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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11164 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-01-07 21:15:43 +00:00
parent 83d75279ae
commit 5f7c2e1f8a
7 changed files with 740 additions and 220 deletions
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2
examples/deposit/in.deposit.molecule
View File

@ -34,7 +34,7 @@ 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 &
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

56
examples/deposit/in.deposit.molecule.shake Normal file
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@ -0,0 +1,56 @@
# sample surface deposition script for molecules
units lj
atom_style bond
boundary p p f
lattice fcc 1.0
region box block 0 5 0 5 0 10
create_box 3 box "bond types" 1 "extra bond per atom" 1
region substrate block INF INF INF INF INF 3
create_atoms 1 region substrate
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
region mobile block 0 5 0 5 2 INF
group mobile region 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
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add lost/bond ignore lost warn
#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

220
examples/deposit/log.deposit.molecule.17Dec13.linux.1
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@ -1,4 +1,4 @@
LAMMPS (16 Dec 2013)
LAMMPS (30 Dec 2013)
# sample surface deposition script for molecules
units lj
@ -41,7 +41,7 @@ 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 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
@ -58,7 +58,7 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.761 Mbytes
Memory usage per processor = 2.76078 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
@ -66,119 +66,119 @@ Step Atoms Temp E_pair TotEng Press
300 356 0.83994737 -6.8170634 -6.7958288 -0.69170868
400 358 0.84042015 -6.7849768 -6.756806 -0.70352248
500 360 0.84184269 -6.7489038 -6.7138265 -0.68386838
600 362 0.84581252 -6.7098504 -6.667791 -0.68282962
700 364 0.87383402 -6.6715895 -6.6211263 -0.66625521
800 366 0.87700584 -6.6397294 -6.5813855 -0.68714738
900 368 0.89799284 -6.6074178 -6.5411933 -0.6633197
1000 370 0.95083484 -6.5900376 -6.5110576 -0.69572146
1100 372 0.82985799 -6.5796732 -6.5020171 -0.64680951
1200 374 0.85651845 -6.569056 -6.4832041 -0.68799376
1300 376 0.95704327 -6.5541436 -6.446087 -0.68860769
1400 378 0.99164463 -6.5980098 -6.4811236 -0.57034819
1500 380 0.77250737 -6.6076789 -6.5065665 -0.6404344
1600 382 0.64450542 -6.5925431 -6.4979083 -0.67080474
1700 384 0.59174558 -6.570604 -6.4836042 -0.63920736
1800 386 0.68425339 -6.570226 -6.4656269 -0.65233974
1900 388 0.62329345 -6.5635189 -6.4650127 -0.63792408
2000 390 0.68456891 -6.5689788 -6.4521732 -0.65509823
2100 392 0.67321061 -6.5811717 -6.4500318 -0.65425662
2200 394 0.54478143 -6.5824499 -6.4589679 -0.69489133
2300 396 0.7025569 -6.6028441 -6.4506792 -0.64336994
2400 398 0.52296791 -6.5865304 -6.4590029 -0.66244621
2500 400 0.51361748 -6.5952192 -6.4571287 -0.73142772
2600 402 0.56909773 -6.6329678 -6.4745546 -0.68833191
2700 404 0.47316324 -6.6191013 -6.4797191 -0.68529766
2800 406 0.4024784 -6.5932129 -6.4753576 -0.72859927
2900 408 0.47244328 -6.5871757 -6.453229 -0.70781408
3000 410 0.46719857 -6.5875097 -6.4597457 -0.72630704
3100 412 0.53920664 -6.6146383 -6.4453004 -0.71086513
3200 414 0.48131175 -6.6451928 -6.4749523 -0.69309105
3300 416 0.41250886 -6.6284687 -6.4822569 -0.74495454
3400 418 0.4434617 -6.6469432 -6.4852748 -0.67332297
3500 420 0.41557109 -6.6594512 -6.4906766 -0.67511353
3600 422 0.42683402 -6.6822906 -6.5032101 -0.71730208
3700 424 0.40725472 -6.6999266 -6.5091665 -0.66350769
3800 426 0.46233068 -6.6939398 -6.4972405 -0.77367408
3900 428 0.46559823 -6.7209898 -6.5128889 -0.65590187
4000 430 0.40285904 -6.7463651 -6.5425884 -0.69952343
4100 432 0.41660438 -6.7760035 -6.5559126 -0.76829413
4200 434 0.3629958 -6.7769429 -6.5539205 -0.71514525
4300 436 0.43292832 -6.7723248 -6.5349078 -0.72086327
4400 438 0.48031456 -6.7909542 -6.5399856 -0.69055364
4500 440 0.43514381 -6.816345 -6.5668484 -0.64504209
4600 442 0.42216902 -6.8369302 -6.5912992 -0.64124177
4700 444 0.35593175 -6.8269085 -6.5961629 -0.75319222
4800 446 0.37281022 -6.8544574 -6.608371 -0.74800751
4900 448 0.38378226 -6.8650757 -6.6074728 -0.71830366
5000 450 0.35692176 -6.8758194 -6.6221425 -0.7445901
5100 452 0.4095119 -6.8844748 -6.6209625 -0.72430291
5200 454 0.36077122 -6.8707148 -6.6227241 -0.71794836
5300 456 0.32219928 -6.8715464 -6.6320277 -0.72291054
5400 458 0.31616802 -6.8698226 -6.6333157 -0.74720215
5500 460 0.31786106 -6.872068 -6.6308287 -0.80360394
5600 462 0.37015248 -6.8956604 -6.6240251 -0.73210594
5700 464 0.3534065 -6.9088566 -6.6327609 -0.71453932
5800 466 0.33251725 -6.9070782 -6.641467 -0.68201092
5900 468 0.30410425 -6.9075384 -6.6426114 -0.72551088
6000 470 0.30851479 -6.8970992 -6.6383198 -0.79668941
6100 472 0.31983822 -6.8935456 -6.6343679 -0.80093887
6200 474 0.34046679 -6.9033232 -6.6366444 -0.60584348
6300 476 0.34341 -6.9228112 -6.6519685 -0.71926688
6400 478 0.34850659 -6.9401172 -6.654428 -0.67959231
6500 480 0.32905065 -6.9511765 -6.6672014 -0.75953777
6600 482 0.34907767 -6.9596072 -6.6681567 -0.88241294
6700 484 0.35028194 -6.9653815 -6.6710713 -0.78275064
6800 486 0.35051323 -6.969352 -6.6763765 -0.66893758
6900 488 0.36217701 -6.9868033 -6.6759619 -0.72513293
7000 490 0.32291745 -6.9917249 -6.6925637 -0.74768371
7100 492 0.30809063 -6.9870686 -6.7043983 -0.73169721
7200 494 0.29851506 -6.9982183 -6.7077915 -0.8299932
7300 496 0.26179616 -6.9846023 -6.7127008 -0.77318
7400 498 0.29514008 -7.0132716 -6.7075934 -0.75316322
7500 500 0.3135944 -7.0285572 -6.7115419 -0.78914193
7600 502 0.30198119 -7.0431055 -6.7121603 -0.7265163
7700 504 0.32873608 -7.0693396 -6.7082228 -0.81872378
7800 506 0.32477424 -7.0818561 -6.7212948 -0.75793697
7900 508 0.31922052 -7.1059386 -6.7389868 -0.8543698
8000 510 0.28136655 -7.1067254 -6.7459867 -0.83979756
8100 512 0.29278742 -7.1165141 -6.7510805 -0.8241496
8200 514 0.33282329 -7.1327987 -6.7472492 -0.84438285
8300 516 0.31127854 -7.1410039 -6.7529902 -0.75630712
8400 518 0.28319374 -7.1327512 -6.7707492 -0.77390852
8500 520 0.32016512 -7.1697563 -6.7823027 -0.82592367
8600 522 0.32447805 -7.1674565 -6.7749588 -0.84309705
8700 524 0.2887839 -7.1818676 -6.7859966 -0.7609437
8800 526 0.30555242 -7.2166233 -6.8001973 -0.70067115
8900 528 0.3443468 -7.2376029 -6.7979364 -0.82279495
9000 530 0.30995579 -7.2506269 -6.8126325 -0.78972208
9100 532 0.30548349 -7.2637762 -6.80996 -0.7147236
9200 534 0.27799866 -7.2455264 -6.8191946 -0.87999072
9300 536 0.31062978 -7.2754833 -6.8217503 -0.84995092
9400 538 0.3169359 -7.2912363 -6.8367367 -0.87666495
9500 540 0.29095311 -7.302781 -6.8411527 -0.7819709
9600 542 0.31893318 -7.3077289 -6.8358361 -0.78035337
9700 544 0.33737303 -7.3293865 -6.8465864 -0.8238632
9800 546 0.31835531 -7.3291308 -6.8519745 -0.77631405
9900 548 0.31244715 -7.3722703 -6.8756185 -0.82478125
10000 550 0.3025952 -7.3985931 -6.8904785 -0.88208948
Loop time of 6.59022 on 1 procs for 10000 steps with 550 atoms
600 362 0.84581137 -6.7098504 -6.6677911 -0.6828296
700 364 0.87382946 -6.6715894 -6.6211265 -0.66625495
800 366 0.87689746 -6.6396776 -6.5813408 -0.68710928
900 368 0.89661715 -6.6072681 -6.5411455 -0.66320699
1000 370 1.00676 -6.5947268 -6.512331 -0.68611219
1100 372 0.86243824 -6.5866848 -6.5042223 -0.67174009
1200 374 0.84425239 -6.5636281 -6.479445 -0.69383244
1300 376 1.0078184 -6.550962 -6.4431087 -0.66633027
1400 378 1.0391938 -6.5969765 -6.4778058 -0.56558987
1500 380 0.74712353 -6.6166281 -6.5240793 -0.66003498
1600 382 0.58302452 -6.5997567 -6.5184528 -0.67167612
1700 384 0.56467802 -6.5776894 -6.4975516 -0.64668082
1800 386 0.71825353 -6.5726227 -6.4691096 -0.65076646
1900 388 0.53975986 -6.5613236 -6.4741837 -0.63639897
2000 390 0.59341094 -6.5769909 -6.4682541 -0.65193031
2100 392 0.68035001 -6.5827033 -6.4574143 -0.62788928
2200 394 0.57776644 -6.589353 -6.4761586 -0.69498055
2300 396 0.5318152 -6.5951551 -6.4885222 -0.60457555
2400 398 0.49568196 -6.6007559 -6.4881834 -0.69316627
2500 400 0.53409937 -6.6072399 -6.4763374 -0.69823432
2600 402 0.45633292 -6.6332159 -6.5034387 -0.65145273
2700 404 0.4892626 -6.6191003 -6.4911656 -0.66150699
2800 406 0.4586448 -6.6101924 -6.4821935 -0.71952986
2900 408 0.50133988 -6.6233932 -6.4820172 -0.69040381
3000 410 0.49942448 -6.6353753 -6.4859797 -0.6737426
3100 412 0.42190611 -6.6280489 -6.4885103 -0.71665975
3200 414 0.41178932 -6.621106 -6.4868768 -0.70387051
3300 416 0.46253061 -6.6361091 -6.4919436 -0.71264477
3400 418 0.42181868 -6.6317908 -6.4923081 -0.66171467
3500 420 0.41797099 -6.6287141 -6.4897821 -0.65879262
3600 422 0.36509229 -6.6214108 -6.4915707 -0.70324811
3700 424 0.39348534 -6.6179504 -6.4817297 -0.68426814
3800 426 0.39474314 -6.6086782 -6.4636684 -0.71591333
3900 428 0.45542305 -6.635636 -6.4706661 -0.68175206
4000 430 0.39042908 -6.6488343 -6.500435 -0.66366199
4100 432 0.39468368 -6.6585928 -6.49931 -0.76227835
4200 434 0.41142379 -6.6557126 -6.4903949 -0.73380042
4300 436 0.48160084 -6.6588571 -6.4749235 -0.71948887
4400 438 0.55431951 -6.698039 -6.4754774 -0.68067319
4500 440 0.4585125 -6.7096071 -6.5073393 -0.68190471
4600 442 0.44221158 -6.7238275 -6.5235013 -0.72486537
4700 444 0.3530253 -6.7116222 -6.5326725 -0.78475189
4800 446 0.39053263 -6.7192087 -6.5305763 -0.7500161
4900 448 0.39195928 -6.7304752 -6.5391648 -0.7414609
5000 450 0.39808899 -6.7364876 -6.5449794 -0.68624334
5100 452 0.40415767 -6.7520155 -6.5566586 -0.77799849
5200 454 0.32066094 -6.7478767 -6.5677968 -0.70955786
5300 456 0.3189586 -6.7748028 -6.5774312 -0.76013414
5400 458 0.28680679 -6.754829 -6.57373 -0.75077874
5500 460 0.3229394 -6.7693127 -6.565559 -0.76453959
5600 462 0.39545678 -6.7962985 -6.5645492 -0.75110236
5700 464 0.41518466 -6.8618036 -6.6026038 -0.79792247
5800 466 0.41117489 -6.8979481 -6.6272973 -0.68505301
5900 468 0.34391673 -6.8959897 -6.6377009 -0.67914717
6000 470 0.30168814 -6.8907915 -6.643955 -0.79643615
6100 472 0.30916205 -6.8885557 -6.6360589 -0.81599518
6200 474 0.35424257 -6.8990909 -6.6305161 -0.75613637
6300 476 0.35703296 -6.9174766 -6.6367178 -0.72950736
6400 478 0.37445271 -6.9445085 -6.6442671 -0.69659454
6500 480 0.329543 -6.9458858 -6.6609468 -0.75534893
6600 482 0.33963739 -6.947355 -6.6559786 -0.86232494
6700 484 0.34574376 -6.9518517 -6.6559314 -0.78159338
6800 486 0.38169407 -6.9787425 -6.6545343 -0.69654215
6900 488 0.36970486 -6.9727516 -6.6668784 -0.73296306
7000 490 0.32030483 -6.9604688 -6.6704554 -0.79884199
7100 492 0.34751955 -6.9885857 -6.6859115 -0.72531587
7200 494 0.34236112 -7.0019964 -6.700804 -0.81526247
7300 496 0.27559869 -7.0056964 -6.7192826 -0.77309778
7400 498 0.31846741 -7.0236162 -6.7200064 -0.84787873
7500 500 0.321674 -7.0382328 -6.7191195 -0.75690059
7600 502 0.31379969 -7.0541204 -6.7245415 -0.84134932
7700 504 0.33442098 -7.0824103 -6.7379709 -0.77808299
7800 506 0.31650445 -7.1121677 -6.7680346 -0.78541215
7900 508 0.30347752 -7.1100388 -6.7724658 -0.89260888
8000 510 0.31695084 -7.121996 -6.7701485 -0.80026292
8100 512 0.29991827 -7.133499 -6.779965 -0.77547985
8200 514 0.32128068 -7.1588222 -6.7891361 -0.85855005
8300 516 0.28103196 -7.1423077 -6.7970623 -0.76011418
8400 518 0.27077784 -7.150974 -6.8102547 -0.8189845
8500 520 0.29179445 -7.1717624 -6.8140245 -0.81319487
8600 522 0.29543603 -7.1666027 -6.8067797 -0.87228723
8700 524 0.27449088 -7.1899692 -6.824729 -0.86748792
8800 526 0.28192057 -7.1737434 -6.8131045 -0.80681355
8900 528 0.29164865 -7.1791336 -6.8042773 -0.83580175
9000 530 0.3473538 -7.2167575 -6.8110439 -0.84061628
9100 532 0.29792019 -7.211711 -6.8136015 -0.7023788
9200 534 0.2856865 -7.2088408 -6.8221795 -0.89143929
9300 536 0.27649993 -7.2299192 -6.8337365 -0.95862494
9400 538 0.29410309 -7.243419 -6.8486336 -0.91099619
9500 540 0.29981454 -7.2655451 -6.8556167 -0.79314135
9600 542 0.2972807 -7.2726656 -6.8578775 -0.77556553
9700 544 0.27946124 -7.2703884 -6.8622493 -0.78651169
9800 546 0.29668633 -7.2869601 -6.8663987 -0.86233713
9900 548 0.27596387 -7.2922319 -6.8749679 -0.78008994
10000 550 0.29155875 -7.2941724 -6.8764764 -0.76577583
Loop time of 6.55461 on 1 procs for 10000 steps with 550 atoms
Pair time (%) = 4.02228 (61.0341)
Bond time (%) = 0.0115879 (0.175834)
Neigh time (%) = 2.18644 (33.177)
Comm time (%) = 0.188319 (2.85755)
Outpt time (%) = 0.00100374 (0.0152308)
Other time (%) = 0.180595 (2.74034)
Pair time (%) = 4.01151 (61.2013)
Bond time (%) = 0.0117879 (0.179841)
Neigh time (%) = 2.16259 (32.9935)
Comm time (%) = 0.187663 (2.86307)
Outpt time (%) = 0.000994444 (0.0151717)
Other time (%) = 0.18006 (2.74707)
Nlocal: 550 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2357 ave 2357 max 2357 min
Nghost: 2375 ave 2375 max 2375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39728 ave 39728 max 39728 min
Neighs: 39585 ave 39585 max 39585 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39728
Ave neighs/atom = 72.2327
Total # of neighbors = 39585
Ave neighs/atom = 71.9727
Ave special neighs/atom = 0.363636
Neighbor list builds = 893
Neighbor list builds = 885
Dangerous builds = 0

218
examples/deposit/log.deposit.molecule.17Dec13.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (16 Dec 2013)
LAMMPS (30 Dec 2013)
# sample surface deposition script for molecules
units lj
@ -41,7 +41,7 @@ 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 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
@ -66,119 +66,119 @@ Step Atoms Temp E_pair TotEng Press
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
600 362 0.8458127 -6.7144697 -6.6724104 -0.66535013
700 364 0.87383242 -6.6725197 -6.6220566 -0.66071708
800 366 0.87696132 -6.6413623 -6.5830213 -0.66927232
900 368 0.89744792 -6.6071502 -6.5409657 -0.62868608
1000 370 0.99832562 -6.591423 -6.509704 -0.68145874
1100 372 0.83690497 -6.5836533 -6.5010396 -0.63926628
1200 374 0.88380837 -6.5576129 -6.4700582 -0.6448691
1300 376 0.93920197 -6.5480148 -6.4485844 -0.67509018
1400 378 1.0819467 -6.5984857 -6.4753138 -0.62854894
1500 380 0.72832384 -6.6161872 -6.5284826 -0.63429953
1600 382 0.63213539 -6.5990997 -6.5150252 -0.67037851
1700 384 0.5824052 -6.588541 -6.5069607 -0.69907025
1800 386 0.72529167 -6.5843125 -6.478207 -0.62283149
1900 388 0.57664201 -6.5677387 -6.4698656 -0.65451624
2000 390 0.65546977 -6.5676639 -6.4578769 -0.67432025
2100 392 0.69516646 -6.5858998 -6.4683877 -0.62289901
2200 394 0.56654159 -6.583766 -6.4770207 -0.70102083
2300 396 0.64110841 -6.598494 -6.4743096 -0.66950817
2400 398 0.52329199 -6.6104218 -6.4917721 -0.69664414
2500 400 0.55744613 -6.6221319 -6.4934736 -0.67790032
2600 402 0.46920185 -6.6192179 -6.5005058 -0.6830418
2700 404 0.56776413 -6.6299774 -6.4918044 -0.68598379
2800 406 0.44695801 -6.6053321 -6.4845111 -0.60979234
2900 408 0.51785351 -6.610722 -6.4741891 -0.62751234
3000 410 0.58665518 -6.6389279 -6.4792835 -0.64022876
3100 412 0.423824 -6.6194712 -6.4927699 -0.66450673
3200 414 0.45133153 -6.6230652 -6.4839389 -0.74364185
3300 416 0.51641116 -6.6567861 -6.49277 -0.64795831
3400 418 0.47621669 -6.6912734 -6.531463 -0.71160352
3500 420 0.38209486 -6.6823272 -6.5355428 -0.69351964
3600 422 0.44576071 -6.6807448 -6.5147154 -0.74737153
3700 424 0.41694154 -6.6822051 -6.5174366 -0.68130033
3800 426 0.40975915 -6.7048899 -6.5360548 -0.72002151
3900 428 0.48398461 -6.7282377 -6.5350708 -0.74439115
4000 430 0.36367577 -6.7208528 -6.5534139 -0.63650412
4100 432 0.34028562 -6.7242165 -6.5649615 -0.70137882
4200 434 0.33582497 -6.722058 -6.5514851 -0.76135001
4300 436 0.3825237 -6.7180169 -6.5381019 -0.70786373
4400 438 0.52062671 -6.7481686 -6.5135064 -0.73624603
4500 440 0.40436975 -6.7359486 -6.5304443 -0.79135494
4600 442 0.44491445 -6.7486865 -6.5249583 -0.76722101
4700 444 0.42190093 -6.7620999 -6.5568957 -0.68635283
4800 446 0.43599741 -6.7597134 -6.5440627 -0.77969628
4900 448 0.47851973 -6.7786447 -6.5458666 -0.74770553
5000 450 0.36262781 -6.8254599 -6.6092673 -0.71317359
5100 452 0.33856471 -6.8140502 -6.6072777 -0.70403037
5200 454 0.39260588 -6.835737 -6.6062808 -0.79831143
5300 456 0.31209864 -6.8230791 -6.6185118 -0.70136268
5400 458 0.31219166 -6.8170389 -6.6118122 -0.75454291
5500 460 0.33107044 -6.8102616 -6.5929746 -0.75347113
5600 462 0.40659306 -6.8413513 -6.5940668 -0.71199073
5700 464 0.35864173 -6.8618978 -6.6302942 -0.68000488
5800 466 0.35595504 -6.8739057 -6.637045 -0.72726368
5900 468 0.30133562 -6.8629749 -6.6404473 -0.79721111
6000 470 0.32080099 -6.860886 -6.631765 -0.79848812
6100 472 0.27961391 -6.8709022 -6.6465395 -0.71256878
6200 474 0.31406154 -6.8829903 -6.6410549 -0.7089865
6300 476 0.36004409 -6.9012979 -6.6442205 -0.77551843
6400 478 0.32635204 -6.8936662 -6.6413458 -0.6682556
6500 480 0.32068722 -6.8935855 -6.6453583 -0.7254097
6600 482 0.32713469 -6.9215037 -6.6558734 -0.76984099
6700 484 0.36721979 -6.9207471 -6.6473085 -0.75359037
6800 486 0.38350491 -6.9354455 -6.6470817 -0.79067926
6900 488 0.3250273 -6.9458853 -6.6769931 -0.67224329
7000 490 0.32830721 -6.9469844 -6.6778539 -0.7619618
7100 492 0.33730308 -6.9374197 -6.6588506 -0.78689069
7200 494 0.30775449 -6.9609022 -6.6952452 -0.67621108
7300 496 0.28573367 -6.9569147 -6.7028926 -0.67991253
7400 498 0.28191768 -6.988469 -6.7220227 -0.87179721
7500 500 0.31351279 -6.9987024 -6.7160563 -0.82937872
7600 502 0.28969341 -7.0254266 -6.7316544 -0.77890838
7700 504 0.28407599 -7.0337382 -6.7311947 -0.80238049
7800 506 0.29761165 -7.0326028 -6.731669 -0.8371957
7900 508 0.34677565 -7.0523551 -6.7260518 -0.8740631
8000 510 0.3118165 -7.0626608 -6.7450993 -0.77834874
8100 512 0.29761479 -7.0754729 -6.7620945 -0.74405688
8200 514 0.30483577 -7.0905149 -6.7644188 -0.85441065
8300 516 0.33684783 -7.1137001 -6.7534121 -0.82965734
8400 518 0.27961357 -7.0957286 -6.7677311 -0.78630354
8500 520 0.30612337 -7.1335883 -6.7809001 -0.83422091
8600 522 0.29624122 -7.1270458 -6.7835376 -0.84386217
8700 524 0.29657024 -7.1402335 -6.7844074 -0.69683349
8800 526 0.3086498 -7.137074 -6.7768455 -0.80569969
8900 528 0.26822775 -7.1262968 -6.7891397 -0.78344768
9000 530 0.29595187 -7.1836398 -6.8037091 -0.80740794
9100 532 0.27991165 -7.178976 -6.8079248 -0.71421566
9200 534 0.27664216 -7.1784888 -6.8037579 -0.84396547
9300 536 0.27879865 -7.2033389 -6.8100683 -0.64262205
9400 538 0.28514769 -7.1987974 -6.8126137 -0.7018808
9500 540 0.32951622 -7.2371185 -6.8151986 -0.88679168
9600 542 0.35683108 -7.2746833 -6.821215 -0.81047037
9700 544 0.29775774 -7.2584568 -6.8336125 -0.85576789
9800 546 0.29002392 -7.2763888 -6.8501209 -0.81455861
9900 548 0.31009857 -7.2950962 -6.852398 -0.93711055
10000 550 0.28745157 -7.3035265 -6.8657121 -0.90926429
Loop time of 5.64819 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)
Pair time (%) = 1.02706 (18.1839)
Bond time (%) = 0.00374371 (0.0662816)
Neigh time (%) = 0.562528 (9.95945)
Comm time (%) = 2.94816 (52.1966)
Outpt time (%) = 0.0134226 (0.237645)
Other time (%) = 1.09327 (19.3561)
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
Nghost: 1917.25 ave 2722 max 455 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 9769 ave 24071 max 1 min
Neighs: 9881.5 ave 24370 max 1 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 39076
Ave neighs/atom = 71.0473
Total # of neighbors = 39526
Ave neighs/atom = 71.8655
Ave special neighs/atom = 0.363636
Neighbor list builds = 884
Neighbor list builds = 879
Dangerous builds = 0

210
examples/deposit/log.deposit.molecule.shake.31Dec13.linux.1 Normal file
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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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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 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
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 = 3.36903 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 0.84041725 -6.7834986 -6.7553282 -0.68860028
500 360 0.84183519 -6.7432451 -6.7081686 -0.72724802
600 362 0.84576393 -6.714465 -6.6724104 -0.66535527
700 364 0.8717559 -6.6683922 -6.6180986 -0.65401104
800 366 0.8972223 -6.6397054 -6.5808712 -0.6644064
900 368 0.89269075 -6.6040689 -6.5385725 -0.6293193
SHAKE stats (type/ave/delta) on step 1000
1 1 1.9984e-15
1000 370 0.8729371 -6.5843837 -6.513605 -0.66197956
1100 372 0.93342483 -6.5845128 -6.501709 -0.66278095
1200 374 0.91864917 -6.5632239 -6.4747977 -0.66231969
1300 376 0.88129406 -6.5508349 -6.4594241 -0.66330811
1400 378 0.88948953 -6.5759309 -6.4770988 -0.65591838
1500 380 0.66619538 -6.5716683 -6.4927768 -0.59010827
1600 382 0.64223132 -6.5753954 -6.4946962 -0.64796777
1700 384 0.71053601 -6.5931071 -6.498739 -0.71037238
1800 386 0.54790722 -6.5681884 -6.4915382 -0.63518672
1900 388 0.52085896 -6.5677463 -6.4912283 -0.67745991
SHAKE stats (type/ave/delta) on step 2000
1 1 2.22045e-15
2000 390 0.53994531 -6.563133 -6.4800645 -0.70555161
2100 392 0.64094961 -6.5675869 -6.4645772 -0.61019297
2200 394 0.50620722 -6.5592797 -6.4744836 -0.63511891
2300 396 0.6301209 -6.5760707 -6.4662769 -0.6545461
2400 398 0.53704268 -6.5642828 -6.4671294 -0.68416557
2500 400 0.64625918 -6.586831 -6.4656574 -0.68064342
2600 402 0.45719634 -6.5878773 -6.4991676 -0.72641767
2700 404 0.45430513 -6.5902202 -6.4991343 -0.64780429
2800 406 0.39401639 -6.5731811 -6.4916604 -0.63232952
2900 408 0.56403499 -6.5944647 -6.4741925 -0.66065801
SHAKE stats (type/ave/delta) on step 3000
1 1 1.88738e-15
3000 410 0.42366175 -6.5762728 -6.4832739 -0.58419502
3100 412 0.46961858 -6.597044 -6.4910379 -0.72500263
3200 414 0.45608063 -6.579384 -6.4736262 -0.66491063
3300 416 0.41525459 -6.6061269 -6.5073043 -0.7034034
3400 418 0.34167228 -6.5966324 -6.5132578 -0.69889479
3500 420 0.35438956 -6.5897102 -6.5011128 -0.69191247
3600 422 0.371945 -6.587433 -6.4922433 -0.74209613
3700 424 0.42415073 -6.5959033 -6.4848638 -0.70963735
3800 426 0.41039811 -6.5821598 -6.4723349 -0.77667535
3900 428 0.49077557 -6.6168589 -6.4826982 -0.73113384
SHAKE stats (type/ave/delta) on step 4000
1 1 2.10942e-15
4000 430 0.40203105 -6.6345318 -6.5223371 -0.71969376
4100 432 0.36787594 -6.6171373 -6.5123949 -0.76807348
4200 434 0.3261302 -6.6032025 -6.5085195 -0.74955499
4300 436 0.38926276 -6.6029583 -6.4877865 -0.72978015
4400 438 0.41086026 -6.621007 -6.4971861 -0.68550032
4500 440 0.3521118 -6.6242377 -6.5162034 -0.76756664
4600 442 0.38603968 -6.6293115 -6.5087832 -0.74258268
4700 444 0.34056733 -6.6415895 -6.5334364 -0.65780725
4800 446 0.37197114 -6.6416079 -6.5215096 -0.82603673
4900 448 0.30132362 -6.6363593 -6.5374874 -0.71862716
SHAKE stats (type/ave/delta) on step 5000
1 1 2.33147e-15
5000 450 0.28288619 -6.6354525 -6.5411571 -0.77201855
5100 452 0.26546305 -6.6297974 -6.5399393 -0.71006539
5200 454 0.30926196 -6.6267464 -6.5204801 -0.81320777
5300 456 0.32583739 -6.6465492 -6.5329349 -0.71621457
5400 458 0.32161442 -6.6474216 -6.5336628 -0.71056186
5500 460 0.34683164 -6.6587332 -6.5343262 -0.81507876
5600 462 0.33207554 -6.6707235 -6.5499688 -0.76405763
5700 464 0.30990462 -6.6765987 -6.5623882 -0.74469148
5800 466 0.38115342 -6.7114459 -6.5691268 -0.76594753
5900 468 0.3045191 -6.7224056 -6.6072349 -0.8010673
SHAKE stats (type/ave/delta) on step 6000
1 1 3.9968e-15
6000 470 0.29295042 -6.7112692 -6.5990754 -0.87488246
6100 472 0.28821962 -6.7201644 -6.6084183 -0.77836483
6200 474 0.27856084 -6.7228536 -6.6135449 -0.84000894
6300 476 0.27590056 -6.7303516 -6.6208028 -0.78812565
6400 478 0.25075258 -6.7209969 -6.6202762 -0.78937406
6500 480 0.2420497 -6.7100555 -6.6117228 -0.84935998
6600 482 0.24559955 -6.7058717 -6.6049822 -0.73869936
6700 484 0.26670092 -6.7106888 -6.5999308 -0.74058907
6800 486 0.27972148 -6.7095837 -6.5921698 -0.85599188
6900 488 0.27556092 -6.7181144 -6.6012268 -0.78080334
SHAKE stats (type/ave/delta) on step 7000
1 1 3.66374e-15
7000 490 0.31988812 -6.7171565 -6.5800616 -0.79439098
7100 492 0.28768419 -6.7050741 -6.5805279 -0.75103962
7200 494 0.27446382 -6.6965124 -6.5765039 -0.7254846
7300 496 0.27613579 -6.6951364 -6.5732136 -0.81917256
7400 498 0.28716597 -6.6931216 -6.5651078 -0.83063101
7500 500 0.29991456 -6.7065993 -6.5716377 -0.84995417
7600 502 0.30054942 -6.7057164 -6.5692119 -0.82453964
7700 504 0.33779908 -6.7355443 -6.5807197 -0.79378799
7800 506 0.27918017 -6.7440838 -6.6149767 -0.80343537
7900 508 0.27474528 -6.757924 -6.6297456 -0.9146801
SHAKE stats (type/ave/delta) on step 8000
1 1 3.21965e-15
8000 510 0.27352726 -6.7606902 -6.6319715 -0.83056014
8100 512 0.24483334 -6.7656728 -6.6494726 -0.81557302
8200 514 0.26136253 -6.776203 -6.6511151 -0.93698626
8300 516 0.22306201 -6.7512948 -6.6436544 -0.84185984
8400 518 0.23781328 -6.7617152 -6.6460223 -0.92614518
8500 520 0.26396807 -6.7687306 -6.6392847 -0.88122061
8600 522 0.27813101 -6.7722102 -6.6347431 -0.86382754
8700 524 0.28109538 -6.7747951 -6.6347838 -0.73669838
8800 526 0.25374762 -6.7712592 -6.643903 -0.81383179
8900 528 0.26572288 -6.7804903 -6.6461191 -0.88882544
SHAKE stats (type/ave/delta) on step 9000
1 1 2.55351e-15
9000 530 0.23242437 -6.7530647 -6.6346599 -0.82067326
9100 532 0.24597332 -6.7582807 -6.6320576 -0.89921536
9200 534 0.23307655 -6.7540042 -6.6335377 -0.94279835
9300 536 0.2252299 -6.7483888 -6.6311516 -0.72691575
9400 538 0.24036406 -6.7561763 -6.6301862 -0.79108419
9500 540 0.24443282 -6.7448693 -6.6158631 -0.89759125
9600 542 0.21936118 -6.725477 -6.6089161 -0.81388326
9700 544 0.24527855 -6.7404349 -6.6092289 -0.88469799
9800 546 0.26358125 -6.746269 -6.6043407 -0.94325913
9900 548 0.30133107 -6.7564789 -6.5931662 -0.95797751
SHAKE stats (type/ave/delta) on step 10000
1 1 2.77556e-15
10000 550 0.24849941 -6.7407813 -6.6052361 -0.88843235
Loop time of 6.0445 on 4 procs for 10000 steps with 550 atoms
Pair time (%) = 1.0029 (16.5919)
Bond time (%) = 0.0037064 (0.0613185)
Neigh time (%) = 0.542864 (8.98112)
Comm time (%) = 2.92824 (48.4448)
Outpt time (%) = 0.00355923 (0.0588838)
Other time (%) = 1.56323 (25.862)
Nlocal: 137.5 ave 298 max 4 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1913.75 ave 2692 max 538 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 9179.5 ave 22892 max 1 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 36718
Ave neighs/atom = 66.76
Ave special neighs/atom = 0.363636
Neighbor list builds = 848
Dangerous builds = 0

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# dimer molecule
2 atoms
1 bonds
Coords
1 0 0 0
2 1 0 0
Types
1 2
2 3
Bonds
1 1 1 2
Special Bond Counts
1 1 0 0
2 1 0 0
Special Bonds
1 2
2 1
Shake Flags
1 2
2 2
Shake Atoms
1 1 2
2 1 2
Shake Bond Types
1 1
2 1