1LAMMPS (30 Aug 2013) 2units real 3atom_style atomic 4# create domain 5#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70) 6# NOTE following 3 lines added for restart 7boundary f p p 8pair_style lj/cut 13.5 9read_data temp.init 10Reading data file ... 11 orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215) 12 2 by 1 by 2 MPI processor grid 13 1440 atoms 14 1440 velocities 15lattice fcc 5.405 origin 0.25 0.25 0.25 16Lattice spacing in x,y,z = 5.405 5.405 5.405 17region simRegion block -12 12 -3 3 -3 3 18# create atoms, NOTE commented out for restart 19#region mdRegion block -5 5 -3 3 -3 3 20#boundary f p p 21#create_box 1 mdRegion 22#create_atoms 1 region mdRegion 23#mass 1 39.95 24# specify interal/ghost atoms 25region mdInternal block -4 4 -3 3 -3 3 26group internal region mdInternal 271152 atoms in group internal 28group ghost subtract all internal 29288 atoms in group ghost 30# velocities have Vcm = 0, NOTE next three lines commented out for restart 31#velocity internal create 40. 87287 mom yes loop geom 32#pair_style lj/cut 13.5 33#pair_coeff 1 1 .238 3.405 13.5 34neighbor 5. bin 35neigh_modify every 10 delay 0 check no 36# ID group atc PhysicsType ParameterFile 37fix AtC internal atc thermal Ar_thermal.mat 38ATC: constructing thermal coupling with parameter file Ar_thermal.mat 39 ATC: version 2.0 40 ATC: peratom PE compute created with ID: 3 41 ATC: 3 materials defined from Ar_thermal.mat 42fix_modify AtC boundary ghost 43# numerical parameters 44fix_modify AtC time_integration fractional_step 45fix_modify AtC internal_quadrature off 46# ID part keywords nx ny nz region 47fix_modify AtC mesh create 12 1 1 simRegion f p p 48 ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements 49fix_modify AtC mesh create_faceset ibndy box -4.0 4.0 -INF INF -INF INF in 50 ATC: created faceset ibndy with 2 faces 51fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -INF INF -INF INF outward 52 ATC: created faceset obndy with 2 faces 53# fix a temperature 54fix_modify AtC fix temperature all 20. 55#fix_modify AtC fix temperature all linear 0 0 0 -0.154 0 0 30. 56#fix_modify AtC fix temperature all quadratic 0 0 0 -0.154 0 0 30. 0.01 0.0 0.0 0 0 0 57# turn on thermostat 58fix_modify AtC control thermal rescale 10 59# output 60thermo 100 61variable xdof equal 3*count(ghost) 62compute_modify thermo_temp extra ${xdof} 63compute_modify thermo_temp extra 864 64thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] 65thermo_modify format 1 %6i format 2 %7.2g 66# equilibrate MD field 67#fix_modify AtC output bar1d_lumped_initFE 1 text 68timestep 5 69run 400 70Setting up run ... 71 ATC: WARNING: material: [vacuum] cannot find heat_flux 72 ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null 73Memory usage per processor = 50.9732 Mbytes 74Step CPU TotEng PotEng AtC[1] Temp AtC[2] 75 0 0 -2573.6428 -2710.8793 412.06718 39.965279 20 76 100 0.78 -2537.6764 -2606.3542 412.06718 20 20 77 200 1.6 -2584.8754 -2653.5532 412.06718 20 20 78 300 2.3 -2575.3126 -2643.9904 412.06718 20 20 79 400 3.1 -2573.4199 -2642.0977 412.06718 20 20 80Loop time of 3.12019 on 4 procs for 400 steps with 1440 atoms 81 82Pair time (%) = 1.50839 (48.343) 83Neigh time (%) = 0.58196 (18.6514) 84Comm time (%) = 0.345325 (11.0674) 85Outpt time (%) = 0.00157982 (0.0506322) 86Other time (%) = 0.682932 (21.8875) 87 88Nlocal: 360 ave 360 max 360 min 89Histogram: 4 0 0 0 0 0 0 0 0 0 90Nghost: 4060 ave 4060 max 4060 min 91Histogram: 4 0 0 0 0 0 0 0 0 0 92Neighs: 104865 ave 104966 max 104653 min 93Histogram: 1 0 0 0 0 0 0 1 0 2 94FullNghs: 209730 ave 209902 max 209521 min 95Histogram: 1 0 0 0 1 0 0 1 0 1 96 97Total # of neighbors = 838918 98Ave neighs/atom = 582.582 99Neighbor list builds = 40 100Dangerous builds = 0 101#run 100 102# change thermostat to hoover 103fix_modify AtC unfix temperature all 104#fix_modify AtC thermal control flux interpolate 105fix_modify AtC control thermal flux faceset obndy 106fix_modify AtC control localized_lambda on 107fix_modify AtC filter type exponential 108fix_modify AtC filter scale 10000.0 109fix_modify AtC filter on 110# add nodesets 111# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax 112fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF 113 ATC: created nodeset lbc with 1 nodes 114fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF 115 ATC: created nodeset rbc with 1 nodes 116fix_modify AtC fix temperature lbc 80. 117fix_modify AtC fix temperature rbc 80. 118# initialize 119thermo 10 120run 100 121Setting up run ... 122 ATC: WARNING: material: [vacuum] cannot find heat_flux 123 ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null 124Memory usage per processor = 55.72 Mbytes 125Step CPU TotEng PotEng AtC[1] Temp AtC[2] 126 400 0 -2573.4199 -2642.0977 412.06718 20 20 127 410 0.09 -2573.3989 -2643.8455 517.30661 20.515089 29.330348 128 420 0.17 -2573.4223 -2646.1083 519.64166 21.16724 29.434964 129 430 0.26 -2573.4498 -2647.2051 521.96898 21.478626 29.539233 130 440 0.34 -2573.4569 -2646.2686 524.27182 21.203839 29.642406 131 450 0.43 -2573.4737 -2644.3159 526.53414 20.63027 29.743762 132 460 0.51 -2573.4879 -2643.0036 528.75499 20.243982 29.843261 133 470 0.59 -2573.4922 -2642.6172 530.94429 20.130226 29.941347 134 480 0.68 -2573.5022 -2642.5663 533.10876 20.112489 30.03832 135 490 0.76 -2573.5141 -2642.9253 535.25201 20.213567 30.134343 136 500 0.85 -2573.5321 -2643.6709 537.37935 20.425453 30.229652 137Loop time of 0.846033 on 4 procs for 100 steps with 1440 atoms 138 139Pair time (%) = 0.37079 (43.8269) 140Neigh time (%) = 0.146187 (17.279) 141Comm time (%) = 0.0834975 (9.86929) 142Outpt time (%) = 0.00396448 (0.468597) 143Other time (%) = 0.241595 (28.5562) 144 145Nlocal: 360 ave 360 max 360 min 146Histogram: 4 0 0 0 0 0 0 0 0 0 147Nghost: 4060 ave 4060 max 4060 min 148Histogram: 4 0 0 0 0 0 0 0 0 0 149Neighs: 104761 ave 105083 max 104555 min 150Histogram: 2 0 0 0 1 0 0 0 0 1 151FullNghs: 209522 ave 209825 max 209318 min 152Histogram: 1 0 1 1 0 0 0 0 0 1 153 154Total # of neighbors = 838090 155Ave neighs/atom = 582.007 156Neighbor list builds = 10 157Dangerous builds = 0 158# relax 159fix_modify AtC unfix temperature all 160# output 161fix_modify AtC output bar1d_lumpedFE 100 text 162 ATC: Warning : text output can create _LARGE_ files 163 ATC: output custom names: 164 165# run with FE 166reset_timestep 0 167thermo 100 168run 10000 169Setting up run ... 170 ATC: WARNING: material: [vacuum] cannot find heat_flux 171 ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null 172Memory usage per processor = 55.72 Mbytes 173Step CPU TotEng PotEng AtC[1] Temp AtC[2] 174 0 0 -2573.5321 -2643.6709 537.37935 20.425453 30.229652 175 100 0.84 -2573.4714 -2644.6628 537.59712 20.731964 29.437439 176 200 1.7 -2573.5166 -2641.7664 537.63735 19.875333 28.850231 177 300 2.5 -2573.3454 -2646.2939 537.8469 21.243688 28.422511 178 400 3.4 -2573.0942 -2641.1809 537.90867 19.827861 28.095231 179 500 4.2 -2572.3083 -2643.707 538.005 20.792348 27.845793 180 600 5 -2571.6518 -2640.8182 538.12895 20.142273 27.652618 181 700 5.9 -2570.5731 -2641.7027 538.24696 20.713971 27.499382 182 800 6.7 -2569.3231 -2640.7761 538.33555 20.808172 27.374616 183 900 7.6 -2568.1073 -2641.2144 538.42259 21.289869 27.27217 184 1000 8.4 -2566.8774 -2641.7627 538.50252 21.807716 27.186491 185 1100 9.2 -2565.6817 -2639.3847 538.60769 21.463413 27.11518 186 1200 10 -2564.5291 -2639.0021 538.6921 21.687625 27.053351 187 1300 11 -2563.046 -2636.8175 538.75291 21.483334 26.998775 188 1400 12 -2561.7374 -2637.9846 538.75622 22.204304 26.948354 189 1500 13 -2560.5922 -2638.0152 538.92825 22.546707 26.911016 190 1600 13 -2559.5712 -2634.9079 538.98874 21.939138 26.873272 191 1700 14 -2558.4498 -2637.4043 539.01552 22.992706 26.83788 192 1800 15 -2557.3572 -2637.6783 539.06504 23.390689 26.806789 193 1900 16 -2556.3318 -2635.4587 539.21528 23.042919 26.783029 194 2000 17 -2555.2491 -2634.8649 539.3077 23.185278 26.759119 195 2100 18 -2554.0813 -2632.5651 539.34324 22.855611 26.734792 196 2200 18 -2552.9667 -2635.7107 539.36679 24.096274 26.711802 197 2300 19 -2552.2327 -2633.1401 539.45717 23.561421 26.693468 198 2400 20 -2551.6044 -2632.5536 539.53752 23.573606 26.676165 199 2500 21 -2551.1734 -2631.6954 539.62757 23.449169 26.660623 200 2600 22 -2550.381 -2634.669 539.66971 24.545902 26.644129 201 2700 23 -2549.624 -2633.4682 539.75068 24.41666 26.630457 202 2800 23 -2548.8206 -2630.6519 539.80156 23.830481 26.616417 203 2900 24 -2547.8861 -2632.5638 539.88361 24.659393 26.604667 204 3000 25 -2547.084 -2627.427 539.9225 23.397054 26.5918 205 3100 26 -2546.394 -2629.4378 539.94648 24.183576 26.579016 206 3200 27 -2545.7683 -2629.3918 540.06149 24.352372 26.571 207 3300 28 -2545.2615 -2631.3813 540.12465 25.079335 26.5613 208 3400 28 -2544.6024 -2630.0895 540.12814 24.895105 26.549518 209 3500 29 -2543.9337 -2628.4156 540.13502 24.602369 26.53844 210 3600 30 -2543.3099 -2628.0721 540.25751 24.684014 26.533053 211 3700 31 -2542.6958 -2628.8619 540.25488 25.092829 26.522541 212 3800 32 -2542.218 -2630.3008 540.2971 25.651004 26.514488 213 3900 33 -2542.2329 -2626.6554 540.40242 24.585058 26.509685 214 4000 33 -2542.345 -2628.0992 540.4246 24.972878 26.501556 215 4100 34 -2542.444 -2628.9863 540.4438 25.202383 26.493668 216 4200 35 -2542.4625 -2630.9619 540.43077 25.772324 26.484689 217 4300 36 -2542.4932 -2628.6896 540.46659 25.101648 26.47823 218 4400 37 -2542.4649 -2626.3615 540.52486 24.431935 26.473089 219 4500 38 -2542.3848 -2629.9464 540.56942 25.49921 26.467627 220 4600 38 -2542.2156 -2630.1917 540.57345 25.619915 26.460625 221 4700 39 -2542.0968 -2628.4423 540.65789 25.145095 26.457485 222 4800 40 -2541.8766 -2630.6991 540.69403 25.866389 26.452428 223 4900 41 -2541.7652 -2628.337 540.65021 25.210979 26.444021 224 5000 42 -2541.667 -2627.5891 540.75066 25.021773 26.442299 225 5100 43 -2541.4455 -2626.9354 540.74526 24.895894 26.436045 226 5200 43 -2541.3524 -2626.9293 540.80011 24.92126 26.432691 227 5300 44 -2541.4921 -2627.9353 540.85481 25.173531 26.429523 228 5400 45 -2541.4091 -2627.4363 540.77756 25.052378 26.420627 229 5500 46 -2541.2364 -2627.0322 540.8409 24.985021 26.418205 230 5600 47 -2541.0146 -2626.1809 540.84749 24.801661 26.41341 231 5700 48 -2540.7658 -2626.3892 540.83392 24.934789 26.407875 232 5800 48 -2540.5557 -2625.5238 540.86784 24.74395 26.404623 233 5900 49 -2540.2613 -2628.8094 540.88157 25.7865 26.400618 234 6000 50 -2540.023 -2628.3564 540.89421 25.723987 26.39671 235 6100 51 -2539.7369 -2626.2678 540.8886 25.199056 26.392126 236 6200 52 -2539.4247 -2626.9787 540.88107 25.496996 26.387593 237 6300 53 -2539.2795 -2628.1038 540.94239 25.866954 26.386278 238 6400 53 -2539.2702 -2625.3721 540.99133 25.07412 26.384539 239 6500 54 -2539.0339 -2627.6649 541.01851 25.810661 26.381951 240 6600 55 -2538.7604 -2630.2595 540.93819 26.645879 26.37467 241 6700 56 -2538.5609 -2627.2764 541.00702 25.835243 26.374189 242 6800 57 -2538.4781 -2628.4908 541.04647 26.213023 26.372508 243 6900 58 -2538.3363 -2626.3948 541.0421 25.643922 26.368975 244 7000 58 -2538.1096 -2624.3062 541.07424 25.101732 26.367185 245 7100 59 -2538.1297 -2625.2825 541.13737 25.380157 26.366889 246 7200 60 -2537.9558 -2625.6952 541.11622 25.550998 26.362917 247 7300 61 -2537.7777 -2623.8467 541.12479 25.064554 26.360375 248 7400 62 -2537.691 -2626.362 541.12857 25.822305 26.357713 249 7500 63 -2537.6017 -2627.6258 541.11665 26.216328 26.354439 250 7600 63 -2537.5881 -2626.5336 541.09525 25.902252 26.350828 251 7700 64 -2537.4503 -2626.5011 541.10444 25.932897 26.348674 252 7800 65 -2537.4247 -2625.6606 541.16841 25.695575 26.349056 253 7900 66 -2537.221 -2626.6494 541.16553 26.042851 26.346524 254 8000 67 -2536.9786 -2624.3886 541.16948 25.455068 26.344375 255 8100 68 -2537.0091 -2626.1267 541.19675 25.952348 26.343346 256 8200 68 -2536.8966 -2626.9415 541.24047 26.222385 26.343126 257 8300 69 -2536.7301 -2627.422 541.17563 26.4108 26.338112 258 8400 70 -2536.5639 -2626.9772 541.22236 26.329686 26.338165 259 8500 71 -2536.2761 -2623.6142 541.20754 25.434125 26.335526 260 8600 72 -2536.1413 -2624.8573 541.2923 25.835401 26.337411 261 8700 73 -2535.8015 -2627.0616 541.217 26.576282 26.332188 262 8800 73 -2535.645 -2625.4677 541.22666 26.157671 26.33083 263 8900 74 -2535.5467 -2622.6362 541.21146 25.361737 26.328417 264 9000 75 -2535.5706 -2622.2805 541.23307 25.251184 26.32771 265 9100 76 -2535.6698 -2627.18 541.28442 26.649119 26.328389 266 9200 77 -2535.6724 -2623.9823 541.29366 25.717136 26.327233 267 9300 78 -2535.4543 -2624.9706 541.21196 26.06848 26.322051 268 9400 78 -2535.4415 -2625.439 541.31268 26.20861 26.325088 269 9500 79 -2535.4949 -2622.6035 541.29414 25.367306 26.322824 270 9600 80 -2535.6083 -2623.7154 541.32785 25.658066 26.322941 271 9700 81 -2535.569 -2624.6231 541.28832 25.933859 26.319815 272 9800 82 -2535.4348 -2624.787 541.27797 26.020648 26.318031 273 9900 83 -2535.3781 -2626.4373 541.30541 26.517775 26.317973 274 10000 83 -2535.4286 -2624.7326 541.30648 26.006646 26.316764 275Loop time of 83.3594 on 4 procs for 10000 steps with 1440 atoms 276 277Pair time (%) = 37.0847 (44.4877) 278Neigh time (%) = 14.6226 (17.5416) 279Comm time (%) = 8.17561 (9.80766) 280Outpt time (%) = 0.0690249 (0.082804) 281Other time (%) = 23.4075 (28.0802) 282 283Nlocal: 360 ave 360 max 360 min 284Histogram: 4 0 0 0 0 0 0 0 0 0 285Nghost: 4060 ave 4060 max 4060 min 286Histogram: 4 0 0 0 0 0 0 0 0 0 287Neighs: 104746 ave 104843 max 104627 min 288Histogram: 1 0 0 0 0 1 1 0 0 1 289FullNghs: 209492 ave 209713 max 209341 min 290Histogram: 1 1 0 0 1 0 0 0 0 1 291 292Total # of neighbors = 837970 293Ave neighs/atom = 581.924 294Neighbor list builds = 1000 295Dangerous builds = 0 296