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

From: Scott M Smith <sms387@...1461...>
Date: Thu, 21 Sep 2017 16:09:50 -0400

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:

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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