From 1fe284dbba8aeb980ce9ef6658bb4b1c4c343ab5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Apr 2021 07:55:43 -0400 Subject: [PATCH] add examples for using fix rigid/nv?/small with fix deposit --- .../in.deposit.molecule.rigid-nve-small | 56 +++++ .../in.deposit.molecule.rigid-nvt-small | 56 +++++ ...r21.deposit.molecule.rigid-nve-small.g++.1 | 218 ++++++++++++++++++ ...r21.deposit.molecule.rigid-nve-small.g++.4 | 218 ++++++++++++++++++ ...r21.deposit.molecule.rigid-nvt-small.g++.1 | 218 ++++++++++++++++++ ...r21.deposit.molecule.rigid-nvt-small.g++.4 | 218 ++++++++++++++++++ 6 files changed, 984 insertions(+) create mode 100644 examples/deposit/in.deposit.molecule.rigid-nve-small create mode 100644 examples/deposit/in.deposit.molecule.rigid-nvt-small create mode 100644 examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.1 create mode 100644 examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.4 create mode 100644 examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.1 create mode 100644 examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.4 diff --git a/examples/deposit/in.deposit.molecule.rigid-nve-small b/examples/deposit/in.deposit.molecule.rigid-nve-small new file mode 100644 index 0000000000..b2af77ac00 --- /dev/null +++ b/examples/deposit/in.deposit.molecule.rigid-nve-small @@ -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 + +molecule dimer molecule.dimer +region slab block 0 5 0 5 8 9 + +group addatoms empty +region mobile block 0 5 0 5 2 INF +group mobile region mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nve/small molecule mol dimer +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 + +#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 diff --git a/examples/deposit/in.deposit.molecule.rigid-nvt-small b/examples/deposit/in.deposit.molecule.rigid-nvt-small new file mode 100644 index 0000000000..9ceb1b3984 --- /dev/null +++ b/examples/deposit/in.deposit.molecule.rigid-nvt-small @@ -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 + +molecule dimer molecule.dimer +region slab block 0 5 0 5 8 9 + +group addatoms empty +region mobile block 0 5 0 5 2 INF +group mobile region mobile + +compute add addatoms temp +compute_modify add dynamic/dof yes extra/dof 0 + +fix 1 addatoms rigid/nvt/small molecule temp 0.1 0.1 0.1 mol dimer +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 + +#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 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.1 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.1 new file mode 100644 index 0000000000..792d3954c1 --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.1 @@ -0,0 +1,218 @@ +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 1 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.001 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) = 5.929 | 5.929 | 5.929 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914 + 200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276 + 300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826 + 400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699 + 500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307 + 600 362 1.026148 -6.7105231 -6.6680032 -0.68314418 + 700 364 1.0683344 -6.6725162 -6.621154 -0.65747369 + 800 366 1.0958953 -6.6412275 -6.5813425 -0.68789615 + 900 368 1.1250034 -6.6101882 -6.541404 -0.66674346 + 1000 370 1.2326365 -6.5993719 -6.5160856 -0.69688655 + 1100 372 1.1397444 -6.5912865 -6.5070312 -0.6333041 + 1200 374 1.0514447 -6.5905753 -6.5062348 -0.71020272 + 1300 376 1.0033284 -6.5747792 -6.4880554 -0.65459641 + 1400 378 0.82996548 -6.5681806 -6.4913319 -0.60438595 + 1500 380 0.90239071 -6.5752982 -6.4862465 -0.66528503 + 1600 382 0.86403681 -6.5692212 -6.4787461 -0.65027922 + 1700 384 0.64748046 -6.5644242 -6.4927629 -0.63046709 + 1800 386 0.74288742 -6.5515741 -6.4649681 -0.67770665 + 1900 388 0.72584537 -6.5565195 -6.4676596 -0.66175025 + 2000 390 0.73351281 -6.5631154 -6.4690753 -0.64686647 + 2100 392 0.76490681 -6.5573734 -6.4549305 -0.68861526 + 2200 394 0.65926638 -6.5511574 -6.4591279 -0.71726284 + 2300 396 0.70267414 -6.5728555 -6.4708258 -0.64360436 + 2400 398 0.60523691 -6.5845973 -6.4933555 -0.63956839 + 2500 400 0.5103586 -6.5812006 -6.5014571 -0.68698448 + 2600 402 0.52401744 -6.6003358 -6.5156066 -0.68987222 + 2700 404 0.46421291 -6.5662747 -6.4887143 -0.72872856 + 2800 406 0.48254258 -6.5724266 -6.4892296 -0.75447872 + 2900 408 0.53073083 -6.5809842 -6.4866754 -0.67592283 + 3000 410 0.55314547 -6.5922077 -6.4910226 -0.74646953 + 3100 412 0.47150308 -6.5907273 -6.5020344 -0.64994935 + 3200 414 0.43047803 -6.5836315 -6.5004473 -0.79764713 + 3300 416 0.46289353 -6.5739439 -6.4821441 -0.76441674 + 3400 418 0.59724106 -6.5980575 -6.4766089 -0.73735626 + 3500 420 0.43571285 -6.5955972 -6.5048237 -0.64145941 + 3600 422 0.42461639 -6.6060271 -6.5154691 -0.70124484 + 3700 424 0.44323254 -6.6059723 -6.5092766 -0.74498147 + 3800 426 0.4037907 -6.592043 -6.5019958 -0.72171799 + 3900 428 0.41668443 -6.5975302 -6.5026079 -0.68327878 + 4000 430 0.44895183 -6.5958671 -6.4914597 -0.73939433 + 4100 432 0.39798052 -6.5952115 -6.5007833 -0.74871822 + 4200 434 0.45156734 -6.6237274 -6.5144772 -0.75111778 + 4300 436 0.48297356 -6.6395283 -6.5204465 -0.76105913 + 4400 438 0.43595234 -6.6347133 -6.5252276 -0.72858275 + 4500 440 0.44683726 -6.6385398 -6.5242916 -0.74280051 + 4600 442 0.47875512 -6.6419903 -6.5174274 -0.75579572 + 4700 444 0.43972605 -6.6406078 -6.5242388 -0.72196509 + 4800 446 0.43572615 -6.6495404 -6.5323047 -0.7135049 + 4900 448 0.38063437 -6.6432385 -6.5391588 -0.77087429 + 5000 450 0.4239223 -6.6617795 -6.5440233 -0.784531 + 5100 452 0.37201988 -6.6581813 -6.5532421 -0.74611403 + 5200 454 0.41765777 -6.6661321 -6.5465385 -0.75422239 + 5300 456 0.38015287 -6.6606624 -6.5502013 -0.78866702 + 5400 458 0.40549607 -6.6807118 -6.5611878 -0.78932883 + 5500 460 0.34444407 -6.6720564 -6.5690976 -0.77859171 + 5600 462 0.36572308 -6.6730078 -6.5621827 -0.85672419 + 5700 464 0.40055073 -6.6976989 -6.574685 -0.74251563 + 5800 466 0.36037213 -6.7022014 -6.5900685 -0.66239625 + 5900 468 0.32810921 -6.6952135 -6.591803 -0.83981757 + 6000 470 0.35110886 -6.6986862 -6.5866302 -0.82474047 + 6100 472 0.29965884 -6.6839503 -6.5871326 -0.7864913 + 6200 474 0.32402637 -6.6902745 -6.5843165 -0.74531083 + 6300 476 0.35042653 -6.6990084 -6.5830585 -0.74839967 + 6400 478 0.32695511 -6.6909459 -6.5815048 -0.76549489 + 6500 480 0.35209088 -6.6902987 -6.5711013 -0.71281516 + 6600 482 0.354106 -6.6890268 -6.567808 -0.81897158 + 6700 484 0.3504816 -6.681739 -6.5604463 -0.811609 + 6800 486 0.37396733 -6.7018369 -6.5710253 -0.80383296 + 6900 488 0.36435774 -6.7010114 -6.5722169 -0.72063651 + 7000 490 0.35631012 -6.7089806 -6.581727 -0.74152078 + 7100 492 0.37646659 -6.719154 -6.5833352 -0.77739001 + 7200 494 0.36546269 -6.7223269 -6.5891623 -0.8288767 + 7300 496 0.37688206 -6.7457243 -6.607053 -0.80062121 + 7400 498 0.30331409 -6.7284953 -6.6158184 -0.79894584 + 7500 500 0.30382936 -6.7333804 -6.6194444 -0.86924602 + 7600 502 0.30163143 -6.7294737 -6.6153104 -0.7689497 + 7700 504 0.30281215 -6.7233976 -6.6077402 -0.8557548 + 7800 506 0.33378009 -6.7244958 -6.5958651 -0.82584084 + 7900 508 0.31843128 -6.7250998 -6.6013002 -0.82424684 + 8000 510 0.35912946 -6.7399052 -6.5990701 -0.81879575 + 8100 512 0.31405017 -6.733487 -6.6092777 -0.72940457 + 8200 514 0.30475 -6.7271485 -6.6056043 -0.87958287 + 8300 516 0.30717434 -6.7277574 -6.6042329 -0.81700937 + 8400 518 0.33032462 -6.7382165 -6.6043011 -0.75436496 + 8500 520 0.32218568 -6.7351971 -6.6035347 -0.77661738 + 8600 522 0.30922651 -6.7275431 -6.6001797 -0.85334327 + 8700 524 0.30728021 -6.7237477 -6.5962029 -0.94977016 + 8800 526 0.31061903 -6.7181672 -6.5882505 -0.86132456 + 8900 528 0.33543344 -6.728929 -6.5875768 -0.87545919 + 9000 530 0.31887735 -6.7265066 -6.5911341 -0.76892061 + 9100 532 0.31888326 -6.7216274 -6.5852629 -0.83190298 + 9200 534 0.33310892 -6.7111349 -6.567661 -0.94282671 + 9300 536 0.34737171 -6.722515 -6.5718361 -0.95235602 + 9400 538 0.32752858 -6.7246204 -6.5815549 -0.86227131 + 9500 540 0.30665764 -6.7225391 -6.5876665 -0.87144326 + 9600 542 0.32747382 -6.7149245 -6.5699176 -0.86863105 + 9700 544 0.32463079 -6.7205757 -6.5758643 -0.85393932 + 9800 546 0.31517825 -6.7178961 -6.5764699 -0.81017759 + 9900 548 0.33649933 -6.7380644 -6.5860871 -0.80769312 + 10000 550 0.37394555 -6.7612874 -6.5913121 -0.82102213 +Loop time of 16.7275 on 1 procs for 10000 steps with 550 atoms + +Performance: 258256.688 tau/day, 597.816 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.2508 | 9.2508 | 9.2508 | 0.0 | 55.30 +Bond | 0.021603 | 0.021603 | 0.021603 | 0.0 | 0.13 +Neigh | 4.5325 | 4.5325 | 4.5325 | 0.0 | 27.10 +Comm | 0.62777 | 0.62777 | 0.62777 | 0.0 | 3.75 +Output | 0.006916 | 0.006916 | 0.006916 | 0.0 | 0.04 +Modify | 2.218 | 2.218 | 2.218 | 0.0 | 13.26 +Other | | 0.07002 | | | 0.42 + +Nlocal: 550.000 ave 550 max 550 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2344.00 ave 2344 max 2344 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36607.0 ave 36607 max 36607 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36607 +Ave neighs/atom = 66.558182 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 847 +Dangerous builds = 0 +Total wall time: 0:00:16 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.4 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.4 new file mode 100644 index 0000000000..e9158cd7ec --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nve-small.g++.4 @@ -0,0 +1,218 @@ +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 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.1 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.1 new file mode 100644 index 0000000000..5abc557d8b --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.1 @@ -0,0 +1,218 @@ +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 1 MPI processor grid + +region substrate block INF INF INF INF INF 3 +create_atoms 1 region substrate +Created 350 atoms + create_atoms CPU = 0.001 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/nvt/small molecule temp 0.1 0.1 0.1 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) = 5.929 | 5.929 | 5.929 Mbytes +Step Atoms Temp E_pair TotEng Press + 0 350 0 -6.9215833 -6.9215833 -1.0052629 + 100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914 + 200 354 1.0081552 -6.8594643 -6.8452248 -0.70421276 + 300 356 1.0085803 -6.8171524 -6.7959042 -0.6917826 + 400 358 1.0099188 -6.7852701 -6.7570601 -0.70371699 + 500 360 1.0140221 -6.7493429 -6.7141338 -0.68415307 + 600 362 1.026148 -6.7105231 -6.6680032 -0.68314418 + 700 364 1.0683344 -6.6725162 -6.621154 -0.65747369 + 800 366 1.0958953 -6.6412275 -6.5813425 -0.68789615 + 900 368 1.1250034 -6.6101882 -6.541404 -0.66674346 + 1000 370 1.2326365 -6.5993719 -6.5160856 -0.69688655 + 1100 372 1.1397444 -6.5912865 -6.5070312 -0.6333041 + 1200 374 1.0514447 -6.5905753 -6.5062348 -0.71020272 + 1300 376 1.0033284 -6.5747792 -6.4880554 -0.65459641 + 1400 378 0.82996548 -6.5681806 -6.4913319 -0.60438595 + 1500 380 0.90239071 -6.5752982 -6.4862465 -0.66528503 + 1600 382 0.86403681 -6.5692212 -6.4787461 -0.65027922 + 1700 384 0.64748046 -6.5644242 -6.4927629 -0.63046709 + 1800 386 0.74288742 -6.5515741 -6.4649681 -0.67770665 + 1900 388 0.72584537 -6.5565195 -6.4676596 -0.66175025 + 2000 390 0.73351281 -6.5631154 -6.4690753 -0.64686647 + 2100 392 0.76490681 -6.5573734 -6.4549305 -0.68861526 + 2200 394 0.65926638 -6.5511574 -6.4591279 -0.71726284 + 2300 396 0.70267414 -6.5728555 -6.4708258 -0.64360436 + 2400 398 0.60523691 -6.5845973 -6.4933555 -0.63956839 + 2500 400 0.5103586 -6.5812006 -6.5014571 -0.68698448 + 2600 402 0.52401744 -6.6003358 -6.5156066 -0.68987222 + 2700 404 0.46421291 -6.5662747 -6.4887143 -0.72872856 + 2800 406 0.48254258 -6.5724266 -6.4892296 -0.75447872 + 2900 408 0.53073083 -6.5809842 -6.4866754 -0.67592283 + 3000 410 0.55314547 -6.5922077 -6.4910226 -0.74646953 + 3100 412 0.47150308 -6.5907273 -6.5020344 -0.64994935 + 3200 414 0.43047803 -6.5836315 -6.5004473 -0.79764713 + 3300 416 0.46289353 -6.5739439 -6.4821441 -0.76441674 + 3400 418 0.59724106 -6.5980575 -6.4766089 -0.73735626 + 3500 420 0.43571285 -6.5955972 -6.5048237 -0.64145941 + 3600 422 0.42461639 -6.6060271 -6.5154691 -0.70124484 + 3700 424 0.44323254 -6.6059723 -6.5092766 -0.74498147 + 3800 426 0.4037907 -6.592043 -6.5019958 -0.72171799 + 3900 428 0.41668443 -6.5975302 -6.5026079 -0.68327878 + 4000 430 0.44895183 -6.5958671 -6.4914597 -0.73939433 + 4100 432 0.39798052 -6.5952115 -6.5007833 -0.74871822 + 4200 434 0.45156734 -6.6237274 -6.5144772 -0.75111778 + 4300 436 0.48297356 -6.6395283 -6.5204465 -0.76105913 + 4400 438 0.43595234 -6.6347133 -6.5252276 -0.72858275 + 4500 440 0.44683726 -6.6385398 -6.5242916 -0.74280051 + 4600 442 0.47875512 -6.6419903 -6.5174274 -0.75579572 + 4700 444 0.43972605 -6.6406078 -6.5242388 -0.72196509 + 4800 446 0.43572615 -6.6495404 -6.5323047 -0.7135049 + 4900 448 0.38063437 -6.6432385 -6.5391588 -0.77087429 + 5000 450 0.4239223 -6.6617795 -6.5440233 -0.784531 + 5100 452 0.37201988 -6.6581813 -6.5532421 -0.74611403 + 5200 454 0.41765777 -6.6661321 -6.5465385 -0.75422239 + 5300 456 0.38015287 -6.6606624 -6.5502013 -0.78866702 + 5400 458 0.40549607 -6.6807118 -6.5611878 -0.78932883 + 5500 460 0.34444407 -6.6720564 -6.5690976 -0.77859171 + 5600 462 0.36572308 -6.6730078 -6.5621827 -0.85672419 + 5700 464 0.40055073 -6.6976989 -6.574685 -0.74251563 + 5800 466 0.36037213 -6.7022014 -6.5900685 -0.66239625 + 5900 468 0.32810921 -6.6952135 -6.591803 -0.83981757 + 6000 470 0.35110886 -6.6986862 -6.5866302 -0.82474047 + 6100 472 0.29965884 -6.6839503 -6.5871326 -0.7864913 + 6200 474 0.32402637 -6.6902745 -6.5843165 -0.74531083 + 6300 476 0.35042653 -6.6990084 -6.5830585 -0.74839967 + 6400 478 0.32695511 -6.6909459 -6.5815048 -0.76549489 + 6500 480 0.35209088 -6.6902987 -6.5711013 -0.71281516 + 6600 482 0.354106 -6.6890268 -6.567808 -0.81897158 + 6700 484 0.3504816 -6.681739 -6.5604463 -0.811609 + 6800 486 0.37396733 -6.7018369 -6.5710253 -0.80383296 + 6900 488 0.36435774 -6.7010114 -6.5722169 -0.72063651 + 7000 490 0.35631012 -6.7089806 -6.581727 -0.74152078 + 7100 492 0.37646659 -6.719154 -6.5833352 -0.77739001 + 7200 494 0.36546269 -6.7223269 -6.5891623 -0.8288767 + 7300 496 0.37688206 -6.7457243 -6.607053 -0.80062121 + 7400 498 0.30331409 -6.7284953 -6.6158184 -0.79894584 + 7500 500 0.30382936 -6.7333804 -6.6194444 -0.86924602 + 7600 502 0.30163143 -6.7294737 -6.6153104 -0.7689497 + 7700 504 0.30281215 -6.7233976 -6.6077402 -0.8557548 + 7800 506 0.33378009 -6.7244958 -6.5958651 -0.82584084 + 7900 508 0.31843128 -6.7250998 -6.6013002 -0.82424684 + 8000 510 0.35912946 -6.7399052 -6.5990701 -0.81879575 + 8100 512 0.31405017 -6.733487 -6.6092777 -0.72940457 + 8200 514 0.30475 -6.7271485 -6.6056043 -0.87958287 + 8300 516 0.30717434 -6.7277574 -6.6042329 -0.81700937 + 8400 518 0.33032462 -6.7382165 -6.6043011 -0.75436496 + 8500 520 0.32218568 -6.7351971 -6.6035347 -0.77661738 + 8600 522 0.30922651 -6.7275431 -6.6001797 -0.85334327 + 8700 524 0.30728021 -6.7237477 -6.5962029 -0.94977016 + 8800 526 0.31061903 -6.7181672 -6.5882505 -0.86132456 + 8900 528 0.33543344 -6.728929 -6.5875768 -0.87545919 + 9000 530 0.31887735 -6.7265066 -6.5911341 -0.76892061 + 9100 532 0.31888326 -6.7216274 -6.5852629 -0.83190298 + 9200 534 0.33310892 -6.7111349 -6.567661 -0.94282671 + 9300 536 0.34737171 -6.722515 -6.5718361 -0.95235602 + 9400 538 0.32752858 -6.7246204 -6.5815549 -0.86227131 + 9500 540 0.30665764 -6.7225391 -6.5876665 -0.87144326 + 9600 542 0.32747382 -6.7149245 -6.5699176 -0.86863105 + 9700 544 0.32463079 -6.7205757 -6.5758643 -0.85393932 + 9800 546 0.31517825 -6.7178961 -6.5764699 -0.81017759 + 9900 548 0.33649933 -6.7380644 -6.5860871 -0.80769312 + 10000 550 0.37394555 -6.7612874 -6.5913121 -0.82102213 +Loop time of 16.6615 on 1 procs for 10000 steps with 550 atoms + +Performance: 259279.806 tau/day, 600.185 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.2639 | 9.2639 | 9.2639 | 0.0 | 55.60 +Bond | 0.021559 | 0.021559 | 0.021559 | 0.0 | 0.13 +Neigh | 4.544 | 4.544 | 4.544 | 0.0 | 27.27 +Comm | 0.62792 | 0.62792 | 0.62792 | 0.0 | 3.77 +Output | 0.0069666 | 0.0069666 | 0.0069666 | 0.0 | 0.04 +Modify | 2.1282 | 2.1282 | 2.1282 | 0.0 | 12.77 +Other | | 0.06897 | | | 0.41 + +Nlocal: 550.000 ave 550 max 550 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2344.00 ave 2344 max 2344 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36607.0 ave 36607 max 36607 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36607 +Ave neighs/atom = 66.558182 +Ave special neighs/atom = 0.36363636 +Neighbor list builds = 847 +Dangerous builds = 0 +Total wall time: 0:00:16 diff --git a/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.4 b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.4 new file mode 100644 index 0000000000..7239fc9bb9 --- /dev/null +++ b/examples/deposit/log.10Mar21.deposit.molecule.rigid-nvt-small.g++.4 @@ -0,0 +1,218 @@ +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/nvt/small molecule temp 0.1 0.1 0.1 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 16.1559 on 4 procs for 10000 steps with 550 atoms + +Performance: 267395.139 tau/day, 618.970 timesteps/s +96.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0035574 | 2.5467 | 7.5373 | 192.6 | 15.76 +Bond | 0.0022929 | 0.0073138 | 0.019471 | 8.3 | 0.05 +Neigh | 0.018645 | 1.2357 | 3.8167 | 138.4 | 7.65 +Comm | 1.1946 | 6.6335 | 11.87 | 158.8 | 41.06 +Output | 0.010714 | 0.014391 | 0.020006 | 3.2 | 0.09 +Modify | 3.4474 | 5.6081 | 11.47 | 143.2 | 34.71 +Other | | 0.1102 | | | 0.68 + +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