219 lines
11 KiB
Groff
219 lines
11 KiB
Groff
LAMMPS (10 Mar 2021)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# 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 = 1.5874011 1.5874011 1.5874011
|
|
region box block 0 5 0 5 0 10
|
|
create_box 3 box bond/types 1 extra/bond/per/atom 1
|
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (7.9370053 7.9370053 15.874011)
|
|
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
|
|
create_atoms CPU = 0.002 seconds
|
|
|
|
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
|
|
|
|
molecule dimer molecule.dimer
|
|
Read molecule template dimer:
|
|
1 molecules
|
|
2 atoms with max type 3
|
|
1 bonds with max type 1
|
|
0 angles with max type 0
|
|
0 dihedrals with max type 0
|
|
0 impropers with max type 0
|
|
region slab block 0 5 0 5 8 9
|
|
|
|
group addatoms empty
|
|
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/dof yes extra/dof 0
|
|
|
|
fix 1 addatoms rigid/nve/small molecule mol dimer
|
|
create bodies CPU = 0.000 seconds
|
|
0 rigid bodies with 0 atoms
|
|
1.0000000 = max distance from body owner to body atom
|
|
fix 2 mobile langevin 0.1 0.1 0.1 587283
|
|
fix 3 mobile nve
|
|
|
|
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 rigid 1
|
|
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 (src/thermo.cpp:468)
|
|
|
|
#dump 1 all atom 50 dump.deposit.atom
|
|
|
|
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
|
|
#dump_modify 2 pad 5
|
|
|
|
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
|
|
#dump_modify 3 pad 5
|
|
|
|
run 10000
|
|
WARNING: Should not allow rigid bodies to bounce off relecting walls (src/fix_wall_reflect.cpp:182)
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 5.3
|
|
ghost atom cutoff = 5.3
|
|
binsize = 2.65, bins = 3 3 6
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.852 | 6.302 Mbytes
|
|
Step Atoms Temp E_pair TotEng Press
|
|
0 350 0 -6.9215833 -6.9215833 -1.0052629
|
|
100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337
|
|
200 354 1.0081552 -6.8645575 -6.850318 -0.69629729
|
|
300 356 1.0085803 -6.821677 -6.8004288 -0.69532657
|
|
400 358 1.0099188 -6.7837923 -6.7555822 -0.68879568
|
|
500 360 1.0140221 -6.7446709 -6.7094618 -0.72991641
|
|
600 362 1.026146 -6.7129201 -6.6704003 -0.67063836
|
|
700 364 1.0683193 -6.6776523 -6.6262908 -0.65572472
|
|
800 366 1.0958894 -6.6402029 -6.5803182 -0.66307282
|
|
900 368 1.1231769 -6.6050912 -6.5364187 -0.64076928
|
|
1000 370 1.1976289 -6.5942508 -6.51333 -0.69249047
|
|
1100 372 1.05061 -6.5772306 -6.4995645 -0.6307289
|
|
1200 374 0.93723829 -6.5732962 -6.4981166 -0.64963821
|
|
1300 376 0.93899122 -6.5578418 -6.476679 -0.65096688
|
|
1400 378 0.87050694 -6.546852 -6.4662495 -0.67613401
|
|
1500 380 0.84462904 -6.5400883 -6.4567368 -0.64376986
|
|
1600 382 0.92417795 -6.5611292 -6.4643567 -0.62092779
|
|
1700 384 0.67296541 -6.5589985 -6.4845167 -0.6779111
|
|
1800 386 0.87159158 -6.5655058 -6.4638954 -0.6582786
|
|
1900 388 0.67504975 -6.5772537 -6.4946123 -0.665098
|
|
2000 390 0.65034978 -6.5717854 -6.4884072 -0.73162072
|
|
2100 392 0.63389859 -6.5652907 -6.4803935 -0.64937411
|
|
2200 394 0.6265637 -6.5582412 -6.4707767 -0.70819854
|
|
2300 396 0.85352983 -6.5750751 -6.4511408 -0.69995918
|
|
2400 398 0.69792348 -6.5938659 -6.4886513 -0.63755214
|
|
2500 400 0.45320495 -6.595022 -6.5242087 -0.70462183
|
|
2600 402 0.46824374 -6.5697613 -6.4940502 -0.75497893
|
|
2700 404 0.46605975 -6.5599272 -6.4820583 -0.66778506
|
|
2800 406 0.50637604 -6.5700492 -6.482743 -0.63812082
|
|
2900 408 0.55335921 -6.5873352 -6.4890054 -0.62891652
|
|
3000 410 0.51731142 -6.5890566 -6.4944264 -0.64305355
|
|
3100 412 0.59439734 -6.6003127 -6.4885025 -0.67140541
|
|
3200 414 0.53413632 -6.595564 -6.4923492 -0.76242248
|
|
3300 416 0.49221593 -6.5990831 -6.5014681 -0.71330819
|
|
3400 418 0.55006126 -6.6015725 -6.4897179 -0.72044309
|
|
3500 420 0.49065348 -6.6329864 -6.5307669 -0.65775397
|
|
3600 422 0.41907335 -6.6219753 -6.5325995 -0.75936391
|
|
3700 424 0.38720116 -6.6153349 -6.5308629 -0.74166397
|
|
3800 426 0.40625994 -6.6150209 -6.5244231 -0.7595111
|
|
3900 428 0.40460547 -6.6122642 -6.5200936 -0.70484465
|
|
4000 430 0.45014991 -6.6254404 -6.5207544 -0.70069933
|
|
4100 432 0.44820466 -6.640222 -6.5338771 -0.805972
|
|
4200 434 0.39767521 -6.6450316 -6.5488199 -0.72841414
|
|
4300 436 0.4155331 -6.6547917 -6.5523381 -0.6894484
|
|
4400 438 0.43034353 -6.6615074 -6.5534303 -0.74026062
|
|
4500 440 0.38062977 -6.6541618 -6.5568417 -0.85911194
|
|
4600 442 0.39357419 -6.6522517 -6.5498512 -0.66232114
|
|
4700 444 0.40296801 -6.6647029 -6.5580616 -0.67307577
|
|
4800 446 0.38194993 -6.6510248 -6.548258 -0.77887746
|
|
4900 448 0.40739835 -6.6601751 -6.5487771 -0.84146416
|
|
5000 450 0.38392807 -6.6560665 -6.5494198 -0.77343399
|
|
5100 452 0.35209286 -6.6481476 -6.5488294 -0.68065755
|
|
5200 454 0.41355143 -6.6615988 -6.543181 -0.81611092
|
|
5300 456 0.42200484 -6.6627494 -6.5401273 -0.7774134
|
|
5400 458 0.37764326 -6.661431 -6.550117 -0.72187808
|
|
5500 460 0.41857405 -6.6674232 -6.542306 -0.74929745
|
|
5600 462 0.41682611 -6.6710961 -6.5447852 -0.7557454
|
|
5700 464 0.44396148 -6.6924346 -6.5560887 -0.78018312
|
|
5800 466 0.37058077 -6.6865013 -6.5711919 -0.74146125
|
|
5900 468 0.346812 -6.681215 -6.57191 -0.81184233
|
|
6000 470 0.34919462 -6.6827931 -6.571348 -0.87330821
|
|
6100 472 0.39360936 -6.6933359 -6.5661634 -0.79237598
|
|
6200 474 0.33270778 -6.6847095 -6.5759127 -0.77978526
|
|
6300 476 0.35973804 -6.6951254 -6.5760944 -0.80340174
|
|
6400 478 0.38124318 -6.7045984 -6.5769857 -0.81628407
|
|
6500 480 0.41188302 -6.7133356 -6.573896 -0.7940289
|
|
6600 482 0.36998039 -6.7079555 -6.5813025 -0.75055442
|
|
6700 484 0.37615026 -6.722917 -6.592741 -0.76534055
|
|
6800 486 0.3466597 -6.7188712 -6.5976116 -0.77986211
|
|
6900 488 0.32902492 -6.7247054 -6.6084005 -0.75702458
|
|
7000 490 0.31856427 -6.7167709 -6.6029979 -0.76014555
|
|
7100 492 0.30233891 -6.7144406 -6.6053651 -0.96246708
|
|
7200 494 0.32557309 -6.7315347 -6.6129049 -0.8122153
|
|
7300 496 0.29919611 -6.7186327 -6.6085455 -0.71917931
|
|
7400 498 0.29778169 -6.7259455 -6.6153238 -0.88199391
|
|
7500 500 0.35535305 -6.7419073 -6.6086499 -0.90344083
|
|
7600 502 0.31979187 -6.7326802 -6.6116434 -0.78324572
|
|
7700 504 0.30821359 -6.72895 -6.6112295 -0.81363335
|
|
7800 506 0.31374993 -6.7255461 -6.6046346 -0.89904197
|
|
7900 508 0.29072338 -6.7177355 -6.6047082 -0.81423073
|
|
8000 510 0.30557494 -6.7208283 -6.600995 -0.85853575
|
|
8100 512 0.30521237 -6.726874 -6.6061601 -0.75361257
|
|
8200 514 0.29622226 -6.7152225 -6.5970794 -0.85766132
|
|
8300 516 0.28337698 -6.7023552 -6.5884003 -0.8985415
|
|
8400 518 0.32860902 -6.7211074 -6.5878875 -0.89758921
|
|
8500 520 0.35483743 -6.7406183 -6.5956126 -0.77602077
|
|
8600 522 0.32928486 -6.7326607 -6.5970358 -0.75070137
|
|
8700 524 0.36008106 -6.7474714 -6.5980103 -0.87093836
|
|
8800 526 0.36082301 -6.743579 -6.5926644 -0.90132107
|
|
8900 528 0.35010285 -6.7501553 -6.6026214 -0.85238959
|
|
9000 530 0.31513985 -6.7411795 -6.6073937 -0.75884529
|
|
9100 532 0.30895083 -6.7421063 -6.6099891 -0.74482692
|
|
9200 534 0.33631849 -6.751265 -6.6064087 -0.95632911
|
|
9300 536 0.33306096 -6.759187 -6.6147156 -0.76275935
|
|
9400 538 0.34582537 -6.7706766 -6.619619 -0.72251598
|
|
9500 540 0.32003146 -6.772057 -6.6313024 -0.88195851
|
|
9600 542 0.32439637 -6.7743569 -6.6307127 -0.90233104
|
|
9700 544 0.33988235 -6.7763721 -6.624862 -0.85185581
|
|
9800 546 0.32877587 -6.7744977 -6.62697 -0.8550905
|
|
9900 548 0.29570051 -6.7623752 -6.6288243 -1.0371157
|
|
10000 550 0.33675914 -6.7757315 -6.6226591 -1.0082157
|
|
Loop time of 16.2553 on 4 procs for 10000 steps with 550 atoms
|
|
|
|
Performance: 265759.101 tau/day, 615.183 timesteps/s
|
|
97.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.0034051 | 2.6646 | 8.0317 | 200.7 | 16.39
|
|
Bond | 0.0022626 | 0.0072971 | 0.019437 | 8.3 | 0.04
|
|
Neigh | 0.018657 | 1.218 | 3.7621 | 137.5 | 7.49
|
|
Comm | 1.1497 | 6.7957 | 12.192 | 164.2 | 41.81
|
|
Output | 0.010692 | 0.01431 | 0.019901 | 3.2 | 0.09
|
|
Modify | 3.1502 | 5.3779 | 11.342 | 149.0 | 33.08
|
|
Other | | 0.1775 | | | 1.09
|
|
|
|
Nlocal: 137.500 ave 299 max 2 min
|
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
|
Nghost: 1903.75 ave 2686 max 529 min
|
|
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
Neighs: 9209.75 ave 23206 max 0 min
|
|
Histogram: 2 0 0 0 0 1 0 0 0 1
|
|
|
|
Total # of neighbors = 36839
|
|
Ave neighs/atom = 66.980000
|
|
Ave special neighs/atom = 0.36363636
|
|
Neighbor list builds = 829
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:16
|