lammps/examples/USER/atc/thermal/bar1d.screen

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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 <temperature> 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 <temperature> 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:
# ouput 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 <temperature> 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