#AtC Thermal Coupling
# This benchmark tests heat conducting into and out of the MD region.  The
# temperature is initially 20 everywhere and the left boundary BC is fixed at
# 40.# The result should show heat diffusing through the FEM to the MD and back
# out # to the FEM on the right.  Insufficient time is captured to reach the
# linear # steady state, but heat crossing both boundaries should be observed.
units		real
atom_style	atomic
# create domain
#lattice	type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
# NOTE following 3 lines added for restart
boundary        f p p
pair_style      lj/cut 13.5
read_data       temp.init
lattice         fcc 5.405 origin 0.25 0.25 0.25
region		simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart
#region		mdRegion block -5 5 -3 3 -3 3
#boundary	f p p
#create_box	1 mdRegion
#create_atoms	1 region mdRegion
#mass		1 39.95
# specify interal/ghost atoms
region		mdInternal block -4 4 -3 3 -3 3
group		internal region mdInternal
group		ghost subtract all internal
# velocities have Vcm = 0, NOTE next three lines commented out for restart
#velocity	internal create 40. 87287 mom yes loop geom
#pair_style	lj/cut 13.5
#pair_coeff  	1 1 .238 3.405 13.5
neighbor	5. bin
neigh_modify	every 10 delay 0 check no
#               ID  group atc PhysicsType ParameterFile
fix             AtC internal   atc thermal     Ar_thermal.mat
fix_modify      AtC boundary ghost
# numerical parameters
fix_modify	AtC time_integration fractional_step
#               ID  part keywords    nx ny nz region
fix_modify      AtC mesh create 12 1  1  simRegion f p p
fix_modify      AtC mesh create_faceset ibndy box -4.0 4.0 -INF INF -INF INF in
fix_modify      AtC mesh create_faceset obndy box -4.0 4.0 -INF INF -INF INF outward
# fix a temperature
fix_modify     	AtC  fix temperature all 20.
#fix_modify	AtC  fix temperature all linear 0 0 0 -0.154 0 0 30.
#fix_modify	AtC  fix temperature all quadratic 0 0 0 -0.154 0 0 30. 0.01 0.0 0.0 0 0 0 
# turn on thermostat
fix_modify	AtC  control thermal rescale 10
# equilibrate MD field
#fix_modify      AtC  output bar1dfe_flux_init 100
timestep	5
variable xdof equal 3*count(ghost)
compute_modify thermo_temp extra ${xdof}
thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2]
thermo_modify  format 1 %6i format 2 %7.2g
thermo		100
run 		400
# change thermostat to hoover
fix_modify	AtC  unfix temperature all
fix_modify	AtC  control thermal none
fix_modify	AtC  control thermal flux interpolate
fix_modify	AtC  control localized_lambda on
#fix_modify	AtC  thermal control flux faceset obndy
fix_modify      AtC  filter type exponential
fix_modify	AtC  filter scale 10000.0
fix_modify	AtC  filter on
# add nodesets
#               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify      AtC mesh create_nodeset lbc -12.1  -11.9   -INF INF   -INF INF
fix_modify      AtC mesh create_nodeset rbc  11.9   12.1   -INF INF   -INF INF
fix_modify      AtC  fix temperature lbc 40.
fix_modify      AtC  fix temperature rbc 20.
# initialize filter
run		100
# set up output, should be before a "run"
fix_modify      AtC  output bar1d_interpolateFE 100 text
# run with FE
reset_timestep 0
thermo		100
#run 		10
run 		10000