forked from lijiext/lammps
542 lines
34 KiB
Groff
542 lines
34 KiB
Groff
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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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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# careful not to slam into wall too hard
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variable v index 0.3
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variable w index 0.08
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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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Time spent = 0.000665188 secs
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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 0.3 $w 0 sum yes
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velocity all set 0.3 0.08 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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create_bonds many all all 1 1.0 1.5
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Neighbor list info ...
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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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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) command create_bonds, occasional
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/2d
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bin: standard
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(2) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/2d/newton
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bin: standard
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Added 1014 bonds, new total = 1014
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6 = max # of 1-2 neighbors
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30 = max # of 1-3 neighbors
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180 = max # of 1-4 neighbors
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36 = 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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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 200 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 40000
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Neighbor list info ...
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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 = 42 29 1
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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/newton
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stencil: half/bin/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 7.02 | 7.048 | 7.096 Mbytes
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Step Temp E_pair Press f_10[3] f_10
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0 0.57437856 0 0.26099453 3.2354571 1.0526316
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100 0.29756515 0 0.10149401 1.0193906 1.0083102
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200 0.35394813 0 0.075159099 1.0304709 1.0193906
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300 0.39245849 0 0.033002384 1.0083102 1.0193906
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400 0.34078347 0 -0.020825841 1.0304709 1.0083102
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500 0.35201095 0 -0.062637506 1.0193906 1.0083102
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600 0.34014717 0 -0.11122965 1.0415512 1.0083102
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700 0.3323524 0 -0.11598015 1.0193906 1.0083102
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800 0.35116047 0 -0.096162395 1.0193906 1.0193906
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900 0.35695352 0 -0.01385176 1.0526316 1.0193906
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1000 0.36986539 0 0.056772858 1.0083102 1.0083102
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1100 0.34584644 0 0.084941323 1.0304709 1.0083102
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1200 0.31921435 0 0.10545078 1.0415512 1.0083102
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1300 0.32952819 0 0.124902 1.0083102 1.0193906
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1400 0.34497365 0 0.12662081 1.0193906 1.0083102
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1500 0.33429243 0 0.096230972 1.0193906 1.0193906
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1600 0.33765387 0 0.025800542 1.0304709 1.0083102
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1700 0.35134464 0 -0.04422593 1.0415512 1.0083102
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1800 0.35003859 0 -0.096745576 1.0304709 1.0083102
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1900 0.33839618 0 -0.095465943 1.0193906 1.0083102
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2000 0.33732078 0 -0.094652802 1.0083102 1.0083102
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2100 0.34552238 0 -0.076729261 1.0304709 1.0083102
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2200 0.34893142 0 -0.036853228 1.0304709 1.0083102
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2300 0.35379341 0 0.021124847 1.0304709 1.0193906
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2400 0.34829744 0 0.09230184 1.0304709 1.0083102
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2500 0.33038141 0 0.1399855 1.0193906 1.0193906
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2600 0.30983019 0 0.12754742 1.0083102 1.0083102
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2700 0.32992561 0 0.10485138 1.0415512 1.0083102
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2800 0.34604747 0 0.066174138 1.0083102 1.0083102
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2900 0.3444791 0 0.036590652 1.0193906 1.0193906
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3000 0.34721342 0 -0.023793368 1.0193906 1.0193906
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3100 0.33404314 0 -0.08374223 1.0415512 1.0083102
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3200 0.33019355 0 -0.12715599 1.0083102 1.0304709
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3300 0.33515177 0 -0.12217394 1.0193906 1.0083102
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3400 0.33628481 0 -0.070877624 1.0193906 1.0083102
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3500 0.34257038 0 -0.021612062 1.0304709 1.0083102
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3600 0.32838009 0 0.030131228 1.0083102 1.0083102
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3700 0.34462142 0 0.074586378 1.0526316 1.0193906
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3800 0.30891825 0 0.10605673 1.0304709 1.0083102
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3900 0.33847951 0 0.13956139 1.0083102 1.0083102
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4000 0.32952079 0 0.12688129 1.0193906 1.0304709
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4100 0.32646772 0 0.081089042 1.0304709 1.0193906
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4200 0.35399503 0 0.013422873 1.0083102 1.0083102
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4300 0.33154914 0 -0.050919508 1.0193906 1.0193906
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4400 0.34113556 0 -0.083171 1.0304709 1.0083102
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4500 0.32651708 0 -0.1063133 1.0304709 1.0083102
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4600 0.34359609 0 -0.1076395 1.0083102 1.0083102
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4700 0.34973537 0 -0.088231606 1.0415512 1.0083102
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4800 0.35198515 0 -0.020901044 1.0415512 1.0083102
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4900 0.35187284 0 0.043645941 1.0415512 1.0083102
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5000 0.34887336 0 0.095698609 1.0193906 1.0083102
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5100 0.30308163 0 0.11649328 1.0193906 1.0083102
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5200 0.32401285 0 0.12072411 1.0193906 1.0083102
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5300 0.33025072 0 0.10933161 1.0193906 1.0083102
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5400 0.33288012 0 0.078356448 1.0083102 1.0193906
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5500 0.35142492 0 0.036958063 1.0193906 1.0083102
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5600 0.35125368 0 -0.041371343 1.0304709 1.0083102
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5700 0.34547744 0 -0.096450846 1.0637119 1.0083102
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5800 0.30939887 0 -0.12356656 1.0083102 1.0193906
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5900 0.32315628 0 -0.11338676 1.0193906 1.0193906
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6000 0.34117485 0 -0.066198961 1.0193906 1.0083102
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6100 0.35298043 0 -0.016172816 1.0304709 1.0193906
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6200 0.35130653 0 0.027660468 1.0415512 1.0083102
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6300 0.35398766 0 0.087221238 1.0083102 1.0083102
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6400 0.30963379 0 0.11990957 1.0415512 1.0083102
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6500 0.3174541 0 0.14103528 1.0193906 1.0193906
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6600 0.31989791 0 0.11575506 1.0304709 1.0193906
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6700 0.33811477 0 0.060747353 1.0415512 1.0193906
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6800 0.3424043 0 0.010357152 1.0193906 1.0083102
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6900 0.34804319 0 -0.042621786 1.0193906 1.0083102
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7000 0.35357865 0 -0.067248959 1.0083102 1.0083102
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7100 0.33556885 0 -0.10983726 1.0193906 1.0083102
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7200 0.33531101 0 -0.112179 1.0304709 1.0083102
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7300 0.35742607 0 -0.078405267 1.0304709 1.0193906
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7400 0.34577559 0 -0.01985432 1.0193906 1.0083102
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7500 0.3498641 0 0.052289439 1.0526316 1.0083102
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7600 0.33773715 0 0.092939035 1.0083102 1.0193906
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7700 0.33093497 0 0.11924405 1.0304709 1.0083102
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7800 0.31435814 0 0.12701724 1.0083102 1.0304709
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7900 0.33132217 0 0.10793075 1.0083102 1.0083102
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8000 0.33451798 0 0.077993125 1.0304709 1.0193906
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8100 0.35188371 0 0.019929977 1.0193906 1.0083102
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8200 0.33645742 0 -0.039302079 1.0193906 1.0193906
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8300 0.3415632 0 -0.098067982 1.0193906 1.0083102
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8400 0.30619282 0 -0.12952879 1.0304709 1.0193906
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8500 0.34446484 0 -0.098084709 1.0083102 1.0083102
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8600 0.33761673 0 -0.07069818 1.0193906 1.0083102
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8700 0.34495452 0 -0.022458056 1.0193906 1.0083102
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8800 0.33502983 0 0.027742411 1.0193906 1.0083102
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8900 0.35418591 0 0.092390134 1.0083102 1.0193906
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9000 0.31648387 0 0.12467398 1.0193906 1.0083102
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9100 0.33994825 0 0.14460327 1.0193906 1.0083102
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9200 0.33822571 0 0.11273284 1.0193906 1.0083102
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9300 0.33260773 0 0.060063671 1.0083102 1.0193906
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9400 0.36140305 0 0.021427642 1.0193906 1.0083102
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9500 0.34273562 0 -0.034064202 1.0193906 1.0083102
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9600 0.33867054 0 -0.089076906 1.0193906 1.0083102
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9700 0.32088235 0 -0.12027075 1.0193906 1.0083102
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9800 0.3320823 0 -0.11602794 1.0415512 1.0083102
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9900 0.33916442 0 -0.080281044 1.0083102 1.0083102
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10000 0.34852268 0 -0.01000914 1.0193906 1.0083102
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10100 0.32955942 0 0.04258493 1.0083102 1.0083102
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10200 0.34487898 0 0.086971308 1.0304709 1.0083102
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10300 0.32325593 0 0.11558149 1.0304709 1.0193906
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10400 0.30927871 0 0.12239437 1.0083102 1.0083102
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10500 0.33176799 0 0.12285937 1.0193906 1.0083102
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10600 0.35120027 0 0.084897432 1.0415512 1.0083102
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10700 0.33129697 0 0.0053089279 1.0193906 1.0193906
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10800 0.36028769 0 -0.04280715 1.0193906 1.0083102
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10900 0.35552287 0 -0.084955999 1.0193906 1.0193906
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11000 0.3406024 0 -0.096554577 1.0083102 1.0083102
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11100 0.33041202 0 -0.10703492 1.0304709 1.0193906
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11200 0.32442686 0 -0.084328121 1.0304709 1.0193906
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11300 0.35952468 0 -0.020191965 1.0304709 1.0083102
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11400 0.34610624 0 0.03440148 1.0193906 1.0193906
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11500 0.3415612 0 0.1041929 1.0193906 1.0083102
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11600 0.34040042 0 0.13215705 1.0304709 1.0083102
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11700 0.33555094 0 0.12738686 1.0415512 1.0193906
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11800 0.3458647 0 0.10963398 1.0083102 1.0193906
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11900 0.33836678 0 0.067253864 1.0193906 1.0193906
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12000 0.34853314 0 0.03201448 1.0193906 1.0083102
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12100 0.34600048 0 -0.034833402 1.0304709 1.0193906
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12200 0.33145631 0 -0.09865675 1.0193906 1.0193906
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12300 0.32848884 0 -0.1248489 1.0193906 1.0083102
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12400 0.3321344 0 -0.11266575 1.0083102 1.0083102
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12500 0.32622305 0 -0.061634993 1.0304709 1.0083102
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12600 0.36213537 0 -0.0090593315 1.0526316 1.0083102
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12700 0.34673866 0 0.036734645 1.0193906 1.0083102
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12800 0.34606618 0 0.086267678 1.0193906 1.0083102
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12900 0.34271431 0 0.12415522 1.0193906 1.0083102
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13000 0.31993287 0 0.13879926 1.0193906 1.0193906
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13100 0.3422918 0 0.11978905 1.0083102 1.0083102
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13200 0.33055236 0 0.062620483 1.0083102 1.0083102
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13300 0.34652207 0 0.0043833459 1.0304709 1.0083102
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13400 0.33574661 0 -0.04691024 1.0304709 1.0083102
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13500 0.33940837 0 -0.074241604 1.0304709 1.0083102
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13600 0.32093414 0 -0.1078027 1.0193906 1.0083102
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13700 0.34336597 0 -0.10544097 1.0193906 1.0083102
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13800 0.35806461 0 -0.072531559 1.0193906 1.0083102
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13900 0.35209713 0 -0.018851408 1.0193906 1.0083102
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14000 0.35702629 0 0.061046366 1.0083102 1.0083102
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14100 0.33234093 0 0.094086465 1.0083102 1.0083102
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14200 0.3459466 0 0.12186656 1.0193906 1.0193906
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14300 0.3327428 0 0.11396572 1.0193906 1.0083102
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14400 0.32409443 0 0.10658903 1.0193906 1.0193906
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14500 0.35022184 0 0.083558031 1.0083102 1.0083102
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|
|
35800 0.3371086 0 -0.0023678632 1.0193906 1.0193906
|
||
|
|
35900 0.33818476 0 0.011197742 1.0193906 1.0083102
|
||
|
|
36000 0.35142144 0 0.022520935 1.0083102 1.0193906
|
||
|
|
36100 0.35147297 0 0.020277852 1.0193906 1.0083102
|
||
|
|
36200 0.33489465 0 0.014564878 1.0415512 1.0193906
|
||
|
|
36300 0.33841515 0 0.036439962 1.0193906 1.0083102
|
||
|
|
36400 0.32301096 0 0.019966746 1.0304709 1.0083102
|
||
|
|
36500 0.35612028 0 0.036509556 1.0083102 1.0083102
|
||
|
|
36600 0.33841597 0 -0.0042180605 1.0193906 1.0193906
|
||
|
|
36700 0.34477654 0 -0.0052770853 1.0193906 1.0083102
|
||
|
|
36800 0.33804317 0 -0.013751733 1.0083102 1.0083102
|
||
|
|
36900 0.35003816 0 -0.0021184393 1.0083102 1.0083102
|
||
|
|
37000 0.32965041 0 -0.020900951 1.0193906 1.0083102
|
||
|
|
37100 0.34653095 0 -0.013667977 1.0193906 1.0083102
|
||
|
|
37200 0.35019871 0 -0.0071740923 1.0193906 1.0304709
|
||
|
|
37300 0.34859745 0 0.02006041 1.0304709 1.0083102
|
||
|
|
37400 0.35739859 0 0.020892822 1.0304709 1.0083102
|
||
|
|
37500 0.34128859 0 0.041072111 1.0193906 1.0193906
|
||
|
|
37600 0.33781905 0 0.023376738 1.0193906 1.0083102
|
||
|
|
37700 0.32961874 0 0.030953741 1.0193906 1.0083102
|
||
|
|
37800 0.343987 0 0.029579795 1.0083102 1.0083102
|
||
|
|
37900 0.33610448 0 0.036836828 1.0415512 1.0304709
|
||
|
|
38000 0.32757228 0 0.020902031 1.0193906 1.0193906
|
||
|
|
38100 0.32735808 0 0.019544751 1.0193906 1.0083102
|
||
|
|
38200 0.35646953 0 0.044607528 1.0083102 1.0304709
|
||
|
|
38300 0.32509773 0 0.03610738 1.0193906 1.0083102
|
||
|
|
38400 0.32111741 0 0.034474043 1.0193906 1.0193906
|
||
|
|
38500 0.30590608 0 0.053461212 1.0304709 1.0083102
|
||
|
|
38600 0.32322402 0 0.053453832 1.0193906 1.0304709
|
||
|
|
38700 0.33843057 0 0.076264534 1.0083102 1.0193906
|
||
|
|
38800 0.31350741 0 0.064733869 1.0415512 1.0083102
|
||
|
|
38900 0.31943061 0 0.067836769 1.0304709 1.0193906
|
||
|
|
39000 0.33775583 0 0.0788316 1.0193906 1.0193906
|
||
|
|
39100 0.34256036 0 0.075874935 1.0083102 1.0193906
|
||
|
|
39200 0.33128527 0 0.071610976 1.0193906 1.0083102
|
||
|
|
39300 0.34519653 0 0.046257301 1.0193906 1.0083102
|
||
|
|
39400 0.34351844 0 0.052422917 1.0304709 1.0304709
|
||
|
|
39500 0.35716037 0 0.048916058 1.0304709 1.0083102
|
||
|
|
39600 0.34000737 0 0.016149089 1.0304709 1.0083102
|
||
|
|
39700 0.34587892 0 0.021619621 1.0526316 1.0083102
|
||
|
|
39800 0.34878036 0 0.0092881327 1.0083102 1.0193906
|
||
|
|
39900 0.35225411 0 -0.011341599 1.0083102 1.0193906
|
||
|
|
40000 0.36309266 0 0.0050869295 1.0304709 1.0083102
|
||
|
|
Loop time of 1.12306 on 4 procs for 40000 steps with 361 atoms
|
||
|
|
|
||
|
|
Performance: 15386559.518 tau/day, 35617.036 timesteps/s
|
||
|
|
90.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 0.023094 | 0.023348 | 0.023582 | 0.1 | 2.08
|
||
|
|
Bond | 0.17827 | 0.19268 | 0.21984 | 3.7 | 17.16
|
||
|
|
Neigh | 0.18144 | 0.18231 | 0.18323 | 0.1 | 16.23
|
||
|
|
Comm | 0.23759 | 0.28095 | 0.30794 | 5.0 | 25.02
|
||
|
|
Output | 0.0062952 | 0.013342 | 0.034226 | 10.4 | 1.19
|
||
|
|
Modify | 0.2379 | 0.24327 | 0.25076 | 0.9 | 21.66
|
||
|
|
Other | | 0.1871 | | | 16.66
|
||
|
|
|
||
|
|
Nlocal: 90.25 ave 91 max 89 min
|
||
|
|
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||
|
|
Nghost: 59.25 ave 61 max 56 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||
|
|
Neighs: 0 ave 0 max 0 min
|
||
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||
|
|
|
||
|
|
Total # of neighbors = 0
|
||
|
|
Ave neighs/atom = 0
|
||
|
|
Ave special neighs/atom = 31.0249
|
||
|
|
Neighbor list builds = 3079
|
||
|
|
Dangerous builds = 0
|
||
|
|
Total wall time: 0:00:01
|