#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.
log bar1d_fluids.log
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
#read_restart	post_eq.dat
lattice         fcc 5.405 origin 0.25 0.25 0.25
# create atoms, NOTE commented out for restart
#region		mdRegion block -7 7 -3 3 -3 3
#boundary	f p p
#create_box	2 mdRegion
#create_atoms	1 region mdRegion
#mass		* 39.95
# specify interal/ghost atoms
#region		mdInternal block -6 6 -3 3 -3 3
#region		mdGhost block -6 6 -3 3 -3 3 side out
#create_atoms    1 region mdGhost
#lattice         fcc 6.5 origin 0.25 0.25 0.25
#create_atoms	2 region mdInternal
group		internal type 2
group		ghost type 1
# velocities have Vcm = 0, NOTE next four lines commented out for restart
#velocity	internal create 100. 87287 mom yes loop geom
#pair_style	lj/cut 13.5
##pair_coeff	1 1 0.010323166 3.405 13.5
#pair_coeff  	* * .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
lattice         fcc 5.405 origin 0.25 0.25 0.25
region		atcRegion block -6.25 6.25 -3 3 -3 3
fix             AtC internal   atc thermal     Ar_thermal.mat
#               ID  part keywords    nx ny nz region    periodicity
fix_modify      AtC mesh create 6 1  1   atcRegion f p p
fix_modify      AtC time_integration fractional_step
fix_modify	AtC atom_element_map eulerian 10 # NOTE this introduces a minor amount of time integration error tracking the atomic temperature
fix_modify      AtC  internal_quadrature off
#fix_modify	AtC  mass_matrix fe
# fix a temperature
fix_modify     	AtC  fix temperature all 100.
# add nodesets
#               ID  mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify      AtC mesh create_nodeset lbc -6.3 -6.2   -INF  INF   -INF  INF
fix_modify      AtC mesh create_nodeset rbc  6.2  6.3   -INF  INF   -INF  INF
#fix_modify      AtC  fix temperature lbc 120.
#fix_modify      AtC  fix temperature rbc 100.
#used for restarting
#fix_modify	AtC  consistent_fe_initialization on
#fix_modify     AtC  initial temperature all 100.
# turn on thermostat
fix_modify	AtC control  thermal rescale 10
# equilibrate MD field
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
#fix_modify      AtC  output bar1d_fluids_eqFE 200 text binary
#dump            D1 all atom 200 dump_eq.bar1d
timestep	2
thermo		200
run 		2000
#write_restart	post_eq.dat
# change thermostat to hoover
reset_timestep 0
fix_modify	AtC  reset_time
fix_modify      AtC  unfix temperature all
variable deltaT equal 2.*2000.
fix_modify      AtC  fix temperature lbc temporal_ramp 100. 120. ${deltaT}
#fix_modify	AtC  fix temperature lbc 100.
fix_modify      AtC  fix temperature rbc 100.
fix_modify      AtC control thermal flux no_boundary
fix_modify	AtC control tolerance 1.e-14
fix_modify	AtC control localized_lambda on
fix_modify      AtC  filter type exponential
fix_modify      AtC  filter scale 1000.0
fix_modify      AtC  filter on
# output commands
fix_modify      AtC  output bar1d_fluidsFE 100 text
#undump          D1
#dump		D2 all atom 200 dump.bar1d
#dump		D2 all custom 200 dump.bar1d id type xs ys zs vx vy vz
# set-up non-equilibrium IC
thermo		100
run 		2000
# run non-equilibrium condition
fix_modify	AtC  fix temperature lbc 120.
run		4000