222 lines
12 KiB
Groff
222 lines
12 KiB
Groff
LAMMPS (17 Feb 2022)
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units lj
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dimension 3
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boundary f f f
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atom_style bond
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special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
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newton on off
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comm_modify vel yes cutoff 2.6
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lattice fcc 1.0
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Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
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region box block -25 15 -22 22 -22 22
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create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
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Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
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1 by 2 by 2 MPI processor grid
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region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
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create_atoms 1 region disk
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Created 7529 atoms
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using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
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create_atoms CPU = 0.001 seconds
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group plate region disk
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7529 atoms in group plate
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region ball sphere 8.0 0.0 0.0 6.0
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create_atoms 1 region ball
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Created 3589 atoms
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using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
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create_atoms CPU = 0.000 seconds
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group projectile region ball
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3589 atoms in group projectile
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displace_atoms all random 0.1 0.1 0.1 134598738
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Displacing atoms ...
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mass 1 1.0
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neighbor 1.0 bin
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pair_style bpm/spring
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pair_coeff 1 1 1.0 1.0 1.0
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fix 1 all nve
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create_bonds many plate plate 1 0.0 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 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2
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ghost atom cutoff = 2.6
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binsize = 1, bins = 64 70 70
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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/3d
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bin: standard
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(2) pair bpm/spring, 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/3d
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bin: standard
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Added 38559 bonds, new total = 38559
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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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15 = max # of 1-2 neighbors
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101 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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create_bonds many projectile projectile 2 0.0 1.5
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generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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WARNING: Bonds are defined but no bond style is set (../force.cpp:192)
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WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:194)
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Added 21869 bonds, new total = 60428
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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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16 = max # of 1-2 neighbors
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101 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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neighbor 0.3 bin
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special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
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bond_style bpm/spring store/local brkbond 100 time id1 id2
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bond_coeff 1 1.0 0.04 1.0
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bond_coeff 2 1.0 0.20 1.0
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velocity projectile set -0.05 0.0 0.0
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compute nbond all nbond/atom
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compute tbond all reduce sum c_nbond
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timestep 0.1
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thermo_style custom step ke pe pxx pyy pzz c_tbond
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thermo 100
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thermo_modify lost ignore lost/bond ignore
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#dump 1 all custom 100 atomDump id x y z c_nbond
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dump 2 all local 100 brokenDump f_brkbond[1] f_brkbond[2] f_brkbond[3]
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dump_modify 2 header no
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run 7500
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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 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.3
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ghost atom cutoff = 2.6
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binsize = 0.65, bins = 98 108 108
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair bpm/spring, 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/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 17.74 | 17.74 | 17.74 Mbytes
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Step KinEng PotEng Pxx Pyy Pzz c_tbond
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0 0.0010167873 0 7.298968e-05 0 0 10.8703
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100 0.0010167873 0 7.298968e-05 -8.7429897e-20 -8.8470837e-20 10.8703
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200 0.0010167873 0 7.298968e-05 -7.2809565e-20 -8.0915788e-20 10.8703
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300 0.0009951439 0 9.9273671e-05 8.1569216e-06 8.0922512e-06 10.868142
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400 0.00095142792 0 0.00012669557 -1.3413721e-05 -1.4800745e-05 10.849793
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500 0.00092272662 0 8.1708784e-05 -9.7488701e-06 -1.3603634e-05 10.819752
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600 0.00088967612 0 6.2587266e-05 -5.1954127e-06 -6.781587e-06 10.797985
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700 0.00086070919 0 8.8529902e-05 -9.9431205e-06 -7.9905211e-06 10.776579
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800 0.00083543943 0 7.5920357e-05 3.6381024e-07 3.7747551e-06 10.759309
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900 0.00081190799 0 6.3678219e-05 5.4158243e-06 1.2751247e-05 10.744199
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1000 0.00078828988 0 7.3079869e-05 -6.6410613e-06 -1.198683e-06 10.728368
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1100 0.00075664718 0 6.2976995e-05 -4.7863299e-06 -3.9814556e-06 10.711819
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1200 0.00072472205 0 4.9680233e-05 9.3093553e-06 4.4426393e-06 10.69401
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1300 0.00070176532 0 5.4048176e-05 1.3051954e-05 7.5448558e-06 10.671164
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1400 0.00068599319 0 5.4062404e-05 9.9930199e-06 1.0353154e-05 10.650117
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1500 0.0006786164 0 4.5038593e-05 8.067571e-06 9.8825461e-06 10.636266
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1600 0.00067466823 0 4.6733251e-05 9.8595584e-06 1.1551081e-05 10.621335
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1700 0.00066847126 0 5.1472453e-05 2.1569974e-07 6.0070599e-06 10.6127
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1800 0.00065711827 0 5.0355189e-05 -8.030203e-06 -3.1395588e-06 10.599568
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1900 0.00063882539 0 4.7146888e-05 -2.0596242e-05 -1.6494542e-05 10.581939
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2000 0.00061717894 0 4.6698781e-05 -2.5473048e-05 -2.7703615e-05 10.567188
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2100 0.00059261327 0 3.7701055e-05 -2.4637803e-05 -3.3919162e-05 10.552617
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2200 0.00056527158 0 3.2239421e-05 -1.8786685e-05 -2.4202734e-05 10.538406
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2300 0.00054054919 0 2.7410334e-05 -6.701111e-06 -7.4354974e-06 10.520777
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2400 0.00051820065 0 2.2997206e-05 1.5623767e-05 1.8687824e-05 10.501889
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2500 0.00049647925 0 1.746693e-05 2.8814144e-05 3.5569425e-05 10.487498
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2600 0.00047837258 0 1.4127067e-05 3.4245611e-05 4.0208577e-05 10.472387
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2700 0.00046626924 0 1.3714876e-05 3.7922196e-05 4.1550346e-05 10.456377
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2800 0.0004560167 0 1.5260976e-05 3.5632577e-05 3.7885738e-05 10.440007
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2900 0.00045331059 0 1.5194832e-05 3.1036124e-05 2.8633755e-05 10.427955
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3000 0.00045227799 0 1.4877378e-05 1.9327028e-05 2.1189487e-05 10.414283
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3100 0.00044866178 0 2.0424612e-05 -2.7242288e-06 7.7121438e-06 10.40349
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3200 0.00044336453 0 2.3276121e-05 -1.979069e-05 -4.2311089e-06 10.395575
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3300 0.00043526526 0 2.3338132e-05 -2.834945e-05 -1.7302033e-05 10.389998
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3400 0.00042817758 0 2.4374527e-05 -2.9870076e-05 -3.0623264e-05 10.382803
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3500 0.00042182658 0 2.6120627e-05 -2.9449521e-05 -3.787776e-05 10.378126
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3600 0.00041794291 0 2.4736957e-05 -2.4098172e-05 -3.0529166e-05 10.373628
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3700 0.0004156005 0 2.7543305e-05 -1.2431749e-05 -1.8626096e-05 10.37075
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3800 0.0004141461 0 2.4630482e-05 -6.345489e-06 -1.7375803e-05 10.368771
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3900 0.00041328832 0 2.2220142e-05 4.1471034e-07 -1.3339476e-05 10.366972
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4000 0.00041121725 0 2.3491321e-05 1.1284551e-05 -5.8651834e-06 10.364634
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4100 0.00040761876 0 2.6688248e-05 1.9721625e-05 3.7536871e-06 10.362655
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4200 0.00040301362 0 2.7601916e-05 1.9212118e-05 9.7175996e-06 10.359417
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4300 0.00040001545 0 2.7243769e-05 1.6889359e-05 1.1857147e-05 10.3551
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4400 0.00039654521 0 2.561083e-05 1.3863551e-05 1.0593597e-05 10.351142
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4500 0.00039435924 0 2.4366458e-05 1.2545563e-05 1.1323962e-05 10.348804
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4600 0.00039250006 0 2.3719127e-05 1.1015167e-05 8.5964046e-06 10.348444
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4700 0.00039145496 0 2.2943915e-05 8.7824224e-06 5.0397129e-06 10.346825
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4800 0.00039105331 0 2.4005757e-05 7.5899773e-06 9.033741e-07 10.344846
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4900 0.0003898798 0 2.3819433e-05 4.9673894e-06 -2.3466459e-06 10.343587
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5000 0.00038747508 0 2.3605028e-05 -1.1717437e-06 -6.1096657e-06 10.343047
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5100 0.00038549022 0 2.3453798e-05 -9.9256693e-06 -9.3584148e-06 10.341788
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5200 0.00038283936 0 2.5243567e-05 -1.5877598e-05 -9.9474447e-06 10.340169
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5300 0.00038140888 0 2.5522223e-05 -1.9331435e-05 -1.1067039e-05 10.33873
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5400 0.00037916674 0 2.5181488e-05 -2.1581255e-05 -1.1252641e-05 10.336931
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5500 0.00037782932 0 2.691805e-05 -1.5768241e-05 -5.6704695e-06 10.334952
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5600 0.00037628832 0 2.5851445e-05 -1.4239811e-05 -1.9122536e-06 10.333153
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5700 0.00037451913 0 2.4758416e-05 -1.3252284e-05 -1.9222041e-06 10.331714
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5800 0.00037328662 0 2.2507032e-05 -9.6704092e-06 -7.5470215e-06 10.330095
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5900 0.00037253111 0 2.3303086e-05 -4.2828034e-06 -7.888056e-06 10.328476
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6000 0.00037171133 0 2.4042456e-05 -4.7684985e-06 -6.5164336e-06 10.327397
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6100 0.00036986726 0 2.4938695e-05 -4.8738316e-06 -4.5380007e-06 10.327037
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6200 0.0003675822 0 2.3322229e-05 -4.6333093e-06 -5.7086464e-06 10.327037
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6300 0.00036552389 0 2.1435354e-05 -4.8971566e-06 -3.5935426e-06 10.327037
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6400 0.00036488091 0 2.0813994e-05 -3.8333319e-06 -3.6595059e-06 10.327037
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6500 0.00036447973 0 2.2241876e-05 8.7797361e-08 -4.141203e-06 10.327037
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6600 0.00036383343 0 2.269485e-05 4.9364593e-06 1.3062133e-06 10.326677
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6700 0.00036305076 0 2.1838759e-05 6.4587048e-06 4.7758772e-06 10.326318
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6800 0.00036226601 0 2.2916622e-05 6.044926e-06 5.0291597e-06 10.325598
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6900 0.00036175279 0 2.2691667e-05 6.9998847e-06 5.8988637e-06 10.324699
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7000 0.00036143633 0 2.1725813e-05 8.1268152e-06 5.0390503e-06 10.324519
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7100 0.0003610248 0 2.1799675e-05 8.65795e-06 3.1360368e-06 10.323439
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7200 0.00036086259 0 2.2198029e-05 5.1764734e-06 5.4798783e-07 10.32308
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7300 0.00036099757 0 2.4160496e-05 1.0310325e-06 -5.115075e-07 10.32254
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7400 0.00036129334 0 2.5325018e-05 -9.4918158e-07 -1.7064957e-06 10.32218
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7500 0.00036136655 0 2.3513198e-05 -3.8618451e-06 -4.4344772e-06 10.321281
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Loop time of 4.51074 on 4 procs for 7500 steps with 11118 atoms
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Performance: 14365719.597 tau/day, 1662.699 timesteps/s
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93.8% 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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Pair | 0.25733 | 0.26952 | 0.28068 | 1.6 | 5.98
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Bond | 1.9391 | 2.0128 | 2.0851 | 3.7 | 44.62
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Neigh | 0.56308 | 0.5941 | 0.62077 | 2.8 | 13.17
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Comm | 0.68282 | 0.80856 | 0.94406 | 10.7 | 17.93
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Output | 0.19287 | 0.1933 | 0.19426 | 0.1 | 4.29
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Modify | 0.53239 | 0.55343 | 0.57349 | 2.0 | 12.27
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Other | | 0.07902 | | | 1.75
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Nlocal: 2779.5 ave 2862 max 2686 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Nghost: 1183.25 ave 1220 max 1134 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Neighs: 11828.8 ave 12387 max 11053 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Total # of neighbors = 47315
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Ave neighs/atom = 4.2557115
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Ave special neighs/atom = 10.321461
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Neighbor list builds = 421
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Dangerous builds = 11
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Total wall time: 0:00:04
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