# virtual atomic force microscope demo
# $Id $
dimension	3
units		lj
atom_style	molecular
bond_style	harmonic
angle_style harmonic
boundary	s s s
newton		on off  # apply newton's 3rd law only for nonbonded.
special_bonds lj/coul 0.0 0.0 1.0

# override original processor grid for maximum performance.
# since there are few atoms in y direction we don't want
# to do domain decomposition in that direction. so optimally
# is should be set to that the middle number is always 1.
# use this for 6 CPUs
#processors  3 1 2
# use this for 7 CPUs
processors  1 1 7

# we are pushing the limits with the time step,
# make sure we don't miss neighbor list updates.
neighbor	0.45 bin
neigh_modify delay 2 every 1 check yes 

# an fcc lattice will be our base lattice
# not really needed with a data file, but...
lattice		fcc 0.9

# system definition
read_data data.afm-plus

# atom masses.
mass	1	 1.0   # substrate, doesn't move so mass doesn't matter.
mass	2	 1.0   # light, soft atoms => liquid.
mass	3	 5.0   # medium weight, medium hard atoms => soft solid.
mass	4	25.0   # heavy, hard atoms => hard solid.
mass	5    0.005 # tip atoms. have to be very light, so we can "feel" something.
mass    6    1.0   # buckyballs.

# surface and buckballs are integrated normally.
group mobile type 2 3 4 6 
velocity mobile create 0.6 46659 mom yes rot yes dist gaussian

# temperature is based on mobile atoms only
compute mobtemp mobile temp

# contain mobile atoms within the original simulation cell
fix bounds  all wall/lj93  xlo -16.0 1.0 1.7 1.36 xhi 16.0 1.0 1.7 1.36 &
                           ylo -16.0 1.0 1.7 1.36 yhi 10.0 1.0 1.7 1.36 &
                           zlo -16.0 1.0 1.7 1.36 zhi 16.0 1.0 1.7 1.36 &
                           units lattice

# make probe rigid and keep it from rotating.
group afm type 5
fix afmtip afm rigid group 1 afm torque * off off off
velocity afm set 0.0 0.0 0.0

# damping through friction makes the probe much easier
# to control and keeps it in place if not grabbed.
fix dampen afm viscous 0.02
# with bouncing walls we need to slow down regular atoms, too
fix frict mobile viscous 0.05

pair_style  lj/cut 2.5
# GPU version dies in cell list.
#pair_style  lj/cut/gpu one/node 1 3.0
pair_coeff  * *  1.0 1.05 
pair_coeff	3 3  2.0 1.05 
pair_coeff	4 4  3.0 1.05 
pair_coeff  6 6  0.2 1.05

# reset parameters for interactions with the tip 
# and make tip atoms a bit hard and large and
# mostly repulsive so that they are more "feely" 
# (not physically correct, but much nicer).
pair_coeff	1 5  3.0 1.30 1.50
pair_coeff	2 5  3.0 1.30 1.50
pair_coeff	3 5  3.0 1.30 1.50
pair_coeff	4 5  3.0 1.30 1.50
pair_coeff	5 6  3.0 1.30 1.50

# buckballs are purely repulsive with 
# type 2 atoms to make them float on top.
pair_coeff  2 6  0.6 1.05 1.178

# buckball bonded parameters, adapted from CHARMM benzene.
bond_coeff	1	340.0   0.72
angle_coeff	1	570.0 120.00 

#
run_style respa 2 3 bond 1 angle 1 dihedral 1 pair 2
timestep	0.015
# use verlet for smoother interactions through higher TimeS/S, 
# but slower progress
#run_style verlet
#timestep   0.005 

fix		integrate 	mobile nve
fix		thermostat	mobile langevin 0.5 0.5 10.0 699483 

thermo_style	custom step pe ke evdwl emol c_mobtemp tpt tps
thermo		    1000
thermo_modify	norm yes
thermo_modify	temp mobtemp

#write_restart	afm-plus.restart

#dump traj all atom 100 afm-plus.lammpstrj
fix  comm       all imd 6789 unwrap off trate 10
#run		10000 
# XXX: need to correct fix imd to handle multiple runs.
run		5000000000