forked from lijiext/lammps
226 lines
11 KiB
Groff
226 lines
11 KiB
Groff
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LAMMPS (15 Feb 2016)
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# 2d circle of particles inside a box with LJ walls
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variable b index 0
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variable x index 50
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variable y index 20
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variable d index 20
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variable v index 5
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variable w index 2
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units lj
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dimension 2
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atom_style bond
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boundary f f p
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lattice hex 0.85
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Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
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region box block 0 $x 0 $y -0.5 0.5
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region box block 0 50 0 $y -0.5 0.5
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region box block 0 50 0 20 -0.5 0.5
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create_box 1 box bond/types 1 extra/bond/per/atom 6
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Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
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2 by 2 by 1 MPI processor grid
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region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
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region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
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region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
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region circle sphere 11 6.7735026918962581988 0.0 10
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create_atoms 1 region circle
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Created 361 atoms
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mass 1 1.0
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velocity all create 0.5 87287 loop geom
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velocity all set $v $w 0 sum yes
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velocity all set 5 $w 0 sum yes
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velocity all set 5 2 0 sum yes
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pair_style lj/cut 2.5
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pair_coeff 1 1 10.0 1.0 2.5
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bond_style harmonic
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bond_coeff 1 10.0 1.2
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# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
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special_bonds lj/coul 0 1 1
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0 = max # of 1-2 neighbors
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1 = max # of special neighbors
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create_bonds all all 1 1.0 1.5
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Neighbor list info ...
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2 neighbor list requests
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update every 1 steps, delay 10 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 = 42 29 1
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Added 1014 bonds, new total = 1014
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6 = max # of 1-2 neighbors
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6 = max # of special neighbors
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 all nve
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fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
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fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
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fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
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fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
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comm_style tiled
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comm_modify cutoff 7.5
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fix 10 all balance 50 0.9 rcb
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#compute 1 all property/atom proc
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#variable p atom (c_1%10)+1
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#dump 2 all custom 50 tmp.dump id v_p x y z
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#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
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#variable colors string # "red green blue yellow white # purple pink orange lime gray"
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#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
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thermo_style custom step temp epair press f_10[3] f_10
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thermo 100
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run 10000
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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 = 7.5
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binsize = 1.4 -> bins = 42 29 1
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Memory usage per processor = 4.49421 Mbytes
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Step Temp E_pair Press 10[3] 10
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0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316
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100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102
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200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906
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300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906
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400 41.660701 -27.615203 8.6214679 1.3518006 1.0083102
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500 37.154928 -24.096947 3.2656178 1.3296399 1.0193906
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600 35.059889 -21.524279 2.372849 1.3296399 1.0083102
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700 36.70516 -21.98396 3.2995108 1.3296399 1.0083102
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800 39.53521 -25.672748 4.3257712 1.3961219 1.0083102
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900 38.566797 -24.778382 4.1874914 1.3739612 1.0083102
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1000 37.506157 -25.381025 5.6634589 1.4182825 1.0193906
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1100 34.186888 -23.460558 5.2123037 1.2963989 1.0083102
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1200 33.302788 -22.509552 4.9394032 1.1745152 1.0193906
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1300 33.271956 -22.831342 4.5519649 1.1966759 1.0083102
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1400 30.344677 -20.654604 4.1641375 1.0969529 1.0193906
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1500 27.292624 -18.180523 1.0686706 1.1412742 1.0083102
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1600 26.787948 -15.907011 1.7236133 1.1745152 1.0193906
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1700 25.708419 -15.568774 0.73006531 1.1080332 1.0193906
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1800 26.523196 -14.641077 0.78443231 1.1301939 1.0083102
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1900 25.151151 -13.927975 1.1760729 1.1080332 1.0193906
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2000 27.637036 -15.055467 1.5903524 1.1301939 1.0083102
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2100 27.642772 -14.038356 2.4101976 1.2077562 1.0083102
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2200 27.178261 -13.277262 1.9252291 1.1745152 1.0193906
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2300 25.615526 -12.67851 0.88527229 1.1634349 1.0083102
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2400 24.918218 -13.029669 0.95714212 1.1966759 1.0193906
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2500 27.302154 -13.02629 1.3556788 1.1080332 1.0193906
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2600 26.798157 -13.78042 2.703198 1.1855956 1.0083102
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2700 27.24573 -16.504845 3.1771274 1.1523546 1.0193906
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2800 24.592313 -14.795322 1.6473982 1.0969529 1.0193906
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2900 22.803769 -13.043913 0.71978239 1.0969529 1.0083102
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3000 21.388681 -13.323114 -1.3437735 1.0858726 1.0083102
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3100 21.929044 -11.627262 -0.38509856 1.1191136 1.0083102
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3200 22.350115 -10.438826 0.7833392 1.0526316 1.0083102
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3300 22.619011 -9.9110914 1.4143766 1.1191136 1.0193906
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3400 24.251234 -11.712256 1.4299187 1.0969529 1.0193906
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3500 25.633796 -12.609976 1.4809529 1.0969529 1.0083102
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3600 23.070279 -11.178798 0.35315388 1.1191136 1.0083102
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3700 22.635771 -10.360523 0.060253018 1.1412742 1.0193906
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3800 20.746426 -9.7066538 0.24549731 1.0526316 1.0083102
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3900 22.467121 -10.469368 0.9854352 1.0969529 1.0193906
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4000 22.658639 -10.781605 0.014232783 1.1191136 1.0083102
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4100 22.839698 -10.528796 1.3995223 1.0526316 1.0083102
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4200 23.52621 -12.150065 0.74863439 1.0747922 1.0193906
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4300 24.401948 -11.703236 0.25019621 1.0637119 1.0193906
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4400 22.769001 -11.763045 -0.033044917 1.1412742 1.0083102
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4500 22.170178 -11.572473 -0.40444128 1.0526316 1.0083102
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4600 22.409231 -10.761099 -0.012942618 1.0747922 1.0083102
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4700 22.953641 -10.999181 0.17199357 1.0637119 1.0083102
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4800 22.746977 -10.69943 -0.050664647 1.0526316 1.0083102
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4900 23.784023 -10.353932 0.55400224 1.0747922 1.0304709
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5000 23.250563 -11.567067 -0.23735032 1.0637119 1.0083102
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5100 22.521138 -10.661998 0.50094359 1.0747922 1.0083102
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5200 21.318659 -9.5996948 0.75683786 1.0637119 1.0193906
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5300 21.603355 -10.042239 -0.2376815 1.0637119 1.0083102
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5400 21.350407 -10.181041 -0.87085628 1.1745152 1.0193906
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5500 22.430002 -10.535576 0.47962005 1.1191136 1.0193906
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5600 22.459036 -11.914086 0.47719353 1.0858726 1.0193906
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5700 23.348257 -12.888911 0.55511547 1.0858726 1.0193906
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5800 23.357742 -12.328566 0.734193 1.0526316 1.0193906
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5900 24.002277 -11.439187 0.23688862 1.0858726 1.0193906
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6000 22.398563 -10.682615 0.28777592 1.0747922 1.0193906
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6100 22.23883 -10.838986 -0.17956279 1.1080332 1.0083102
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6200 21.930735 -11.182485 0.044031465 1.0526316 1.0193906
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6300 22.658226 -11.142419 0.060550217 1.0526316 1.0193906
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6400 22.375935 -11.1764 -0.027267206 1.0526316 1.0193906
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6500 21.553541 -9.9609653 1.0562139 1.0858726 1.0193906
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6600 23.339323 -10.988956 0.19462502 1.0526316 1.0083102
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6700 22.506968 -11.276791 0.50225378 1.0969529 1.0083102
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6800 22.991741 -10.292043 1.3278137 1.0858726 1.0193906
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6900 22.716461 -10.540264 1.090723 1.0304709 1.0083102
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7000 20.88433 -10.566053 -0.47976012 1.0969529 1.0193906
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7100 22.034864 -10.27774 0.24169213 1.0193906 1.0083102
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7200 23.107403 -10.304771 0.39888005 1.0969529 1.0304709
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7300 22.734104 -9.8038963 1.1986757 1.0858726 1.0083102
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7400 23.566402 -10.560548 1.0213434 1.1080332 1.0193906
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7500 23.651346 -10.596902 1.290057 1.0969529 1.0083102
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7600 23.181407 -10.247073 0.80701327 1.0526316 1.0083102
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7700 23.778698 -10.659208 0.54327672 1.0304709 1.0193906
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7800 22.655159 -10.183303 0.81382393 1.0747922 1.0193906
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7900 22.897008 -10.849819 0.56424197 1.0415512 1.0083102
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8000 23.698074 -10.398048 0.42170034 1.0747922 1.0083102
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8100 22.726563 -9.8563277 0.30293638 1.0193906 1.0193906
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8200 23.424699 -10.687885 0.54222367 1.0415512 1.0083102
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8300 22.921826 -10.919492 0.55264172 1.0747922 1.0083102
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8400 23.220159 -9.7725217 1.2872547 1.1080332 1.0083102
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8500 23.606204 -9.7070499 1.0340181 1.0747922 1.0193906
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8600 23.008166 -10.451507 -0.42524326 1.0747922 1.0083102
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8700 22.4959 -10.278782 0.19535494 1.0858726 1.0083102
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8800 25.153658 -10.757 1.5966743 1.0193906 1.0193906
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8900 23.206798 -10.486994 1.2031737 1.0637119 1.0083102
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9000 22.726684 -10.406196 0.10165144 1.0858726 1.0304709
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9100 22.504045 -9.638919 -0.80560991 1.0747922 1.0083102
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9200 21.431928 -9.073801 0.3773795 1.0415512 1.0193906
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9300 23.596502 -11.045041 -0.3135787 1.0858726 1.0083102
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9400 25.308669 -11.931174 1.3143518 1.0526316 1.0193906
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9500 24.394499 -10.661499 0.82236963 1.0969529 1.0193906
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9600 21.987451 -9.5632699 0.30728292 1.0858726 1.0193906
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9700 22.150748 -9.5707928 -0.1239396 1.0526316 1.0193906
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9800 23.347328 -9.7899306 0.29737715 1.0193906 1.0083102
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9900 20.310207 -9.4839992 -1.2980277 1.0193906 1.0193906
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10000 22.978427 -9.9593786 -0.45943368 1.0526316 1.0083102
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Loop time of 0.815364 on 4 procs for 10000 steps with 361 atoms
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Performance: 5298244.819 tau/day, 12264.456 timesteps/s
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98.9% CPU use with 4 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 | 0.12547 | 0.13632 | 0.14796 | 2.6 | 16.72
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Bond | 0.05547 | 0.06023 | 0.064582 | 1.7 | 7.39
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Neigh | 0.28201 | 0.28972 | 0.298 | 1.1 | 35.53
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Comm | 0.16858 | 0.19467 | 0.22096 | 4.3 | 23.88
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Output | 0.0017931 | 0.0019639 | 0.0023253 | 0.5 | 0.24
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Modify | 0.039718 | 0.040559 | 0.041364 | 0.4 | 4.97
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Other | | 0.09189 | | | 11.27
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Nlocal: 90.25 ave 91 max 90 min
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Histogram: 3 0 0 0 0 0 0 0 0 1
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Nghost: 195.25 ave 202 max 185 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Neighs: 629.5 ave 731 max 543 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Total # of neighbors = 2518
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Ave neighs/atom = 6.97507
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Ave special neighs/atom = 5.61773
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Neighbor list builds = 4874
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Dangerous builds = 0
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Total wall time: 0:00:00
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