# DPD 3-d flow simulation

dimension          3
boundary           p p p

atom_style         atomic
units              lj
comm_modify        vel yes
neighbor           0.3 bin
neigh_modify       delay 5

# create geometry
lattice            fcc 1
region             box block 0 10 0 10 0 12
create_box         3 box
create_atoms       2 box

mass               1 1.0
mass               2 1.0
mass               3 1.0

# potentials
pair_style        dpd   1.0 2.5 419084618
pair_coeff        * *   25.0 4.5

# define groups
region            1 block INF INF INF INF INF 1
group             lower region 1
region            2 block INF INF INF INF 11 INF
group             upper region 2
group             boundary union lower upper
group             flow subtract all boundary

set	              group lower type 1
set	              group upper type 3

# initial velocities
compute           mobile flow temp
velocity          flow create 1.0 482748 temp mobile
fix               1 all nve
fix               2 flow temp/rescale 100 1.0 1.0 0.02 1.0
fix_modify        2 temp mobile

# Couette flow
velocity          upper set 3.0 0.0 0.0
velocity          lower set 0.0 0.0 0.0
fix               3 boundary setforce 0.0 0.0 0.0
fix	              4 flow addforce 0.5 0.0 0.0

# Run
timestep          0.005
thermo		      100
thermo_modify	  temp mobile

dump              1 all  atom  5  dump3.flow
run               5000

# Compute the diffusion coefficient

variable        dt equal 1.0


fix             5 all nvt temp 1.0 1.0 0.01

compute         msd all msd com yes
variable        twopoint equal c_msd[4]/6/(step*${dt}+1.0e-6)  
fix             9 all vector 10 c_msd[4]

variable        fitslope equal slope(f_9)/6/(10*${dt}) 
thermo_style	custom step temp press c_msd[4] v_twopoint v_fitslope 

thermo          1000
run             500000