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# 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
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