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