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Re: [lammps-users] Polymer/CO2 system not time integrating when using fix rigid/nve/small
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Re: [lammps-users] Polymer/CO2 system not time integrating when using fix rigid/nve/small

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 11 May 2018 18:21:30 -0400


thanks for providing illustrative and complete input examples. that helps a lot in figuring out what might be a problem.

i am seeing two issues:
1) your CO2 geometries are not "precise" enough, so i had to change the TOLERANCE setting in the rigid fix
​ source code and recompile ​
for it to accept those as linear molecules.
2) you have a rather high potential energy initial configuration and there seems to be some conflict with CO2 molecules in combination with the langevin settings, which then makes the time integrator become unstable.

​when i change the middle part of your input to do just one step without any progressions, everything looks like it is straightening out and then a stable MD seems to be following.
see below for the modified input and please give it a try.


print                          .
print =====================================
print "Step2: Heating: NVE dynamics with Langevin thermostat"
print =====================================
print            .

reset_timestep  0
timestep        2.0
fix             fixshake poly shake 0.0001 20 0 b 3 7
fix             fixnve poly nve
fix             fixrigid co2 rigid/nve/small molecule
run             0
unfix           fixrigid
fix             fixlangevin poly langevin ${itemp} ${ftemp} 100.0 699483
fix             fixrigid co2 rigid/nvt/small molecule temp ${itemp} ${ftemp} 100.0
thermo          100
thermo_style    custom time temp pe etotal press density

On Thu, May 10, 2018 at 4:09 PM, Bill K Wheatle <bkw686@...4851...> wrote:
Good afternoon,

I am trying to simulate a system of polymer mixed with some CO2 molecules in the 16Mar18 version of LAMMPS with 24 MPI threads. I've attached the input file and the simplified data file containing 1 polymer chain and 20 CO2 molecules. In short, when I apply the rigid/nve/small or rigid/small fixes, the LAMMPS output stops at Timestep: 2.0 without ever showing any thermodynamic data. In contrast, if I simply delete the CO2 from the system and remove the fix, thermodynamic data is produced quite easily. Are there any particular commands that I may be missing in my input file for a mixed system like mine to work correctly?

All the best,

Bill K. Wheatle | Doctoral Candidate
The University of Texas at Austin | McKetta Department of Chemical Engineering | Cockrell School of Engineering
200 E. Dean Keeton St. Austin, TX 78712 | CPE 3.472 | bkw686@...4851... 

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Dr. Axel Kohlmeyer  akohlmey@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.