261 lines
9.2 KiB
Groff
261 lines
9.2 KiB
Groff
LAMMPS (29 Mar 2019)
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using 1 OpenMP thread(s) per MPI task
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# 2d micelle simulation
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dimension 2
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neighbor 0.3 bin
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neigh_modify delay 5
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atom_style bond
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# Soft potential push-off
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read_data data.micelle
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orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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1200 atoms
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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300 bonds
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.000422001 secs
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read_data CPU = 0.00473404 secs
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special_bonds fene
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2 = max # of 1-2 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.000183344 secs
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pair_style soft 1.12246
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pair_coeff * * 0.0 1.12246
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bond_style harmonic
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bond_coeff 1 50.0 0.75
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velocity all create 0.45 2349852
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variable prefactor equal ramp(1.0,20.0)
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fix 1 all nve
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fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
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fix 3 all adapt 1 pair soft a * * v_prefactor
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fix 4 all enforce2d
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thermo 50
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run 500
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.42246
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ghost atom cutoff = 1.42246
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binsize = 0.71123, bins = 51 51 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair soft, 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) = 3.758 | 3.85 | 4.126 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
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50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
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100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
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150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
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200 0.45 1.01454 0.10663502 1.5708 4.7598476
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250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
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300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
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350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
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400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
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450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
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500 0.45 0.66669513 0.13695201 1.2532721 6.807146
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Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms
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Performance: 5066547.720 tau/day, 11728.120 timesteps/s
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98.7% 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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Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16
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Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95
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Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95
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Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78
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Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62
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Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28
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Other | | 0.002669 | | | 6.26
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Nlocal: 300 ave 304 max 292 min
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Histogram: 1 0 0 0 0 0 0 0 2 1
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Nghost: 103.5 ave 108 max 98 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Neighs: 773.5 ave 792 max 735 min
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Histogram: 1 0 0 0 0 0 0 0 2 1
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Total # of neighbors = 3094
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Ave neighs/atom = 2.57833
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Ave special neighs/atom = 0.5
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Neighbor list builds = 52
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Dangerous builds = 0
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unfix 3
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# Main run
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pair_style lj/cut 2.5
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# solvent/head - full-size and long-range
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pair_coeff 1 1 1.0 1.0 2.5
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pair_coeff 2 2 1.0 1.0 2.5
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pair_coeff 1 2 1.0 1.0 2.5
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# tail/tail - size-averaged and long-range
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pair_coeff 3 3 1.0 0.75 2.5
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pair_coeff 4 4 1.0 0.50 2.5
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pair_coeff 3 4 1.0 0.67 2.5
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# solvent/tail - full-size and repulsive
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pair_coeff 1 3 1.0 1.0 1.12246
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pair_coeff 1 4 1.0 1.0 1.12246
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# head/tail - size-averaged and repulsive
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pair_coeff 2 3 1.0 0.88 1.12246
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pair_coeff 2 4 1.0 0.75 1.12246
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thermo 50
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#dump 1 all atom 2000 dump.micelle
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#dump 2 all image 2000 image.*.jpg type type zoom 1.6
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#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
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#dump 3 all movie 2000 movie.mpg type type zoom 1.6
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#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
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reset_timestep 0
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group solvent molecule 0
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750 atoms in group solvent
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group solute subtract all solvent
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450 atoms in group solute
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unfix 1
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unfix 2
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unfix 4
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fix 1 solvent nve
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fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
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fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
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150 rigid bodies with 450 atoms
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fix 4 all enforce2d
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run 500
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Neighbor list info ...
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update every 1 steps, delay 5 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 = 26 26 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) = 5.251 | 5.282 | 5.374 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
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50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
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100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
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150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
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200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
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250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
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300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
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350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
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400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
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450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
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500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
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Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms
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Performance: 2434100.210 tau/day, 5634.491 timesteps/s
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98.9% 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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Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74
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Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30
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Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32
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Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30
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Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29
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Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73
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Other | | 0.002938 | | | 3.31
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Nlocal: 300 ave 309 max 291 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Nghost: 218.75 ave 223 max 216 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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Neighs: 2192.25 ave 2251 max 2113 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Total # of neighbors = 8769
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Ave neighs/atom = 7.3075
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Ave special neighs/atom = 0.5
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Neighbor list builds = 47
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Dangerous builds = 2
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unfix 2
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unfix 4
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unfix 5
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fix 5 solute rigid/small molecule
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create bodies CPU = 7.70092e-05 secs
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150 rigid bodies with 450 atoms
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1.30435 = max distance from body owner to body atom
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fix 4 all enforce2d
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run 500
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Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes
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Step Temp E_pair E_mol TotEng Press
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500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
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550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
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600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
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650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
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700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
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750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
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800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
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850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
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900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
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950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332
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1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141
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Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms
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Performance: 3671840.233 tau/day, 8499.630 timesteps/s
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98.3% 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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Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47
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Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93
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Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98
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Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29
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Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42
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Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11
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Other | | 0.00224 | | | 3.81
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Nlocal: 300 ave 303 max 295 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 219 ave 224 max 215 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Neighs: 2185.75 ave 2244 max 2143 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Total # of neighbors = 8743
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Ave neighs/atom = 7.28583
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Ave special neighs/atom = 0.5
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Neighbor list builds = 40
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Dangerous builds = 0
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Total wall time: 0:00:00
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