256 lines
14 KiB
Groff
256 lines
14 KiB
Groff
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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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 = 1.1655347 2.0187654 1.1655347
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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 -0.58276737) to (58.276737 40.375308 0.58276737)
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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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using lattice units in orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
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create_atoms CPU = 0.001 seconds
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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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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors 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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special bonds CPU = 0.000 seconds
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create_bonds many all all 1 1.0 1.5
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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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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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
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bin: standard
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Added 1014 bonds, new total = 1014
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors coul: 0 1 1
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6 = max # of 1-2 neighbors
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6 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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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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timestep 0.001
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run 10000
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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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
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.123 | 5.142 | 5.176 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 25.57187 -2.2902218 2.9990153 1.0526316 1.0193906
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200 25.532511 -2.5273097 2.8286231 1.0526316 1.0083102
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300 25.860246 -3.0674998 2.6725358 1.0415512 1.0083102
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400 26.628011 -4.394738 2.6618897 1.0526316 1.0083102
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500 27.627309 -6.2305012 2.6564278 1.0415512 1.0083102
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600 28.881803 -8.2757766 2.8249236 1.0526316 1.0083102
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700 29.941402 -9.9816088 2.9828232 1.0526316 1.0083102
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800 31.118457 -12.199787 3.2044549 1.0304709 1.0083102
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900 32.393498 -14.204491 2.9496587 1.0747922 1.0193906
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1000 33.392657 -15.747519 3.1613807 1.0637119 1.0193906
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1100 34.671769 -17.728904 3.019138 1.0526316 1.0193906
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1200 35.632627 -19.846347 3.1061176 1.0637119 1.0193906
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1300 36.77272 -21.156179 3.2353009 1.0415512 1.0193906
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1400 38.241608 -22.744765 4.1163075 1.0637119 1.0083102
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1500 40.072478 -25.139827 5.3032535 1.0415512 1.0193906
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1600 40.665382 -25.901697 5.4330761 1.0858726 1.0083102
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1700 40.957034 -26.28667 7.1881521 1.1080332 1.0083102
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1800 41.536831 -27.393841 6.6814405 1.0969529 1.0193906
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1900 41.952676 -28.123051 7.4683871 1.0858726 1.0193906
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2000 42.201937 -28.685743 7.4624284 1.0747922 1.0083102
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2100 41.509082 -27.909225 6.8666955 1.0969529 1.0083102
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2200 40.794912 -27.085519 5.259945 1.0415512 1.0083102
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2300 38.749709 -25.14601 4.2936222 1.0526316 1.0083102
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2400 38.418065 -24.593596 3.1418049 1.1191136 1.0083102
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2500 36.932588 -23.407613 1.9397982 1.0637119 1.0083102
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2600 35.979181 -23.066748 2.1678902 1.0637119 1.0193906
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2700 35.84858 -22.55645 2.0798013 1.0858726 1.0193906
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2800 35.795795 -22.092149 2.6849882 1.0637119 1.0193906
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2900 35.754958 -21.662138 2.4892921 1.0526316 1.0083102
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3000 36.548644 -21.943203 2.8497192 1.0747922 1.0083102
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3100 36.755531 -22.081384 3.6960187 1.0858726 1.0193906
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3200 36.606921 -22.538438 3.7047874 1.0415512 1.0193906
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3300 37.185396 -23.077004 3.4202006 1.0858726 1.0083102
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3400 37.136687 -23.617745 2.9763794 1.0858726 1.0083102
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3500 37.908279 -24.364631 3.5155218 1.0304709 1.0083102
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3600 38.459203 -25.01024 4.3313693 1.0747922 1.0083102
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3700 39.108683 -25.636756 4.4707992 1.0415512 1.0083102
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3800 38.67059 -25.126486 5.3753987 1.0747922 1.0083102
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3900 38.395639 -25.140269 5.1661495 1.0858726 1.0193906
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4000 38.552057 -24.871721 5.0206769 1.0747922 1.0083102
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4100 39.065683 -25.344035 4.4042913 1.0858726 1.0083102
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4200 37.714294 -24.728278 5.1978439 1.0304709 1.0083102
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4300 38.785555 -25.380643 3.7033369 1.0304709 1.0193906
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4400 38.341445 -25.13442 3.4298833 1.1191136 1.0193906
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4500 37.720522 -24.702087 3.4450752 1.0637119 1.0083102
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4600 37.509806 -24.477444 3.6155741 1.0858726 1.0083102
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4700 37.319957 -23.722654 4.7111338 1.0526316 1.0193906
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4800 38.233154 -24.653472 4.25263 1.0637119 1.0083102
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4900 37.309164 -24.21353 4.8513758 1.0637119 1.0193906
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5000 37.559292 -24.720651 5.409312 1.0415512 1.0193906
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5100 37.449783 -25.21538 6.0099692 1.0747922 1.0083102
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5200 38.187982 -25.16709 6.1425844 1.0415512 1.0083102
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5300 36.91668 -24.616017 4.7873357 1.0304709 1.0083102
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5400 35.103465 -23.85158 5.1950262 1.0304709 1.0193906
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5500 35.299351 -23.946174 4.8038223 1.0526316 1.0083102
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5600 35.713482 -24.962908 3.5111314 1.0193906 1.0193906
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5700 33.740794 -23.77699 4.5783011 1.0304709 1.0193906
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5800 33.791635 -23.536627 3.1317306 1.0415512 1.0193906
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5900 34.039769 -23.068008 4.0189755 1.0415512 1.0083102
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6000 32.809103 -22.085195 4.0827943 1.0637119 1.0193906
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6100 32.522642 -21.979287 4.1437901 1.0637119 1.0083102
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6200 32.347924 -21.661359 4.1436759 1.0526316 1.0193906
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6300 32.099974 -21.114688 5.5745084 1.0193906 1.0193906
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6400 33.767704 -23.489786 4.1038662 1.0526316 1.0193906
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6500 32.283906 -22.076822 7.2664805 1.0526316 1.0083102
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6600 33.25146 -23.191973 6.01093 1.0526316 1.0083102
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6700 31.7665 -22.1476 6.4256074 1.0747922 1.0193906
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6800 30.775727 -21.513059 5.1709188 1.0304709 1.0083102
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6900 30.964501 -21.153634 5.1077701 1.0193906 1.0193906
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7000 31.292268 -20.800916 3.6047789 1.0193906 1.0193906
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7100 31.460811 -20.280043 3.2369395 1.0193906 1.0083102
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7200 30.871387 -19.340893 2.9615798 1.0193906 1.0083102
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7300 28.983475 -18.709174 3.1686601 1.0304709 1.0083102
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7400 28.032829 -18.200801 1.8738157 1.0304709 1.0193906
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7500 28.088176 -17.117863 3.5604961 1.0304709 1.0083102
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7600 27.456327 -17.011025 1.7822114 1.0526316 1.0304709
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7700 26.483887 -16.024179 1.258431 1.0415512 1.0193906
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7800 26.023393 -15.532176 1.3663841 1.0304709 1.0083102
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7900 26.154386 -14.738286 1.5214339 1.0415512 1.0193906
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8000 25.755121 -14.487715 1.0185064 1.0415512 1.0304709
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8100 25.468927 -14.273205 1.3553057 1.0526316 1.0304709
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8200 25.74216 -14.606852 0.13693979 1.0193906 1.0083102
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8300 24.457219 -14.529941 -0.0032579349 1.0304709 1.0193906
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8400 24.054076 -13.704387 0.80714443 1.0193906 1.0193906
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8500 23.742098 -13.699968 0.41096573 1.0304709 1.0193906
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8600 24.060806 -13.289555 0.22489663 1.0193906 1.0083102
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8700 23.831533 -13.025052 -0.090244538 1.0304709 1.0193906
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8800 23.823082 -13.407662 -0.28029605 1.0304709 1.0083102
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8900 23.982182 -12.862338 0.50556065 1.0193906 1.0193906
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9000 24.876045 -13.400416 1.1475671 1.0415512 1.0193906
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9100 25.018155 -13.625286 0.74749825 1.0304709 1.0083102
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9200 25.671195 -13.850993 0.88340554 1.0526316 1.0083102
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9300 26.076502 -13.935292 1.2705214 1.0526316 1.0083102
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9400 25.847786 -13.626034 1.5676611 1.0415512 1.0193906
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9500 25.963986 -14.23672 1.4791684 1.0304709 1.0083102
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9600 26.58066 -14.74703 1.3431841 1.0526316 1.0083102
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9700 27.401448 -14.568412 2.4488742 1.0747922 1.0083102
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9800 27.927894 -15.254362 2.8516414 1.0415512 1.0083102
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9900 28.204891 -15.219892 3.0631109 1.0415512 1.0083102
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10000 27.30902 -14.939134 2.8235246 1.0304709 1.0083102
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Loop time of 0.317224 on 4 procs for 10000 steps with 361 atoms
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Performance: 2723630.892 tau/day, 31523.506 timesteps/s, 11.380 Matom-step/s
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89.4% CPU use with 4 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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---------------------------------------------------------------
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Pair | 0.066318 | 0.073612 | 0.081352 | 2.6 | 23.21
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Bond | 0.01886 | 0.020483 | 0.022893 | 1.1 | 6.46
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Neigh | 0.051128 | 0.052747 | 0.054345 | 0.5 | 16.63
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Comm | 0.093881 | 0.11329 | 0.13156 | 4.2 | 35.71
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Output | 0.0011573 | 0.0013205 | 0.0016444 | 0.5 | 0.42
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Modify | 0.025957 | 0.026647 | 0.027249 | 0.3 | 8.40
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Other | | 0.02913 | | | 9.18
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Nlocal: 90.25 ave 91 max 89 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Nghost: 260.75 ave 265 max 256 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Neighs: 889.5 ave 1035 max 794 min
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Histogram: 1 1 0 0 1 0 0 0 0 1
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Total # of neighbors = 3558
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Ave neighs/atom = 9.8559557
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Ave special neighs/atom = 5.6177285
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Neighbor list builds = 1192
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Dangerous builds = 0
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Total wall time: 0:00:00
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