echo          screen
units          real                    
dimension      3                       
atom_style     full                    
neighbor         2.0 bin
neigh_modify     delay 0 every 1 check yes
boundary        p p s                   

bond_style       harmonic               
angle_style      harmonic                
dihedral_style   nharmonic
pair_style      lj/cut 12.5  
pair_modify      mix geometric 
pair_modify      shift yes mix geometric

        
read_data   msd400w.data

 
# Settings
dielectric       1.0

run_style        verlet
timestep       0.5
special_bonds    lj/coul 0 0 1 
reset_timestep 0

# Output
thermo_style     custom step vol density temp  
thermo           1000
thermo_modify    flush yes
 


reset_timestep 0
 

group poly type 1
group poly include molecule
group group2 subtract all poly


fix 01 poly nvt temp 300.0 300.0 100.0 
fix 02 group2  nvt temp 300.0 300.0 100.0 

velocity all create 300.0 12345
run 0                             # temperature may not be 300K
velocity all scale 300.0          # now it should be


compute         layers0 all chunk/atom bin/1d z lower 5 units box
fix       10   all ave/chunk 10 1000 10000 layers0 temp file temp00_profile.dat

dump 120 all custom 5000 all.lammpstrj id type mass mol  x y z

run 1000000


unfix 01 
unfix 02
unfix 10  




fix 01 all nvt temp 300.0 300.0 100.0 


fix       10   all ave/chunk 10 1000 10000 layers0 temp file temp010_profile.dat


dump 220 all custom 10000 allu.lammpstrj id type mass mol  xu yu zu

compute rou12 poly chunk/atom bin/1d z lower 0.1 units box
compute rou13 all chunk/atom bin/1d z lower 0.1 units box
fix rou12 poly ave/chunk 100 200 20000  rou12 density/mass file 1_densitypol.out
fix rou13 all ave/chunk 100 200 20000   rou13 density/mass file 1_densityall.out 


run   1000000