forked from lijiext/lammps
243 lines
12 KiB
Groff
243 lines
12 KiB
Groff
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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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 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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Time spent = 0.000778913 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 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 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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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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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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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) = 5.156 | 5.167 | 5.177 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 2 1.0193906
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100 27.623422 -6.228166 2.6542136 1.0803324 1.0027701
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200 33.35302 -15.746749 3.2018248 1.1246537 1.0027701
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300 39.17734 -24.1557 4.9116986 1.1468144 1.0027701
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400 41.660701 -27.615203 8.6214678 1.2077562 1.0027701
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500 37.154935 -24.096954 3.2656298 1.2243767 1.0083102
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600 35.062196 -21.527799 2.3688444 1.1800554 1.0027701
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700 36.962955 -22.265373 3.0233424 1.1800554 1.0083102
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800 38.514356 -24.625735 5.2876402 1.2077562 1.0027701
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900 37.840168 -24.069158 4.443617 1.2022161 1.0083102
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1000 36.429396 -23.978878 7.2603394 1.1966759 1.0027701
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1100 34.75827 -22.743232 6.6304628 1.1745152 1.0083102
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1200 31.057199 -21.46544 3.7869701 1.1634349 1.0083102
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1300 33.127345 -22.426161 5.824726 1.0858726 1.0027701
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1400 31.678654 -21.604473 3.2219261 1.0360111 1.0083102
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1500 28.345212 -18.030807 0.93335223 1.1191136 1.0027701
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1600 26.031412 -15.389052 0.82549542 1.1080332 1.0027701
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1700 25.082832 -13.48625 1.0006592 1.0858726 1.0027701
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1800 25.673875 -13.965883 0.54607043 1.0692521 1.0027701
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1900 26.530842 -13.979318 2.0285449 1.1024931 1.0027701
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2000 25.910771 -14.244515 1.9592232 1.1191136 1.0027701
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2100 28.505636 -16.220559 1.7154775 1.1191136 1.0027701
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2200 28.142753 -15.564302 2.9946076 1.1135734 1.0027701
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2300 26.606225 -13.734442 1.4589278 1.0083102 1.0083102
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2400 25.664988 -12.389759 1.3450183 1.0360111 1.0027701
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2500 25.145328 -11.815173 0.48162788 1.0360111 1.0027701
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2600 26.654868 -13.916929 2.8361012 1.0581717 1.0083102
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2700 27.3758 -15.495452 4.1206412 1.0360111 1.0027701
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2800 23.60864 -14.520038 1.8948923 1.0193906 1.0027701
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2900 20.604557 -12.901121 0.17526991 1.0138504 1.0027701
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3000 20.852473 -12.756946 -0.44987285 1.0360111 1.0027701
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3100 21.934986 -12.797691 0.76186765 1.0415512 1.0027701
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3200 23.293263 -12.368233 0.021937309 1.0526316 1.0027701
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3300 22.091492 -10.88605 0.013006632 1.0415512 1.0083102
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3400 23.535429 -10.937804 2.0738989 1.0360111 1.0027701
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3500 24.503573 -12.202994 1.126785 1.0581717 1.0027701
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3600 23.54503 -12.745709 0.39022194 1.0858726 1.0027701
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3700 22.658187 -10.986188 -0.18869692 1.0692521 1.0027701
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3800 21.282045 -9.7879088 -0.061253454 1.0193906 1.0027701
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3900 20.571754 -9.1157993 -1.0178917 1.0526316 1.0027701
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4000 23.779702 -10.230328 1.0778525 1.0581717 1.0083102
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4100 23.675854 -10.63724 0.59402249 1.0415512 1.0027701
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4200 24.058963 -11.89505 0.3866378 1.0526316 1.0027701
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4300 22.683721 -11.358978 1.8269036 1.0470914 1.0083102
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4400 23.002345 -11.081443 0.4529456 1.0415512 1.0027701
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4500 21.984542 -10.233276 -0.60718244 1.0415512 1.0083102
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4600 22.079237 -9.979061 0.53013572 1.0415512 1.0027701
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4700 22.336961 -10.323583 -0.37512832 1.0249307 1.0027701
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4800 23.351699 -10.143724 0.95694397 1.0470914 1.0027701
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4900 23.643954 -10.687354 1.6062522 1.0858726 1.0083102
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5000 25.158132 -11.532398 1.3083639 1.0914127 1.0027701
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5100 23.755521 -10.978548 0.60587307 1.0470914 1.0027701
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5200 21.842692 -10.443216 -0.41185899 1.0637119 1.0027701
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5300 22.828066 -10.871114 1.1754353 1.0470914 1.0027701
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5400 24.883977 -12.39165 0.65101173 1.0470914 1.0027701
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5500 22.908286 -11.419431 1.4712698 1.0637119 1.0027701
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5600 22.718634 -12.083974 1.5706808 1.0526316 1.0027701
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5700 23.080763 -11.464882 1.2979578 1.0304709 1.0083102
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5800 21.877026 -11.483185 0.279772 1.0360111 1.0027701
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5900 22.526809 -10.868636 0.37121786 1.0637119 1.0083102
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6000 22.908857 -10.311118 0.58244569 1.0526316 1.0083102
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6100 22.399847 -10.222706 0.87875674 1.0858726 1.0027701
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6200 22.623463 -10.035541 -0.25811274 1.0304709 1.0027701
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6300 21.518006 -10.017552 -0.98187611 1.0470914 1.0083102
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6400 21.269816 -11.297716 0.20058535 1.0138504 1.0027701
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6500 23.362834 -11.263306 0.47670072 1.0692521 1.0027701
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6600 23.705236 -12.358492 -0.63286237 1.0027701 1.0027701
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6700 22.410623 -10.849516 0.57027834 1.0581717 1.0083102
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6800 21.661639 -9.3981379 0.38726515 1.0470914 1.0027701
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6900 21.856521 -8.8451751 0.053822789 1.0304709 1.0027701
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7000 21.069495 -8.6443387 -0.10412144 1.0193906 1.0027701
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7100 22.305494 -10.098469 -0.22662961 1.0581717 1.0027701
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7200 23.52884 -11.055929 -0.099869868 1.0692521 1.0027701
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7300 24.042008 -11.411758 2.0528788 1.0415512 1.0027701
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7400 22.870777 -12.408763 0.33346225 1.0249307 1.0027701
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7500 21.290152 -10.963058 0.26940112 1.0083102 1.0027701
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7600 21.702686 -10.36214 0.84057004 1.0083102 1.0027701
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7700 22.478034 -10.832724 -0.70855164 1.0747922 1.0027701
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7800 22.856853 -11.161008 -0.88354803 1.0083102 1.0083102
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7900 22.579842 -10.789899 0.40865274 1.0360111 1.0027701
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8000 24.364281 -12.116023 -0.44788445 1.0249307 1.0083102
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8100 22.993409 -10.261331 0.44712215 1.0193906 1.0027701
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8200 23.006207 -10.723372 1.2357091 1.0415512 1.0083102
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8300 23.292233 -10.041314 2.143692 1.0581717 1.0027701
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8400 21.658087 -10.089378 -0.25838681 1.0083102 1.0027701
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8500 23.268456 -10.356603 0.089787317 1.0526316 1.0083102
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8600 22.572019 -10.32801 0.12320758 1.0526316 1.0027701
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8700 22.970465 -10.662456 0.57027398 1.0581717 1.0083102
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8800 23.515552 -10.415842 1.0048598 1.0138504 1.0083102
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8900 22.733961 -10.343495 0.19917627 1.0360111 1.0083102
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9000 21.835458 -9.8740971 -1.0653164 1.0193906 1.0027701
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9100 22.062821 -9.2303832 0.21428267 1.0415512 1.0083102
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9200 23.020404 -10.321542 -0.48757848 1.0193906 1.0083102
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9300 22.529362 -9.2916938 0.57056277 1.0415512 1.0027701
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9400 23.301911 -10.538876 0.80637627 1.0138504 1.0027701
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9500 21.984286 -9.4754676 -0.19048233 1.0193906 1.0027701
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9600 23.710224 -10.274983 0.72268146 1.0249307 1.0027701
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9700 22.317038 -9.3509008 -0.45727658 1.0360111 1.0027701
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9800 23.41615 -10.026331 -0.45909049 1.0415512 1.0027701
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9900 22.130299 -11.18528 -0.15359132 1.0747922 1.0027701
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10000 23.273859 -11.337403 0.4036321 1.0304709 1.0083102
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Loop time of 1.18289 on 2 procs for 10000 steps with 361 atoms
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Performance: 3652073.393 tau/day, 8453.874 timesteps/s
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97.0% 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 | 0.25191 | 0.25685 | 0.2618 | 1.0 | 21.71
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Bond | 0.097655 | 0.098332 | 0.099009 | 0.2 | 8.31
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Neigh | 0.53258 | 0.53993 | 0.54728 | 1.0 | 45.65
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Comm | 0.13457 | 0.15372 | 0.17288 | 4.9 | 13.00
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Output | 0.0013587 | 0.0016007 | 0.0018427 | 0.6 | 0.14
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Modify | 0.074109 | 0.074314 | 0.074518 | 0.1 | 6.28
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Other | | 0.05813 | | | 4.91
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Nlocal: 180.5 ave 182 max 179 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 172.5 ave 175 max 170 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 1421 ave 1488 max 1354 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 2842
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Ave neighs/atom = 7.87258
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Ave special neighs/atom = 5.61773
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Neighbor list builds = 4884
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Dangerous builds = 0
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Total wall time: 0:00:01
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