LAMMPS (30 Aug 2013) units metal variable INF equal 1000 variable T equal 20 atom_style atomic lattice fcc 5.405 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 5.405 5.405 5.405 region FE block -8 8 -6 6 0 3 region MD block -7 7 -6 0 0 3 region FREE block -4 4 -6 0 0 3 boundary f f p # create atoms #create_box 1 FE #create_atoms 1 region MD #group internal region FREE #mass 1 39.95 #read_data cutout.data #pair_coeff * * .238 3.405 13.5 #velocity internal create 40 87287 mom yes loop geom #fix NVE internal nve #thermo 100 #dump CONFIG all atom 100 cutout.dump ##run 1000 #unfix NVE #write_restart cutout.rst pair_style lj/cut 13.5 read_data cutout.init Reading data file ... orthogonal box = (-43.24 -32.43 0) to (43.24 32.43 16.215) 2 by 2 by 1 MPI processor grid 1008 atoms 1008 velocities group internal region FREE 576 atoms in group internal group ghost subtract all internal 432 atoms in group ghost timestep 0.002 thermo 20 # allow initial state to relax fix NVT internal nvt temp $T $T 10 drag 0.2 fix NVT internal nvt temp 20 $T 10 drag 0.2 fix NVT internal nvt temp 20 20 10 drag 0.2 fix RESCALE internal temp/rescale 25 $T $T 0.05 1.0 fix RESCALE internal temp/rescale 25 20 $T 0.05 1.0 fix RESCALE internal temp/rescale 25 20 20 0.05 1.0 run 200 Setting up run ... Memory usage per processor = 2.20651 Mbytes Step Temp E_pair E_mol TotEng Press 0 22.840119 -1789.5949 0 -1786.6219 -15765.333 20 13.566839 -1788.3853 0 -1786.6194 -15277.27 40 33.553913 -1791.7417 0 -1787.3741 -14707.846 60 19.256223 -1794.1032 0 -1791.5967 -14029.132 80 13.368297 -1796.2574 0 -1794.5173 -13523.457 100 11.42006 -1798.2698 0 -1796.7833 -13103.079 120 21.491111 -1799.819 0 -1797.0216 -12688.96 140 16.977999 -1801.1896 0 -1798.9797 -12265.345 160 13.938224 -1802.0525 0 -1800.2382 -11790.033 180 12.23396 -1802.7 0 -1801.1076 -11276.872 200 11.42006 -1803.1286 0 -1801.6421 -10730.804 Loop time of 0.502293 on 4 procs for 200 steps with 1008 atoms Pair time (%) = 0.237447 (47.2725) Neigh time (%) = 0 (0) Comm time (%) = 0.253115 (50.3918) Outpt time (%) = 0.000676036 (0.13459) Other time (%) = 0.0110559 (2.20109) Nlocal: 252 ave 504 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 1368 ave 1656 max 1080 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 36492 ave 74116 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 145968 Ave neighs/atom = 144.81 Neighbor list builds = 0 Dangerous builds = 0 unfix RESCALE run 800 Setting up run ... Memory usage per processor = 2.20651 Mbytes Step Temp E_pair E_mol TotEng Press 200 11.42006 -1803.1286 0 -1801.6421 -10730.804 220 12.634668 -1803.4525 0 -1801.8079 -10188.88 240 12.389545 -1803.5125 0 -1801.8998 -9656.8881 260 11.317877 -1803.4182 0 -1801.945 -9236.1616 280 9.7270274 -1803.2416 0 -1801.9754 -8947.2355 300 7.9370805 -1803.0419 0 -1802.0087 -8750.7074 320 6.4067491 -1802.861 0 -1802.027 -8623.9069 340 5.3573492 -1802.7311 0 -1802.0338 -8577.8953 360 4.9188235 -1802.6872 0 -1802.0469 -8637.0036 380 4.8156229 -1802.6667 0 -1802.0399 -8806.2763 400 5.0090105 -1802.6545 0 -1802.0025 -9077.449 420 5.6421616 -1802.6821 0 -1801.9477 -9435.9659 440 6.5180667 -1802.7415 0 -1801.8931 -9843.0718 460 7.8021978 -1802.8463 0 -1801.8307 -10243.525 480 9.1986451 -1802.9578 0 -1801.7604 -10581.685 500 10.560896 -1803.0497 0 -1801.675 -10833.653 520 11.604474 -1803.1302 0 -1801.6197 -11011.347 540 11.844791 -1803.1128 0 -1801.571 -11122.58 560 11.304866 -1803.0402 0 -1801.5687 -11161.742 580 9.8313387 -1802.8722 0 -1801.5925 -11124.258 600 7.7333706 -1802.6641 0 -1801.6575 -11030.299 620 5.3793592 -1802.408 0 -1801.7078 -10901.73 640 3.3272825 -1802.1725 0 -1801.7394 -10761.774 660 2.0314815 -1802.0222 0 -1801.7578 -10622.656 680 2.0077988 -1802.0353 0 -1801.7739 -10487.867 700 3.3843921 -1802.2247 0 -1801.7842 -10372.664 720 5.9780298 -1802.565 0 -1801.7869 -10302.637 740 9.0173322 -1802.9596 0 -1801.7858 -10280.842 760 11.766779 -1803.3181 0 -1801.7865 -10288.676 780 13.733393 -1803.5291 0 -1801.7415 -10302.17 800 14.164962 -1803.566 0 -1801.7222 -10302.618 820 12.863097 -1803.4368 0 -1801.7625 -10272.719 840 10.393884 -1803.1903 0 -1801.8374 -10192.543 860 7.4184997 -1802.8426 0 -1801.877 -10058.512 880 4.3613644 -1802.4882 0 -1801.9205 -9897.1119 900 2.2361845 -1802.2402 0 -1801.9491 -9736.3308 920 1.7719305 -1802.1979 0 -1801.9672 -9590.9833 940 2.9237629 -1802.3563 0 -1801.9757 -9472.0013 960 5.061993 -1802.6395 0 -1801.9806 -9381.0823 980 7.6242849 -1802.9731 0 -1801.9807 -9319.9173 1000 10.04544 -1803.2677 0 -1801.9601 -9298.5324 Loop time of 2.04514 on 4 procs for 800 steps with 1008 atoms Pair time (%) = 0.971291 (47.4926) Neigh time (%) = 0 (0) Comm time (%) = 1.03072 (50.3986) Outpt time (%) = 0.00227565 (0.111271) Other time (%) = 0.0408522 (1.99752) Nlocal: 252 ave 504 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 1368 ave 1656 max 1080 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 37230.2 ave 75593 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 148921 Ave neighs/atom = 147.739 Neighbor list builds = 0 Dangerous builds = 0 unfix NVT # ID group atc PhysicsType ParameterFile fix AtC internal atc two_temperature Ar_ttm.mat ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: WARNING: material units real do not match lammps ATC: WARNING: material units real do not match lammps ATC: 2 materials defined from Ar_ttm.mat ATC: creating two_temperature extrinsic model ATC: WARNING: material units real do not match lammps ATC: WARNING: material units real do not match lammps ATC: 2 materials defined from Ar_ttm.mat # ID part keywords nx ny nz region fix_modify AtC mesh create 8 6 1 FE f f p ATC: created uniform mesh with 126 nodes, 63 unique nodes, and 48 elements fix_modify AtC mesh create_elementset wire -4 4 -INF 0 -INF INF ATC: created elementset wire with 12 elements fix_modify AtC mesh create_nodeset gap -4 4 -0 INF -INF INF ATC: created nodeset gap with 20 nodes fix_modify AtC mesh create_elementset gap -4 4 -0 INF -INF INF ATC: created elementset gap with 12 elements fix_modify AtC mesh delete_elements gap fix_modify AtC mesh create_faceset bndy box -4 4 -INF 0 -INF INF ATC: created faceset bndy with 10 faces fix_modify AtC control thermal flux faceset bndy # fix a temperature fix_modify AtC initial temperature all 20.0 fix_modify AtC initial electron_temperature all 30.0 fix_modify AtC initial temperature gap 0.0 # relaxation thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] fix_modify AtC output cutoutFE 10 text ATC: Warning : text output can create _LARGE_ files ATC: output custom names: fix_modify AtC extrinsic electron_integration implicit # heating fix_modify AtC mesh create_nodeset lbc -8 -8 -INF INF -INF INF ATC: created nodeset lbc with 7 nodes fix_modify AtC mesh create_nodeset rbc 8 8 -INF INF -INF INF ATC: created nodeset rbc with 7 nodes fix_modify AtC fix electron_temperature lbc 20. fix_modify AtC fix electron_temperature rbc 20. fix_modify AtC source electron_temperature wire 0.001 run 200 Setting up run ... Memory usage per processor = 52.1308 Mbytes Step CPU AtC[1] AtC[2] AtC[3] AtC[4] 1000 0 7.5905384e-06 13.650794 1.7918648e-05 30 1020 0.33390522 8.0867497e-06 14.386397 0.00011143616 168.06236 1040 0.66419816 8.2236256e-06 14.569133 0.00020569969 308.34605 1060 0.99323916 7.9547417e-06 14.139358 0.00029996263 448.62886 1080 1.3224351 7.47106e-06 13.387177 0.00039422497 588.91078 1100 1.6522331 6.9291851e-06 12.597525 0.00048848671 729.19182 1120 1.9804182 6.4666101e-06 11.970788 0.00058274785 869.47196 1140 2.310976 6.1269287e-06 11.536337 0.0006770084 1009.7512 1160 2.6388621 5.9463401e-06 11.304155 0.00077126834 1150.0296 1180 2.9668522 5.7757317e-06 11.035914 0.0008655277 1290.307 1200 3.294523 5.6534832e-06 10.819941 0.00095978645 1430.5836 Loop time of 3.29723 on 4 procs for 200 steps with 1008 atoms Pair time (%) = 0.376869 (11.4298) Neigh time (%) = 0 (0) Comm time (%) = 0.394623 (11.9683) Outpt time (%) = 0.0362152 (1.09835) Other time (%) = 2.48953 (75.5035) Nlocal: 252 ave 504 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 1368 ave 1656 max 1080 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 37569 ave 75414 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 75138 ave 150278 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 300552 Ave neighs/atom = 298.167 Neighbor list builds = 0 Dangerous builds = 0 # relaxation fix_modify AtC remove_source electron_temperature wire run 200 Setting up run ... Memory usage per processor = 52.1308 Mbytes Step CPU AtC[1] AtC[2] AtC[3] AtC[4] 1200 0 5.6534832e-06 10.819941 0.00095978645 1430.5836 1220 0.33387113 5.6247016e-06 10.745001 0.0009597804 1430.5746 1240 0.66027904 5.6705058e-06 10.77004 0.00095977436 1430.5656 1260 0.98564315 5.9348763e-06 11.132668 0.00095976831 1430.5566 1280 1.311569 6.3878919e-06 11.792006 0.00095976227 1430.5477 1300 1.6400352 6.8588119e-06 12.489994 0.00095975623 1430.5387 1320 1.968184 7.3682728e-06 13.289603 0.00095975019 1430.5297 1340 2.2977772 7.8680354e-06 14.125224 0.00095974416 1430.5207 1360 2.624141 8.1759187e-06 14.694182 0.00095973813 1430.5117 1380 2.9510572 8.187909e-06 14.802618 0.0009597321 1430.5028 1400 3.2788641 7.7666161e-06 14.187723 0.00095972607 1430.4938 Loop time of 3.28154 on 4 procs for 200 steps with 1008 atoms Pair time (%) = 0.373896 (11.3939) Neigh time (%) = 0 (0) Comm time (%) = 0.391092 (11.9179) Outpt time (%) = 0.0359665 (1.09602) Other time (%) = 2.48059 (75.5921) Nlocal: 252 ave 504 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 1368 ave 1656 max 1080 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 37178.8 ave 74546 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 FullNghs: 74357.5 ave 148715 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 297430 Ave neighs/atom = 295.069 Neighbor list builds = 0 Dangerous builds = 0