# =====================================
# Capillary filling of a CNT with water
# =====================================

# Typical input script used to investigate the dynamics
# of water uptake by a carbon nanotube, as detailed in: 
# L. Joly, J. Chem. Phys. 135, 214705 (2011)
# http://link.aip.org/link/doi/10.1063/1.3664622


# =======================================
# gamma coefficient of the DPD thermostat
# =======================================
variable        gamma equal 0.1  # eta ~ 0.3 mPa s, timestep = 2 fs

units           real
boundary        p p p
communicate     single vel yes

atom_style      full
bond_style      harmonic
angle_style     harmonic
pair_style      hybrid/overlay lj/cut/coul/long 14.0 10.0 dpd/tstat 300.0 300.0 10.0 38262
kspace_style    pppm 1.0e-4

read_data	data.cnt

pair_coeff      * * lj/cut/coul/long 0.086 3.4
pair_coeff      1 * lj/cut/coul/long 0.0 0.0
pair_coeff      5 8 lj/cut/coul/long 0.02330 3.275
pair_coeff      6*7 8 lj/cut/coul/long 0.1144 3.275
pair_coeff      8 8 lj/cut/coul/long 0.1521 3.151

pair_coeff      1 1 dpd/tstat ${gamma}
pair_coeff      1 8 dpd/tstat ${gamma}
pair_coeff      8 8 dpd/tstat ${gamma}

bond_coeff      1 0.0 0.9572
angle_coeff     1 0.0 104.5

group 	        water   type 1 8
group 	        oxygen  type 8
group           wall    type 5 6
group           plug    type 7

neighbor        2.0 bin
neigh_modify    delay 5
neigh_modify    exclude group wall wall
neigh_modify    exclude group wall plug
neigh_modify    exclude group plug plug

compute         Tliq water temp
compute         Tpar water temp/partial 1 1 0

fix             shakeh2o water shake 1.0e-4 200 0 b 1 a 1
fix             constnve water nve

# ===========================================================================
# output density profile and water mass inside the tube as a function of time
# ===========================================================================
fix	        dens oxygen ave/spatial 100 100 10000 z lower 1.0 density/number units box file rho.cnt
region          cnt cylinder z 0.0 0.0 20.3 0.0 98.4 units box
variable        ncnt equal count(oxygen,cnt)
region          eff cylinder z 0.0 0.0 18.7 -1.6 100.0 units box
variable        neff equal count(oxygen,eff)
region          cal cylinder z 0.0 0.0 20.3 25.0 75.0 units box
variable        ncal equal count(oxygen,cal)/50.0
fix             nmoy all ave/time 10 100 1000 v_ncnt v_neff v_ncal file nmoy.cnt

# =====================================================
# dump atom positions for visualization, e.g. using VMD
# =====================================================
dump            dumpwall wall xyz 10000000 dump.wall.xyz
dump_modify     dumpwall flush yes
dump            dumpwater water xyz 1000 dump.water.xyz
dump_modify     dumpwater flush yes

thermo_style    custom step cpu c_Tliq c_Tpar etotal
thermo          100
thermo_modify   flush yes

timestep        2.0
velocity        water create 300.0 34239
run             60000
write_restart   restart.eq

# ====================================
# remove the plug at the tube entrance
# ====================================
neigh_modify    exclude group plug all
run             240000