forked from lijiext/lammps
226 lines
11 KiB
Groff
226 lines
11 KiB
Groff
LAMMPS (5 Oct 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 10.0 # because bonds stretch a long ways
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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 = 10
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binsize = 1.4 -> bins = 42 29 1
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Memory usage per processor = 4.49479 Mbytes
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Step Temp E_pair Press f_10[3] f_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 35.05989 -21.524279 2.3728488 1.3296399 1.0083102
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700 36.705654 -21.984526 3.2984899 1.3296399 1.0083102
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800 39.631254 -25.783472 4.1595658 1.3961219 1.0083102
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900 38.122407 -24.836728 5.3619155 1.3628809 1.0083102
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1000 38.369965 -25.098561 4.5613077 1.3074792 1.0083102
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1100 36.448264 -25.295817 4.0134469 1.1966759 1.0193906
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1200 33.216313 -21.813423 4.48954 1.1634349 1.0304709
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1300 30.361077 -20.323335 4.8079549 1.0637119 1.0083102
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1400 29.368132 -18.532543 3.8449914 1.1191136 1.0083102
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1500 27.699395 -15.990271 2.1565226 1.1523546 1.0304709
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1600 25.304973 -14.626675 0.91025038 1.1301939 1.0083102
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1700 26.335273 -14.499134 1.2878263 1.1855956 1.0083102
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1800 25.755278 -13.121269 0.78425366 1.1745152 1.0193906
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1900 25.454743 -13.903724 -0.16644734 1.1080332 1.0083102
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2000 25.54829 -13.271068 1.9214248 1.0969529 1.0083102
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2100 26.663083 -13.423796 1.9699997 1.1080332 1.0083102
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2200 27.707332 -13.759474 1.5528121 1.1412742 1.0304709
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2300 26.649636 -14.246313 0.91466777 1.1412742 1.0193906
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2400 25.92802 -13.16271 1.0298936 1.1301939 1.0193906
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2500 24.992275 -12.299161 1.3078979 1.1301939 1.0083102
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2600 26.235185 -13.363142 2.0756764 1.2188366 1.0083102
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2700 27.235116 -15.57943 2.1120604 1.1745152 1.0083102
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2800 25.313585 -14.352196 2.1442169 1.0637119 1.0083102
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2900 23.472278 -13.686216 0.69404738 1.0637119 1.0193906
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3000 21.02552 -11.646464 0.56287643 1.0747922 1.0083102
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3100 20.746946 -10.721207 -0.67351842 1.0858726 1.0193906
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3200 20.330655 -10.307715 -0.30221601 1.0637119 1.0083102
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3300 22.84995 -11.104879 0.0039310975 1.1191136 1.0083102
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3400 23.23878 -11.827018 0.80792932 1.1301939 1.0193906
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3500 25.262491 -12.191616 0.83249221 1.0747922 1.0193906
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3600 25.08542 -13.10456 1.3164581 1.0969529 1.0193906
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3700 22.649046 -11.300822 0.20123604 1.0526316 1.0193906
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3800 20.516849 -9.7738907 -0.45160364 1.0637119 1.0083102
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3900 20.227823 -9.8156456 -1.4386994 1.0637119 1.0083102
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4000 21.511004 -9.6074826 0.83933362 1.1080332 1.0083102
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4100 24.569081 -12.671563 0.60105671 1.0858726 1.0193906
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4200 24.739215 -11.654269 0.66172409 1.0969529 1.0083102
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4300 22.433043 -10.921392 1.2813391 1.1634349 1.0083102
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4400 22.520504 -10.59901 0.10799908 1.0193906 1.0083102
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4500 21.799185 -9.5801426 0.057062661 1.1191136 1.0193906
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4600 22.537171 -9.9647087 -0.70915155 1.1412742 1.0083102
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4700 22.380783 -10.974234 -0.73703011 1.0858726 1.0083102
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4800 23.991602 -11.171402 1.3314176 1.0415512 1.0193906
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4900 23.077116 -12.281132 0.73818416 1.0858726 1.0083102
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5000 23.180253 -11.702364 0.84176858 1.1080332 1.0193906
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5100 21.079712 -11.204743 0.50038687 1.0747922 1.0083102
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5200 21.348945 -10.802581 -0.28651467 1.1634349 1.0193906
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5300 21.332913 -10.352697 0.46738209 1.0858726 1.0193906
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5400 22.283885 -10.635637 -0.31446485 1.0415512 1.0083102
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5500 21.404737 -9.7733531 0.61106958 1.0858726 1.0193906
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5600 23.013417 -10.291315 1.0562031 1.0969529 1.0083102
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5700 22.087964 -10.931365 0.071180576 1.0415512 1.0193906
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5800 24.011278 -11.080032 1.3901123 1.0637119 1.0193906
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5900 22.320482 -10.616071 0.57726663 1.1412742 1.0193906
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6000 23.348377 -12.116776 0.59306932 1.1191136 1.0193906
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6100 22.20822 -11.545749 0.035299394 1.0747922 1.0193906
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6200 22.810467 -10.598645 0.3296656 1.0415512 1.0083102
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6300 21.398957 -10.058479 0.66795602 1.0415512 1.0193906
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6400 21.945005 -10.358622 -1.0094405 1.0415512 1.0083102
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6500 22.906408 -10.767788 1.0948374 1.0858726 1.0083102
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6600 23.326617 -11.264481 0.82773039 1.0747922 1.0083102
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6700 22.491386 -10.27014 0.043938534 1.0526316 1.0193906
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6800 22.294374 -10.664685 0.048726237 1.1191136 1.0083102
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6900 22.221286 -10.697394 1.0354647 1.0415512 1.0193906
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7000 21.693738 -10.009277 0.64426437 1.0858726 1.0083102
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7100 22.775615 -11.372061 0.069159076 1.1191136 1.0193906
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7200 22.274683 -11.583382 -0.35907789 1.0858726 1.0193906
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7300 21.410706 -11.005479 -0.66394825 1.1080332 1.0083102
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7400 21.910735 -9.9354265 0.78899083 1.0526316 1.0083102
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7500 21.526738 -9.7787506 -0.38232161 1.0415512 1.0083102
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7600 21.833898 -10.289457 0.058939882 1.0747922 1.0193906
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7700 21.606736 -9.6807332 0.50127515 1.0526316 1.0083102
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7800 22.294657 -10.790285 0.8685065 1.0637119 1.0083102
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7900 23.269713 -11.375434 0.84634431 1.0969529 1.0304709
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8000 22.865151 -10.960251 1.0270422 1.0526316 1.0304709
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8100 21.656008 -10.504825 1.2228537 1.0304709 1.0193906
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8200 24.494122 -12.282009 0.16316531 1.0526316 1.0193906
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8300 22.974267 -11.287149 -0.035076799 1.0747922 1.0193906
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8400 21.052237 -11.243181 -0.099450689 1.0747922 1.0193906
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8500 22.661383 -11.090107 -0.22913242 1.0969529 1.0193906
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8600 21.403272 -9.5267458 -0.28047198 1.0637119 1.0193906
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8700 22.786699 -10.403836 0.40752047 1.0415512 1.0193906
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8800 24.504694 -10.706052 1.1870205 1.0969529 1.0193906
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8900 23.22256 -11.182967 0.64166445 1.0747922 1.0304709
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9000 23.734203 -10.422277 1.3143506 1.1191136 1.0304709
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9100 23.517258 -11.247418 -0.13540081 1.0193906 1.0193906
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9200 23.128204 -9.9181617 1.0928284 1.1412742 1.0083102
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9300 23.281107 -10.523942 0.011923998 1.0969529 1.0193906
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9400 21.800282 -10.359413 -0.62145559 1.1412742 1.0193906
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9500 24.910955 -11.786562 1.6227559 1.1301939 1.0193906
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9600 24.331432 -11.802048 0.62882542 1.1191136 1.0083102
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9700 22.340782 -10.531555 0.29842716 1.0415512 1.0193906
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9800 22.371239 -10.384104 0.34253854 1.0415512 1.0083102
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9900 22.289367 -9.9488634 0.29499176 1.1412742 1.0083102
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10000 22.518865 -10.279548 -0.48356734 1.1745152 1.0083102
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Loop time of 0.879172 on 4 procs for 10000 steps with 361 atoms
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Performance: 4913715.115 tau/day, 11374.341 timesteps/s
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99.2% 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 | 0.11586 | 0.13009 | 0.14055 | 2.7 | 14.80
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Bond | 0.054003 | 0.058475 | 0.063238 | 1.8 | 6.65
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Neigh | 0.2865 | 0.29554 | 0.3049 | 1.2 | 33.62
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Comm | 0.20988 | 0.24193 | 0.27748 | 4.9 | 27.52
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Output | 0.0021532 | 0.0023131 | 0.00266 | 0.4 | 0.26
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Modify | 0.043945 | 0.045592 | 0.047122 | 0.6 | 5.19
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Other | | 0.1052 | | | 11.97
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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: 250.25 ave 257 max 247 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Neighs: 624.75 ave 739 max 519 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Total # of neighbors = 2499
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Ave neighs/atom = 6.92244
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Ave special neighs/atom = 5.61773
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Neighbor list builds = 4881
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Dangerous builds = 0
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Total wall time: 0:00:00
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