
# LAMMPS supports a large number of force-field styles. We must select
# which ones we need. This information belongs in the "In Init" section (and
# (you can specify it anywhere in your LT files, multiple times if you like).
# If different molecules use different force-field styles, you can use hybrid
# styles.  (In this example the molecules share the same pair_style.)

write_once("In Init") {
  units           real
  atom_style      full
  bond_style      harmonic
  angle_style     harmonic
  dihedral_style  opls
  pair_style      lj/cut 9.0
  # If you have charged molecules immersed in a salty implicit
  # solvent, you might try something like this this instead:
  #    pair_style      lj/cut/coul/debye 0.1 9.0
  pair_modify     mix arithmetic
  dielectric      80.0
  special_bonds   lj 0.0 0.0 0.0
}


write_once("Data Boundary") {
  0.0 36.0 xlo xhi
  0.0 36.0 ylo yhi
  0.0 36.0 zlo zhi
}


import "solvent.lt"

import "walls.lt"

import "polymer.lt"

polymer = new Polymer
polymer.rot(-90.0, 0,0,1)    # rotate it -90 degrees around the Y axis
polymer.move(19.5,22.5,16.5) # move it near the openning of the hole



####################### Notes: #########################
#
# In this example we deleted solvent and wall molecule objects.
# You can also delete a monomer inside the polymer.  To do that use:
#   delete polymer/monomers[6]
# You can also delete individual atoms, bonds, angles, dihedrals, & impropers
# from existing molecules.  For example to delete an atom in the middle 
# of the polymer try this.  (Bonds and other interactions will also be removed.)
#   delete polymer/monomers[6]/CA
# To delete a bond, try this
#   delete polymer/bb6
# Note: This will not delete the angular interactions. Delete them manually
# Note: In both cases the two molecule fragments will keep the same mol counter.
