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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.

Scott

Attachment: lammps_files_2017.tar.gz
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