update log files for peptide, peri, pour and python examples
This commit is contained in:
Axel Kohlmeyer
217
examples/python/log.27Nov18.pair_python_melt.g++.4
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217
examples/python/log.27Nov18.pair_python_melt.g++.4
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 10 0 10 0 10
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create_box 1 box
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Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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Time spent = 0.000413418 secs
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mass * 1.0
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velocity all create 3.0 87287
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pair_style python 2.5
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pair_coeff * * py_pot.LJCutMelt lj
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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thermo 50
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run 250
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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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 = 12 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair python, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 3 -6.7733681 0 -2.2744931 -3.7033504
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50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
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100 1.6503357 -4.756014 0 -2.2811293 5.8050524
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150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
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200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
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250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
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Loop time of 3.21263 on 4 procs for 250 steps with 4000 atoms
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Performance: 33617.340 tau/day, 77.818 timesteps/s
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98.6% 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 | 2.9309 | 2.9942 | 3.1071 | 3.9 | 93.20
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Neigh | 0.024111 | 0.024518 | 0.024765 | 0.2 | 0.76
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Comm | 0.075799 | 0.1889 | 0.25258 | 15.5 | 5.88
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Output | 0.00018406 | 0.00030106 | 0.00065088 | 0.0 | 0.01
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Modify | 0.0038259 | 0.0038511 | 0.0038726 | 0.0 | 0.12
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Other | | 0.0009047 | | | 0.03
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Nlocal: 1000 ave 1010 max 982 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Nghost: 2703.75 ave 2713 max 2689 min
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Histogram: 1 0 0 0 0 0 0 2 0 1
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Neighs: 37915.5 ave 39239 max 36193 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Total # of neighbors = 151662
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Ave neighs/atom = 37.9155
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Neighbor list builds = 12
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Dangerous builds not checked
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write_data melt.data
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write_restart melt.restart
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart melt.restart
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restoring atom style atomic from restart
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orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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1 by 2 by 2 MPI processor grid
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pair style python stores no restart info
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4000 atoms
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pair_style python 2.5
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pair_coeff * * py_pot.LJCutMelt lj
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fix 1 all nve
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thermo 50
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run 250
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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 = 12 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair python, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.829 | 2.83 | 2.83 Mbytes
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Step Temp E_pair E_mol TotEng Press
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250 1.6323462 -4.7292062 0 -2.2812991 5.9762168
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300 1.6451788 -4.7488091 0 -2.2816578 5.8375485
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350 1.6171909 -4.7064928 0 -2.2813129 6.0094235
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400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
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450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
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500 1.643316 -4.7454222 0 -2.2810644 5.8454817
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Loop time of 3.16401 on 4 procs for 250 steps with 4000 atoms
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Performance: 34133.894 tau/day, 79.014 timesteps/s
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99.0% 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 | 2.9254 | 2.9723 | 3.0639 | 3.2 | 93.94
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Neigh | 0.04915 | 0.050266 | 0.050704 | 0.3 | 1.59
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Comm | 0.044051 | 0.13579 | 0.18379 | 15.0 | 4.29
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Output | 0.00016141 | 0.00028008 | 0.00063109 | 0.0 | 0.01
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Modify | 0.0037544 | 0.003895 | 0.0041802 | 0.3 | 0.12
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Other | | 0.001474 | | | 0.05
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Nlocal: 1000 ave 1012 max 983 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Nghost: 2699 ave 2706 max 2693 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Neighs: 37930.8 ave 39292 max 36264 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Total # of neighbors = 151723
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Ave neighs/atom = 37.9308
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Neighbor list builds = 25
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Dangerous builds = 25
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clear
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using 1 OpenMP thread(s) per MPI task
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units lj
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atom_style atomic
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read_data melt.data
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orthogonal box = (0 0 0) to (16.796 16.796 16.796)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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4000 atoms
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reading velocities ...
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4000 velocities
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pair_style python 2.5
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pair_coeff * * py_pot.LJCutMelt lj
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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fix 1 all nve
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thermo 50
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run 250
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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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 = 12 12 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair python, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.329 | 2.33 | 2.33 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.6323462 -4.7292062 0 -2.2812991 5.9762168
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50 1.6450626 -4.7488948 0 -2.2819177 5.8370409
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100 1.6169004 -4.7066969 0 -2.2819526 6.0082546
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150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
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200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
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250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
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Loop time of 3.16461 on 4 procs for 250 steps with 4000 atoms
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Performance: 34127.383 tau/day, 78.999 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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---------------------------------------------------------------
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Pair | 2.9135 | 2.9842 | 3.0594 | 3.1 | 94.30
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Neigh | 0.024132 | 0.024319 | 0.024553 | 0.1 | 0.77
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Comm | 0.075955 | 0.15106 | 0.22174 | 13.9 | 4.77
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Output | 0.00016856 | 0.00028443 | 0.00062919 | 0.0 | 0.01
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Modify | 0.0037944 | 0.0038335 | 0.0038977 | 0.1 | 0.12
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Other | | 0.0008717 | | | 0.03
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Nlocal: 1000 ave 1013 max 989 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Nghost: 2695.5 ave 2706 max 2682 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Neighs: 37927.2 ave 39002 max 36400 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Total # of neighbors = 151709
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Ave neighs/atom = 37.9273
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Neighbor list builds = 12
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Dangerous builds not checked
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shell rm melt.data melt.restart
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Total wall time: 0:00:09
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