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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: Bill K Wheatle <bkw686@...4851...>
Date: Sun, 13 May 2018 17:03:28 -0500

Hello Axel,

Before I use the modified input script, I have a couple of questions. First, what do you mean "precise"? Is the CO2 angle not 180 degrees in my data file? If not, then would simply minimizing the molecule without any pair interactions turned on help in the future? Second, what did you change your TOLERANCE setting to in the fix rigid source code?

Thanks again for your help.

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... 


On Fri, May 11, 2018 at 5:21 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:
bill,

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.

axel.​


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@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.