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Re: [lammps-users] barostat in systems with rigid and non-rigid bodies
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Re: [lammps-users] barostat in systems with rigid and non-rigid bodies

From: Stefan Paquay <stefanpaquay@...24...>
Date: Mon, 25 Sep 2017 11:31:23 -0400

No one picked this up yet, unfortunately. I am no expert in how rigid is supposed to work with pressure, but I will at least try to reproduce the issue. Hopefully others will chime at some point.

On Thu, Sep 21, 2017 at 4:09 PM, Scott M Smith <sms387@...1461...> wrote:
Hello lammps users,

I am running into an issue of the barostat not achieving the target pressure (zero) in a system with rigid and non-rigid bodies. This issue was discussed previously on the forum, with the subject titled "global pressure with rigid and non-rigid bodies." I was unsuccessful in replying to the old thread, so I have started a new one. From the old thread, I was not able to figure out why the barostat (nose-hoover) was not achieving the target pressure, and so I eventually moved forward with a Berendsen barostat because it was reaching the target pressure as desired. However, my latest simulations require calculation of a bulk modulus, and Berendsen does not capture the correct physics for a bulk modulus determination. I recently tried going back to the Nose-Hoover barostat, and not surprisingly, the pressure issue has returned.  

I believe there is a bug in the way the pressure is handled for systems with rigid and non-rigid bodies when using a Nose-Hoover barostat, and I have provided supporting evidence below. 

In my system, I use fix rigid/nvt on the rigid bodies and npt on the non-rigid. I have attached a sample input file and data file for a system with 16 rigid bodies in a polymer melt; I apply a small amount of positive pressure initially (ramp the LJ pressure from 0.01 to 0 to prevent the system from vaporizing) and then switch the target pressure to zero and monitor the pressure. To reduce noise in the output, I have also printed a pressure that is averaged over 1000 timesteps using the fix ave/time command. In my experience, this output reveals a positive pressure that scales linearly in the number of rigid bodies included in the simulation (although the target pressure is zero in each case), as shown in the attachment.

I am running the March 2017 version of lammps. The following list includes troubleshooting techniques that I have employed in trying to understand what is going on with the system:
  • Using "neigh_modify exclude molecule/intra" to prevent bogus pressure contributions due to intraparticle forces
  • reducing the timestep from 0.005 tau LJ to 0.001 tau LJ (no change in the results)
  • changing the pressure damping parameter from 2 tau to 20 tau (no change in the results)
  • Use "compute pressure" to get the pressure that the barostat uses/computes to make box volume adjustments (this number is consistently positive and fluctuates around a value greater than zero; I am not sure why the barostat does not increase the box volume to reduce the pressure to the target value of zero)
  • invoking the barostat on the rigid body time integration: fix rigid/npt for rigid body, fix nvt for non-rigid (this throws many FENE bond warnings, and the pressure still does not go to the target value of zero)
  • using "aniso" instead of "iso" for altering the box dimensions due to pressure fluctuations (no change)
  • I am allowing the rigid body COM's to dilate with the changing box size ("dilate all"; this command is a default anyways)
  • Reducing the volume fraction of rigid bodies to rule out possible jamming effects

I want to emphasize that this is not an issue of fluctuations in the pressure; I am seeing fluctuations around a mean pressure value that is not the target value. I would greatly appreciate if someone could confirm this result by running the attached sample system and observing the pressure magnitude in the thermo output. Thank you for any feedback.


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