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.
Lennard-Jones atoms interacting with 9-3 wall interaction
boundary p p f
neighbor 0.3 bin
neigh_modify delay 5
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 1 region box
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
velocity all create 0.1 482748
fix 1 all nve
fix 2 all wall/lj93 zlo -2 1.0 1.0 2.5
fix 3 all wall/reflect zhi
dump 1 all atom 500 dump.lennard_jones_substrate