# This is a small version of a carbon-nanotube, water capillary system.  It was
# inspired by this paper: Laurent Joly, J. Chem. Phys. 135(21):214705 (2011)

import "graphene_walls.lt"

import "nanotube.lt"

import "water_box.lt"


# ------------ boundary conditions ------------

write_once("Data Boundary") {
 -15.98682895386 15.98682895386  xlo xhi
 -14.91          14.91           ylo yhi
    0.0          80.00           zlo zhi
}

# ---------------------------------------------



write_once("In Init") {
  # -- override any earlier pair_style settings: --
  # If some of the junction carbon atoms have non-zero partial charge, try this
  #pair_style  hybrid  lj/charmm/coul/long 10.0 10.5 10.5

  # If all graphened atoms have zero charge, you can use this:
  pair_style  hybrid  lj/charmm/coul/long 10.0 10.5 10.5 &
                      lj/cut  10.0

  # I was too lazy to figure out what these partial charges would be, so I set
  # them to zero, but a serious investigation into carbon-nanotube-graphene
  # junctions would adjust the charge and geometry of the boundary atoms.
}


write_once("In Settings") {
  # --- We must eventually specify the interactions between the atoms ---
  # --- in different molecule types (graphene-water interactions).    ---
  # (See Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) for details

  pair_coeff @atom:Graphene/C @atom:SPCE/O lj/charmm/coul/long 0.114 3.28
  pair_coeff @atom:Graphene/C @atom:SPCE/H lj/charmm/coul/long 0.0   3.28
}

