forked from lijiext/lammps
226 lines
11 KiB
Groff
226 lines
11 KiB
Groff
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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1 by 1 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 = 4.44301 Mbytes
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Step Temp E_pair Press 10[3] 10
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0 25.701528 -2.2032569 3.1039469 1 1
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100 27.623422 -6.228166 2.6542136 1 1
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200 33.35302 -15.746749 3.2018248 1 1
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300 39.17734 -24.1557 4.9116986 1 1
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400 41.660701 -27.615203 8.6214678 1 1
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500 37.154935 -24.096962 3.2656162 1 1
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600 35.061294 -21.52655 2.3693223 1 1
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700 37.204395 -22.313267 2.7108913 1 1
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800 39.050704 -24.972147 5.5398741 1 1
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900 38.37275 -24.777769 3.9291488 1 1
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1000 39.147816 -26.003699 4.3586203 1 1
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1100 36.084337 -24.88638 4.5496174 1 1
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1200 32.404559 -20.810803 6.0760128 1 1
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1300 32.625538 -19.709411 4.3718289 1 1
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1400 32.246777 -18.785184 3.435959 1 1
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1500 29.174368 -17.434726 2.2702916 1 1
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1600 27.359273 -15.40756 1.033659 1 1
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1700 26.046626 -14.318045 0.87714473 1 1
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1800 24.540401 -13.017686 0.84464169 1 1
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1900 26.259688 -12.777739 0.80954004 1 1
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2000 27.491023 -13.363863 1.4519188 1 1
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2100 27.839831 -13.709118 3.0184763 1 1
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2200 26.669065 -12.710422 1.4560094 1 1
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2300 26.86742 -12.730386 0.16986139 1 1
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2400 26.375504 -12.476682 1.907352 1 1
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2500 26.581263 -12.530908 1.5507765 1 1
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2600 27.67091 -12.922702 2.0391206 1 1
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2700 27.158784 -13.306789 3.7355268 1 1
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2800 25.635671 -13.502047 2.9431633 1 1
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2900 24.648357 -12.388002 0.44910075 1 1
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3000 22.988768 -10.685349 0.37214853 1 1
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3100 21.788719 -10.171928 -0.95734833 1 1
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3200 22.707514 -9.6682633 -0.32868418 1 1
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3300 22.907772 -10.612766 -0.024319089 1 1
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3400 24.276426 -10.802246 0.44731188 1 1
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3500 25.086959 -10.797849 2.3218091 1 1
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3600 26.064365 -12.589537 1.2460738 1 1
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3700 24.656426 -11.956895 0.57862216 1 1
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3800 22.316856 -11.174148 -0.7567936 1 1
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3900 22.590299 -9.5928781 0.4127727 1 1
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4000 22.353461 -9.5887736 -0.34247396 1 1
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4100 24.103395 -9.76584 0.98989862 1 1
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4200 23.92261 -10.566828 -0.71536268 1 1
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4300 24.44409 -11.358378 0.37166197 1 1
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4400 24.772419 -11.324888 0.26732853 1 1
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4500 23.150748 -11.309892 -0.43134573 1 1
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4600 24.008361 -10.212365 0.43277527 1 1
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4700 25.107401 -9.5753673 0.020406689 1 1
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4800 23.658604 -8.9131426 0.46554745 1 1
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4900 22.530251 -9.023311 -0.014405315 1 1
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5000 23.110692 -9.6567397 0.9033234 1 1
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5100 23.760144 -9.7623416 0.32059726 1 1
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5200 25.048012 -9.6748253 0.66411561 1 1
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5300 24.09835 -9.7867216 0.61128267 1 1
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5400 22.984982 -9.9464053 0.28096544 1 1
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5500 22.502003 -9.9294451 -0.53666181 1 1
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5600 23.712298 -10.054318 0.64334761 1 1
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5700 23.350796 -10.217344 2.1979894 1 1
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5800 25.246549 -12.458753 0.055553025 1 1
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5900 24.422272 -10.641177 0.82506839 1 1
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6000 22.478315 -10.629525 -0.774321 1 1
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6100 22.970846 -10.218868 0.59819592 1 1
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6200 24.500063 -10.355481 0.55427078 1 1
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6300 22.358071 -9.9041539 0.89500518 1 1
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6400 23.924951 -11.121442 0.045999129 1 1
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6500 24.83773 -10.464191 2.0048038 1 1
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6600 24.752158 -9.9939162 0.53794465 1 1
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6700 23.073765 -9.3662561 0.38618685 1 1
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6800 21.940219 -8.4948475 -0.25184019 1 1
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6900 22.23783 -8.8668868 0.0072863367 1 1
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7000 25.667836 -10.473211 0.59852886 1 1
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7100 23.352123 -9.0862268 0.85289283 1 1
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7200 24.072107 -9.4020576 0.090222808 1 1
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7300 22.806746 -8.4687857 -0.46892989 1 1
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7400 24.798425 -9.1144357 -0.38738146 1 1
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7500 24.748499 -9.1560558 0.94929896 1 1
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7600 25.364753 -10.176533 0.2649225 1 1
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7700 25.137988 -9.6617897 1.3920543 1 1
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7800 25.502583 -10.320832 0.64812816 1 1
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7900 24.5208 -9.9466543 -0.084071026 1 1
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8000 24.653522 -10.312942 0.32535023 1 1
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8100 23.129565 -9.6250435 0.016356303 1 1
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8200 23.82421 -9.7608023 0.11631418 1 1
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8300 25.081262 -9.3510452 0.92337854 1 1
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8400 24.328205 -9.2875396 0.28266968 1 1
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8500 25.041711 -11.254976 -0.21368615 1 1
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8600 24.111473 -9.0389585 1.2102938 1 1
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8700 23.50066 -9.0926498 0.78819229 1 1
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8800 23.840962 -9.3434474 0.091313007 1 1
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8900 23.081841 -9.0635966 0.56672001 1 1
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9000 24.712103 -9.3243213 0.60301629 1 1
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9100 24.457422 -9.439298 -0.60457515 1 1
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9200 25.070662 -9.1945782 1.2399235 1 1
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9300 25.019869 -8.7910068 0.42340497 1 1
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9400 24.23662 -9.3111098 -0.75379175 1 1
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9500 24.836827 -8.7324281 0.81857501 1 1
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9600 24.901993 -8.6624128 0.84890877 1 1
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9700 24.936686 -8.9869503 1.9627894 1 1
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9800 25.393368 -9.8538595 0.45344428 1 1
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9900 25.942336 -9.7854728 0.68352091 1 1
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10000 24.636319 -9.3369442 0.62793231 1 1
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Loop time of 1.67474 on 1 procs for 10000 steps with 361 atoms
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Performance: 2579511.004 tau/day, 5971.090 timesteps/s
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99.8% CPU use with 1 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 | 0.47884 | 0.47884 | 0.47884 | 0.0 | 28.59
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Bond | 0.24918 | 0.24918 | 0.24918 | 0.0 | 14.88
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Neigh | 0.82974 | 0.82974 | 0.82974 | 0.0 | 49.54
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Comm | 0.01265 | 0.01265 | 0.01265 | 0.0 | 0.76
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Output | 0.00085878 | 0.00085878 | 0.00085878 | 0.0 | 0.05
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Modify | 0.075636 | 0.075636 | 0.075636 | 0.0 | 4.52
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Other | | 0.02783 | | | 1.66
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Nlocal: 361 ave 361 max 361 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 2421 ave 2421 max 2421 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2421
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Ave neighs/atom = 6.70637
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Ave special neighs/atom = 5.61773
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Neighbor list builds = 4937
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Dangerous builds = 5
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Total wall time: 0:00:01
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