forked from lijiext/lammps
219 lines
8.1 KiB
Groff
219 lines
8.1 KiB
Groff
LAMMPS (29 Mar 2019)
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using 1 OpenMP thread(s) per MPI task
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# 2d micelle simulation
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dimension 2
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neighbor 0.3 bin
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neigh_modify delay 5
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atom_style bond
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# Soft potential push-off
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read_data data.micelle
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orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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1200 atoms
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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300 bonds
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.000413656 secs
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read_data CPU = 0.00487924 secs
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special_bonds fene
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2 = max # of 1-2 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.000178576 secs
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pair_style soft 1.12246
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pair_coeff * * 0.0 1.12246
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bond_style harmonic
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bond_coeff 1 50.0 0.75
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velocity all create 0.45 2349852
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variable prefactor equal ramp(1.0,20.0)
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fix 1 all nve
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fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
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fix 3 all adapt 1 pair soft a * * v_prefactor
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fix 4 all enforce2d
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thermo 50
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.42246
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ghost atom cutoff = 1.42246
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binsize = 0.71123, bins = 51 51 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair soft, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
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50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
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100 0.45 0.73046745 0.054836584 1.234929 2.3196516
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150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
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200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
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250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
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300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
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350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
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400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
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450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
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500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
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550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
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600 0.45 0.58193041 0.088386617 1.119942 5.131481
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650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
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700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
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750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
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800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
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850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
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900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
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950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
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1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
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Loop time of 0.0906248 on 4 procs for 1000 steps with 1200 atoms
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Performance: 4766906.584 tau/day, 11034.506 timesteps/s
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98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 0.036572 | 0.039266 | 0.041216 | 1.0 | 43.33
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Bond | 0.0023205 | 0.0024512 | 0.0025697 | 0.2 | 2.70
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Neigh | 0.0088909 | 0.0089301 | 0.0089679 | 0.0 | 9.85
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Comm | 0.022308 | 0.024047 | 0.027175 | 1.3 | 26.53
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Output | 0.00057411 | 0.00061274 | 0.00071025 | 0.0 | 0.68
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Modify | 0.0083182 | 0.0092374 | 0.0098341 | 0.6 | 10.19
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Other | | 0.006081 | | | 6.71
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Nlocal: 300 ave 305 max 292 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 100.25 ave 108 max 93 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 784 ave 815 max 739 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Total # of neighbors = 3136
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Ave neighs/atom = 2.61333
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Ave special neighs/atom = 0.5
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Neighbor list builds = 92
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Dangerous builds = 0
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unfix 3
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# Main run
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pair_style lj/cut 2.5
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# solvent/head - full-size and long-range
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pair_coeff 1 1 1.0 1.0 2.5
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pair_coeff 2 2 1.0 1.0 2.5
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pair_coeff 1 2 1.0 1.0 2.5
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# tail/tail - size-averaged and long-range
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pair_coeff 3 3 1.0 0.75 2.5
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pair_coeff 4 4 1.0 0.50 2.5
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pair_coeff 3 4 1.0 0.67 2.5
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# solvent/tail - full-size and repulsive
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pair_coeff 1 3 1.0 1.0 1.12246
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pair_coeff 1 4 1.0 1.0 1.12246
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# head/tail - size-averaged and repulsive
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pair_coeff 2 3 1.0 0.88 1.12246
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pair_coeff 2 4 1.0 0.75 1.12246
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thermo 50
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#dump 1 all atom 2000 dump.micelle
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#dump 2 all image 2000 image.*.jpg type type zoom 1.6
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#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
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#dump 3 all movie 2000 movie.mpg type type zoom 1.6
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#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
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reset_timestep 0
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run 1000
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 26 26 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
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50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557
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100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661
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150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373
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200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655
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250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682
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300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947
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350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532
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400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066
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450 0.47220236 -1.9468502 0.065625625 -1.4094157 2.0984288
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500 0.4684673 -1.9444333 0.076696285 -1.3996601 2.0528682
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550 0.47683128 -1.958676 0.070589721 -1.4116523 2.0856023
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600 0.46851245 -1.9338267 0.070605469 -1.3950992 2.26405
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650 0.46874143 -1.9462493 0.069134686 -1.4087638 2.1070262
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700 0.4643739 -1.9309953 0.071977511 -1.3950309 2.225692
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750 0.47326259 -1.9484258 0.075435808 -1.4001218 2.0880235
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800 0.45 -1.9646003 0.06415956 -1.4508158 2.0612703
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850 0.46748278 -1.9705588 0.06038513 -1.4430804 1.9472884
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900 0.46909438 -1.9537221 0.062470305 -1.4225483 2.0223008
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950 0.45631508 -1.9387742 0.067536066 -1.4153033 2.063854
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1000 0.45 -1.9727651 0.058608085 -1.464532 1.9982447
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Loop time of 0.0878521 on 4 procs for 1000 steps with 1200 atoms
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Performance: 4917357.613 tau/day, 11382.772 timesteps/s
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99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 0.043517 | 0.044455 | 0.046903 | 0.7 | 50.60
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Bond | 0.0020199 | 0.0022303 | 0.0024347 | 0.4 | 2.54
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Neigh | 0.012207 | 0.012335 | 0.012512 | 0.1 | 14.04
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Comm | 0.014938 | 0.018265 | 0.020068 | 1.5 | 20.79
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Output | 0.00061369 | 0.00064814 | 0.00073504 | 0.0 | 0.74
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Modify | 0.0052264 | 0.0053691 | 0.0055039 | 0.2 | 6.11
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Other | | 0.00455 | | | 5.18
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Nlocal: 300 ave 305 max 296 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Nghost: 219.5 ave 228 max 214 min
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Histogram: 1 0 1 1 0 0 0 0 0 1
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Neighs: 2146.5 ave 2201 max 2114 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Total # of neighbors = 8586
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Ave neighs/atom = 7.155
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Ave special neighs/atom = 0.5
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Neighbor list builds = 86
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Dangerous builds = 0
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Total wall time: 0:00:00
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