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lammps/examples/deposit/log.deposit.molecule.17Dec13.linux.4
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LAMMPS (16 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 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
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 2 100 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:439)
#dump 1 all atom 50 dump.deposit.atom
#dump 1 all movie 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
#dump 1 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.83497 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 0.83994737 -6.8946578 -6.8874992 -0.73775337
200 354 0.83994737 -6.8644786 -6.8502422 -0.69623155
300 356 0.83994737 -6.821588 -6.8003534 -0.69525265
400 358 0.84042015 -6.783499 -6.7553282 -0.68860116
500 360 0.84184269 -6.7432459 -6.7081686 -0.72724605
600 362 0.84581206 -6.714469 -6.6724097 -0.66534959
700 364 0.87383596 -6.6725214 -6.6220581 -0.66071834
800 366 0.87713015 -6.6413724 -6.5830204 -0.66928287
900 368 0.90018655 -6.6073735 -6.5409855 -0.62892884
1000 370 0.96227808 -6.5868064 -6.5074907 -0.68749702
1100 372 0.84208591 -6.5856173 -6.5061644 -0.64781569
1200 374 0.86272285 -6.5582926 -6.4731764 -0.63543562
1300 376 0.95773406 -6.5544141 -6.4487816 -0.67940605
1400 378 0.93803076 -6.5912608 -6.4787926 -0.63035119
1500 380 0.76188302 -6.609601 -6.507431 -0.62936804
1600 382 0.64812925 -6.6158742 -6.5225057 -0.66629492
1700 384 0.57104425 -6.5834801 -6.4973389 -0.69201022
1800 386 0.68121441 -6.5913511 -6.4849854 -0.66274766
1900 388 0.59071249 -6.5693977 -6.4707313 -0.66442628
2000 390 0.52513894 -6.5668567 -6.4711301 -0.67507629
2100 392 0.64263416 -6.5743168 -6.464217 -0.65041002
2200 394 0.5522363 -6.5755738 -6.4617061 -0.64108615
2300 396 0.60202284 -6.5810207 -6.4607912 -0.69126827
2400 398 0.5502913 -6.5914085 -6.4766683 -0.70577646
2500 400 0.58838656 -6.5797348 -6.4493383 -0.66940146
2600 402 0.52515002 -6.6008189 -6.4720071 -0.70528448
2700 404 0.53401562 -6.6009928 -6.4682401 -0.6736596
2800 406 0.55645674 -6.5964808 -6.4666926 -0.62821291
2900 408 0.5010237 -6.6058796 -6.4773043 -0.61911753
3000 410 0.47849773 -6.6269143 -6.4812007 -0.63008018
3100 412 0.41094701 -6.6268204 -6.4948979 -0.69597934
3200 414 0.47271593 -6.6185525 -6.4739318 -0.76685926
3300 416 0.48687338 -6.6387845 -6.485648 -0.65914049
3400 418 0.41665 -6.6436505 -6.5127368 -0.67432882
3500 420 0.39038075 -6.6289835 -6.498372 -0.65549289
3600 422 0.34117471 -6.6226464 -6.5023435 -0.72876441
3700 424 0.39179203 -6.6292939 -6.4916715 -0.70961805
3800 426 0.45549191 -6.6355863 -6.4828955 -0.75810311
3900 428 0.46330056 -6.6426861 -6.479373 -0.6989264
4000 430 0.42092635 -6.6709567 -6.5036845 -0.6880803
4100 432 0.38694735 -6.6644049 -6.4971039 -0.71471482
4200 434 0.37777641 -6.6603214 -6.488897 -0.72601053
4300 436 0.43182044 -6.6654281 -6.4824146 -0.73109185
4400 438 0.45572414 -6.6798984 -6.4832598 -0.71210332
4500 440 0.43104607 -6.6862396 -6.4864417 -0.71733998
4600 442 0.43149918 -6.6995102 -6.4971938 -0.70850012
4700 444 0.39399217 -6.7016909 -6.503212 -0.72214549
4800 446 0.39037156 -6.6935218 -6.4868921 -0.77055747
4900 448 0.37753842 -6.707923 -6.4903142 -0.75393104
5000 450 0.42220551 -6.7301507 -6.4988577 -0.73394915
5100 452 0.42497529 -6.7619403 -6.5159525 -0.72393516
5200 454 0.41455722 -6.7847454 -6.5348956 -0.74296171
5300 456 0.37062474 -6.8072062 -6.5579493 -0.69921697
5400 458 0.40599849 -6.8406565 -6.5728968 -0.75919888
5500 460 0.34392525 -6.8358415 -6.5921562 -0.80486225
5600 462 0.4757898 -6.8765422 -6.5865976 -0.7406693
5700 464 0.38072464 -6.897556 -6.6319606 -0.72639904
5800 466 0.32103715 -6.8973169 -6.6501111 -0.69518251
5900 468 0.33232797 -6.9213547 -6.658116 -0.79603128
6000 470 0.29700153 -6.8996291 -6.6504065 -0.74837616
6100 472 0.32894406 -6.912751 -6.6463385 -0.80262352
6200 474 0.30835766 -6.9245814 -6.6478388 -0.76247382
6300 476 0.297769 -6.9133945 -6.6465479 -0.75942017
6400 478 0.33564944 -6.9244855 -6.6365737 -0.71744787
6500 480 0.35950195 -6.9438674 -6.6373008 -0.79583688
6600 482 0.35852398 -6.9471083 -6.6345034 -0.84850956
6700 484 0.37746341 -6.9631113 -6.6387598 -0.70828084
6800 486 0.37927455 -6.9770207 -6.6478759 -0.77149809
6900 488 0.37385451 -6.9751669 -6.6384794 -0.79839428
7000 490 0.41326552 -7.0109364 -6.6510976 -0.73572519
7100 492 0.40109886 -7.0371818 -6.6787269 -0.82747312
7200 494 0.33962506 -7.0383357 -6.7000108 -0.7310352
7300 496 0.32727099 -7.043221 -6.7062747 -0.78908544
7400 498 0.35009463 -7.079117 -6.7254804 -0.79946569
7500 500 0.35210197 -7.0921525 -6.7263024 -0.83049592
7600 502 0.34235777 -7.1152929 -6.739115 -0.8539266
7700 504 0.35260408 -7.1402842 -6.7444179 -0.77281485
7800 506 0.31704586 -7.1539324 -6.7601853 -0.85345291
7900 508 0.28865083 -7.1430332 -6.7640433 -0.77523459
8000 510 0.31369319 -7.1398358 -6.7550426 -0.74734362
8100 512 0.30997857 -7.1833379 -6.7738104 -0.76399943
8200 514 0.31923033 -7.1972291 -6.7754992 -0.70540601
8300 516 0.31824159 -7.1938739 -6.7770826 -0.80861798
8400 518 0.32665366 -7.2270765 -6.7898354 -0.82435696
8500 520 0.29657718 -7.2279397 -6.8001913 -0.86391198
8600 522 0.36713485 -7.2533129 -6.7964761 -0.84088775
8700 524 0.33860436 -7.2733474 -6.8293145 -0.70211305
8800 526 0.38774267 -7.3423046 -6.8318829 -0.69503174
8900 528 0.36336749 -7.3685203 -6.8610493 -0.83072975
9000 530 0.3621714 -7.367274 -6.8680611 -0.73399135
9100 532 0.31443182 -7.3655292 -6.89329 -0.78935196
9200 534 0.31575618 -7.3757175 -6.8951715 -0.88062913
9300 536 0.33643287 -7.4005087 -6.9019497 -0.76181889
9400 538 0.31285273 -7.4149817 -6.9143533 -0.64113419
9500 540 0.29107993 -7.4010991 -6.9280937 -0.76468717
9600 542 0.32545351 -7.4388103 -6.9269868 -0.81079634
9700 544 0.287295 -7.444308 -6.9440494 -0.79138369
9800 546 0.28728225 -7.4460341 -6.9621294 -0.76946227
9900 548 0.26717995 -7.4465158 -6.9695501 -0.90635358
10000 550 0.25556281 -7.4491924 -6.9758166 -0.91347995
Loop time of 5.77993 on 4 procs for 10000 steps with 550 atoms
Pair time (%) = 1.03264 (17.866)
Bond time (%) = 0.0038864 (0.0672396)
Neigh time (%) = 0.579989 (10.0345)
Comm time (%) = 3.02126 (52.2716)
Outpt time (%) = 0.0154074 (0.266568)
Other time (%) = 1.12674 (19.494)
Nlocal: 137.5 ave 298 max 3 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1935 ave 2745 max 468 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 9769 ave 24071 max 1 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 39076
Ave neighs/atom = 71.0473
Ave special neighs/atom = 0.363636
Neighbor list builds = 884
Dangerous builds = 0
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