# LAMMPS Input File (License CC BY 4.0)

# By Simon Gravelle, Jacob R. Gissinger, and Axel Kohlmeyer

# The DOI will be added upon publication

# Find more on GitHub: https://github.com/lammpstutorials

# 1) Initialization

units lj

dimension 3

atom_style atomic

boundary p p p

# 2) System definition

pair_style lj/cut 4.0

read_data improved.min.data

region cyl_in cylinder z 0 0 10 INF INF side in

region cyl_out cylinder z 0 0 10 INF INF side out

group grp_t1 type 1

group grp_t2 type 2

group grp_in region cyl_in

group grp_out region cyl_out

group grp_t1_in intersect grp_t1 grp_in

group grp_t2_out intersect grp_t2 grp_out

delete_atoms group grp_t1_in

delete_atoms group grp_t2_out

# delete no longer needed groups

group grp_in delete

group grp_out delete

group grp_t1_in delete

group grp_t2_out delete

variable n1_in equal count(grp_t1,cyl_in)

variable n2_in equal count(grp_t2,cyl_in)

compute coor12 grp_t1 coord/atom cutoff 2.0 group grp_t2

compute sumcoor12 grp_t1 reduce ave c_coor12

# 3) Settings

# 4) Visualization

thermo 1000

thermo_style custom step temp pe ke etotal &

press v_n1_in v_n2_in c_sumcoor12

dump viz all image 1000 myimage-*.ppm type type &

shiny 0.1 box no 0.01 view 0 0 zoom 1.8 fsaa yes size 800 800

dump_modify viz adiam 1 1 adiam 2 3 acolor 1 &

turquoise acolor 2 royalblue backcolor white

# 5) Run

velocity all create 1.0 49284 mom yes dist gaussian

fix mynve all nve

fix mylgv all langevin 1.0 1.0 0.1 10917 zero yes

timestep 0.005

run 300000