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lammps/examples/deposit/log.deposit.molecule.shake.31Dec13.linux.1
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LAMMPS (30 Dec 2013)
# 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
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:439)
#dump 1 all atom 50 dump.deposit.atom
#dump 1 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
#dump 1 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000
SHAKE stats (type/ave/delta) on step 0
Memory usage per processor = 3.29483 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 0.83994737 -6.8170634 -6.7958288 -0.69170868
400 358 0.84041725 -6.7849764 -6.756806 -0.7035216
500 360 0.84183519 -6.748903 -6.7138265 -0.68387035
600 362 0.8457626 -6.7098456 -6.6677911 -0.68283488
700 364 0.87175336 -6.6714189 -6.6211254 -0.66640179
800 366 0.89727068 -6.6401774 -6.58134 -0.6884522
900 368 0.8910839 -6.6065228 -6.5411444 -0.66350953
SHAKE stats (type/ave/delta) on step 1000
1 1 2.22045e-15
1000 370 0.91133967 -6.588373 -6.5144806 -0.66697456
1100 372 0.94335272 -6.5833353 -6.4996508 -0.67903461
1200 374 0.99444649 -6.5738934 -6.4781713 -0.69968884
1300 376 0.90431799 -6.5527637 -6.4589648 -0.65395726
1400 378 0.87224945 -6.5791233 -6.4822067 -0.59735159
1500 380 0.70715888 -6.5873408 -6.5035983 -0.66564852
1600 382 0.62213024 -6.5772707 -6.4990972 -0.64409364
1700 384 0.68070957 -6.5844244 -6.4940176 -0.64134987
1800 386 0.57401946 -6.5665002 -6.4861969 -0.67470049
1900 388 0.5881638 -6.5787142 -6.4923087 -0.63724246
SHAKE stats (type/ave/delta) on step 2000
1 1 1.9984e-15
2000 390 0.51745341 -6.5676275 -6.4880193 -0.64186008
2100 392 0.64333766 -6.5649026 -6.4615091 -0.69333804
2200 394 0.57593118 -6.5450453 -6.4485695 -0.68021805
2300 396 0.53492565 -6.5584624 -6.4652557 -0.62345783
2400 398 0.45661041 -6.544717 -6.4621142 -0.65654987
2500 400 0.58215641 -6.5446545 -6.4355002 -0.66883882
2600 402 0.43995697 -6.5607405 -6.4753757 -0.67436771
2700 404 0.4466557 -6.5533428 -6.4637906 -0.70117445
2800 406 0.42040295 -6.54221 -6.4552301 -0.72050093
2900 408 0.49200481 -6.5487677 -6.4438549 -0.67794849
SHAKE stats (type/ave/delta) on step 3000
1 1 1.66533e-15
3000 410 0.5342337 -6.5660827 -6.4488119 -0.68521246
3100 412 0.41569551 -6.5482164 -6.4543822 -0.65929253
3200 414 0.41434893 -6.5508493 -6.4547684 -0.73417701
3300 416 0.46561679 -6.574876 -6.4640682 -0.74107992
3400 418 0.39535512 -6.5649131 -6.4684388 -0.69006358
3500 420 0.39411087 -6.5718133 -6.4732856 -0.69106958
3600 422 0.37682035 -6.5696319 -6.4731945 -0.67828428
3700 424 0.37674329 -6.5708333 -6.4722048 -0.7295631
3800 426 0.37554504 -6.5551508 -6.4546528 -0.74098651
3900 428 0.47716365 -6.5863941 -6.4559545 -0.69775764
SHAKE stats (type/ave/delta) on step 4000
1 1 2.33147e-15
4000 430 0.39309652 -6.5839434 -6.474242 -0.67165044
4100 432 0.36137922 -6.5755863 -6.4726936 -0.75284168
4200 434 0.33665675 -6.5709582 -6.4732191 -0.70384507
4300 436 0.3946452 -6.5707735 -6.4540092 -0.69853666
4400 438 0.39629282 -6.5795369 -6.4601062 -0.67823491
4500 440 0.42475465 -6.6042384 -6.473916 -0.71292755
4600 442 0.34909419 -6.5857221 -6.4767288 -0.68062333
4700 444 0.33643716 -6.585937 -6.4790954 -0.71038994
4800 446 0.3811408 -6.5930525 -6.4699936 -0.74063911
4900 448 0.3779954 -6.6042774 -6.4802477 -0.70390914
SHAKE stats (type/ave/delta) on step 5000
1 1 2.66454e-15
5000 450 0.35790409 -6.6297715 -6.5104702 -0.67849435
5100 452 0.31862212 -6.6444655 -6.5366133 -0.69854773
5200 454 0.32789016 -6.6469195 -6.5342524 -0.77180002
5300 456 0.31629858 -6.6421111 -6.5318228 -0.68835335
5400 458 0.36152066 -6.6602984 -6.5324243 -0.66682577
5500 460 0.30603254 -6.6639673 -6.5541948 -0.75705636
5600 462 0.34658631 -6.6700688 -6.5440374 -0.75945094
5700 464 0.28458079 -6.6579566 -6.5530788 -0.7766899
5800 466 0.34190507 -6.6915819 -6.5639178 -0.6929815
5900 468 0.26172244 -6.6714593 -6.5724745 -0.70329441
SHAKE stats (type/ave/delta) on step 6000
1 1 2.88658e-15
6000 470 0.30325244 -6.6862834 -6.5701442 -0.82109242
6100 472 0.25803236 -6.6686757 -6.5686335 -0.75984602
6200 474 0.25736768 -6.6766546 -6.5756622 -0.67984915
6300 476 0.3530954 -6.7208307 -6.580631 -0.77335637
6400 478 0.3006363 -6.7044803 -6.5837227 -0.66974614
6500 480 0.27597377 -6.7071947 -6.5950803 -0.75642311
6600 482 0.2706662 -6.7070144 -6.5958279 -0.88321143
6700 484 0.27555986 -6.7058949 -6.5914578 -0.82283176
6800 486 0.2955121 -6.7016169 -6.5775747 -0.72199097
6900 488 0.2913952 -6.6993267 -6.5757226 -0.69282245
SHAKE stats (type/ave/delta) on step 7000
1 1 2.22045e-15
7000 490 0.27981191 -6.7009662 -6.5810468 -0.73943132
7100 492 0.31685264 -6.7152099 -6.5780359 -0.78601605
7200 494 0.26385909 -6.7026224 -6.5872508 -0.76508099
7300 496 0.2419927 -6.6912656 -6.584418 -0.89055484
7400 498 0.28044404 -6.6920358 -6.5670186 -0.79518453
7500 500 0.2762337 -6.7027512 -6.5784461 -0.76793505
7600 502 0.26902486 -6.6930632 -6.5708766 -0.80819618
7700 504 0.30012554 -6.7092162 -6.5716587 -0.83589424
7800 506 0.27717017 -6.718352 -6.5901745 -0.74594843
7900 508 0.28519942 -6.7259778 -6.5929221 -0.77889998
SHAKE stats (type/ave/delta) on step 8000
1 1 2.44249e-15
8000 510 0.28557016 -6.7262354 -6.5918494 -0.75257718
8100 512 0.32553601 -6.7486118 -6.5941094 -0.78328454
8200 514 0.28944387 -6.7379705 -6.5994429 -0.82277182
8300 516 0.28225288 -6.7447383 -6.6085349 -0.82524964
8400 518 0.29766781 -6.7537921 -6.6089808 -0.81172437
8500 520 0.28078531 -6.7473953 -6.6097025 -0.78667487
8600 522 0.29606157 -6.7504868 -6.6041575 -0.75691538
8700 524 0.28041746 -6.7552926 -6.615619 -0.79512658
8800 526 0.26962722 -6.7491997 -6.6138735 -0.8259819
8900 528 0.25123819 -6.7474166 -6.62037 -0.71869124
SHAKE stats (type/ave/delta) on step 9000
1 1 2.55351e-15
9000 530 0.24967063 -6.7564864 -6.6292957 -0.80484783
9100 532 0.255677 -6.7481047 -6.616902 -0.79613772
9200 534 0.24927075 -6.7427408 -6.6139042 -0.78203944
9300 536 0.24128001 -6.7505335 -6.6249418 -0.89696509
9400 538 0.23135126 -6.7432631 -6.6219972 -0.8704287
9500 540 0.24351964 -6.7393856 -6.6108613 -0.75482267
9600 542 0.26958835 -6.7406647 -6.5974148 -0.74586395
9700 544 0.29017813 -6.7545832 -6.5993592 -0.82279021
9800 546 0.28529127 -6.7509448 -6.5973264 -0.82084768
9900 548 0.28362819 -6.7624889 -6.6087707 -0.70739129
SHAKE stats (type/ave/delta) on step 10000
1 1 3.10862e-15
10000 550 0.26759148 -6.766521 -6.620562 -0.73792582
Loop time of 6.38249 on 1 procs for 10000 steps with 550 atoms
Pair time (%) = 3.88742 (60.9075)
Bond time (%) = 0.0116096 (0.181897)
Neigh time (%) = 2.05303 (32.1666)
Comm time (%) = 0.18659 (2.92347)
Outpt time (%) = 0.000954866 (0.0149607)
Other time (%) = 0.242887 (3.80551)
Nlocal: 550 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2367 ave 2367 max 2367 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 37090 ave 37090 max 37090 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 37090
Ave neighs/atom = 67.4364
Ave special neighs/atom = 0.363636
Neighbor list builds = 845
Dangerous builds = 0
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