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lammps/examples/deposit/log.15Feb16.deposit.molecule.shake.g++.4
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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 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
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 = 4.51485 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337
200 354 1.0079368 -6.8644786 -6.8502422 -0.69623155
300 356 1.0098741 -6.8219324 -6.800657 -0.69552497
400 358 1.015821 -6.775427 -6.7470521 -0.67240912
500 360 1.0431742 -6.7311558 -6.6949345 -0.69505765
600 362 1.0978772 -6.7107816 -6.6652895 -0.66124338
700 364 1.0536993 -6.6818292 -6.6311706 -0.67789771
800 366 1.0615655 -6.6354474 -6.5774383 -0.64710621
900 368 1.1688557 -6.614281 -6.5428156 -0.64842218
SHAKE stats (type/ave/delta) on step 1000
1 1 1.22125e-15
1000 370 1.2172009 -6.5772424 -6.4949991 -0.67942188
1100 372 1.1031034 -6.55895 -6.4774034 -0.65896897
1200 374 1.040192 -6.5874108 -6.503973 -0.62919433
1300 376 0.94890463 -6.5897148 -6.5076952 -0.63346087
1400 378 0.78945672 -6.5952649 -6.522167 -0.67613271
1500 380 0.82876461 -6.5798609 -6.4980749 -0.65306056
1600 382 0.73883758 -6.5591084 -6.4817432 -0.62749488
1700 384 0.73539709 -6.5556021 -6.4742105 -0.66817567
1800 386 0.67455206 -6.5535874 -6.474948 -0.57721026
1900 388 0.66352723 -6.5469905 -6.4657597 -0.69276627
SHAKE stats (type/ave/delta) on step 2000
1 1 2.22045e-15
2000 390 0.81013116 -6.5567994 -6.4529364 -0.71579948
2100 392 0.72889872 -6.5689128 -6.4712924 -0.65504494
2200 394 0.57901901 -6.552299 -6.4714715 -0.67723953
2300 396 0.59157803 -6.5485081 -6.4626098 -0.66397554
2400 398 0.70712699 -6.5593644 -6.4527623 -0.70641253
2500 400 0.7569242 -6.576119 -6.4578496 -0.69907756
2600 402 0.6662505 -6.6038869 -6.4961599 -0.66941055
2700 404 0.51455113 -6.6038412 -6.5178704 -0.69578494
2800 406 0.58401979 -6.6058664 -6.5051733 -0.70647457
2900 408 0.50129416 -6.6138934 -6.5248154 -0.64390758
SHAKE stats (type/ave/delta) on step 3000
1 1 2.66454e-15
3000 410 0.44807689 -6.6222658 -6.5403005 -0.68340233
3100 412 0.45962393 -6.6204312 -6.5339728 -0.66309459
3200 414 0.50182826 -6.6295842 -6.5326126 -0.74122586
3300 416 0.48471205 -6.6424495 -6.5463227 -0.69764601
3400 418 0.36856546 -6.6251783 -6.5502308 -0.76543921
3500 420 0.4203509 -6.6198957 -6.5323226 -0.64154608
3600 422 0.54795097 -6.6410801 -6.5242185 -0.7463818
3700 424 0.51183952 -6.6521145 -6.5404514 -0.70304908
3800 426 0.39414561 -6.6456807 -6.5577844 -0.74178922
3900 428 0.40589341 -6.6564647 -6.5640007 -0.78327027
SHAKE stats (type/ave/delta) on step 4000
1 1 1.88738e-15
4000 430 0.43166847 -6.6566443 -6.5562563 -0.73290988
4100 432 0.40408931 -6.6500622 -6.5541845 -0.73057986
4200 434 0.35377187 -6.6356255 -6.5500355 -0.76557381
4300 436 0.4291929 -6.657321 -6.5514993 -0.78608144
4400 438 0.43151668 -6.6494979 -6.5411262 -0.70820395
4500 440 0.44315446 -6.6596739 -6.5463674 -0.82000058
4600 442 0.41285261 -6.6553044 -6.547888 -0.76115447
4700 444 0.38354616 -6.6502515 -6.54875 -0.6954286
4800 446 0.39108666 -6.648355 -6.5431299 -0.72779836
4900 448 0.3799768 -6.6517925 -6.5478926 -0.79771549
SHAKE stats (type/ave/delta) on step 5000
1 1 3.10862e-15
5000 450 0.39260452 -6.6598567 -6.5507999 -0.76677324
5100 452 0.41475009 -6.6627963 -6.5458038 -0.70468384
5200 454 0.4115583 -6.6658575 -6.5480104 -0.78115993
5300 456 0.3753641 -6.6631393 -6.5540696 -0.78711192
5400 458 0.36565536 -6.6545908 -6.5468103 -0.74549556
5500 460 0.33271655 -6.6418893 -6.542436 -0.76780862
5600 462 0.36832168 -6.6440805 -6.5324679 -0.75143503
5700 464 0.39059076 -6.6481163 -6.5281612 -0.78380485
5800 466 0.36650802 -6.6430337 -6.5289916 -0.75502025
5900 468 0.35914314 -6.6418801 -6.5286886 -0.67704807
SHAKE stats (type/ave/delta) on step 6000
1 1 2.22045e-15
6000 470 0.39116517 -6.6612874 -6.5364474 -0.84800605
6100 472 0.38421704 -6.6693489 -6.545211 -0.78734456
6200 474 0.38216918 -6.6812774 -6.5563065 -0.81814647
6300 476 0.34722048 -6.6730701 -6.5581809 -0.77616674
6400 478 0.32907391 -6.6719973 -6.5618471 -0.7458085
6500 480 0.31094699 -6.6715976 -6.566329 -0.83282406
6600 482 0.35169592 -6.6680323 -6.5476384 -0.85138473
6700 484 0.36350925 -6.6706468 -6.5448456 -0.71970784
6800 486 0.38133383 -6.6922722 -6.5588839 -0.77339402
6900 488 0.34810579 -6.6746177 -6.551568 -0.77360649
SHAKE stats (type/ave/delta) on step 7000
1 1 3.66374e-15
7000 490 0.3590117 -6.683101 -6.5548825 -0.80004574
7100 492 0.38269726 -6.688913 -6.5508464 -0.81445922
7200 494 0.31934554 -6.6944357 -6.578075 -0.74069497
7300 496 0.32758627 -6.6955862 -6.5750529 -0.78679117
7400 498 0.3660502 -6.7111626 -6.5751801 -0.78104263
7500 500 0.32569889 -6.6953555 -6.5732185 -0.74496853
7600 502 0.33737271 -6.6971694 -6.5694785 -0.90240288
7700 504 0.35222518 -6.7006509 -6.5661204 -0.86220892
7800 506 0.31834385 -6.6988433 -6.5761614 -0.78723443
7900 508 0.35977076 -6.7264843 -6.5866128 -0.8568963
SHAKE stats (type/ave/delta) on step 8000
1 1 2.22045e-15
8000 510 0.35931856 -6.7266146 -6.5857054 -0.85544232
8100 512 0.36797798 -6.739034 -6.5934958 -0.82062699
8200 514 0.40277035 -6.7571847 -6.5965467 -0.82121365
8300 516 0.32568144 -6.7419653 -6.6109984 -0.78580816
8400 518 0.33705466 -6.7532799 -6.6166361 -0.83332745
8500 520 0.30158673 -6.7342587 -6.6110142 -0.8578352
8600 522 0.32525112 -6.7446972 -6.6107336 -0.96759
8700 524 0.32985772 -6.7480971 -6.611181 -0.78464535
8800 526 0.32397396 -6.7465569 -6.6110545 -0.81041129
8900 528 0.33669589 -6.7543874 -6.6125032 -0.87866197
SHAKE stats (type/ave/delta) on step 9000
1 1 3.88578e-15
9000 530 0.32538398 -6.7436298 -6.6054951 -0.79985713
9100 532 0.3336509 -6.7541485 -6.6114688 -0.84449566
9200 534 0.31516122 -6.7553334 -6.6195898 -0.88997909
9300 536 0.30963064 -6.7627673 -6.6284593 -0.75349544
9400 538 0.34228518 -6.7754099 -6.6258988 -0.77001741
9500 540 0.29032769 -6.7737667 -6.6460763 -0.85854407
9600 542 0.31033087 -6.7764458 -6.63903 -0.8553105
9700 544 0.33657054 -6.7798228 -6.629789 -0.91356823
9800 546 0.30235172 -6.7634263 -6.6277557 -0.92787364
9900 548 0.3446797 -6.7794717 -6.6237998 -0.88766558
SHAKE stats (type/ave/delta) on step 10000
1 1 2.55351e-15
10000 550 0.30296128 -6.7756768 -6.6379672 -0.84420968
Loop time of 5.79101 on 4 procs for 10000 steps with 550 atoms
Performance: 745983.597 tau/day, 1726.814 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 | 0.0016487 | 1.0205 | 2.974 | 120.1 | 17.62
Bond | 0.0012839 | 0.003953 | 0.010697 | 6.2 | 0.07
Neigh | 0.0035315 | 0.52893 | 1.691 | 94.9 | 9.13
Comm | 0.57816 | 2.7844 | 4.9123 | 99.7 | 48.08
Output | 0.0024757 | 0.0037841 | 0.0065219 | 2.7 | 0.07
Modify | 0.41353 | 1.2632 | 3.4168 | 111.3 | 21.81
Other | | 0.1862 | | | 3.22
Nlocal: 137.5 ave 300 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1874.5 ave 2648 max 509 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 9185.75 ave 23231 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 36743
Ave neighs/atom = 66.8055
Ave special neighs/atom = 0.363636
Neighbor list builds = 833
Dangerous builds = 0
Total wall time: 0:00:05
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