Lost atoms

I am simulating a lattice and using periodic boundary conditions in x and y and fixed boundary condition in z direction. I have also considered making my simulation cell a bit larger in z-direction to give the atoms some room to vibrate. But still I find atoms get lost .

I first equilibrated the sample my using NPT ensemble as shown:

fix 4 all npt temp 1000 1000 1.0 x 0.0 0.0 1.0 y 0.0 0.0 1.0 couple xy
run 50000

During equilibration no atoms lost

Then heating the sample from 1000K to 3500 K using NPT as :
fix 5 all npt temp 1000 3500 1.0 x 0.0 0.0 100.0 y 0.0 0.0 100.0 couple xy
run 1000000

Time step is 0.5 fms

You don’t give enough info to comment.

The LAMMPS manual (error section for your error message) explains many

ways atoms can be lost.


This is what I would expect. At these elevated temperatures, even if the solid remains unmelted, it is very likely that one or more atoms are ejected from the free surfaces and manage to cross the fixed boundary. I suggest you run with shrink-wrapped boundary until you understand your system better.