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sjplimp 2013-12-18 13:30:37 +00:00
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commit 627fd232e9
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1
examples/README
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@ -54,6 +54,7 @@ body: body particles, 2d system
colloid: big colloid particles in a small particle solvent, 2d system
comb: models using the COMB potential
crack: crack propagation in a 2d solid
deposit: deposition of atoms and molecules onto a 3d substrate
dipole: point dipolar particles, 2d system
dreiding: methanol via Dreiding FF
eim: NaCl using the EIM potential

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# sample surface deposition script for atoms
units lj
atom_style atomic
boundary p p f
lattice fcc 1.0
region box block 0 5 0 5 0 10
create_box 2 box
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
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 1.0 1.0 0.1 587283
fix 3 mobile nve
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 2 100 12345 region slab near 1.0 &
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
#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 movie.mpg type type &
# axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000

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examples/deposit/in.deposit.molecule Normal file
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# 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
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
#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

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examples/deposit/log.deposit.atom.17Dec13.linux.1 Normal file
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LAMMPS (16 Dec 2013)
# sample surface deposition script for atoms
units lj
atom_style atomic
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 2 box
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
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 1.0 1.0 0.1 587283
fix 3 mobile nve
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 2 100 12345 region slab near 1.0 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
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 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.12546 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 351 0.83994737 -6.3459678 -6.3423783 -0.12047746
200 352 0.83994737 -6.2377119 -6.2305533 -0.3420432
300 353 0.84063802 -6.102615 -6.0918986 -0.40610132
400 354 0.84248131 -6.0284461 -6.0141667 -0.46041042
500 355 0.84689832 -5.9201486 -5.9022564 -0.44565465
600 356 0.86694405 -5.8676653 -5.8457482 -0.45310439
700 357 0.93585062 -5.8080247 -5.7804997 -0.4235135
800 358 0.87721962 -5.7667317 -5.7373277 -0.47514081
900 359 0.98586832 -5.7397849 -5.7027118 -0.53506606
1000 360 1.1977372 -5.7043822 -5.6544765 -0.5143915
1100 361 0.86840339 -5.6974093 -5.6577177 -0.57133639
1200 362 0.91410157 -5.6449104 -5.5994579 -0.54863872
1300 363 1.0317704 -5.6108925 -5.5554668 -0.63480165
1400 364 0.78937966 -5.5995247 -5.5539836 -0.54633211
1500 365 1.0022364 -5.592367 -5.5305854 -0.61542058
1600 366 1.36861 -5.5602006 -5.4704557 -0.5557092
1700 367 1.2584928 -5.6125569 -5.5251139 -0.54474262
1800 368 1.2395052 -5.5575635 -5.4666216 -0.39432632
1900 369 1.4424114 -5.5511809 -5.4397751 -0.39219555
2000 370 1.0355115 -5.5657056 -5.4817452 -0.42684751
2100 371 1.0710232 -5.621664 -5.5307281 -0.60685079
2200 372 1.1723348 -5.5425772 -5.4385798 -0.53815496
2300 373 1.0854557 -5.6087637 -5.5083664 -0.6673737
2400 374 1.1021474 -5.5084817 -5.4023926 -0.52097008
2500 375 1.2269864 -5.4265984 -5.3038998 -0.49657202
2600 376 1.039955 -5.476211 -5.3683434 -0.62204764
2700 377 1.0944057 -5.407846 -5.2902772 -0.63977966
2800 378 1.0323171 -5.39575 -5.2810481 -0.62614235
2900 379 1.1065423 -5.3744087 -5.2474045 -0.57270499
3000 380 1.0281199 -5.3681406 -5.2463895 -0.66444016
3100 381 1.043599 -5.3317419 -5.2043735 -0.65417699
3200 382 1.0445598 -5.3089303 -5.1776767 -0.63427235
3300 383 1.1112429 -5.2607562 -5.117136 -0.57989768
3400 384 1.2829004 -5.2907632 -5.120378 -0.56018912
3500 385 1.0963306 -5.2325275 -5.0830279 -0.55177255
3600 386 1.0791899 -5.2303202 -5.0793455 -0.62981193
3700 387 0.94844753 -5.1732719 -5.0372543 -0.54632838
3800 388 1.0521937 -5.221439 -5.0668642 -0.66965407
3900 389 0.9826229 -5.2181425 -5.0703702 -0.63446515
4000 390 0.91368716 -5.181823 -5.0412558 -0.60085212
4100 391 0.89544864 -5.1919255 -5.0510813 -0.54221581
4200 392 0.75657889 -5.1831443 -5.0615513 -0.67325177
4300 393 0.93900487 -5.126951 -4.9728395 -0.48335997
4400 394 0.8593926 -5.2046256 -5.0606665 -0.61020127
4500 395 0.95412643 -5.2094621 -5.0464152 -0.66934949
4600 396 0.92666909 -5.2451094 -5.0836443 -0.60939327
4700 397 1.01953 -5.250453 -5.069403 -0.59800998
4800 398 0.79158616 -5.2564791 -5.1132776 -0.65741727
4900 399 1.0354176 -5.2890436 -5.0983088 -0.62373201
5000 400 1.0952161 -5.348647 -5.143294 -0.68192295
5100 401 0.93545388 -5.3669167 -5.1884573 -0.70799109
5200 402 1.1494382 -5.3432275 -5.1202022 -0.63752184
5300 403 0.99548049 -5.2792244 -5.0828455 -0.64833221
5400 404 1.1403496 -5.2690808 -5.0404463 -0.59847109
5500 405 1.1603116 -5.2594419 -5.0230821 -0.57039169
5600 406 1.0631193 -5.2339182 -5.0139625 -0.65214332
5700 407 0.96112361 -5.1115962 -4.9096894 -0.49296687
5800 408 1.0057273 -5.2149323 -5.0004758 -0.6288722
5900 409 1.0081842 -5.2677684 -5.0496161 -0.66956189
6000 410 1.1018378 -5.197239 -4.9553722 -0.56197903
6100 411 0.95491378 -5.2192405 -5.0066502 -0.57092889
6200 412 1.1257567 -5.2427379 -4.9886229 -0.60501573
6300 413 0.92515533 -5.2911514 -5.0794633 -0.71296835
6400 414 0.88193756 -5.2485519 -5.0440447 -0.62228066
6500 415 1.1421168 -5.258063 -4.9897344 -0.58398767
6600 416 1.1202205 -5.1905351 -4.9239442 -0.57396572
6700 417 0.95130512 -5.1665766 -4.9373053 -0.54725501
6800 418 1.1527843 -5.1757857 -4.8944842 -0.67073304
6900 419 1.0361942 -5.1545229 -4.8985656 -0.54846926
7000 420 0.99630188 -5.1619249 -4.9128494 -0.55694385
7100 421 0.9361364 -5.1977715 -4.9609579 -0.6844444
7200 422 1.0798692 -5.2022654 -4.9259007 -0.68276117
7300 423 1.1813674 -5.1407348 -4.8349198 -0.48578088
7400 424 1.172588 -5.1454198 -4.8384451 -0.56027825
7500 425 1.1057774 -5.1871818 -4.894476 -0.63993616
7600 426 1.1182194 -5.0981279 -4.7988861 -0.51535988
7700 427 1.2199143 -5.1427322 -4.8127554 -0.52888993
7800 428 1.1962566 -5.1524711 -4.825457 -0.48097947
7900 429 1.1264027 -5.171705 -4.8605658 -0.65075724
8000 430 1.1333818 -5.1429716 -4.826679 -0.66899357
8100 431 1.0571341 -5.0912822 -4.7932734 -0.59186526
8200 432 1.0064557 -5.1167265 -4.8301662 -0.59922344
8300 433 0.9988262 -5.1878937 -4.9007024 -0.65115476
8400 434 1.1031119 -5.1400663 -4.819808 -0.4893497
8500 435 1.1480133 -5.2265686 -4.8900819 -0.61178303
8600 436 1.1295109 -5.1695862 -4.8353961 -0.58399158
8700 437 1.0054231 -5.1692361 -4.8689896 -0.6618483
8800 438 0.97531325 -5.1627328 -4.8688028 -0.65722388
8900 439 1.0594641 -5.107595 -4.7854117 -0.62363978
9000 440 1.1400991 -5.1098088 -4.7600057 -0.58529871
9100 441 0.99798612 -5.0390174 -4.7301169 -0.46665264
9200 442 1.1110124 -5.1181538 -4.7712766 -0.71646157
9300 443 1.048379 -5.118944 -4.7888111 -0.57591241
9400 444 0.90506078 -5.1264418 -4.8390239 -0.76401152
9500 445 0.96451217 -5.0675273 -4.7586666 -0.64381165
9600 446 1.0823286 -5.0664171 -4.7169657 -0.5345442
9700 447 1.1847976 -5.1194594 -4.7338038 -0.62633623
9800 448 1.0307519 -5.1036157 -4.7654002 -0.59954885
9900 449 1.0182147 -5.0987073 -4.7619481 -0.58646377
10000 450 0.96233181 -5.146377 -4.8255998 -0.68930839
Loop time of 5.53702 on 1 procs for 10000 steps with 450 atoms
Pair time (%) = 3.04622 (55.0154)
Neigh time (%) = 2.15803 (38.9745)
Comm time (%) = 0.164064 (2.96303)
Outpt time (%) = 0.000992537 (0.0179255)
Other time (%) = 0.16772 (3.02906)
Nlocal: 450 ave 450 max 450 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1996 ave 1996 max 1996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 28228 ave 28228 max 28228 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 28228
Ave neighs/atom = 62.7289
Neighbor list builds = 1143
Dangerous builds = 0

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examples/deposit/log.deposit.atom.17Dec13.linux.4 Normal file
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LAMMPS (16 Dec 2013)
# sample surface deposition script for atoms
units lj
atom_style atomic
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 2 box
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
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 1.0 1.0 0.1 587283
fix 3 mobile nve
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 2 100 12345 region slab near 1.0 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
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 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.19138 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 351 0.83994737 -6.3596932 -6.3561037 -0.10696131
200 352 0.83994737 -6.3044678 -6.2973092 -0.38494392
300 353 0.84063802 -6.164881 -6.1541646 -0.41223901
400 354 0.84248131 -6.0388811 -6.0246018 -0.31496573
500 355 0.84688124 -6.0084178 -5.990526 -0.37482638
600 356 0.86681079 -6.0286531 -6.0067393 -0.54868509
700 357 0.93465165 -5.9564751 -5.9289854 -0.48728319
800 358 0.86905333 -5.8498868 -5.8207565 -0.4146325
900 359 0.90267243 -5.7844092 -5.7504647 -0.38165702
1000 360 0.92357983 -5.777549 -5.7390665 -0.38381524
1100 361 1.3481334 -5.7713272 -5.7097089 -0.44738093
1200 362 1.15494 -5.7155857 -5.6581577 -0.38961524
1300 363 0.97329529 -5.6445379 -5.5922534 -0.37655267
1400 364 1.2187161 -5.6818221 -5.6115115 -0.60238965
1500 365 1.2026123 -5.66813 -5.5939963 -0.56317155
1600 366 1.4012284 -5.6764268 -5.584543 -0.49098723
1700 367 1.3618781 -5.6121414 -5.517515 -0.47893702
1800 368 0.9670811 -5.5551479 -5.4841935 -0.3409573
1900 369 1.002089 -5.6037307 -5.5263336 -0.45325785
2000 370 1.3599868 -5.5793818 -5.4691126 -0.44566809
2100 371 1.0007794 -5.585692 -5.5007201 -0.54221497
2200 372 1.1061186 -5.5172266 -5.4191031 -0.46551394
2300 373 0.99747295 -5.556485 -5.4642255 -0.55670261
2400 374 1.0990417 -5.5538565 -5.4480664 -0.63197286
2500 375 1.1415126 -5.5118583 -5.3977071 -0.515634
2600 376 1.0106197 -5.5221131 -5.4172882 -0.54958102
2700 377 1.0964027 -5.4985654 -5.3807821 -0.54044665
2800 378 0.93035607 -5.4391662 -5.3357933 -0.52401636
2900 379 0.93052107 -5.5146104 -5.4078092 -0.69426617
3000 380 1.0256715 -5.4314645 -5.3100034 -0.55807748
3100 381 1.1165704 -5.441198 -5.3049236 -0.67260986
3200 382 1.0516479 -5.3743543 -5.2422101 -0.55726796
3300 383 1.3015716 -5.393488 -5.2252692 -0.55526352
3400 384 1.2021373 -5.4152522 -5.2555933 -0.63254327
3500 385 1.0712229 -5.3875667 -5.2414908 -0.53868713
3600 386 0.83109486 -5.3651207 -5.2488536 -0.65516002
3700 387 0.91939065 -5.3500756 -5.218225 -0.6090015
3800 388 1.1887187 -5.4422838 -5.2676524 -0.69893677
3900 389 1.0816342 -5.3817634 -5.2191012 -0.58777145
4000 390 0.85854697 -5.3988171 -5.2667329 -0.68550599
4100 391 1.0028015 -5.3760402 -5.2183106 -0.61280389
4200 392 1.1063074 -5.373048 -5.1952486 -0.69264824
4300 393 0.94803569 -5.2768075 -5.1212139 -0.4968846
4400 394 1.0358207 -5.2313016 -5.0577885 -0.47759843
4500 395 0.99463555 -5.2840763 -5.1141069 -0.65377832
4600 396 1.1336626 -5.2732108 -5.0756787 -0.68505207
4700 397 1.043989 -5.3177843 -5.1323907 -0.66352488
4800 398 1.1880124 -5.2919552 -5.0770384 -0.5760075
4900 399 1.03793 -5.2870595 -5.0958618 -0.42225723
5000 400 0.94525219 -5.3621262 -5.1848915 -0.57578045
5100 401 1.0012033 -5.2951115 -5.1041089 -0.49619424
5200 402 0.9093106 -5.323038 -5.1466046 -0.63808588
5300 403 1.0780126 -5.3297725 -5.1171125 -0.54697182
5400 404 1.1821134 -5.3408341 -5.1038263 -0.54142347
5500 405 1.0861151 -5.3794714 -5.1582257 -0.62078287
5600 406 0.99813873 -5.2575404 -5.051029 -0.46334991
5700 407 1.0024386 -5.3416556 -5.1310696 -0.67522177
5800 408 1.0499128 -5.2805967 -5.0567182 -0.51745165
5900 409 1.0175995 -5.2346622 -5.0144725 -0.56525137
6000 410 1.0580253 -5.3059195 -5.0736701 -0.72405837
6100 411 1.0301092 -5.2456791 -5.0163483 -0.63734034
6200 412 1.0936687 -5.2986069 -5.0517351 -0.65680297
6300 413 1.1588036 -5.2889356 -5.0237856 -0.68692669
6400 414 1.0738578 -5.2626417 -5.0136312 -0.61945759
6500 415 1.0799598 -5.2267416 -4.9730161 -0.54000165
6600 416 1.0654575 -5.2904664 -5.036908 -0.79867075
6700 417 1.1409741 -5.2288709 -4.953888 -0.61287225
6800 418 0.91721071 -5.2193327 -4.9955158 -0.67288058
6900 419 0.99562084 -5.2164082 -4.9704732 -0.59995412
7000 420 0.98493772 -5.1472091 -4.9009747 -0.5672666
7100 421 1.1650853 -5.1686492 -4.8739186 -0.65830934
7200 422 1.1058038 -5.1915304 -4.9085285 -0.71319305
7300 423 1.0695793 -5.1082351 -4.8313581 -0.47793146
7400 424 1.0205032 -5.1187042 -4.8515441 -0.45596744
7500 425 1.0509541 -5.119854 -4.8416602 -0.53998089
7600 426 0.94300051 -5.1572926 -4.9049403 -0.6117655
7700 427 0.97832544 -5.1763299 -4.9117009 -0.76832421
7800 428 0.99162405 -5.1076903 -4.8366155 -0.53958966
7900 429 1.0777105 -5.1240548 -4.8263655 -0.63632393
8000 430 1.0810155 -5.1582004 -4.8565216 -0.58803291
8100 431 1.0168798 -5.1415512 -4.8548902 -0.59356121
8200 432 1.1324612 -5.1323524 -4.8099155 -0.51666326
8300 433 1.0225017 -5.1357067 -4.841708 -0.53308683
8400 434 1.0938048 -5.1370091 -4.8194529 -0.50683321
8500 435 0.98749809 -5.1760393 -4.8866002 -0.63777967
8600 436 0.9696005 -5.1684071 -4.8815299 -0.60457804
8700 437 1.1714664 -5.2563529 -4.9065214 -0.64901375
8800 438 1.1068684 -5.1834342 -4.8498574 -0.448558
8900 439 1.048918 -5.2496241 -4.9306479 -0.51509876
9000 440 1.3045868 -5.2790483 -4.8787774 -0.63054863
9100 441 1.1505177 -5.2631527 -4.90704 -0.60158373
9200 442 1.0838443 -5.2358506 -4.8974558 -0.66026866
9300 443 0.99074033 -5.1267153 -4.8147328 -0.36508529
9400 444 1.120907 -5.2081858 -4.8522221 -0.70153485
9500 445 1.1571034 -5.2002705 -4.8297374 -0.39376803
9600 446 1.1427182 -5.1948759 -4.8259266 -0.50433867
9700 447 1.1386351 -5.1960248 -4.8253953 -0.55647471
9800 448 0.94339428 -5.1379682 -4.828417 -0.49931715
9900 449 0.9187318 -5.1851142 -4.8812575 -0.5929999
10000 450 1.1185411 -5.2444214 -4.8715743 -0.61322449
Loop time of 4.76332 on 4 procs for 10000 steps with 450 atoms
Pair time (%) = 0.82251 (17.2676)
Neigh time (%) = 0.589647 (12.3789)
Comm time (%) = 2.44321 (51.2921)
Outpt time (%) = 0.011445 (0.240274)
Other time (%) = 0.89651 (18.8211)
Nlocal: 112.5 ave 250 max 5 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 1496 ave 2221 max 416 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 7344.75 ave 16734 max 4 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 29379
Ave neighs/atom = 65.2867
Neighbor list builds = 1150
Dangerous builds = 0

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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 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
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 = 2.761 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 0.84042015 -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
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)
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
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39728 ave 39728 max 39728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39728
Ave neighs/atom = 72.2327
Ave special neighs/atom = 0.363636
Neighbor list builds = 893
Dangerous builds = 0

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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

28
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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