LAMMPS (30 Aug 2013)
units    real
atom_style  atomic

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

lattice         fcc 5.405 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.405 5.405 5.405
boundary  f f f

# region to create atoms
region		bigCyl cylinder z 0. 0. ${lg} -$w $w
region		bigCyl cylinder z 0. 0. 10 -$w $w
region		bigCyl cylinder z 0. 0. 10 -2 $w
region		bigCyl cylinder z 0. 0. 10 -2 2
region		offsetPlane block -${lg} $g -${lg} ${lg} -$w $w
region		offsetPlane block -10 $g -${lg} ${lg} -$w $w
region		offsetPlane block -10 2 -${lg} ${lg} -$w $w
region		offsetPlane block -10 2 -10 ${lg} -$w $w
region		offsetPlane block -10 2 -10 10 -$w $w
region		offsetPlane block -10 2 -10 10 -2 $w
region		offsetPlane block -10 2 -10 10 -2 2
region		mdRegion intersect 2 bigCyl offsetPlane
#create_box 1 mdRegion
pair_style  lj/cut 13.5
read_data	semicircle.init
Reading data file ...
  orthogonal box = (-54.05 -54.05 -10.81) to (10.81 54.05 10.81)
  2 by 2 by 1 MPI processor grid
  3168 atoms
  3168 velocities

# region for internal atoms
region     mdInternalCyl cylinder z 0. 0. $l -$w $w
region     mdInternalCyl cylinder z 0. 0. 8 -$w $w
region     mdInternalCyl cylinder z 0. 0. 8 -2 $w
region     mdInternalCyl cylinder z 0. 0. 8 -2 2
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
1624 atoms in group internal
group	 ghost region mdGhost
904 atoms in group ghost
#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
ATC: constructing thermal coupling with parameter file Ar_ttm.mat
 ATC: version 2.0
 ATC: peratom PE compute created with ID: 3
 ATC: 2 materials defined from Ar_ttm.mat
fix_modify	AtC boundary ghost
fix_modify	AtC mesh read semicircle.mesh  f f p
 ATC: read 398 nodes
 ATC: read 176 HEX8 elements
 ATC: P1, writing periodicity corrected mesh: periodic_semicircle.mesh
 ATC: P3, writing periodicity corrected mesh: periodic_semicircle.mesh
 ATC: condensed 199 periodic nodes in the 3 direction
 ATC: created nodeset 1 with 44 nodes
 ATC: created nodeset 2 with 4 nodes
 ATC: P2, writing periodicity corrected mesh: periodic_semicircle.mesh
 ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive
 ATC: P0, writing periodicity corrected mesh: periodic_semicircle.mesh
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
Setting up run ...
Memory usage per processor = 52.3462 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    20.498895   -5250.6971            0   -5057.1829   -1088.0506 
     100    10.255763   -5131.7808            0   -5034.9641   -671.92179 
     200    10.255763   -5194.8934            0   -5098.0766   -664.20614 
     300    10.255763   -5191.6455            0   -5094.8288   -564.44341 
     400    10.255763   -5185.5031            0   -5088.6864   -611.34498 
     500    10.255763   -5185.1021            0   -5088.2853   -686.81479 
Loop time of 9.08358 on 4 procs for 500 steps with 3168 atoms

Pair  time (%) = 2.5019 (27.5431)
Neigh time (%) = 0.0543029 (0.597814)
Comm  time (%) = 0.724279 (7.97349)
Outpt time (%) = 0.000456929 (0.00503028)
Other time (%) = 5.80264 (63.8806)

Nlocal:    792 ave 944 max 640 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:    860 ave 888 max 832 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs:    95743.8 ave 114417 max 76793 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs:  191488 ave 228943 max 153856 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 765950
Ave neighs/atom = 241.777
Neighbor list builds = 5
Dangerous builds = 0

# 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}
fix_modify      AtC source temperature hole temporal_ramp 0. 0.0000000001 5000

# 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
 ATC: Warning : text output can create _LARGE_ files
 ATC: output custom names:

#undump		D1
#dump            D1 all atom 100 semicircle_equil.dmp

# run
fix_modify	AtC reset_time 0.
reset_timestep  0
thermo 100
run    1000
Setting up run ...
Memory usage per processor = 65.9216 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    10.255763   -5185.1021            0   -5088.2853   -686.81479 
     100    9.9160769   -5177.6646            0   -5084.0545   -753.44628 
     200    10.215779   -5182.5539            0   -5086.1147   -721.64916 
     300    10.609664   -5183.8798            0   -5083.7222   -672.99308 
     400    10.754797   -5188.6804            0   -5087.1527   -620.77678 
     500    10.271869   -5184.1487            0     -5087.18   -643.71337 
     600    10.214975   -5184.0211            0   -5087.5894   -687.47365 
     700    10.231487    -5182.315            0   -5085.7274   -719.65308 
     800    10.245262   -5181.8268            0   -5085.1092   -707.19351 
     900    10.342331   -5183.9012            0   -5086.2673   -667.21622 
    1000    10.446039   -5184.9612            0   -5086.3482   -647.13367 
Loop time of 25.9666 on 4 procs for 1000 steps with 3168 atoms

Pair  time (%) = 4.93896 (19.0204)
Neigh time (%) = 0.0919983 (0.354294)
Comm  time (%) = 1.34195 (5.16797)
Outpt time (%) = 0.0565627 (0.217828)
Other time (%) = 19.5372 (75.2395)

Nlocal:    792 ave 944 max 640 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:    860 ave 888 max 832 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs:    95600.8 ave 114809 max 76836 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs:  191202 ave 228917 max 153483 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 764806
Ave neighs/atom = 241.416
Neighbor list builds = 8
Dangerous builds = 0

# 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
