#===========================================================================#
# polymer test                                                              #
#                                                                           #
# Run consists of a lone 32-bead coarse-grained polymer                     #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid.            #
#                                                                           #
# Here, gamma (used in the calculation of the monomer-fluid interaction     #
#   force) is set by the user (gamma = 0.03 for this simulation...this      #
#   value has been calibrated a priori through simulations of the drag      #
#   force acting on a single particle of the same radius).                  #
# Sample output from this run can be found in the file:                     #
#   'dump.polymer.lammpstrj'                                                #
# and viewed using, e.g., the VMD software.                                 #
#                                                                           #
# Santtu Ollila                                                             #
# santtu.ollila@aalto.fi                                                    #
# Aalto University                                                          #
# August 14, 2013                                                           #
#===========================================================================#

units	   	nano
dimension	3
boundary	p p p
atom_style	hybrid molecular
special_bonds	fene
read_data	data.polymer

#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
#   to ensure that the particles belonging to a given processor remain inside
#   that processors lattice-Boltzmann grid.
#----------------------------------------------------------------------------
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1

#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
#   each monomer (use a truncated and shifted Lennard-Jones potential).
#----------------------------------------------------------------------------
bond_style	fene
bond_coeff	1 60.0 2.25 4.14195 1.5
pair_style	lj/cut 1.68369
pair_coeff	1 1 4.14195 1.5 1.68369
pair_coeff	1 2 4.14195 1.5 1.68369
pair_coeff	2 2 0 1.0

mass * 0.000000771064
timestep 0.00003

#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which
#   do not interact with the fluid, but are used to implement the hard-sphere
#   interactions.
# FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2

#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
#   (however, this fix does not explicitly apply a force back on to these
#    particles. This is accomplished through the use of the rigid_pc_sphere
#    fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
#   this integration scheme should be used when a large user set value for
#   gamma is specified), a fluid viscosity = 0.023333333,
#   fluid density= 0.0000166368,
#   value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
#   seed=15003).  This enables the particles to undergo Brownian motion in
#   the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003

#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
#   motion, constraining them to move and rotate together as a single rigid
#   spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
#   shell) should move and rotate together, this fix is applied to all of
#   the atoms in the system.  However, since the central atoms should not
#   feel a force due to the fluid, they are excluded from the force
#   calculation through the use of the 'innerNodes' keyword.
# NOTE: This fix should only be used when the user specifies a value for
#   gamma (through the setGamma keyword) in the lb_fluid fix.
#----------------------------------------------------------------------------
fix   2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms

#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
#   system, the momentum_lb fix is used every 10000 timesteps to zero out the
#   total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix   3 all lb/momentum 10000 linear 1 1 1

#----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------

dump		1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz
run		2000001