I am simulating a system of polymer and nanoparticles under confinement (I have walls [LJ 12-6] at the edges of the box in z-direction).
My nanoparticle diameter is 4 sigma and polymer size is 1 sigma. I am using the following commands for fixing the walls
fix 2 pol wall/lj126 zlo EDGE 1.0 0.5 0.56123 zhi EDGE 1.0 0.5 0.56123 units box
fix 3 nan wall/lj126 zlo EDGE 1.0 2.0 2.24492 zhi EDGE 1.0 2.0 2.24492 units box
My box dimensions in z-direction are zlo = -21 and zhi = +21.
I am using nvt ensemble for equilibration with a time step of 0.003. I ran the simulation for 10 million time steps.
When I analyze the nanoparticle trajectory file, I notice that some particles have penetrated the wall. Since my NP size is 4, I do not expect to see the center of any NP from -19 to -21 in the ‘lo’ direction and from +19 to +21 in the ‘hi’ direction. However, I do see that some particles have z-coordinates in those ranges (mentioned above) (eg. z = -19.35). LAMMPS did NOT give me an error, “Particles inside/on the wall”. I was wondering if someone else has also experienced something like this or could give me an explanation as to why this is happening.
I would also like to mention that if the particles are way to inside the wall during generation of my system, then LAMMPS immediately stops giving me the error. However, in this case, my simulations ran completely without any error and I see particles ‘slightly’ inside the wall through out my simulation.
Thanks in advance.
from the vague information you provide, it is difficult to tell
whether you just made a mistake in your input, or there is a problem
with your overall setup, or you triggered a bug in LAMMPS. since there
is nothing extraordinary here, i would assume that the problem is with
your setup or concept. if you still are convinced that there is a bug
in LAMMPS, please prepare a small input that reproduces the issue
quickly, so that it can be properly looked into.
Thanks for your email. As per your suggestion, I have prepared a small system of 100 particles, which contains 50 particles with diameter 1 sigma and the other 50 with diameter 4 sigma. I have maintained the same density (a total packing fraction of 0.415) as my larger polymer-nanoparticle system.
I am attaching the input and data files so that you could run it quickly in your machine and check. I still see that some (big) particles are slightly penetrating the walls. However, the extent of penetration is small now (I believe its dependent on the overall size of the simulations box; I don’t know why though). I’d appreciate it if you could please take a look and share your comments.
data.beads (15.8 KB)
in.poly (685 Bytes)
Fix wall/lj126 doesn’t know anything about nanoparticles
and their “size” as you are defining it. It computes a force
based on r = distance between wall and particle coord,
which is the center of what you are calling a NP. So those
particles are not “inside” the wall as far as wall/lj16 cares.
What you might want is fix wall/colloid, which computes
a force between the wall and finite-size particle.
The doc page for these commands explains the difference.