forked from lijiext/lammps
215 lines
7.2 KiB
Groff
215 lines
7.2 KiB
Groff
LAMMPS (4 May 2017)
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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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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) = 2.69 | 2.69 | 2.69 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 5.83903 on 4 procs for 250 steps with 4000 atoms
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Performance: 18496.226 tau/day, 42.815 timesteps/s
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98.2% 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 | 5.152 | 5.5209 | 5.7679 | 9.6 | 94.55
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Neigh | 0.022809 | 0.023364 | 0.023891 | 0.3 | 0.40
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Comm | 0.041927 | 0.28952 | 0.65893 | 42.2 | 4.96
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Output | 0.0002389 | 0.00024772 | 0.00026727 | 0.0 | 0.00
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Modify | 0.0036368 | 0.0036796 | 0.0037563 | 0.1 | 0.06
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Other | | 0.001328 | | | 0.02
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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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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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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) = 2.815 | 2.816 | 2.816 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 5.85683 on 4 procs for 250 steps with 4000 atoms
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Performance: 18440.001 tau/day, 42.685 timesteps/s
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98.4% 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 | 5.2483 | 5.5095 | 5.7744 | 8.0 | 94.07
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Neigh | 0.047228 | 0.047998 | 0.049293 | 0.4 | 0.82
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Comm | 0.027134 | 0.29341 | 0.55554 | 34.6 | 5.01
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Output | 0.00020003 | 0.00021219 | 0.0002358 | 0.0 | 0.00
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Modify | 0.0035472 | 0.0036988 | 0.0038681 | 0.2 | 0.06
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Other | | 0.001984 | | | 0.03
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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) = 2.315 | 2.316 | 2.316 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 5.86684 on 4 procs for 250 steps with 4000 atoms
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Performance: 18408.545 tau/day, 42.612 timesteps/s
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98.4% 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 | 5.3207 | 5.5695 | 5.8071 | 7.6 | 94.93
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Neigh | 0.023073 | 0.023405 | 0.023834 | 0.2 | 0.40
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Comm | 0.030558 | 0.2686 | 0.51789 | 34.7 | 4.58
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Output | 0.00028825 | 0.00036758 | 0.00042987 | 0.0 | 0.01
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Modify | 0.0034878 | 0.0036733 | 0.0039375 | 0.3 | 0.06
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Other | | 0.001259 | | | 0.02
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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: 0:00:18
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