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lammps/examples/deposit/log.15Feb16.deposit.molecule.shake.g++.1
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LAMMPS (15 Feb 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.shake
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 shake 6
fix 5 addatoms wall/reflect zhi EDGE
fix 6 all shake 0.0001 20 1000 b 1 mol dimer
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
0 = # of frozen angles
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: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 tmp.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
SHAKE stats (type/ave/delta) on step 0
Memory usage per processor = 4.44065 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914
200 354 1.0079368 -6.8593854 -6.845149 -0.70414703
300 356 1.0098741 -6.8174079 -6.7961324 -0.691981
400 358 1.015821 -6.7853803 -6.7570054 -0.70383202
500 360 1.0431742 -6.7504367 -6.7142154 -0.68490175
600 362 1.0978772 -6.7139711 -6.6684789 -0.6851563
700 364 1.0536935 -6.6722083 -6.62155 -0.66701737
800 366 1.0615842 -6.6397391 -6.581729 -0.68874151
900 368 1.1690777 -6.6124387 -6.5409597 -0.6631748
SHAKE stats (type/ave/delta) on step 1000
1 1 2.33147e-15
1000 370 1.2238341 -6.5840994 -6.501408 -0.68752603
1100 372 1.0648652 -6.557204 -6.4784841 -0.67502685
1200 374 1.1172515 -6.5811189 -6.4914998 -0.67901522
1300 376 0.90409242 -6.5843683 -6.506222 -0.63816276
1400 378 0.7557157 -6.5929671 -6.5229934 -0.58917374
1500 380 0.84878624 -6.5750822 -6.4913204 -0.68236463
1600 382 0.7649257 -6.5590761 -6.4789792 -0.66149637
1700 384 0.7158335 -6.5532553 -6.4740289 -0.59288863
1800 386 0.71794608 -6.5599255 -6.4762271 -0.61004271
1900 388 0.65121754 -6.5536032 -6.4738794 -0.64961438
SHAKE stats (type/ave/delta) on step 2000
1 1 2.9976e-15
2000 390 0.69034633 -6.5451174 -6.4566114 -0.67204138
2100 392 0.64581391 -6.5535183 -6.4670253 -0.65563645
2200 394 0.65761022 -6.5431965 -6.4513982 -0.72677062
2300 396 0.6528782 -6.554984 -6.4601848 -0.64557524
2400 398 0.65836233 -6.5570075 -6.4577569 -0.69592521
2500 400 0.6411519 -6.5498234 -6.4496434 -0.72785753
2600 402 0.55292699 -6.5815848 -6.4921812 -0.64848109
2700 404 0.49353048 -6.5774182 -6.4949596 -0.72662195
2800 406 0.55912601 -6.5808134 -6.4844124 -0.75266257
2900 408 0.51233032 -6.571748 -6.4807089 -0.67844491
SHAKE stats (type/ave/delta) on step 3000
1 1 1.9984e-15
3000 410 0.47624368 -6.5904636 -6.5033458 -0.72887592
3100 412 0.45076116 -6.5887249 -6.5039336 -0.67815331
3200 414 0.50910708 -6.5995831 -6.501205 -0.78059594
3300 416 0.45275554 -6.5991184 -6.5093291 -0.71529909
3400 418 0.38977308 -6.6018891 -6.522629 -0.69785747
3500 420 0.43625362 -6.6049671 -6.5140809 -0.69363556
3600 422 0.48184349 -6.613181 -6.5104182 -0.72994587
3700 424 0.39971995 -6.5997664 -6.5125634 -0.68093342
3800 426 0.43158248 -6.6067065 -6.5104616 -0.7865976
3900 428 0.39156456 -6.591465 -6.5022651 -0.72788973
SHAKE stats (type/ave/delta) on step 4000
1 1 1.66533e-15
4000 430 0.45520202 -6.6043002 -6.4984393 -0.76339306
4100 432 0.37804217 -6.5825484 -6.4928509 -0.677846
4200 434 0.44408719 -6.6044968 -6.4970564 -0.72092913
4300 436 0.45187505 -6.6214439 -6.5100298 -0.71003531
4400 438 0.44634852 -6.6370982 -6.5250016 -0.7259646
4500 440 0.44774369 -6.6482048 -6.5337249 -0.75067855
4600 442 0.38004568 -6.6303883 -6.5315076 -0.70235189
4700 444 0.39828448 -6.6228295 -6.5174277 -0.78272067
4800 446 0.44085367 -6.6270343 -6.508419 -0.66562901
4900 448 0.47288585 -6.660755 -6.5314503 -0.74826687
SHAKE stats (type/ave/delta) on step 5000
1 1 1.77636e-15
5000 450 0.43761136 -6.6799555 -6.5583968 -0.78360367
5100 452 0.411973 -6.678564 -6.5623548 -0.70194168
5200 454 0.40797743 -6.6866303 -6.5698086 -0.80152835
5300 456 0.34469092 -6.6716537 -6.5714968 -0.67613535
5400 458 0.34013914 -6.6730911 -6.5728318 -0.76078338
5500 460 0.34154783 -6.6605085 -6.5584154 -0.77667767
5600 462 0.36897691 -6.659394 -6.5475828 -0.81373456
5700 464 0.3540965 -6.6625103 -6.553763 -0.78251629
5800 466 0.4082091 -6.6773565 -6.5503387 -0.70767517
5900 468 0.447614 -6.7033749 -6.5623 -0.71623466
SHAKE stats (type/ave/delta) on step 6000
1 1 2.9976e-15
6000 470 0.40113913 -6.679345 -6.5513219 -0.76250746
6100 472 0.42232629 -6.6963163 -6.5598656 -0.86594326
6200 474 0.39623605 -6.7100181 -6.5804473 -0.73732824
6300 476 0.37197778 -6.7159803 -6.5928994 -0.77305419
6400 478 0.33247467 -6.7128004 -6.6015118 -0.64546345
6500 480 0.34120281 -6.7088232 -6.5933119 -0.90961564
6600 482 0.3342529 -6.7056782 -6.5912555 -0.82385057
6700 484 0.34349872 -6.7152033 -6.5963272 -0.73664697
6800 486 0.33490767 -6.7243451 -6.6071963 -0.71978984
6900 488 0.36292075 -6.7126402 -6.5843536 -0.74097013
SHAKE stats (type/ave/delta) on step 7000
1 1 2.55351e-15
7000 490 0.37409279 -6.7221689 -6.5885643 -0.71570235
7100 492 0.3742131 -6.7256916 -6.5906859 -0.70045361
7200 494 0.35928736 -6.7227141 -6.5917997 -0.83125489
7300 496 0.31306304 -6.7132829 -6.5980934 -0.80568965
7400 498 0.381634 -6.7248419 -6.5830702 -0.81697798
7500 500 0.36301318 -6.7268458 -6.5907159 -0.78210607
7600 502 0.34015711 -6.7204559 -6.5917112 -0.81197949
7700 504 0.33268221 -6.7140074 -6.5869413 -0.80133
7800 506 0.32240031 -6.7139558 -6.5897106 -0.78091826
7900 508 0.28597508 -6.7091152 -6.5979339 -0.80994821
SHAKE stats (type/ave/delta) on step 8000
1 1 2.44249e-15
8000 510 0.3444676 -6.7275437 -6.5924583 -0.83444712
8100 512 0.34432983 -6.7402771 -6.604092 -0.79667718
8200 514 0.30652597 -6.7275717 -6.6053191 -0.79549578
8300 516 0.34347028 -6.7383117 -6.6001914 -0.81425668
8400 518 0.31465002 -6.7319759 -6.6044151 -0.77354562
8500 520 0.32120885 -6.7340886 -6.6028253 -0.83177871
8600 522 0.32040584 -6.71864 -6.5866721 -0.78525843
8700 524 0.34513435 -6.7414459 -6.5981888 -0.8520753
8800 526 0.32652464 -6.7316364 -6.5950672 -0.79191959
8900 528 0.29931888 -6.723678 -6.5975445 -0.86587625
SHAKE stats (type/ave/delta) on step 9000
1 1 2.10942e-15
9000 530 0.34199152 -6.7390429 -6.5938579 -0.8478443
9100 532 0.32986081 -6.7434023 -6.6023434 -0.8020183
9200 534 0.32008917 -6.7313919 -6.5935258 -0.73850848
9300 536 0.31879033 -6.745493 -6.6072118 -0.88838081
9400 538 0.31905323 -6.7359144 -6.596551 -0.90024213
9500 540 0.30837753 -6.7292799 -6.5936509 -0.81564405
9600 542 0.34603468 -6.7371426 -6.583917 -0.78921543
9700 544 0.31957585 -6.7248739 -6.582416 -0.76240549
9800 546 0.32315085 -6.7357573 -6.5907537 -0.92679394
9900 548 0.34107078 -6.7519889 -6.5979469 -0.73569227
SHAKE stats (type/ave/delta) on step 10000
1 1 2.44249e-15
10000 550 0.31059632 -6.7463923 -6.6052122 -0.75225652
Loop time of 6.33784 on 1 procs for 10000 steps with 550 atoms
Performance: 681620.330 tau/day, 1577.825 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 | 3.9751 | 3.9751 | 3.9751 | 0.0 | 62.72
Bond | 0.012007 | 0.012007 | 0.012007 | 0.0 | 0.19
Neigh | 2.0003 | 2.0003 | 2.0003 | 0.0 | 31.56
Comm | 0.13159 | 0.13159 | 0.13159 | 0.0 | 2.08
Output | 0.00095081 | 0.00095081 | 0.00095081 | 0.0 | 0.02
Modify | 0.17719 | 0.17719 | 0.17719 | 0.0 | 2.80
Other | | 0.04064 | | | 0.64
Nlocal: 550 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2331 ave 2331 max 2331 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 36458 ave 36458 max 36458 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 36458
Ave neighs/atom = 66.2873
Ave special neighs/atom = 0.363636
Neighbor list builds = 839
Dangerous builds = 0
Total wall time: 0:00:06
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