# this input can be used to generate the benchmark for in.gaussianIC2d_hex_uniform
echo both
units    real
atom_style  atomic

variable l equal 8
variable g equal 2
variable lg equal $l+$g
variable w equal 2

lattice         fcc 5.405 origin 0.25 0.25 0.25
boundary  f f f

# region to create atoms
region		bigCyl cylinder z 0. 0. ${lg} -$w $w
region		offsetPlane block -${lg} $g -${lg} ${lg} -$w $w
region		mdRegion intersect 2 bigCyl offsetPlane
#create_box 1 mdRegion
pair_style  lj/cut 13.5
read_data	semicircle.init

# region for internal atoms
region     mdInternalCyl cylinder z 0. 0. $l -$w $w
region		leftHalfPlane block INF 0. INF INF INF INF
region		mdInternal intersect 2 mdInternalCyl leftHalfPlane

# region for coupling ghosts
region		rightHalfPlane block 0. INF INF INF INF INF
region		mdGhost union 2 rightHalfPlane mdInternal side out

#create_atoms 1 region mdRegion
#create_atoms 1 region mdInternal
#create_atoms 2 region mdGhost
#region	outerGhost intersect 2 rightHalfPlane mdRegion
#create_atoms 3 region outerGhost

#pair_style  lj/cut 13.5
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
#mass    1 39.95
#pair_coeff    1 1 .238 3.405 13.5
group    internal region mdInternal
group	 ghost region mdGhost
#velocity internal create 40 102486 mom yes rot yes dist gaussian
#write_restart semicircle_init.rst

# ATC commands
fix	AtC internal atc thermal Ar_ttm.mat
fix_modify	AtC boundary ghost
fix_modify	AtC mesh read semicircle.mesh  f f p 
fix_modify	AtC mesh nodeset_to_elementset 2 hole min
fix_modify	AtC internal_quadrature off
fix_modify	AtC time_integration fractional_step

# initial conditions
fix_modify	AtC fix temperature all 20.
fix_modify	AtC control thermal rescale 10
fix_modify      AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results

# initial output
#fix_modify	AtC mesh output semicircle_mesh
#fix_modify	AtC output semicircle_init 100 text binary
#dump		D1 all atom 100 semicircle_init.dmp

# run
timestep  5.0
thermo    100
run       500

# boundary conditions
fix_modify	AtC unfix temperature all
fix_modify	AtC fix temperature 1 20.
fix_modify	AtC control thermal flux
fix_modify	AtC control localized_lambda on

# NOTE appears to be a problem with the temporal ramp function
variable delta_t equal 1000*5.
fix_modify      AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t}

# equilibrate filter
fix_modify	AtC filter type exponential
fix_modify	AtC filter scale 1000.
fix_modify	AtC filter on

# equilibration output
fix_modify      AtC output semicircleFE 100 full_text #binary
#undump		D1
#dump            D1 all atom 100 semicircle_equil.dmp

# run
fix_modify	AtC reset_time 0.
reset_timestep  0
thermo 100
run    1000

# heat source
# NOTE second run omitted as it causes diffs in parallel execution after just one timestep, not sure why
#fix_modify	AtC source temperature hole 0.0000000001
#fix_modify      AtC output semicircleFE 1 full_text #binary
#undump          D1
#dump            D1 all atom 100 semicircle.dmp
#run    1#000