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lammps/examples/USER/atc/bar1d_thermal/bar1d.log
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LAMMPS (7 Jul 2009)
#AtC Thermal Coupling
# This benchmark tests heat conducting into and out of the MD region. The
# temperature is intially 20 everywhere and the left boundary BC is fixed at 40.
# The result should show heat diffusing through the FEM to the MD and back out
# to the FEM on the right. Insufficient time is captured to reach the linear
# steady state, but heat crossing both boundaries should be observed.
units real
atom_style atomic
# 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
orthogonal box = (-27.025 -16.215 -16.215) to (27.025 16.215 16.215)
1 by 1 by 1 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
# ID part keywords nx ny nz region
#fix_modify AtC fem create mesh 12 2 2 simRegion f p p
fix_modify AtC fem create mesh 12 1 1 simRegion f p p
# specify atom types
#fix_modify AtC transfer internal type internal
fix_modify AtC transfer boundary type ghost
# fix a temperature
fix_modify AtC transfer fix temperature all 20.
# turn on thermostat
fix_modify AtC transfer thermal control rescale 10
# equilibrate MD field
#dump D1 all atom 100 dump.bar1d
#fix_modify AtC transfer 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
Memory usage per processor = 8.7506 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
0 0 -2573.6428 -2710.8793 412.06718 39.965279 20
100 2.7 -2537.6764 -2606.3542 412.06718 20 20
200 5.5 -2584.8754 -2653.5532 412.06718 20 20
300 8.2 -2575.3126 -2643.9904 412.06718 20 20
400 11 -2573.4199 -2642.0977 412.06718 20 20
Loop time of 10.9925 on 1 procs for 400 steps with 1440 atoms
Pair time (%) = 4.30201 (39.1358)
Neigh time (%) = 1.867 (16.9842)
Comm time (%) = 0.0373757 (0.34001)
Outpt time (%) = 0.00606346 (0.0551598)
Other time (%) = 4.78008 (43.4848)
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5320 ave 5320 max 5320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 419459 ave 419459 max 419459 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 838918 ave 838918 max 838918 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 838918
Ave neighs/atom = 582.582
Neighbor list builds = 40
Dangerous builds = 0
# change thermostat to hoover
fix_modify AtC transfer unfix temperature all
fix_modify AtC transfer thermal control hoover
fix_modify AtC transfer filter type exponential
fix_modify AtC transfer filter scale 10000.0
fix_modify AtC transfer filter on
fix_modify AtC transfer internal_quadrature off
# add nodesets
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -12 12 -12 12
fix_modify AtC transfer fix temperature lbc 40.
fix_modify AtC transfer fix temperature rbc 20.
# initialize filter
#thermo 1
run 100
Memory usage per processor = 8.97948 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
400 0 -2573.4199 -2642.0977 274.71145 20 20
500 2.7 -2573.7738 -2643.7447 295.61002 20.376549 21.713472
Loop time of 2.67287 on 1 procs for 100 steps with 1440 atoms
Pair time (%) = 1.07427 (40.1917)
Neigh time (%) = 0.466434 (17.4507)
Comm time (%) = 0.00930166 (0.348003)
Outpt time (%) = 0.00103688 (0.0387928)
Other time (%) = 1.12183 (41.9709)
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5320 ave 5320 max 5320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 419059 ave 419059 max 419059 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 838118 ave 838118 max 838118 min
Histogram: 1 0 0 0 0 0 0 0 0 0
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 transfer output bar1dFE 100 text
# ouput command
#dump D1 all atom 1000 dump.bar1d
fix_modify AtC transfer atomic_output bar1dMD 100
# run with FE
reset_timestep 0
thermo 100
run 10000
Memory usage per processor = 8.97948 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
0 0 -2573.7738 -2643.7447 295.61002 20.376549 21.713472
100 2.7 -2573.654 -2645.0562 298.997 20.793359 21.86901
200 5.4 -2574.0035 -2642.057 302.05784 19.818184 22.007349
300 8 -2573.5186 -2646.5507 304.88852 21.268004 22.143129
400 11 -2573.2662 -2641.032 307.48549 19.734394 22.262531
500 13 -2573.5673 -2644.7553 309.92162 20.730998 22.376015
600 16 -2572.9368 -2641.5818 312.18796 19.990452 22.483808
700 19 -2573.2457 -2642.9406 314.3431 20.296183 22.586025
800 21 -2573.215 -2642.7311 316.37915 20.244129 22.681635
900 24 -2572.7227 -2643.5215 318.29866 20.617655 22.772405
1000 27 -2572.411 -2644.5969 320.08215 21.021606 22.85772
1100 29 -2571.4099 -2642.08 321.74721 20.580181 22.940424
1200 32 -2570.5495 -2641.7296 323.29152 20.728698 23.01806
1300 35 -2570.2491 -2640.8115 324.79381 20.548784 23.09183
1400 37 -2570.159 -2641.2853 326.14846 20.713008 23.158731
1500 40 -2569.5061 -2642.2055 327.46482 21.171117 23.230527
1600 43 -2568.7522 -2639.5246 328.68994 20.609988 23.295442
1700 45 -2569.1809 -2642.0975 329.85636 21.234392 23.355365
1800 48 -2568.7484 -2643.2103 330.95066 21.684387 23.414458
1900 51 -2568.258 -2641.5017 332.02069 21.329638 23.476702
2000 54 -2568.192 -2641.4646 333.04827 21.338079 23.534077
2100 56 -2568.0746 -2639.9335 334.04476 20.926349 23.588633
2200 59 -2567.2717 -2642.2868 334.99014 21.84549 23.639739
2300 62 -2566.7209 -2639.9022 335.89195 21.311463 23.692327
2400 64 -2566.6054 -2638.8118 336.73569 21.02756 23.743177
2500 67 -2565.7629 -2639.6423 337.51835 21.514764 23.792702
2600 70 -2565.9251 -2642.5797 338.26277 22.322947 23.837067
2700 72 -2564.9995 -2640.0503 339.00006 21.855897 23.885327
2800 75 -2565.2468 -2638.033 339.72187 21.196396 23.929976
2900 78 -2565.0496 -2639.4905 340.4486 21.678289 23.975728
3000 80 -2565.1382 -2637.5132 341.15766 21.076651 24.018275
3100 83 -2564.4793 -2636.786 341.85076 21.056788 24.060818
3200 86 -2564.1799 -2637.5024 342.51347 21.352563 24.105465
3300 88 -2564.4531 -2641.3463 343.13584 22.392438 24.145599
3400 91 -2564.2323 -2641.0072 343.75483 22.357976 24.184764
3500 94 -2563.378 -2635.3819 344.36945 20.968577 24.22365
3600 96 -2563.5014 -2637.8324 345.00242 21.646292 24.265399
3700 99 -2563.4092 -2638.0479 345.63031 21.73589 24.302306
3800 1e+02 -2563.0307 -2637.5397 346.23705 21.698125 24.340069
3900 1e+02 -2562.1415 -2637.2704 346.79157 21.878655 24.379583
4000 1.1e+02 -2561.9968 -2637.3928 347.2934 21.956417 24.413166
4100 1.1e+02 -2560.7688 -2636.0902 347.76126 21.934696 24.449405
4200 1.1e+02 -2561.3033 -2638.2325 348.21187 22.402893 24.48165
4300 1.2e+02 -2560.9897 -2637.0909 348.67188 22.161792 24.517482
4400 1.2e+02 -2561.1676 -2638.5003 349.1221 22.52042 24.551399
4500 1.2e+02 -2560.4797 -2637.3716 349.57016 22.392068 24.58389
4600 1.2e+02 -2560.5787 -2637.0577 350.03085 22.2718 24.616821
4700 1.3e+02 -2560.9645 -2639.5114 350.46283 22.874034 24.648359
4800 1.3e+02 -2560.445 -2637.6681 350.93668 22.488484 24.682119
4900 1.3e+02 -2559.5243 -2635.9383 351.38797 22.252882 24.713605
5000 1.3e+02 -2559.4948 -2637.7238 351.82736 22.781448 24.746433
5100 1.4e+02 -2559.6822 -2636.169 352.25581 22.274077 24.77752
5200 1.4e+02 -2559.6398 -2637.3169 352.67163 22.620718 24.810244
5300 1.4e+02 -2558.6285 -2634.5293 353.06226 22.103426 24.836256
5400 1.4e+02 -2558.6394 -2637.9486 353.46662 23.096021 24.869663
5500 1.5e+02 -2558.1403 -2636.176 353.85792 22.725147 24.897758
5600 1.5e+02 -2558.0703 -2635.1367 354.27521 22.442874 24.929906
5700 1.5e+02 -2558.0656 -2636.7197 354.66462 22.905238 24.956168
5800 1.6e+02 -2557.3776 -2634.8266 355.06619 22.554271 24.987034
5900 1.6e+02 -2557.2526 -2635.9743 355.44501 22.924934 25.016353
6000 1.6e+02 -2557.3833 -2637.2292 355.80121 23.252296 25.043949
6100 1.6e+02 -2556.0263 -2633.5408 356.13412 22.573353 25.072447
6200 1.7e+02 -2555.7442 -2634.4378 356.46167 22.916748 25.100704
6300 1.7e+02 -2555.855 -2635.6231 356.75569 23.22965 25.127725
6400 1.7e+02 -2555.933 -2634.2031 357.04516 22.793407 25.152406
6500 1.7e+02 -2555.6529 -2635.6086 357.33016 23.28426 25.178081
6600 1.8e+02 -2554.8702 -2633.8043 357.60713 22.986754 25.203066
6700 1.8e+02 -2555.4594 -2637.4198 357.91044 23.868096 25.228913
6800 1.8e+02 -2555.1344 -2633.0306 358.23055 22.684511 25.254519
6900 1.8e+02 -2555.203 -2635.8935 358.56704 23.498239 25.281995
7000 1.9e+02 -2554.4151 -2634.9963 358.89735 23.466408 25.305952
7100 1.9e+02 -2555.5652 -2636.9959 359.27174 23.713819 25.334106
7200 1.9e+02 -2554.6218 -2632.7376 359.62885 22.748439 25.361455
7300 2e+02 -2553.7347 -2633.5173 359.96531 23.233845 25.386903
7400 2e+02 -2553.6833 -2632.7482 360.28731 23.024868 25.412373
7500 2e+02 -2554.1584 -2634.2224 360.62311 23.31579 25.437173
7600 2e+02 -2553.7146 -2636.4165 360.95078 24.084027 25.461273
7700 2.1e+02 -2553.0976 -2633.1652 361.2731 23.316874 25.488376
7800 2.1e+02 -2553.7234 -2633.641 361.58496 23.273177 25.51462
7900 2.1e+02 -2553.1572 -2635.2359 361.88331 23.902505 25.537243
8000 2.1e+02 -2553.0069 -2632.9284 362.20064 23.274304 25.562883
8100 2.2e+02 -2552.2172 -2632.9342 362.5047 23.505977 25.58597
8200 2.2e+02 -2552.6328 -2633.7047 362.84446 23.609337 25.610996
8300 2.2e+02 -2553.0514 -2636.536 363.15344 24.311943 25.634632
8400 2.3e+02 -2551.9163 -2634.5593 363.4457 24.066867 25.656569
8500 2.3e+02 -2551.1621 -2632.5819 363.73408 23.710645 25.680723
8600 2.3e+02 -2551.3228 -2631.8791 364.03489 23.459181 25.706041
8700 2.3e+02 -2551.3997 -2634.1928 364.32604 24.110586 25.728322
8800 2.4e+02 -2551.5524 -2635.9592 364.60259 24.58049 25.751881
8900 2.4e+02 -2550.9861 -2634.5125 364.87711 24.324098 25.772874
9000 2.4e+02 -2550.3983 -2630.9444 365.15409 23.456228 25.797098
9100 2.4e+02 -2550.2259 -2632.4851 365.42126 23.955067 25.819654
9200 2.5e+02 -2549.7275 -2633.251 365.67315 24.323271 25.84363
9300 2.5e+02 -2549.2312 -2632.0116 365.91463 24.106861 25.865763
9400 2.5e+02 -2549.1796 -2631.7916 366.12014 24.057833 25.884164
9500 2.5e+02 -2549.3237 -2632.8582 366.34704 24.326456 25.907195
9600 2.6e+02 -2548.7761 -2630.2005 366.56572 23.711991 25.926896
9700 2.6e+02 -2548.5538 -2631.9243 366.75569 24.278711 25.946464
9800 2.6e+02 -2548.3631 -2632.4881 366.94867 24.498431 25.965165
9900 2.7e+02 -2548.2213 -2631.2185 367.15325 24.169994 25.986899
10000 2.7e+02 -2547.7789 -2631.2241 367.37155 24.30047 26.007162
Loop time of 267.8 on 1 procs for 10000 steps with 1440 atoms
Pair time (%) = 107.528 (40.1525)
Neigh time (%) = 46.6868 (17.4335)
Comm time (%) = 0.952441 (0.355655)
Outpt time (%) = 0.106937 (0.0399319)
Other time (%) = 112.525 (42.0184)
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5320 ave 5320 max 5320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 419294 ave 419294 max 419294 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 838588 ave 838588 max 838588 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 838588
Ave neighs/atom = 582.353
Neighbor list builds = 1000
Dangerous builds = 0
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