forked from lijiext/lammps
226 lines
8.4 KiB
Groff
226 lines
8.4 KiB
Groff
LAMMPS (13 Oct 2016)
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# sample LAMMPS input script for thermal conductivity of liquid LJ
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# use fix ehex to add/subtract energy from 2 regions
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# settings
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variable x equal 10
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variable y equal 10
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variable z equal 20
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variable rho equal 0.6
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variable t equal 1.35
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variable rc equal 2.5
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#variable rho equal 0.85
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#variable t equal 0.7
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#variable rc equal 3.0
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# setup problem
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units lj
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atom_style atomic
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lattice fcc ${rho}
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lattice fcc 0.6
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Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
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region box block 0 $x 0 $y 0 $z
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region box block 0 10 0 $y 0 $z
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region box block 0 10 0 10 0 $z
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region box block 0 10 0 10 0 20
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create_box 1 box
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Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
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2 by 1 by 4 MPI processor grid
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create_atoms 1 box
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Created 8000 atoms
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mass 1 1.0
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velocity all create $t 87287
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velocity all create 1.35 87287
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pair_style lj/cut ${rc}
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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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neighbor 0.3 bin
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neigh_modify delay 0 every 1
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# heat layers
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region hot block INF INF INF INF 0 1
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region cold block INF INF INF INF 10 11
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compute Thot all temp/region hot
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compute Tcold all temp/region cold
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# 1st equilibration run
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fix 1 all nvt temp $t $t 0.5
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fix 1 all nvt temp 1.35 $t 0.5
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fix 1 all nvt temp 1.35 1.35 0.5
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thermo 100
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run 1000
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 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 = 14 14 27
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Memory usage per processor = 2.55761 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.35 -4.1241917 0 -2.0994448 -3.1961612
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100 1.1819832 -3.7640881 0 -1.991335 0.53985757
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200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
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300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
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400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
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500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
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600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
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700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
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800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
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900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
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1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
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Loop time of 0.889114 on 8 procs for 1000 steps with 8000 atoms
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Performance: 485876.777 tau/day, 1124.715 timesteps/s
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99.3% CPU use with 8 MPI tasks x no 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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---------------------------------------------------------------
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Pair | 0.48042 | 0.50311 | 0.52772 | 1.9 | 56.59
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Neigh | 0.22997 | 0.23203 | 0.23466 | 0.3 | 26.10
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Comm | 0.081187 | 0.10484 | 0.1285 | 4.2 | 11.79
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Output | 0.00027299 | 0.00028226 | 0.000314 | 0.1 | 0.03
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Modify | 0.028298 | 0.032276 | 0.037612 | 2.0 | 3.63
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Other | | 0.01658 | | | 1.86
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Nlocal: 1000 ave 1020 max 982 min
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Histogram: 1 0 2 1 0 1 1 1 0 1
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Nghost: 2299.5 ave 2331 max 2268 min
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Histogram: 1 1 1 1 0 0 0 3 0 1
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Neighs: 27122 ave 28382 max 26337 min
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Histogram: 2 0 2 1 1 0 0 1 0 1
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Total # of neighbors = 216976
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Ave neighs/atom = 27.122
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Neighbor list builds = 162
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Dangerous builds = 0
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velocity all scale $t
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velocity all scale 1.35
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unfix 1
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# 2nd equilibration run
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fix 1 all nve
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fix hot all ehex 1 100.0 region hot
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fix cold all ehex 1 -100.0 region cold
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thermo_style custom step temp c_Thot c_Tcold
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thermo 1000
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run 10000
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Memory usage per processor = 2.80761 Mbytes
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Step Temp c_Thot c_Tcold
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1000 1.35 1.431295 1.2955644
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2000 1.3537291 1.6418772 1.1875127
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3000 1.3615152 1.6451299 1.1769094
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4000 1.3612129 1.5281727 1.2022419
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5000 1.3552182 1.6672955 1.2212864
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6000 1.3643442 1.6072213 1.2390567
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7000 1.3665773 1.6909819 1.1466611
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8000 1.375741 1.6144274 1.1691231
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9000 1.3701136 1.8238424 1.136342
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10000 1.3563004 1.8059065 1.1547129
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11000 1.3794051 1.692299 1.0515688
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Loop time of 10.5555 on 8 procs for 10000 steps with 8000 atoms
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Performance: 409265.976 tau/day, 947.375 timesteps/s
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99.4% CPU use with 8 MPI tasks x no 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 | 4.1863 | 5.0134 | 5.8326 | 28.0 | 47.50
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Neigh | 2.1559 | 2.4232 | 2.6516 | 14.2 | 22.96
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Comm | 0.80561 | 1.8126 | 2.8852 | 58.4 | 17.17
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Output | 0.00044537 | 0.00064856 | 0.00077057 | 0.5 | 0.01
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Modify | 0.81915 | 0.94285 | 1.0571 | 9.5 | 8.93
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Other | | 0.3628 | | | 3.44
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Nlocal: 1000 ave 1105 max 883 min
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Histogram: 1 1 2 0 0 0 0 0 2 2
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Nghost: 2319.38 ave 2502 max 2114 min
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Histogram: 1 3 0 0 0 0 0 0 0 4
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Neighs: 27387.9 ave 32453 max 21803 min
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Histogram: 2 2 0 0 0 0 0 0 0 4
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Total # of neighbors = 219103
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Ave neighs/atom = 27.3879
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Neighbor list builds = 1696
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Dangerous builds = 0
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# thermal conductivity calculation
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compute ke all ke/atom
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variable temp atom c_ke/1.5
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compute layers all chunk/atom bin/1d z lower 0.05 units reduced
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fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.ehex
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variable tdiff equal f_2[11][3]-f_2[1][3]
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fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000
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thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
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run 20000
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Memory usage per processor = 3.0578 Mbytes
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Step Temp c_Thot c_Tcold v_tdiff f_ave
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11000 1.3794051 1.6903393 1.0515688 0 0
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12000 1.3799777 1.8004888 1.1032219 -0.63860014 0
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13000 1.3733605 1.7823094 1.0553582 -0.65827891 -0.65827891
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14000 1.3749743 1.7852256 1.1674016 -0.68463005 -0.67145448
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15000 1.3863795 1.8538127 1.0056247 -0.73524813 -0.69271903
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16000 1.3731955 1.7518546 1.0741458 -0.74810775 -0.70656621
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17000 1.3771856 1.9016869 1.0090502 -0.73999567 -0.7132521
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18000 1.3766032 1.7616195 1.1142155 -0.73769104 -0.71732526
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19000 1.3815934 1.7791247 1.1406987 -0.73617832 -0.72001855
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20000 1.3725543 1.8637436 1.0799364 -0.73435569 -0.7218107
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21000 1.3817369 1.8808771 1.0642524 -0.76702329 -0.72683432
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22000 1.3968704 1.840287 1.072304 -0.82496419 -0.7366473
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23000 1.3895558 1.9427293 1.0766665 -0.75363908 -0.73819201
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24000 1.3900493 1.9883976 1.1081017 -0.86394774 -0.74867166
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25000 1.3838912 1.8853041 1.0795751 -0.83043902 -0.75496145
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26000 1.3912105 1.9330259 1.1070335 -0.79880182 -0.75809291
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27000 1.3891151 1.8548451 1.0676153 -0.81856523 -0.7621244
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28000 1.3942624 1.9796706 1.1251407 -0.81762456 -0.76559316
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29000 1.3819302 1.8619138 1.0495292 -0.78627491 -0.76680973
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30000 1.3968366 1.883107 1.1004588 -0.83902548 -0.77082172
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31000 1.3822489 1.8220413 1.0322271 -0.7550338 -0.76999077
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Loop time of 22.7579 on 8 procs for 20000 steps with 8000 atoms
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Performance: 379649.018 tau/day, 878.817 timesteps/s
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99.3% CPU use with 8 MPI tasks x no 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 | 7.4811 | 10.102 | 12.63 | 68.7 | 44.39
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Neigh | 4.0495 | 4.9884 | 5.8366 | 37.8 | 21.92
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Comm | 1.6695 | 4.9483 | 8.493 | 130.7 | 21.74
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Output | 0.0010517 | 0.0017769 | 0.0019059 | 0.7 | 0.01
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Modify | 1.6903 | 1.9371 | 2.2355 | 14.8 | 8.51
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Other | | 0.7799 | | | 3.43
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Nlocal: 1000 ave 1121 max 857 min
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Histogram: 2 0 1 1 0 0 0 0 1 3
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Nghost: 2299.75 ave 2541 max 2067 min
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Histogram: 3 1 0 0 0 0 0 0 2 2
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Neighs: 27487.2 ave 33361 max 20651 min
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Histogram: 2 1 1 0 0 0 0 0 0 4
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Total # of neighbors = 219898
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Ave neighs/atom = 27.4872
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Neighbor list builds = 3474
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Dangerous builds = 0
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Total wall time: 0:00:34
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