 -0400



On Fri, Aug 25, 2017 at 1:23 AM, ZhaoChuan Fan <fzc727@...24...> wrote:
Dear All,

I have been using LAMMPS doing simulations for some systems consisting of rigid bodies. I recently found that using the "fix rigid" commands with a barostat (i.e., fix rigid/nve or rigid/nve/small combined with a Berdenson barostat, or fix rigid/npt, rigid/nph (with or without "/small")), the rigid bodies will slightly distorted about 0.1% of their length scale. For instant, if I run a simulation for a system consisting of 2-nm-sized rigid dimers in a NPT ensemble (300K, 1atm). The distance between the two beads in a dimer will slightly change between 19.99 to 20.01 Angstrom. I found this happened regardless the shape of the rigid bodies (dimers, polyhedrons, small molecules). The deform of the rigid body does not happen if no barostat is used (e.g., NVE, NVT ensembles)

The distortion is tiny, however, this precision does not meet the requirement for my current study. Therefore, I post this to seek helps. Any comments, suggestions, or answers are welcome. I suspect that the slight shape change of the rigid body is caused by the remapping procedure when applying a barostat (either Berdenson or Nose-Hoover). Does anyone know if this is true? More specifically, is it due to the (low) precision of the FFT used in the remap? If so, is there any way to increase the accuracy? Many thanks for your helps!!!

​there are no FFTs used when changing the box size or switching from fractional to regular coordinates and back. where did you get the idea that FFTs are involved?

​what happens if you run fix rigid like this (or fix press/berendsen):

group none type 999
fix 1 all rigid/npt [...​] dilate none

outside of that, please see: ​http://lammps.sandia.gov/guidelines.html

axel.


 

Best Wishes,
Zhaochuan Fan

Department of Chemistry,
University of Utah

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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.