I want to delete some atoms from a simulation box, I was working with the LAMMPS granular modules. The code is shown below.
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
comm_modify vel yes
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran hooke/history 2000.0 NULL 50.0 NULL 0.5 0 &
zplane 0.0 2000.0
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
region void block -10 0 -10 10 -0.5 14 units box
delete_atoms region void
#fix 10 all indent 0.1 plane x 14.5 lo
compute 1 all erotate/sphere
compute 3 all voronoi/atom neighbors yes peratom yes
compute 4 all coord/atom cutoff 1.00
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic/dof yes
dump id all atom 200 dump.pour
dump 1 all custom 200 positions.lammpstrj id x y z vx vy vz diameter
#dump id all atom 1000 dump.pour
#dump 2 all image 1000 image.*.jpg type type &
# axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type &
# axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 25000
unfix ins
#fix 2 all gravity 1.0 chute 26.0
run 25000
But no atoms are deleted from the simulation box. May I get any idea of how to delete these atoms?
I am also attaching a screenshot of my desired atom deletion.
