237 lines
18 KiB
Plaintext
237 lines
18 KiB
Plaintext
LAMMPS (9 Sep 2013)
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# SRD viscosity demo - dimer particles
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units lj
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atom_style sphere
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atom_modify map array first big
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dimension 2
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# read in clusters of rigid bodies
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fix molprop all property/atom mol
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read_data data.dimer fix molprop NULL Molecules
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orthogonal box = (-9.34165 -9.34165 -0.5) to (9.34165 9.34165 0.5)
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4 by 2 by 1 MPI processor grid
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200 atoms
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set type 1 mass 1.0
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200 settings made for mass
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group big type 1
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200 atoms in group big
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velocity big create 1.44 87287 loop geom
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# equilibrate big particles
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pair_style soft 1.12
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pair_coeff 1 1 0.0
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pair_coeff 2 2 0.0 0.0
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pair_coeff 1 2 0.0 0.0
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variable prefactor equal ramp(0,60)
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fix soft all adapt 1 pair soft a * * v_prefactor
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fix 1 big rigid molecule
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100 rigid bodies with 200 atoms
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fix 2 all enforce2d
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#dump 1 all atom 10 dump.dimer.equil
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thermo 100
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run 1000
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Memory usage per processor = 3.10291 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 3.4028231 0 0 0.83369167 -0.55065517
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100 9.5167872 2.392105 0 4.7237178 2.8319556
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200 13.564465 3.0352634 0 6.3585572 3.6388732
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300 13.133051 4.3835112 0 7.6011086 4.060051
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400 14.584346 5.5141254 0 9.0872901 4.4231056
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500 15.331515 6.6554832 0 10.411704 4.847642
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600 16.953755 7.4794317 0 11.633102 5.2020696
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700 16.503256 8.8572339 0 12.900532 5.6694613
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800 17.006131 9.877343 0 14.043845 5.5483363
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900 17.305927 11.081594 0 15.321546 6.2908201
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1000 18.122491 12.126462 0 16.566472 5.7536055
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Loop time of 0.0627978 on 8 procs for 1000 steps with 200 atoms
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Pair time (%) = 0.00222558 (3.54404)
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Neigh time (%) = 0.000630498 (1.00401)
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Comm time (%) = 0.0138363 (22.0331)
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Outpt time (%) = 0.000252694 (0.402393)
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Other time (%) = 0.0458528 (73.0165)
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Nlocal: 25 ave 30 max 20 min
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Histogram: 1 0 1 1 0 0 3 1 0 1
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Nghost: 28.375 ave 36 max 22 min
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Histogram: 1 0 1 2 1 0 2 0 0 1
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Neighs: 33.125 ave 45 max 22 min
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Histogram: 1 0 2 1 0 1 1 0 1 1
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Total # of neighbors = 265
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Ave neighs/atom = 1.325
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Neighbor list builds = 99
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Dangerous builds = 96
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#undump 1
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unfix soft
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unfix 1
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unfix 2
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# add small particles as hi density lattice
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region plane block INF INF INF INF -0.001 0.001 units box
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lattice sq 85.0
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Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
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create_atoms 2 region plane
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Created 29929 atoms
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set type 2 mass 0.1
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29929 settings made for mass
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group small type 2
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29929 atoms in group small
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velocity small create 1.0 593849 loop geom
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# delete overlaps
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# must set 1-2 cutoff to non-zero value
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.0 1.0 0.0
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pair_coeff 1 2 0.0 1.0 0.5
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delete_atoms overlap 0.5 small big
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Deleted 12759 atoms, new total = 17370
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# SRD run
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reset_timestep 0
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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communicate multi group big vel yes
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neigh_modify include big
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# no pairwise interactions with small particles
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 0.0 1.0 0.0
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pair_coeff 1 2 0.0 1.0 0.0
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# use fix SRD to push small particles out from inside big ones
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# if comment out, big particles won't see SRD particles
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timestep 0.001
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fix 1 big rigid molecule
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100 rigid bodies with 200 atoms
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fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
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fix 3 small viscosity 10 x y 50
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fix 4 all enforce2d
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# diagnostics
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compute tbig big temp/sphere
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variable pebig equal pe*atoms/count(big)
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variable ebig equal etotal*atoms/count(big)
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thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
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thermo_modify temp tbig
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WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
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thermo 1000
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#dump 1 all atom 500 dump.dimer.mp
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#dump 1 all image 500 image.*.jpg type type zoom 1.6
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#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
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run 50000
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SRD info:
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SRD/big particles = 17170 200
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big particle diameter max/min = 1 1
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SRD temperature & lamda = 1 0.0632456
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SRD max distance & max velocity = 0.252982 12.6491
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SRD grid counts: 75 75 1
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SRD grid size: request, actual (xyz) = 0.25, 0.249111 0.249111 1
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SRD per actual grid cell = 5.5499
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SRD viscosity = 0.235551
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big/SRD mass density ratio = 0.142367
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# of rescaled SRD velocities = 0
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ave/max small velocity = 4.20347 7.72323
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ave/max big velocity = 2.64047 6.60911
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Memory usage per processor = 6.81079 Mbytes
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Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
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0 6.9744766 0 0.30175295 21.011259 26.207244 2.7219332 0 0 0 0 0 0 0 0 0 0 0 0
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1000 1.2992959 3806 0.24766681 20.541887 21.509863 8.3137867 13254 64 64 1 616 40320 5625 3806 1.0164848 0 4 0
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2000 1.358528 3797 0.2484409 20.564988 21.577092 11.810557 13539 50 50 1 1526 40320 5625 3797 1.0411843 0 45 0
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3000 1.4548846 3805 0.24912964 20.553021 21.63691 9.5926803 13468 60 60 4 2398 40320 5625 3805 1.0497533 0 45 0
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4000 1.8791843 3815 0.2520188 20.48784 21.887833 8.2746056 13404 60 60 0 3383 40320 5625 3815 1.0373399 0 45 0
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5000 1.6477948 3808 0.25003987 20.488356 21.715963 4.4265304 13161 48 48 1 4419 40320 5625 3808 1.0272144 0 45 0
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6000 1.6158929 3793 0.24939304 20.455945 21.659785 8.3817061 13207 59 59 0 5558 40320 5625 3793 1.0368342 0 45 0
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7000 2.0865667 3806 0.25391685 20.498186 22.052678 8.0322269 13079 60 60 0 6843 40320 5625 3806 1.0325798 0 107 0
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8000 2.2197829 3778 0.25451747 20.451104 22.104842 11.453866 13081 49 49 0 8004 40320 5625 3778 1.0191928 0 107 0
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9000 2.1397074 3798 0.25441886 20.502196 22.096278 7.8765329 13080 52 52 0 9214 40320 5625 3798 1.0344843 0 107 0
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10000 2.3083585 3791 0.25615794 20.52759 22.247317 7.8816479 12974 48 48 3 10555 40320 5625 3791 1.0281033 0 107 0
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11000 2.5639164 3803 0.25817577 20.512448 22.422565 6.768962 13177 50 50 1 11917 40320 5625 3803 1.0394491 0 107 0
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12000 2.737192 3757 0.26051986 20.586941 22.626149 7.6808761 13072 48 48 6 13993 40320 5625 3757 1.0643581 0 269 0
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13000 8.1232914 3761 0.30582339 20.508909 26.560761 10.80899 13074 48 48 20 15818 40320 5625 3761 1.029561 0 269 0
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14000 2.961704 3786 0.26050848 20.418692 22.625162 9.7685216 13369 59 59 3 17423 40320 5625 3786 1.0121975 0 269 0
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15000 2.5821822 3789 0.25834133 20.513218 22.436944 6.9498412 13183 46 46 3 18931 40320 5625 3789 1.0375525 0 269 0
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16000 2.6225045 3756 0.25795343 20.449489 22.403255 10.405912 12646 66 66 1 20473 40320 5625 3756 1.032942 0 269 0
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17000 4.1283061 3701 0.27197048 20.545048 23.620636 8.4471446 13224 65 66 15 24398 40320 5625 3701 1.0687815 0 604 0
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18000 2.8741237 3777 0.26027375 20.463553 22.604775 7.6566907 13020 61 61 1 26636 40320 5625 3777 1.0098706 0 604 0
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19000 2.713854 3784 0.25853001 20.43151 22.453331 9.1078878 12941 58 58 2 28367 40320 5625 3784 0.98796076 0 604 0
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20000 3.0035093 3791 0.2624204 20.553597 22.791212 5.8950854 12710 50 50 0 30004 40320 5625 3791 1.0127104 0 604 0
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21000 2.8304858 3794 0.25987392 20.461338 22.57005 7.4867736 13025 58 58 3 31801 40320 5625 3794 1.0303174 0 604 0
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22000 2.8055694 3785 0.26137505 20.610274 22.700423 10.823968 13074 64 64 17 33863 40320 5625 3785 1.0205053 0 604 0
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23000 2.9712363 3794 0.26117889 20.469816 22.683387 8.6172464 13263 55 55 1 35391 40320 5625 3794 1.0051398 0 604 0
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24000 2.8762937 3771 0.26137187 20.557308 22.700146 9.8024879 13172 57 57 0 36915 40320 5625 3771 1.0144035 0 604 0
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25000 2.9852963 3782 0.26142335 20.480572 22.704618 9.0597755 13168 67 67 0 38577 40320 5625 3782 1.0230792 0 604 0
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26000 2.918217 3797 0.26186781 20.569148 22.743219 5.6274781 13407 47 47 1 40096 40320 5625 3797 1.0271045 0 604 0
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27000 2.9863542 3781 0.26202524 20.532058 22.756892 6.2490454 13008 45 45 1 41815 40320 5625 3781 1.0516123 0 604 0
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28000 2.9994869 3815 0.26226247 20.542878 22.777496 7.127401 13211 59 59 0 43562 40320 5625 3815 1.0282567 0 604 0
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29000 2.8020211 3769 0.26039919 20.528164 22.61567 4.8931362 13302 46 46 1 45189 40320 5625 3769 1.0011147 0 604 0
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30000 2.9966437 3749 0.26157845 20.485589 22.718088 10.22032 12525 50 51 0 46781 40320 5625 3749 1.0337902 0 604 0
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31000 3.0907131 3807 0.26212089 20.462618 22.765199 9.2934356 12725 67 67 1 48839 40320 5625 3807 1.0232166 0 604 0
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32000 2.8402863 3804 0.25963296 20.433109 22.549122 7.7909674 12830 58 58 0 50434 40320 5625 3804 1.0068925 0 604 0
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33000 2.8936979 3788 0.26075387 20.490668 22.646473 10.184685 12687 60 60 1 51939 40320 5625 3788 1.0201495 0 604 0
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34000 2.9459329 3801 0.26184842 20.546816 22.741536 8.5616047 12962 64 64 1 53500 40320 5625 3801 0.99938958 0 604 0
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35000 2.6106008 3775 0.2586892 20.52226 22.467157 5.6792512 12967 45 45 1 55087 40320 5625 3775 1.0183544 0 604 0
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36000 5.8747699 3809 0.28651929 20.507497 24.8842 9.1933878 12750 53 53 5 56604 40320 5625 3809 1.0079212 0 604 0
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37000 3.1946428 3802 0.26494145 20.630156 23.010165 6.6564892 13029 53 53 5 58460 40320 5625 3802 1.0088282 0 604 0
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38000 2.8700233 3818 0.26040611 20.478103 22.61627 9.2908419 13033 52 52 0 60287 40320 5625 3818 1.0127385 0 604 0
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39000 2.7656892 3812 0.25998902 20.519608 22.580046 10.920034 12894 52 52 1 61786 40320 5625 3812 1.0034298 0 604 0
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40000 2.7523262 3773 0.26006389 20.536066 22.586549 11.157355 12846 68 68 1 63576 40320 5625 3773 1.0398336 0 604 0
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41000 2.9840686 3785 0.26079459 20.426879 22.65001 6.4161076 12739 51 51 1 65115 40320 5625 3785 1.0116164 0 604 0
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42000 2.7562499 3778 0.25907668 20.447404 22.50081 9.4791152 12698 53 53 2 66584 40320 5625 3778 1.0021024 0 604 0
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43000 2.5912808 3787 0.25812876 20.487979 22.418483 7.9217055 12886 50 50 1 68191 40320 5625 3787 1.0093332 0 604 0
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44000 3.0967473 3775 0.26370565 20.595759 22.902836 5.328598 12716 56 56 0 69792 40320 5625 3775 1.0050084 0 604 0
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45000 2.6575446 3777 0.25781099 20.411014 22.390885 10.088161 12878 62 62 0 71801 40320 5625 3777 1.0237185 0 604 0
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46000 2.9186207 3793 0.25950844 20.363936 22.538308 7.0759867 13243 54 54 1 73365 40320 5625 3793 0.99552398 0 604 0
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47000 2.5812503 3793 0.25694255 20.392429 22.315461 9.5971531 12615 64 64 0 74935 40320 5625 3793 1.0014236 0 604 0
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48000 3.192993 3759 0.26332768 20.491229 22.870009 10.811248 12801 68 68 2 76480 40320 5625 3759 1.0208642 0 604 0
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49000 2.5266504 3780 0.25653188 20.397439 22.279794 6.1860477 12935 67 67 1 77986 40320 5625 3780 1.0105053 0 604 0
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50000 2.8382589 3798 0.25970071 20.440504 22.555006 4.0746424 12612 62 62 1 79447 40320 5625 3798 1.0071327 0 604 0
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Loop time of 11.6101 on 8 procs for 50000 steps with 17370 atoms
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Pair time (%) = 0.175835 (1.5145)
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Neigh time (%) = 0.643515 (5.54273)
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Comm time (%) = 0.862317 (7.42731)
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Outpt time (%) = 0.00260469 (0.0224348)
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Other time (%) = 9.92581 (85.493)
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Nlocal: 2171.25 ave 2372 max 1614 min
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Histogram: 1 0 0 0 0 1 0 0 4 2
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Nghost: 60.5 ave 69 max 54 min
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Histogram: 2 0 2 0 1 0 0 1 0 2
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Neighs: 167.375 ave 282 max 128 min
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Histogram: 3 2 1 1 0 0 0 0 0 1
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Total # of neighbors = 1339
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Ave neighs/atom = 0.0770869
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Neighbor list builds = 2593
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Dangerous builds = 2
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Please see the log.cite file for references relevant to this simulation
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