forked from lijiext/lammps
229 lines
10 KiB
Groff
229 lines
10 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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processors * 1 1
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 10 0 10 0 10
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create_box 3 box
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Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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2 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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Time spent = 0.000553608 secs
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mass * 1.0
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region long block 3 6 0 10 0 10
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set region long type 2
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1400 settings made for type
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velocity all create 1.0 87287
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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pair_coeff * 2 1.0 1.0 5.0
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neighbor 0.3 bin
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neigh_modify every 2 delay 4 check yes
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fix p all property/atom d_WEIGHT
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fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.8 weight store WEIGHT
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compute p all property/atom d_WEIGHT
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variable maximb equal f_0[1]
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variable iter equal f_0[2]
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variable prev equal f_0[3]
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variable final equal f_0
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#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
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fix 1 all nve
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#dump id all atom 50 dump.melt
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#dump id all custom 50 dump.lammpstrj id type x y z c_p
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#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 2 pad 3
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#dump 3 all movie 25 movie.mp4 c_p type # axes yes 0.8 0.02 view 60 -30
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#dump_modify 3 pad 3 amap 0.0 2.0 cf 0.1 3 min blue 0.5 green max red
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thermo 50
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run 500
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Neighbor list info ...
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update every 2 steps, delay 4 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 5.3
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ghost atom cutoff = 5.3
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binsize = 2.65, bins = 7 7 7
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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/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65)
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Per MPI rank memory allocation (min/avg/max) = 4.562 | 4.753 | 4.944 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
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50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
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100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
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150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
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200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
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250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
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300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137
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350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137
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400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137
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450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137
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500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
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Loop time of 3.92718 on 2 procs for 500 steps with 4000 atoms
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Performance: 55001.290 tau/day, 127.318 timesteps/s
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99.2% CPU use with 2 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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---------------------------------------------------------------
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Pair | 2.2902 | 2.6102 | 2.9303 | 19.8 | 66.47
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Neigh | 0.89715 | 0.89718 | 0.8972 | 0.0 | 22.85
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Comm | 0.074355 | 0.39408 | 0.7138 | 50.9 | 10.03
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Output | 0.0003202 | 0.00035989 | 0.00039959 | 0.0 | 0.01
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Modify | 0.016438 | 0.016832 | 0.017226 | 0.3 | 0.43
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Other | | 0.008523 | | | 0.22
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Nlocal: 2000 ave 2056 max 1944 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10457.5 ave 10508 max 10407 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 298070 ave 333007 max 263132 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 596139
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Ave neighs/atom = 149.035
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Neighbor list builds = 51
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Dangerous builds = 0
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run 500
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Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.758 | 4.946 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
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550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137
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600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 4738.2137
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650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 4738.2137
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700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 4738.2137
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750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 4738.2137
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800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 4738.2137
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850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 4738.2137
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900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137
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950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137
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1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
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Loop time of 3.83028 on 2 procs for 500 steps with 4000 atoms
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Performance: 56392.741 tau/day, 130.539 timesteps/s
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99.6% CPU use with 2 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 | 2.263 | 2.5605 | 2.858 | 18.6 | 66.85
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Neigh | 0.8789 | 0.88341 | 0.88791 | 0.5 | 23.06
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Comm | 0.068052 | 0.36076 | 0.65347 | 48.7 | 9.42
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Output | 0.0003016 | 0.0003438 | 0.000386 | 0.0 | 0.01
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Modify | 0.016381 | 0.016829 | 0.017277 | 0.3 | 0.44
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Other | | 0.008426 | | | 0.22
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Nlocal: 2000 ave 2049 max 1951 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10389 ave 10436 max 10342 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 300836 ave 335987 max 265684 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 601671
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Ave neighs/atom = 150.418
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Neighbor list builds = 51
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Dangerous builds = 0
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run 500
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Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.758 | 4.946 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
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1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137
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1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 4738.2137
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1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 4738.2137
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1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 4738.2137
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1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418134 4738.2137
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1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137
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1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137
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1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137
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1450 0.5421844 -6.2574683 0 -5.444395 -1.7901189 4738.2137
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1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137
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Loop time of 3.81946 on 2 procs for 500 steps with 4000 atoms
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Performance: 56552.445 tau/day, 130.908 timesteps/s
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99.6% CPU use with 2 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 | 2.2594 | 2.5549 | 2.8504 | 18.5 | 66.89
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Neigh | 0.86746 | 0.87203 | 0.8766 | 0.5 | 22.83
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Comm | 0.06715 | 0.36699 | 0.66684 | 49.5 | 9.61
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Output | 0.00029325 | 0.00033867 | 0.00038409 | 0.0 | 0.01
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Modify | 0.016529 | 0.016817 | 0.017105 | 0.2 | 0.44
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Other | | 0.008371 | | | 0.22
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Nlocal: 2000 ave 2034 max 1966 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10386 ave 10936 max 9836 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 302958 ave 337188 max 268729 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 605917
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Ave neighs/atom = 151.479
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Neighbor list builds = 51
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Dangerous builds = 0
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run 500
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Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.758 | 4.946 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137
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1550 0.53713593 -6.2504069 0 -5.4449044 -1.764709 4738.2137
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1600 0.54679556 -6.2646482 0 -5.4446599 -1.8115775 4738.2137
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1650 0.53806577 -6.2519006 0 -5.4450037 -1.7409142 4738.2137
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1700 0.5347951 -6.2468962 0 -5.4449041 -1.7162331 4738.2137
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1750 0.53714568 -6.2506577 0 -5.4451406 -1.7340499 4738.2137
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1800 0.52749839 -6.2358664 0 -5.4448167 -1.6874961 4738.2137
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1850 0.54585956 -6.2629394 0 -5.4443547 -1.7758764 4738.2137
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1900 0.53010831 -6.2387561 0 -5.4437925 -1.6381825 4738.2137
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1950 0.54288557 -6.2583073 0 -5.4441826 -1.7368524 4738.2137
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2000 0.52765923 -6.2348572 0 -5.4435663 -1.5588839 4738.2137
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Loop time of 3.78423 on 2 procs for 500 steps with 4000 atoms
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Performance: 57078.976 tau/day, 132.127 timesteps/s
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99.4% CPU use with 2 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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---------------------------------------------------------------
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Pair | 2.2449 | 2.5388 | 2.8328 | 18.4 | 67.09
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Neigh | 0.85527 | 0.85828 | 0.86129 | 0.3 | 22.68
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Comm | 0.065453 | 0.36215 | 0.65885 | 49.3 | 9.57
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Output | 0.00030518 | 0.00032794 | 0.00035071 | 0.0 | 0.01
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Modify | 0.016444 | 0.016597 | 0.01675 | 0.1 | 0.44
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Other | | 0.008044 | | | 0.21
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Nlocal: 2000 ave 2031 max 1969 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 10334 ave 10921 max 9747 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 303988 ave 338808 max 269168 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 607976
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Ave neighs/atom = 151.994
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Neighbor list builds = 51
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Dangerous builds = 0
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Total wall time: 0:00:15
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