"Must shrink-wrap piston boundary"

Hi Steve,

Just a lil background on my sample: I have ran simulations using the structure with periodic boundary conditions, and checked all the relevant thermal-physical properties including Tg for my polymeric system. I want to use this sample to simulate shock compression (NEMD). To prepare the sample for shock, I replicated the polymer sample. The final sample has dimensions of 8.9 nm X8.9 nmx 717nm in x, y, and z dimensions respectively. The first attempt to simulate shock

I used the:

  1. fix 2 all wall/lj126 zhi 750 1.0 1.0 2.5 units box, and I got the same error
    (Bond/angle/dihedral extent > half of periodic box length)
    To resolve this problem, wrote a script to identify the atoms/bond/angles/dihedrals and improper within a certain distance in top and bottom the z direction. This methods, produced a structure that was able to generate wave propagation, however, we are concerned about changing the physics and structure of the system. Additionally, since we are using the pppm solver a slab for our non periodic system with a factor of 2.0. The data showed some variations, and looking further, got a lil concerned with removal of bonds that may be exscaping in the slab area, but still being captured in the shock simulation.(So we resolved to not remove bonds and change the potential)

2> The second approach, we got rid of the slab approach, and modified the pairwise interaction to lj/cut as opposed to lj/long. Doubled checked the effect of changing the pairwise interactions, by running both NPT and NVT, and comparing the energy variations. Comparing the results, no major/alarming variations.

In this case, not trying to remove the bonds at all, to preserve the physics of the structure. I have tried to change the periodic structure to non-periodic using “boundary p p sm” and

using both

fix 2 all wall/piston zlo pos 0.0 0.0 0.0 vel 0.0 0.0 0.0 units box
fix 3 all wall/reflect zlo EDGE zhi EDGE units box.

And got the same error: Bond/angle/dihedral extent > half of periodic box length

Thus in all three cases, I have gotten the same error

You say that, lammps has no way to check which periodic image of atoms/bonds…etc to use, if that is the case, how does one determine what if. happening? I have no idea why this is happening and somehow not making sense to me, unless I am totally missing something. Any suggestions??

You don't say what your box size is, or which dims are periodic.
If you can just post your data file and input script which fails
immediately with this error, we can run it. It's a puzzling
error to me.

Steve