diff --git a/examples/deposit/in.deposit.molecule b/examples/deposit/in.deposit.molecule index 6aa3ee5cfc..471f13a5af 100644 --- a/examples/deposit/in.deposit.molecule +++ b/examples/deposit/in.deposit.molecule @@ -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 diff --git a/examples/deposit/in.deposit.molecule.shake b/examples/deposit/in.deposit.molecule.shake new file mode 100644 index 0000000000..2497f0ce3f --- /dev/null +++ b/examples/deposit/in.deposit.molecule.shake @@ -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 diff --git a/examples/deposit/log.deposit.molecule.17Dec13.linux.1 b/examples/deposit/log.deposit.molecule.17Dec13.linux.1 index 3f0532c544..09543b1a5e 100644 --- a/examples/deposit/log.deposit.molecule.17Dec13.linux.1 +++ b/examples/deposit/log.deposit.molecule.17Dec13.linux.1 @@ -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 diff --git a/examples/deposit/log.deposit.molecule.17Dec13.linux.4 b/examples/deposit/log.deposit.molecule.17Dec13.linux.4 index 47a4d9bf9d..9c1cf4f669 100644 --- a/examples/deposit/log.deposit.molecule.17Dec13.linux.4 +++ b/examples/deposit/log.deposit.molecule.17Dec13.linux.4 @@ -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 diff --git a/examples/deposit/log.deposit.molecule.shake.31Dec13.linux.1 b/examples/deposit/log.deposit.molecule.shake.31Dec13.linux.1 new file mode 100644 index 0000000000..8ef13b73cb --- /dev/null +++ b/examples/deposit/log.deposit.molecule.shake.31Dec13.linux.1 @@ -0,0 +1,210 @@ +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 diff --git a/examples/deposit/log.deposit.molecule.shake.31Dec13.linux.4 b/examples/deposit/log.deposit.molecule.shake.31Dec13.linux.4 new file mode 100644 index 0000000000..e8562fab55 --- /dev/null +++ b/examples/deposit/log.deposit.molecule.shake.31Dec13.linux.4 @@ -0,0 +1,210 @@ +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 diff --git a/examples/deposit/molecule.dimer.shake b/examples/deposit/molecule.dimer.shake new file mode 100644 index 0000000000..fd2cac0d02 --- /dev/null +++ b/examples/deposit/molecule.dimer.shake @@ -0,0 +1,44 @@ +# 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 +