LAMMPS (30 Aug 2013) # create domain #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) # NOTE following 3 lines added for restart boundary f p p pair_style lj/cut 13.5 read_data temp.init Reading data file ... orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215) 2 by 1 by 2 MPI processor grid 1440 atoms 1440 velocities lattice fcc 5.405 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 5.405 5.405 5.405 region simRegion block -12 12 -3 3 -3 3 # create atoms, NOTE commented out for restart #region mdRegion block -5 5 -3 3 -3 3 #boundary f p p #create_box 1 mdRegion #create_atoms 1 region mdRegion #mass 1 39.95 # specify interal/ghost atoms region mdInternal block -4 4 -3 3 -3 3 group internal region mdInternal 1152 atoms in group internal group ghost subtract all internal 288 atoms in group ghost # velocities have Vcm = 0, NOTE next four lines commented out for restart #velocity internal create 40. 87287 mom yes loop geom #pair_style lj/cut 13.5 ##pair_coeff 1 1 0.010323166 3.405 13.5 #pair_coeff 1 1 .238 3.405 13.5 neighbor 5. bin neigh_modify every 10 delay 0 check no # ID group atc PhysicsType ParameterFile fix AtC internal atc thermal Ar_thermal.mat ATC: constructing thermal coupling with parameter file Ar_thermal.mat ATC: version 2.0 ATC: peratom PE compute created with ID: 3 ATC: 3 materials defined from Ar_thermal.mat fix_modify AtC boundary ghost # ID part keywords nx ny nz region fix_modify AtC mesh create 12 1 1 simRegion f p p ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements fix_modify AtC internal_quadrature off # fix a temperature fix_modify AtC fix temperature all 20. # turn on thermostat fix_modify AtC control thermal rescale 10 # equilibrate MD field #dump D1 all atom 100 dump.bar1d #fix_modify AtC output bar1dfe 100 timestep 5 variable xdof equal 3*count(ghost) compute_modify thermo_temp extra ${xdof} compute_modify thermo_temp extra 864 thermo_style custom step cpu etotal pe f_AtC[1] temp f_AtC[2] thermo_modify format 1 %6i format 2 %7.2g thermo 100 run 400 Setting up run ... ATC: WARNING: material: [vacuum] cannot find heat_flux ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null Memory usage per processor = 51.6077 Mbytes Step CPU TotEng PotEng AtC[1] Temp AtC[2] 0 0 -2573.6428 -2710.8793 412.06718 39.965279 20 100 0.76 -2537.6764 -2606.3542 412.06718 20 20 200 1.5 -2584.8754 -2653.5532 412.06718 20 20 300 2.3 -2575.3126 -2643.9904 412.06718 20 20 400 3 -2573.4199 -2642.0977 412.06718 20 20 Loop time of 3.03371 on 4 procs for 400 steps with 1440 atoms Pair time (%) = 1.4429 (47.5623) Neigh time (%) = 0.579483 (19.1015) Comm time (%) = 0.320691 (10.5709) Outpt time (%) = 0.00164133 (0.0541031) Other time (%) = 0.688994 (22.7113) Nlocal: 360 ave 360 max 360 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 4060 ave 4060 max 4060 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 104865 ave 104966 max 104653 min Histogram: 1 0 0 0 0 0 0 1 0 2 FullNghs: 209730 ave 209902 max 209521 min Histogram: 1 0 0 0 1 0 0 1 0 1 Total # of neighbors = 838918 Ave neighs/atom = 582.582 Neighbor list builds = 40 Dangerous builds = 0 # change thermostat to hoover fix_modify AtC unfix temperature all fix_modify AtC control thermal hoover #fix_modify AtC localized_lambda on fix_modify AtC filter type exponential fix_modify AtC filter scale 10000.0 fix_modify AtC filter on # add nodesets # ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF ATC: created nodeset lbc with 1 nodes fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF ATC: created nodeset rbc with 1 nodes fix_modify AtC fix temperature lbc 40. fix_modify AtC fix temperature rbc 20. # initialize filter thermo 1 run 100 Setting up run ... ATC: WARNING: material: [vacuum] cannot find heat_flux ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null Memory usage per processor = 58.8926 Mbytes Step CPU TotEng PotEng AtC[1] Temp AtC[2] 400 0 -2573.4199 -2642.0977 412.06718 20 20 401 0.012 -2573.5379 -2642.2158 429.25134 20.000012 21.53912 402 0.018 -2573.4004 -2642.3419 429.29708 20.076799 21.541169 403 0.024 -2573.3868 -2642.4862 429.33475 20.122758 21.542857 404 0.031 -2573.3802 -2642.6479 429.37421 20.171764 21.544624 405 0.037 -2573.3733 -2642.8193 429.41377 20.223699 21.546397 406 0.043 -2573.3728 -2643.0062 429.45349 20.278247 21.548176 407 0.049 -2573.3755 -2643.204 429.49335 20.335089 21.549963 408 0.056 -2573.3816 -2643.412 429.53339 20.393863 21.551756 409 0.062 -2573.3884 -2643.6259 429.57359 20.454205 21.553557 410 0.091 -2573.3953 -2643.8441 429.61398 20.515714 21.555367 411 0.097 -2573.4089 -2644.0714 429.65455 20.577971 21.557184 412 0.1 -2573.4267 -2644.3041 429.6953 20.640548 21.55901 413 0.11 -2573.4529 -2644.5448 429.73625 20.702991 21.560845 414 0.12 -2573.4717 -2644.7759 429.7774 20.764845 21.562688 415 0.12 -2573.5043 -2645.0173 429.81873 20.825642 21.56454 416 0.13 -2573.5302 -2645.2467 429.86025 20.884902 21.5664 417 0.14 -2573.5593 -2645.4724 429.90195 20.942141 21.568269 418 0.14 -2573.5932 -2645.6943 429.94383 20.996891 21.570145 419 0.15 -2573.6251 -2645.904 429.98588 21.048675 21.572029 420 0.18 -2573.6624 -2646.1074 430.02808 21.097055 21.57392 421 0.18 -2573.6984 -2646.2964 430.07043 21.141602 21.575817 422 0.19 -2573.7375 -2646.474 430.11292 21.18192 21.57772 423 0.2 -2573.7763 -2646.6355 430.15552 21.217657 21.579629 424 0.2 -2573.8162 -2646.7812 430.19823 21.248493 21.581543 425 0.21 -2573.8561 -2646.9093 430.24102 21.274165 21.58346 426 0.22 -2573.8966 -2647.0195 430.28388 21.294459 21.58538 427 0.22 -2573.9335 -2647.1071 430.32678 21.309211 21.587302 428 0.23 -2573.9753 -2647.1802 430.36971 21.318326 21.589225 429 0.24 -2574.0177 -2647.2343 430.41264 21.321759 21.591149 430 0.26 -2574.0542 -2647.2632 430.45557 21.319529 21.593072 431 0.27 -2574.0893 -2647.2714 430.49845 21.311706 21.594993 432 0.28 -2574.1218 -2647.2584 430.54128 21.298422 21.596912 433 0.28 -2574.1494 -2647.2222 430.58404 21.279877 21.598828 434 0.29 -2574.1718 -2647.1636 430.62669 21.256291 21.600739 435 0.3 -2574.1959 -2647.0904 430.66924 21.227951 21.602645 436 0.3 -2574.2185 -2647.0005 430.71165 21.195192 21.604545 437 0.31 -2574.2382 -2646.8938 430.75391 21.158381 21.606438 438 0.31 -2574.2544 -2646.7711 430.796 21.117926 21.608324 439 0.32 -2574.2684 -2646.6352 430.83792 21.074254 21.610202 440 0.35 -2574.2803 -2646.4876 430.87965 21.027836 21.612072 441 0.36 -2574.29 -2646.3302 430.92117 20.979146 21.613932 442 0.36 -2574.2973 -2646.1642 430.96249 20.928684 21.615783 443 0.37 -2574.2996 -2645.9888 431.00359 20.876959 21.617625 444 0.38 -2574.3031 -2645.8122 431.04447 20.824481 21.619456 445 0.38 -2574.3006 -2645.6285 431.08512 20.771751 21.621277 446 0.39 -2574.3011 -2645.4489 431.12555 20.719271 21.623089 447 0.39 -2574.2997 -2645.2697 431.16576 20.667516 21.62489 448 0.4 -2574.2971 -2645.0935 431.20574 20.616927 21.626681 449 0.41 -2574.2869 -2644.915 431.24551 20.567927 21.628463 450 0.44 -2574.2793 -2644.7458 431.28506 20.520897 21.630235 451 0.44 -2574.2719 -2644.5849 431.32441 20.476174 21.631998 452 0.45 -2574.2668 -2644.4351 431.36357 20.434037 21.633752 453 0.46 -2574.2579 -2644.2912 431.40254 20.394702 21.635498 454 0.46 -2574.2474 -2644.1558 431.44133 20.358337 21.637236 455 0.47 -2574.2432 -2644.0372 431.47995 20.32504 21.638967 456 0.47 -2574.2322 -2643.9226 431.51842 20.294867 21.64069 457 0.48 -2574.2189 -2643.8163 431.55675 20.267801 21.642407 458 0.49 -2574.2071 -2643.7221 431.59494 20.243771 21.644118 459 0.49 -2574.1934 -2643.6358 431.633 20.222664 21.645824 460 0.52 -2574.1793 -2643.5588 431.67095 20.204321 21.647524 461 0.53 -2574.1703 -2643.4956 431.70879 20.188542 21.649219 462 0.54 -2574.1553 -2643.4345 431.74654 20.175109 21.65091 463 0.54 -2574.1453 -2643.3856 431.78419 20.163775 21.652597 464 0.55 -2574.1349 -2643.3426 431.82176 20.154293 21.654281 465 0.55 -2574.1233 -2643.3039 431.85926 20.146405 21.65596 466 0.56 -2574.1118 -2643.2699 431.89667 20.139872 21.657637 467 0.57 -2574.1002 -2643.2397 431.93402 20.134447 21.65931 468 0.57 -2574.0858 -2643.2098 431.97129 20.129927 21.66098 469 0.58 -2574.0679 -2643.1789 432.0085 20.126126 21.662647 470 0.61 -2574.0569 -2643.1567 432.04565 20.12288 21.664311 471 0.62 -2574.045 -2643.1352 432.08273 20.12008 21.665973 472 0.62 -2574.037 -2643.1188 432.11976 20.117624 21.667631 473 0.63 -2574.0257 -2643.1002 432.15672 20.115487 21.669287 474 0.63 -2574.0093 -2643.0774 432.19362 20.113646 21.67094 475 0.64 -2573.9926 -2643.0555 432.23046 20.112125 21.672591 476 0.65 -2573.9757 -2643.0347 432.26724 20.110991 21.674239 477 0.65 -2573.9616 -2643.0183 432.30397 20.110332 21.675884 478 0.66 -2573.9411 -2642.9975 432.34064 20.110255 21.677527 479 0.67 -2573.9247 -2642.9833 432.37726 20.110902 21.679168 480 0.7 -2573.9059 -2642.9698 432.41383 20.112418 21.680807 481 0.7 -2573.8934 -2642.966 432.45036 20.114955 21.682443 482 0.71 -2573.8763 -2642.9617 432.48684 20.118662 21.684078 483 0.71 -2573.8572 -2642.9598 432.52329 20.12368 21.685711 484 0.72 -2573.849 -2642.9738 432.55971 20.130144 21.687342 485 0.73 -2573.8322 -2642.9844 432.59611 20.138143 21.688973 486 0.73 -2573.8196 -2643.0048 432.63249 20.14774 21.690603 487 0.74 -2573.8071 -2643.0308 432.66886 20.158959 21.692232 488 0.75 -2573.7953 -2643.063 432.70522 20.171771 21.693861 489 0.75 -2573.7877 -2643.1046 432.74158 20.186108 21.695491 490 0.78 -2573.7797 -2643.1507 432.77796 20.201849 21.69712 491 0.79 -2573.775 -2643.2042 432.81435 20.2188 21.698751 492 0.79 -2573.7691 -2643.2599 432.85076 20.236743 21.700382 493 0.8 -2573.7648 -2643.3196 432.88719 20.255394 21.702014 494 0.81 -2573.7622 -2643.3825 432.92365 20.274433 21.703647 495 0.81 -2573.7617 -2643.4475 432.96013 20.293506 21.705282 496 0.82 -2573.7632 -2643.5133 432.99665 20.312253 21.706918 497 0.83 -2573.7622 -2643.5743 433.03319 20.330297 21.708555 498 0.83 -2573.7649 -2643.6353 433.06975 20.347265 21.710193 499 0.84 -2573.7697 -2643.6933 433.10634 20.362796 21.711833 500 0.87 -2573.7738 -2643.7447 433.14294 20.376549 21.713472 Loop time of 0.86855 on 4 procs for 100 steps with 1440 atoms Pair time (%) = 0.36643 (42.1888) Neigh time (%) = 0.145526 (16.755) Comm time (%) = 0.0606832 (6.98672) Outpt time (%) = 0.0380786 (4.38416) Other time (%) = 0.257832 (29.6854) Nlocal: 360 ave 360 max 360 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 4060 ave 4060 max 4060 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 104765 ave 105086 max 104556 min Histogram: 2 0 0 0 1 0 0 0 0 1 FullNghs: 209530 ave 209833 max 209326 min Histogram: 1 0 1 1 0 0 0 0 0 1 Total # of neighbors = 838118 Ave neighs/atom = 582.026 Neighbor list builds = 10 Dangerous builds = 0 # set up output, should be before a "run" fix_modify AtC output bar1dFE 100 text binary ATC: Warning : text output can create _LARGE_ files ATC: output custom names: # output command #dump D1 all atom 1000 dump.bar1d # run with FE reset_timestep 0 thermo 100 run 10000 Setting up run ... ATC: WARNING: material: [vacuum] cannot find heat_flux ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for physics and will be treated as null Memory usage per processor = 58.8926 Mbytes Step CPU TotEng PotEng AtC[1] Temp AtC[2] 0 0 -2573.7738 -2643.7447 433.14294 20.376549 21.713472 100 0.83 -2573.654 -2645.0562 436.6146 20.793359 21.86901 200 1.7 -2574.0035 -2642.057 439.70235 19.818183 22.007349 300 2.5 -2573.5186 -2646.5507 442.73301 21.268004 22.143129 400 3.3 -2573.2662 -2641.032 445.39809 19.734394 22.262531 500 4.1 -2573.5673 -2644.7553 447.93109 20.730998 22.376015 600 5 -2572.9368 -2641.5818 450.33706 19.990452 22.483808 700 5.8 -2573.2457 -2642.9406 452.61859 20.296182 22.586025 800 6.6 -2573.215 -2642.7311 454.75264 20.244128 22.681635 900 7.4 -2572.7227 -2643.5215 456.77865 20.617654 22.772405 1000 8.3 -2572.411 -2644.5969 458.68289 21.021605 22.857719 1100 9.1 -2571.4099 -2642.08 460.52888 20.580181 22.940424 1200 9.9 -2570.5495 -2641.7296 462.26173 20.728698 23.01806 1300 11 -2570.2491 -2640.8115 463.9083 20.548784 23.09183 1400 12 -2570.159 -2641.2853 465.40156 20.713007 23.158731 1500 12 -2569.5061 -2642.2055 467.00405 21.171116 23.230527 1600 13 -2568.7522 -2639.5247 468.45299 20.609988 23.295442 1700 14 -2569.1809 -2642.0975 469.79048 21.23439 23.355365 1800 15 -2568.7484 -2643.2103 471.10946 21.684386 23.414458 1900 16 -2568.2581 -2641.5017 472.49875 21.329637 23.476701 2000 17 -2568.192 -2641.4647 473.7794 21.338078 23.534077 2100 17 -2568.0746 -2639.9335 474.99711 20.926347 23.588633 2200 18 -2567.2717 -2642.2868 476.13779 21.845489 23.639738 2300 19 -2566.7209 -2639.9022 477.31159 21.311461 23.692327 2400 20 -2566.6054 -2638.8118 478.44655 21.027558 23.743176 2500 21 -2565.7629 -2639.6423 479.55196 21.514764 23.792701 2600 22 -2565.9248 -2642.5794 480.54223 22.322945 23.837067 2700 22 -2564.9995 -2640.0503 481.61938 21.855895 23.885326 2800 23 -2565.2468 -2638.033 482.61597 21.196395 23.929975 2900 24 -2565.0496 -2639.4905 483.63717 21.678286 23.975727 3000 25 -2565.1382 -2637.5132 484.58683 21.076652 24.018275 3100 26 -2564.4793 -2636.7861 485.5364 21.056785 24.060817 3200 26 -2564.1799 -2637.5024 486.53294 21.352561 24.105465 3300 27 -2564.4531 -2641.3463 487.42873 22.392434 24.145598 3400 28 -2564.2323 -2641.0072 488.30292 22.357973 24.184764 3500 29 -2563.378 -2635.3819 489.17087 20.968574 24.22365 3600 30 -2563.5014 -2637.8324 490.1027 21.646291 24.265398 3700 31 -2563.4092 -2638.0479 490.92648 21.735889 24.302305 3800 31 -2563.0307 -2637.5397 491.76937 21.698123 24.340068 3900 32 -2562.1415 -2637.2704 492.65132 21.878653 24.379582 4000 33 -2561.9969 -2637.3928 493.4009 21.956415 24.413165 4100 34 -2560.7688 -2636.0902 494.20978 21.934699 24.449405 4200 35 -2561.3033 -2638.2324 494.92948 22.402886 24.481649 4300 36 -2560.9897 -2637.0909 495.72929 22.161791 24.517482 4400 36 -2561.1677 -2638.5004 496.4863 22.520422 24.551398 4500 37 -2560.4797 -2637.3716 497.21153 22.392069 24.58389 4600 38 -2560.5787 -2637.0577 497.94655 22.271795 24.61682 4700 39 -2560.9645 -2639.5115 498.65048 22.874032 24.648358 4800 40 -2560.4451 -2637.6681 499.40401 22.488483 24.682118 4900 40 -2559.5243 -2635.9383 500.10679 22.252874 24.713604 5000 41 -2559.4948 -2637.7238 500.83953 22.781444 24.746432 5100 42 -2559.6822 -2636.169 501.53339 22.274071 24.777518 5200 43 -2559.6398 -2637.3169 502.26381 22.620718 24.810243 5300 44 -2558.6285 -2634.5293 502.8444 22.103424 24.836255 5400 45 -2558.6394 -2637.9487 503.59005 23.096025 24.869662 5500 45 -2558.1403 -2636.176 504.21716 22.725144 24.897757 5600 46 -2558.0703 -2635.1367 504.9347 22.442865 24.929905 5700 47 -2558.0656 -2636.7197 505.52087 22.905225 24.956167 5800 48 -2557.3777 -2634.8266 506.20982 22.554253 24.987033 5900 49 -2557.2526 -2635.9743 506.86422 22.924918 25.016352 6000 50 -2557.3833 -2637.2291 507.48018 23.25228 25.043948 6100 50 -2556.0263 -2633.5407 508.11625 22.573338 25.072446 6200 51 -2555.7442 -2634.4379 508.74696 22.916758 25.100703 6300 52 -2555.855 -2635.6232 509.35007 23.229653 25.127723 6400 53 -2555.9332 -2634.2034 509.90097 22.793416 25.152405 6500 54 -2555.6529 -2635.6085 510.47402 23.284242 25.178079 6600 55 -2554.8702 -2633.8042 511.0317 22.986719 25.203064 6700 55 -2555.4594 -2637.4199 511.60862 23.868095 25.228911 6800 56 -2555.1345 -2633.0307 512.18015 22.684507 25.254517 6900 57 -2555.2031 -2635.8935 512.79344 23.498217 25.281994 7000 58 -2554.4149 -2634.996 513.32816 23.466386 25.305951 7100 59 -2555.5655 -2636.9961 513.95657 23.713805 25.334105 7200 59 -2554.6219 -2632.7377 514.567 22.748451 25.361454 7300 60 -2553.7348 -2633.5176 515.135 23.233924 25.386901 7400 61 -2553.6835 -2632.7483 515.7035 23.024829 25.412371 7500 62 -2554.1585 -2634.2224 516.25704 23.315779 25.437171 7600 63 -2553.7146 -2636.4167 516.79495 24.084074 25.461271 7700 64 -2553.0976 -2633.1654 517.39991 23.316903 25.488375 7800 64 -2553.7234 -2633.6408 517.98568 23.273102 25.514618 7900 65 -2553.1575 -2635.2362 518.49062 23.902519 25.537241 8000 66 -2553.0069 -2632.9282 519.06292 23.274267 25.562881 8100 67 -2552.2172 -2632.9349 519.57824 23.506176 25.585969 8200 68 -2552.6329 -2633.705 520.13682 23.609392 25.610994 8300 69 -2553.0514 -2636.5364 520.66438 24.312051 25.63463 8400 69 -2551.9158 -2634.5593 521.15401 24.066989 25.656566 8500 70 -2551.162 -2632.582 521.69313 23.710703 25.68072 8600 71 -2551.323 -2631.8792 522.25824 23.459141 25.706039 8700 72 -2551.3995 -2634.1924 522.75555 24.110486 25.728319 8800 73 -2551.5524 -2635.9593 523.28139 24.580545 25.751878 8900 73 -2550.9859 -2634.5116 523.74996 24.3239 25.772871 9000 74 -2550.3986 -2630.9451 524.29066 23.456323 25.797095 9100 75 -2550.2258 -2632.4852 524.79409 23.955138 25.81965 9200 76 -2549.7276 -2633.251 525.32924 24.323252 25.843626 9300 77 -2549.2309 -2632.0111 525.82326 24.1068 25.86576 9400 78 -2549.1793 -2631.7908 526.23399 24.057681 25.884161 9500 78 -2549.3234 -2632.8586 526.74802 24.326659 25.907191 9600 79 -2548.7761 -2630.2005 527.18774 23.711964 25.926891 9700 80 -2548.5531 -2631.9225 527.62451 24.27839 25.946459 9800 81 -2548.3632 -2632.4871 528.04194 24.49812 25.965161 9900 82 -2548.2216 -2631.2195 528.52701 24.170186 25.986893 10000 83 -2547.7787 -2631.2232 528.97935 24.300246 26.007159 Loop time of 82.5249 on 4 procs for 10000 steps with 1440 atoms Pair time (%) = 35.7754 (43.351) Neigh time (%) = 14.5036 (17.5748) Comm time (%) = 7.45016 (9.02777) Outpt time (%) = 0.0984205 (0.119262) Other time (%) = 24.6974 (29.9271) Nlocal: 360 ave 360 max 360 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 4060 ave 4060 max 4060 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 104823 ave 104983 max 104416 min Histogram: 1 0 0 0 0 0 0 0 0 3 FullNghs: 209646 ave 209959 max 209315 min Histogram: 1 0 1 0 0 0 0 0 1 1 Total # of neighbors = 838584 Ave neighs/atom = 582.35 Neighbor list builds = 1000 Dangerous builds = 0