#AtC Thermal Coupling
# This benchmark tests heat conducting into an MD region at a fixed temperature at one end.  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 the boundaries should be observed,
# as should the interaction of the two themostat types.
#echo both
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 -16 4 -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
region		mdGhost block -5 -4 -3 3 -3 3
group		ghost region mdGhost
# velocities have Vcm = 0, NOTE next four lines commented out for restart
#velocity	internal create 40. 87287 mom yes loop geom
#pair_style	lj/cut 13.5
##pair_coeff	1 1 0.010323166 3.405 13.5
#pair_coeff  	1 1 .238 3.405 13.5
neighbor	5. bin
neigh_modify	every 10 delay 0 check no
#write_restart	tinit.dat
#               ID  group atc PhysicsType ParameterFile
fix             AtC internal   atc thermal     Ar_thermal.mat
fix_modify      AtC boundary ghost
fix_modify      AtC time_integration fractional_step
fix_modify	AtC internal_quadrature off
#               ID  part keywords    nx ny nz region
fix_modify      AtC mesh create 10 1  1  simRegion f p p
fix_modify      AtC mesh create_faceset ibndy box -4.0 40.0 -INF INF -INF INF in
fix_modify      AtC mesh create_faceset obndy box -4.0 40.0 -INF INF -INF INF outward
# fix a temperature
fix_modify     	AtC  fix temperature all 20.
# turn on thermostat
fix_modify	AtC  control thermal rescale 10
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
# equilibrate MD field
#fix_modify      AtC  output bar1dfe_combined_init 100
timestep	5
thermo		10
run 		400
# change thermostat to flux
fix_modify	AtC unfix temperature all
fix_modify  	AtC control thermal flux faceset obndy 
#fix_modify	AtC control thermal hoover
fix_modify	AtC control localized_lambda on
#fix_modify      AtC  control tolerance 1.e-16 # this tolerance seems necessary to prevent noticeable drift
# add nodesets
#               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify      AtC mesh create_nodeset lbc -16.1  -15.9   -INF INF   -INF INF
fix_modify      AtC mesh create_nodeset rbc  3.9   4.1   -INF INF   -INF INF
fix_modify      AtC  fix temperature lbc 40.
fix_modify      AtC  fix temperature rbc 20.

# equilibrate filter
fix_modify      AtC  filter type exponential
fix_modify      AtC  filter scale 1000.0
#fix_modify      AtC  filter on
thermo		100
#run		100

# set up output, should be before a "run"
fix_modify      AtC  output bar1d_combinedFE 100 text
# ouput command
#dump            D1 all atom 100 dump.bar1d_combined
# run with FE
reset_timestep 0
thermo		100
run 		5000