I’m trying to simulate the interaction of lj atoms with a solid wall.
I put a wall at the lower z-dimension using the wall/lj93 fix, and I also have a reflecting wall at the upper z-dimension using the wall/reflect fix.
The x, and y dimensions are periodic.
However I’m still losing atoms.
I thought periodic boundary conditions meant that atoms that leave through one end would wrap around to the other side of the cells in the periodic dimensions.
below is the input and output along with the error.
****Input
Lennard-Jones atoms interacting with 9-3 wall interaction
dimension 3
boundary p p f
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
create geometry
lattice fcc 0.01
region box block 0 20 0 22 -1.0 10.0
create_box 1 box
mass 1 1.0
create atoms
create_atoms 1 region box
LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
initial velocities
velocity all create 0.1 482748
fixes
fix 1 all nve
fix 2 all wall/lj93 zlo -2 1.0 1.0 2.5
fix 3 all wall/reflect zhi
Run
timestep 0.0025
thermo 1000
dump 1 all atom 500 dump.lennard_jones_substrate
run 20000