Densify a PLA - Aluminum Interface

LAMMPS LAMMPS General Discussion
1

Hello dear all,

I want to model PLA - Aluminum interface using the PCFF - IFF forcefield. I have correctry -I think- set the potential parameters to the same unit system to avoid mistakes. My general methodology is the following:

  1. Create a relatevely large box periodic in x, y and fixed boundary in z.
  2. Create an aluminum latice in the botomm
  3. Random pack PLA molecules on top of the Al latice
  4. Slowly compress in z direction to densify the box and then perform polymerisation.

I have succesfully created the initial box with all atoms in place. To avoid atoms crossing the boundaries I tgought to have two small vaccum slabs in a small distance from the zlo and zhi boundaries. To create that vaccum I found out in the documantation and in the forum that I can create “virtual enegy walls” with the comand:

fix wall/reflect

I have created two regions one on top and one on the bottom of the simulation box in order to use their outside surface as a wall to compress the system. The simulation is working but I face some issues.

First I get ofteth the lost atoms error in lammps so that maybe indicates large forces in the simulation wall. I saw in the documentantion that

Convex points/edges are like the corners of a cube as seen by particles exterior to the cube, i.e. the points jut into the volume where particles are present. LAMMPS does NOT compute the location of these convex points directly, and hence wall/particle forces in the cutoff volume around these points suffer from inaccuracies. The basic problem is that the outward normal of the surface is not continuous at these points. This can cause particles to feel no force (they don’t “see” the wall) when in one location, then move a distance epsilon, and suddenly feel a large force because they now “see” the wall. In a worst-case scenario, this can blow particles out of the simulation box. Thus, as a general rule you should not use the fix wall/gran/region command with union or interesect regions that have convex points or edges resulting from the union/intersection (convex points/edges in the union/intersection due to a single sub-region are still OK).

I do not think that is my case.

Second how to be sure that the parameters of the 126lj wall are corect. In my mind I just try different parameters just to ensure that it is ok but if there is a better way I would like to know.

I attatch my files for clearance.

Thanks in advance!

force_field.data (28.1 KB)
in.initial_structure (5.4 KB)
PLA_trimer_typed_IFF_merged.lmpmol (11.2 KB)
Al_jnp_real.eam (20.2 KB)