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lammps/examples/deposit/log.5Oct16.deposit.molecule.g++.1
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LAMMPS (5 Oct 2016)
# sample surface deposition script for molecules
units lj
atom_style bond
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 3 box bond/types 1 extra/bond/per/atom 1
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
bond_style harmonic
bond_coeff 1 5.0 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 0.1 0.1 0.1 587283
fix 3 mobile nve
molecule dimer molecule.dimer
Read molecule dimer:
2 atoms with 3 types
1 bonds with 1 types
0 angles with 0 types
0 dihedrals with 0 types
0 impropers with 0 types
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer 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 lost/bond ignore lost warn
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 = 3.56565 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 0.83994737 -6.8875167 -6.8803581 -0.73353914
200 354 0.83994737 -6.8593854 -6.845149 -0.70414703
300 356 0.84169616 -6.8174189 -6.7961324 -0.69200581
400 358 0.84705847 -6.785416 -6.7570071 -0.70386101
500 360 0.87562973 -6.7507562 -6.714217 -0.68491831
600 362 0.89546097 -6.7133515 -6.6684358 -0.68373096
700 364 0.86923875 -6.6724351 -6.6215093 -0.6663574
800 366 0.93007871 -6.6448092 -6.5816911 -0.68706422
900 368 1.0020611 -6.6164541 -6.540933 -0.66074734
1000 370 1.0082042 -6.5845669 -6.5014101 -0.69453732
1100 372 0.96783727 -6.5649235 -6.4753076 -0.6717256
1200 374 0.97597749 -6.5935771 -6.4925926 -0.69360182
1300 376 0.80208918 -6.5923852 -6.5033139 -0.64868248
1400 378 0.66705029 -6.582928 -6.5082634 -0.6111322
1500 380 0.67555528 -6.5640796 -6.4816473 -0.67638117
1600 382 0.65916245 -6.551728 -6.4662574 -0.62833932
1700 384 0.718469 -6.5624935 -6.4643654 -0.64737567
1800 386 0.59257091 -6.5604373 -6.4675604 -0.61982866
1900 388 0.63118529 -6.5638788 -6.467728 -0.63403973
2000 390 0.6013361 -6.571937 -6.473428 -0.62753885
2100 392 0.48508625 -6.5519559 -6.4663394 -0.66580902
2200 394 0.50266444 -6.5357335 -6.4395422 -0.71780255
2300 396 0.52557785 -6.5469569 -6.4355521 -0.65421156
2400 398 0.66055178 -6.5509266 -6.4186172 -0.65273326
2500 400 0.69210544 -6.5578062 -6.4211169 -0.68232818
2600 402 0.64576434 -6.6050398 -6.4574266 -0.64849208
2700 404 0.56298016 -6.6350083 -6.503562 -0.746185
2800 406 0.49149694 -6.6482516 -6.5155551 -0.76320999
2900 408 0.48366321 -6.6606024 -6.5257882 -0.65612432
3000 410 0.47356141 -6.6756446 -6.5312692 -0.70811639
3100 412 0.47568619 -6.6934709 -6.5474974 -0.72316681
3200 414 0.38708973 -6.6932142 -6.5659264 -0.73056797
3300 416 0.43665017 -6.6999962 -6.5567504 -0.75890315
3400 418 0.34923989 -6.7185629 -6.5909531 -0.66986444
3500 420 0.33999089 -6.6922536 -6.5729709 -0.70698979
3600 422 0.37659 -6.6827522 -6.5521249 -0.68796169
3700 424 0.34150483 -6.6973468 -6.5698573 -0.68312043
3800 426 0.41110243 -6.7043016 -6.5510735 -0.71352712
3900 428 0.40957994 -6.7172729 -6.5557011 -0.70233721
4000 430 0.42723175 -6.7170007 -6.5537357 -0.7497547
4100 432 0.37176212 -6.7218812 -6.5574518 -0.7098714
4200 434 0.33265381 -6.7082458 -6.5637164 -0.70399102
4300 436 0.43029564 -6.7142231 -6.5431037 -0.76230436
4400 438 0.38216708 -6.7315576 -6.5614315 -0.6674734
4500 440 0.35981631 -6.7496554 -6.583264 -0.73404044
4600 442 0.36073617 -6.7479258 -6.5907772 -0.71067075
4700 444 0.35705292 -6.7678184 -6.5973053 -0.75325156
4800 446 0.37426281 -6.7869581 -6.6010006 -0.67542828
4900 448 0.33524109 -6.7800476 -6.6026334 -0.66398211
5000 450 0.31770101 -6.7884069 -6.6064017 -0.74655689
5100 452 0.31791473 -6.7695361 -6.5901194 -0.77591531
5200 454 0.37320367 -6.7756559 -6.5809165 -0.76247336
5300 456 0.32228579 -6.7786007 -6.5856918 -0.67574614
5400 458 0.31274193 -6.7828483 -6.5928063 -0.72466782
5500 460 0.30708694 -6.7858555 -6.5973813 -0.76883863
5600 462 0.32849848 -6.7983978 -6.6021343 -0.76855876
5700 464 0.35124617 -6.8131288 -6.5975496 -0.78865946
5800 466 0.35055399 -6.8184367 -6.6060092 -0.70530424
5900 468 0.33326299 -6.8299034 -6.6095077 -0.68840817
6000 470 0.40104727 -6.8633145 -6.6132375 -0.77187971
6100 472 0.29105598 -6.8410097 -6.6311104 -0.7715889
6200 474 0.30288813 -6.8634336 -6.6428858 -0.78760673
6300 476 0.34293767 -6.9005784 -6.6534079 -0.74817698
6400 478 0.34963015 -6.9292987 -6.666687 -0.71175243
6500 480 0.319367 -6.9395521 -6.6743587 -0.76432283
6600 482 0.29016877 -6.9324045 -6.679475 -0.90715919
6700 484 0.35436305 -6.9551643 -6.6789059 -0.79939008
6800 486 0.327512 -6.9608693 -6.687362 -0.70392295
6900 488 0.32349315 -6.9513424 -6.6847712 -0.75205809
7000 490 0.35355467 -6.9907283 -6.7038887 -0.80881264
7100 492 0.32140685 -6.9979325 -6.7169278 -0.68673022
7200 494 0.32242041 -7.0116346 -6.728848 -0.79432529
7300 496 0.26266524 -6.9966902 -6.7334152 -0.86050198
7400 498 0.31564904 -7.0133015 -6.7158904 -0.81615792
7500 500 0.36973921 -7.0516561 -6.717083 -0.79423832
7600 502 0.33599186 -7.0516408 -6.7296713 -0.83610882
7700 504 0.29691416 -7.0495062 -6.738076 -0.83634675
7800 506 0.3244215 -7.0434148 -6.7342677 -0.7170135
7900 508 0.29167542 -7.0637209 -6.7576924 -0.78857188
8000 510 0.34198998 -7.1041546 -6.7635656 -0.83376311
8100 512 0.33068905 -7.1341746 -6.7960028 -0.78639771
8200 514 0.29688969 -7.136245 -6.8093036 -0.85753154
8300 516 0.29829676 -7.1313196 -6.8076328 -0.76960702
8400 518 0.31096049 -7.1559166 -6.8202327 -0.72775356
8500 520 0.26677854 -7.1413516 -6.8361967 -0.81908087
8600 522 0.28811568 -7.1390821 -6.8248702 -0.88515896
8700 524 0.27520272 -7.1501541 -6.8311651 -0.81462692
8800 526 0.28763152 -7.1525343 -6.8281253 -0.74124759
8900 528 0.29917883 -7.1547953 -6.8229151 -0.81440712
9000 530 0.28474306 -7.1612717 -6.8236771 -0.79150099
9100 532 0.29409713 -7.1748026 -6.8272211 -0.7916524
9200 534 0.26767862 -7.1646362 -6.8313179 -0.79362392
9300 536 0.27111075 -7.1719185 -6.8399556 -0.9578129
9400 538 0.33952348 -7.207044 -6.8368639 -0.89888939
9500 540 0.3284439 -7.2371916 -6.8625844 -0.7659201
9600 542 0.31256223 -7.2266123 -6.8655682 -0.82722861
9700 544 0.30268239 -7.2315617 -6.8705788 -0.81448482
9800 546 0.26835398 -7.2214231 -6.8757262 -0.86029096
9900 548 0.31676744 -7.264604 -6.884266 -0.74053962
10000 550 0.31368419 -7.2759575 -6.8979611 -0.76153366
Loop time of 6.51779 on 1 procs for 10000 steps with 550 atoms
Performance: 662801.655 tau/day, 1534.263 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 | 4.0744 | 4.0744 | 4.0744 | 0.0 | 62.51
Bond | 0.01209 | 0.01209 | 0.01209 | 0.0 | 0.19
Neigh | 2.1316 | 2.1316 | 2.1316 | 0.0 | 32.70
Comm | 0.13266 | 0.13266 | 0.13266 | 0.0 | 2.04
Output | 0.0008409 | 0.0008409 | 0.0008409 | 0.0 | 0.01
Modify | 0.12403 | 0.12403 | 0.12403 | 0.0 | 1.90
Other | | 0.04216 | | | 0.65
Nlocal: 550 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2349 ave 2349 max 2349 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39710 ave 39710 max 39710 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39710
Ave neighs/atom = 72.2
Ave special neighs/atom = 0.363636
Neighbor list builds = 877
Dangerous builds = 0
Total wall time: 0:00:06
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