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lammps/examples/deposit/log.5Oct16.deposit.atom.g++.1
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LAMMPS (5 Oct 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 1 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:474)
#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 = 2.54053 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 351 0.83994737 -6.3459678 -6.3423783 -0.12047746
200 352 0.83994737 -6.2377119 -6.2305533 -0.3420432
300 353 0.84063802 -6.102615 -6.0918986 -0.40610132
400 354 0.84248131 -6.0284461 -6.0141667 -0.46041042
500 355 0.84689832 -5.9201486 -5.9022564 -0.44565465
600 356 0.86694405 -5.8676653 -5.8457482 -0.45310439
700 357 0.93585062 -5.8080247 -5.7804997 -0.4235135
800 358 0.87721962 -5.7667317 -5.7373277 -0.47514081
900 359 0.98586832 -5.7397849 -5.7027118 -0.53506606
1000 360 1.1977372 -5.7043822 -5.6544765 -0.5143915
1100 361 0.86840339 -5.6974093 -5.6577177 -0.57133639
1200 362 0.91410157 -5.6449104 -5.5994579 -0.54863872
1300 363 1.0317704 -5.6108925 -5.5554668 -0.63480165
1400 364 0.78937966 -5.5995247 -5.5539836 -0.54633211
1500 365 1.0022364 -5.592367 -5.5305854 -0.61542058
1600 366 1.36861 -5.5602006 -5.4704557 -0.5557092
1700 367 1.2584928 -5.6125569 -5.5251139 -0.54474262
1800 368 1.2395052 -5.5575635 -5.4666216 -0.39432632
1900 369 1.4424114 -5.5511809 -5.4397751 -0.39219555
2000 370 1.0355115 -5.5657056 -5.4817452 -0.42684751
2100 371 1.0710232 -5.621664 -5.5307281 -0.60685079
2200 372 1.1723348 -5.5425772 -5.4385798 -0.53815496
2300 373 1.0854557 -5.6087637 -5.5083664 -0.6673737
2400 374 1.1021474 -5.5084817 -5.4023926 -0.52097006
2500 375 1.2269861 -5.4265984 -5.3038998 -0.49657196
2600 376 1.0399561 -5.476211 -5.3683432 -0.62204748
2700 377 1.0944051 -5.4078459 -5.2902772 -0.63977962
2800 378 1.0323162 -5.3957488 -5.281047 -0.62614071
2900 379 1.1065509 -5.3744068 -5.2474017 -0.57270098
3000 380 1.0280773 -5.3681364 -5.2463904 -0.66444652
3100 381 1.04368 -5.3317133 -5.2043351 -0.65414012
3200 382 1.0449176 -5.3088894 -5.1775909 -0.63418281
3300 383 1.1102316 -5.2604462 -5.1169568 -0.57913921
3400 384 1.2757372 -5.2904271 -5.1209933 -0.56059979
3500 385 1.0652825 -5.2267633 -5.0814975 -0.54269026
3600 386 1.0229877 -5.2277887 -5.0846764 -0.61796376
3700 387 0.96408893 -5.1769745 -5.0387137 -0.55113976
3800 388 1.0505509 -5.2197338 -5.0654003 -0.70804854
3900 389 0.95266837 -5.1605736 -5.017306 -0.52702995
4000 390 1.0413134 -5.2352309 -5.0750288 -0.66067611
4100 391 1.1486876 -5.2288717 -5.0481958 -0.65810366
4200 392 1.042156 -5.2716813 -5.1041919 -0.66967821
4300 393 0.9698966 -5.197189 -5.0380075 -0.46525386
4400 394 0.77874089 -5.257629 -5.12718 -0.67739426
4500 395 1.0157317 -5.2445238 -5.0709494 -0.5922696
4600 396 1.1447586 -5.2710072 -5.0715417 -0.62651602
4700 397 1.1902582 -5.311166 -5.0997978 -0.7459111
4800 398 0.95725223 -5.2619858 -5.0888146 -0.49253005
4900 399 1.0409188 -5.271542 -5.0797938 -0.56590831
5000 400 1.0870091 -5.2619328 -5.0581186 -0.61273172
5100 401 0.90909459 -5.3465255 -5.1730948 -0.61196826
5200 402 0.86456113 -5.2535951 -5.0858445 -0.47565663
5300 403 0.92212118 -5.27055 -5.0886427 -0.55555966
5400 404 0.96914771 -5.2702613 -5.075952 -0.58082428
5500 405 0.96828577 -5.263648 -5.0664046 -0.59818023
5600 406 1.0567855 -5.2988668 -5.0802215 -0.76787404
5700 407 1.0085537 -5.2053833 -4.9935127 -0.55232589
5800 408 0.86382168 -5.2038339 -5.0196367 -0.58471077
5900 409 0.98477929 -5.1862354 -4.9731475 -0.54570637
6000 410 1.0777582 -5.2410631 -5.004482 -0.6711063
6100 411 1.1113596 -5.1775001 -4.9300806 -0.54007427
6200 412 0.86878402 -5.1939794 -4.9978704 -0.64766373
6300 413 1.0174495 -5.2156346 -4.9828284 -0.60249161
6400 414 1.1184824 -5.2250149 -4.9656567 -0.64875897
6500 415 1.1607873 -5.2674286 -4.9947135 -0.65956525
6600 416 0.98987615 -5.2384031 -5.0028316 -0.66246801
6700 417 0.86291514 -5.2362314 -5.0282627 -0.56707491
6800 418 0.97203041 -5.2323576 -4.9951636 -0.54330037
6900 419 0.92972764 -5.2416508 -5.0119926 -0.58029478
7000 420 1.1472637 -5.3052417 -5.0184258 -0.64366532
7100 421 0.9275385 -5.3077824 -5.0731438 -0.54374736
7200 422 0.91492781 -5.3012606 -5.0671084 -0.55376032
7300 423 0.85621578 -5.3016071 -5.0799626 -0.56221777
7400 424 0.94571335 -5.2212917 -4.9737111 -0.52202896
7500 425 1.0819864 -5.2109452 -4.924537 -0.47511017
7600 426 1.1449289 -5.2138905 -4.9075011 -0.62518982
7700 427 0.98061711 -5.2129268 -4.9476779 -0.56003723
7800 428 1.0450011 -5.1652647 -4.8795985 -0.51780393
7900 429 0.98731276 -5.1520883 -4.879369 -0.46982802
8000 430 1.058201 -5.2605391 -4.9652272 -0.69798004
8100 431 1.1031976 -5.2428971 -4.9319029 -0.64564967
8200 432 0.99653694 -5.2790505 -4.9953143 -0.70353076
8300 433 1.2188348 -5.2664086 -4.9159584 -0.56779776
8400 434 1.0610032 -5.2291848 -4.9211516 -0.44040649
8500 435 0.88475193 -5.2938308 -5.034507 -0.70250793
8600 436 0.98427323 -5.2350748 -4.9438564 -0.54824635
8700 437 0.99048279 -5.2379591 -4.9421742 -0.68060327
8800 438 0.92407001 -5.1922203 -4.9137335 -0.67045436
8900 439 0.99630902 -5.1772321 -4.8742543 -0.66221601
9000 440 0.95766319 -5.1605694 -4.8667409 -0.68216304
9100 441 1.0231065 -5.1295203 -4.8128445 -0.52553274
9200 442 0.87783667 -5.1084284 -4.8343527 -0.54144063
9300 443 0.93581944 -5.1737089 -4.8790208 -0.68780812
9400 444 0.99373921 -5.1548474 -4.839268 -0.57996189
9500 445 0.95187515 -5.1408039 -4.8359899 -0.56491542
9600 446 0.91625338 -5.1555381 -4.8597074 -0.62931435
9700 447 0.9526195 -5.1025432 -4.7924624 -0.51046895
9800 448 0.97167962 -5.185173 -4.8663406 -0.56989109
9900 449 1.0038671 -5.1540302 -4.8220162 -0.56356384
10000 450 0.95642062 -5.2046982 -4.8858913 -0.70500643
Loop time of 5.63963 on 1 procs for 10000 steps with 450 atoms
Performance: 766007.688 tau/day, 1773.166 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.1973 | 3.1973 | 3.1973 | 0.0 | 56.69
Neigh | 2.1646 | 2.1646 | 2.1646 | 0.0 | 38.38
Comm | 0.11922 | 0.11922 | 0.11922 | 0.0 | 2.11
Output | 0.00081301 | 0.00081301 | 0.00081301 | 0.0 | 0.01
Modify | 0.11702 | 0.11702 | 0.11702 | 0.0 | 2.07
Other | | 0.04063 | | | 0.72
Nlocal: 450 ave 450 max 450 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1973 ave 1973 max 1973 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 29176 ave 29176 max 29176 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 29176
Ave neighs/atom = 64.8356
Neighbor list builds = 1143
Dangerous builds = 0
Total wall time: 0:00:05
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