forked from lijiext/lammps
251 lines
8.4 KiB
Groff
251 lines
8.4 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 hybrid
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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 2 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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region half block -0.1 4.9 0 10 0 10
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set region half type 2
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2000 settings made for type
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velocity all create 3.0 87287
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pair_style hybrid lj/cut 2.5 python 2.5
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pair_coeff * * python py_pot.LJCutMelt lj NULL
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pair_coeff * 2 lj/cut 1.0 1.0
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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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3 neighbor lists, perpetual/occasional/extra = 3 0 0
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(1) pair lj/cut, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair python, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) neighbor class addition, 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) = 3.953 | 3.953 | 3.953 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 2.71748 on 4 procs for 250 steps with 4000 atoms
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Performance: 39742.745 tau/day, 91.997 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 | 2.4777 | 2.5639 | 2.6253 | 3.9 | 94.35
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Neigh | 0.024626 | 0.025331 | 0.02598 | 0.3 | 0.93
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Comm | 0.061933 | 0.12297 | 0.20987 | 18.0 | 4.53
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Output | 0.00026131 | 0.00027591 | 0.00031352 | 0.0 | 0.01
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Modify | 0.0036087 | 0.0036573 | 0.0037553 | 0.1 | 0.13
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Other | | 0.001337 | | | 0.05
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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: 21469.8 ave 22167 max 20546 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Total # of neighbors = 85879
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Ave neighs/atom = 21.4698
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Neighbor list builds = 12
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Dangerous builds not checked
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write_data hybrid.data
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write_restart hybrid.restart
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart hybrid.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 hybrid lj/cut 2.5 python 2.5
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pair_coeff * * python py_pot.LJCutMelt lj NULL
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pair_coeff * 2 lj/cut 1.0 1.0
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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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3 neighbor lists, perpetual/occasional/extra = 3 0 0
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(1) pair lj/cut, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair python, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) neighbor class addition, 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) = 3.612 | 3.612 | 3.612 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 2.75827 on 4 procs for 250 steps with 4000 atoms
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Performance: 39155.038 tau/day, 90.637 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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---------------------------------------------------------------
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Pair | 2.3631 | 2.5412 | 2.6672 | 7.2 | 92.13
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Neigh | 0.050358 | 0.052316 | 0.053312 | 0.5 | 1.90
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Comm | 0.032793 | 0.15893 | 0.33904 | 29.1 | 5.76
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Output | 0.00018525 | 0.00020212 | 0.00024509 | 0.0 | 0.01
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Modify | 0.0034482 | 0.0035321 | 0.0036578 | 0.1 | 0.13
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Other | | 0.002039 | | | 0.07
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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: 21802 ave 22700 max 21236 min
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Histogram: 1 1 0 1 0 0 0 0 0 1
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Total # of neighbors = 87208
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Ave neighs/atom = 21.802
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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 hybrid.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 hybrid lj/cut 2.5 python 2.5
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pair_coeff * * python py_pot.LJCutMelt lj NULL
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pair_coeff * 2 lj/cut 1.0 1.0
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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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3 neighbor lists, perpetual/occasional/extra = 3 0 0
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(1) pair lj/cut, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair python, perpetual, skip from (3)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) neighbor class addition, 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) = 3.112 | 3.112 | 3.112 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 2.71936 on 4 procs for 250 steps with 4000 atoms
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Performance: 39715.257 tau/day, 91.933 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 | 2.3769 | 2.5432 | 2.6447 | 6.6 | 93.52
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Neigh | 0.024088 | 0.025093 | 0.025748 | 0.4 | 0.92
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Comm | 0.044614 | 0.14598 | 0.31339 | 27.5 | 5.37
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Output | 0.00026488 | 0.00028872 | 0.00034189 | 0.0 | 0.01
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Modify | 0.0034099 | 0.0035709 | 0.0036535 | 0.2 | 0.13
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Other | | 0.001215 | | | 0.04
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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: 21792 ave 22490 max 21457 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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Total # of neighbors = 87168
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Ave neighs/atom = 21.792
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Neighbor list builds = 12
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Dangerous builds not checked
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shell rm hybrid.data hybrid.restart
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Total wall time: 0:00:08
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