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lammps/examples/deposit/log.15Feb16.deposit.atom.g++.4
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LAMMPS (15 Feb 2016)
# sample surface deposition script for atoms
units lj
atom_style atomic
boundary p p f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region box block 0 5 0 5 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
1 by 1 by 4 MPI processor grid
region substrate block INF INF INF INF INF 3
create_atoms 1 region substrate
Created 350 atoms
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 1.0 1.0 5.0
mass * 1.0
neigh_modify delay 0
group addatoms type 2
0 atoms in group addatoms
region mobile block 0 5 0 5 2 INF
group mobile region mobile
150 atoms in group mobile
compute add addatoms temp
compute_modify add dynamic yes extra 0
fix 1 addatoms nve
fix 2 mobile langevin 1.0 1.0 0.1 587283
fix 3 mobile nve
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 2 100 12345 region slab near 1.0 vz -1.0 -1.0
fix 5 addatoms wall/reflect zhi EDGE
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
#dump 1 all atom 50 dump.deposit.atom
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65 -> bins = 3 3 6
Memory usage per processor = 2.60645 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 351 0.83994737 -6.3596932 -6.3561037 -0.10696131
200 352 0.83994737 -6.3044678 -6.2973092 -0.38494392
300 353 0.84063802 -6.164881 -6.1541646 -0.41223901
400 354 0.84248131 -6.0388811 -6.0246018 -0.31496573
500 355 0.84688124 -6.0084178 -5.990526 -0.37482638
600 356 0.86681079 -6.0286531 -6.0067393 -0.54868509
700 357 0.93465165 -5.9564751 -5.9289854 -0.48728319
800 358 0.86905333 -5.8498868 -5.8207565 -0.4146325
900 359 0.90267243 -5.7844092 -5.7504647 -0.38165702
1000 360 0.92357983 -5.777549 -5.7390665 -0.38381524
1100 361 1.3481334 -5.7713272 -5.7097089 -0.44738093
1200 362 1.15494 -5.7155857 -5.6581577 -0.38961524
1300 363 0.97329529 -5.6445379 -5.5922534 -0.37655267
1400 364 1.2187161 -5.6818221 -5.6115115 -0.60238965
1500 365 1.2026123 -5.66813 -5.5939963 -0.56317155
1600 366 1.4012284 -5.6764268 -5.584543 -0.49098723
1700 367 1.3618781 -5.6121414 -5.517515 -0.47893702
1800 368 0.9670811 -5.5551479 -5.4841935 -0.3409573
1900 369 1.002089 -5.6037307 -5.5263336 -0.45325785
2000 370 1.3599869 -5.5793818 -5.4691126 -0.44566809
2100 371 1.0007793 -5.585692 -5.5007201 -0.54221497
2200 372 1.1061185 -5.5172265 -5.4191031 -0.46551381
2300 373 0.99747278 -5.556485 -5.4642254 -0.55670256
2400 374 1.0990419 -5.5538566 -5.4480664 -0.63197307
2500 375 1.1415073 -5.5118583 -5.3977075 -0.51563393
2600 376 1.010645 -5.5221148 -5.4172873 -0.5495753
2700 377 1.0964314 -5.4985586 -5.3807722 -0.54042329
2800 378 0.93010494 -5.4391153 -5.3357703 -0.52395276
2900 379 0.93021935 -5.5144863 -5.4077197 -0.69409861
3000 380 1.0264349 -5.4314217 -5.3098702 -0.55798648
3100 381 1.1612003 -5.4088381 -5.2671168 -0.53167304
3200 382 1.087873 -5.4402561 -5.30356 -0.71158961
3300 383 1.048209 -5.4309208 -5.2954473 -0.67551183
3400 384 1.0275111 -5.4536819 -5.3172156 -0.73761551
3500 385 1.2716758 -5.4036871 -5.2302768 -0.63612803
3600 386 1.2154857 -5.4003006 -5.2302586 -0.61641823
3700 387 1.3376196 -5.4279619 -5.2361328 -0.59689863
3800 388 1.2523858 -5.358924 -5.1749395 -0.55321551
3900 389 1.1650111 -5.333714 -5.1585131 -0.55412715
4000 390 0.98352817 -5.2980477 -5.1467357 -0.68167218
4100 391 1.2779827 -5.297845 -5.0968324 -0.65191886
4200 392 1.0255535 -5.2295551 -5.064734 -0.4761042
4300 393 1.1237891 -5.2225392 -5.0381005 -0.52734107
4400 394 0.97683493 -5.2029168 -5.0392846 -0.59056934
4500 395 1.0041363 -5.1999674 -5.0283744 -0.72038887
4600 396 1.180431 -5.1922463 -4.9865652 -0.55948152
4700 397 1.0627588 -5.2298403 -5.0411136 -0.56208516
4800 398 1.1202971 -5.2121979 -5.0095311 -0.46793143
4900 399 1.2006424 -5.286657 -5.0654861 -0.63042465
5000 400 1.0893045 -5.2512329 -5.0469883 -0.6377186
5100 401 1.1454769 -5.2580965 -5.0395704 -0.59767673
5200 402 0.9467869 -5.249752 -5.0660471 -0.71059143
5300 403 0.96324471 -5.1724796 -4.9824599 -0.50261414
5400 404 1.1634679 -5.1969879 -4.9637184 -0.5555004
5500 405 0.99830529 -5.1678627 -4.9645042 -0.59796761
5600 406 1.0065294 -5.1718443 -4.9635968 -0.59208276
5700 407 0.97182891 -5.2110109 -5.0068552 -0.63948837
5800 408 1.1234056 -5.167964 -4.9284143 -0.53293706
5900 409 1.0124687 -5.1828555 -4.9637761 -0.4922831
6000 410 1.0804251 -5.2275621 -4.9903956 -0.52329411
6100 411 1.0772335 -5.26665 -5.0268279 -0.56252803
6200 412 1.0954219 -5.2051974 -4.9579299 -0.42238433
6300 413 1.0546562 -5.3045877 -5.0632681 -0.61171278
6400 414 1.0985486 -5.335815 -5.0810791 -0.67859848
6500 415 1.0416817 -5.2636237 -5.0188913 -0.61917889
6600 416 0.86231375 -5.1755229 -4.9703088 -0.51453403
6700 417 0.91939084 -5.2111481 -4.9895683 -0.5239181
6800 418 1.1242247 -5.240558 -4.9662256 -0.50836149
6900 419 1.0578099 -5.2020602 -4.9407635 -0.50665054
7000 420 0.98040609 -5.1860531 -4.9409516 -0.63496783
7100 421 0.99357521 -5.1989655 -4.9476216 -0.53673646
7200 422 1.1168255 -5.1850834 -4.8992607 -0.59194739
7300 423 1.0465199 -5.1485597 -4.877652 -0.4964202
7400 424 0.91999946 -5.1379187 -4.8970698 -0.45185782
7500 425 0.94098172 -5.2197403 -4.9706569 -0.6452508
7600 426 0.92305237 -5.2489345 -5.0019205 -0.67135987
7700 427 1.0692215 -5.2004352 -4.9112195 -0.60227676
7800 428 0.98946072 -5.2168971 -4.9464137 -0.61326494
7900 429 1.1578277 -5.2222386 -4.9024191 -0.6841757
8000 430 1.1057865 -5.2447073 -4.9361157 -0.57784399
8100 431 1.0527643 -5.2189715 -4.9221945 -0.5484357
8200 432 1.058862 -5.2236909 -4.9222094 -0.66008275
8300 433 1.0543331 -5.2105622 -4.907411 -0.60403808
8400 434 1.204621 -5.193864 -4.8441353 -0.57011085
8500 435 1.0247837 -5.1910294 -4.8906617 -0.6081565
8600 436 1.0314146 -5.1732662 -4.8680999 -0.59109692
8700 437 0.98196719 -5.144054 -4.8508121 -0.56483113
8800 438 1.1013378 -5.1980036 -4.8660936 -0.60785883
8900 439 1.1016903 -5.1251846 -4.7901603 -0.49838338
9000 440 1.0926008 -5.1360049 -4.8007751 -0.54767492
9100 441 1.1454324 -5.2217858 -4.8672472 -0.67308812
9200 442 1.059963 -5.1945332 -4.8635945 -0.54419884
9300 443 1.2168669 -5.2244149 -4.8412254 -0.49530257
9400 444 1.0656851 -5.1556938 -4.8172667 -0.41869179
9500 445 0.99794121 -5.2447091 -4.9251436 -0.638328
9600 446 1.1717194 -5.247915 -4.869602 -0.65769093
9700 447 1.2345494 -5.1717485 -4.7698985 -0.54917447
9800 448 1.187781 -5.1672598 -4.7775192 -0.55482592
9900 449 0.99538785 -5.1593424 -4.8301329 -0.5886329
10000 450 0.95030539 -5.1408028 -4.8240344 -0.4992403
Loop time of 4.67299 on 4 procs for 10000 steps with 450 atoms
Performance: 924461.293 tau/day, 2139.957 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0024376 | 0.84903 | 2.165 | 97.5 | 18.17
Neigh | 0.0053134 | 0.57645 | 1.783 | 95.1 | 12.34
Comm | 0.54729 | 2.3753 | 4.0958 | 83.6 | 50.83
Output | 0.0022168 | 0.00986 | 0.028065 | 10.7 | 0.21
Modify | 0.0059755 | 0.037876 | 0.085638 | 16.4 | 0.81
Other | | 0.8245 | | | 17.64
Nlocal: 112.5 ave 250 max 9 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 1522.75 ave 2248 max 440 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 7415.25 ave 17049 max 23 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 29661
Ave neighs/atom = 65.9133
Neighbor list builds = 1164
Dangerous builds = 0
Total wall time: 0:00:04
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