provide reference output for python pair style inputs
This commit is contained in:
Axel Kohlmeyer
250
examples/python/log.4May2017.pair_python_hybrid.g++.4
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250
examples/python/log.4May2017.pair_python_hybrid.g++.4
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LAMMPS (4 May 2017)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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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 1 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 hybrid lj/cut 2.5 python 2.5
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pair_coeff * * python lj-melt-potential.py 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) = 4.044 | 4.044 | 4.044 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 1.6758903 -4.7955425 0 -2.2823355 5.670064
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100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
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150 1.6324555 -4.7286791 0 -2.280608 5.9589514
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200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
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250 1.6275257 -4.7224992 0 -2.281821 5.9567365
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Loop time of 33.3499 on 2 procs for 250 steps with 4000 atoms
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Performance: 3238.386 tau/day, 7.496 timesteps/s
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31.8% CPU use with 2 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 | 31.739 | 32.45 | 33.16 | 12.5 | 97.30
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Neigh | 0.12882 | 0.1292 | 0.12959 | 0.1 | 0.39
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Comm | 0.04094 | 0.75173 | 1.4625 | 82.0 | 2.25
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Output | 0.000352 | 0.0004115 | 0.000471 | 0.0 | 0.00
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Modify | 0.014923 | 0.01509 | 0.015257 | 0.1 | 0.05
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Other | | 0.003902 | | | 0.01
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Nlocal: 2000 ave 2006 max 1994 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 3942 ave 3967 max 3917 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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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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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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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 1 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 lj-melt-potential.py 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) = 3.747 | 3.747 | 3.747 Mbytes
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Step Temp E_pair E_mol TotEng Press
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250 1.6275257 -4.7224992 0 -2.281821 5.9567365
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300 1.645592 -4.7496711 0 -2.2819002 5.8734193
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350 1.6514972 -4.7580756 0 -2.2814491 5.810167
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400 1.6540555 -4.7622999 0 -2.281837 5.8200413
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450 1.6264734 -4.7200865 0 -2.2809863 5.9546991
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500 1.6366891 -4.7350979 0 -2.2806781 5.9369284
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Loop time of 33.4436 on 2 procs for 250 steps with 4000 atoms
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Performance: 3229.315 tau/day, 7.475 timesteps/s
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31.8% CPU use with 2 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 | 31.79 | 32.446 | 33.101 | 11.5 | 97.02
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Neigh | 0.26891 | 0.26902 | 0.26912 | 0.0 | 0.80
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Comm | 0.051997 | 0.70764 | 1.3633 | 77.9 | 2.12
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Output | 0.000332 | 0.000396 | 0.00046 | 0.0 | 0.00
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Modify | 0.01539 | 0.015553 | 0.015717 | 0.1 | 0.05
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Other | | 0.005483 | | | 0.02
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Nlocal: 2000 ave 2000 max 2000 min
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Histogram: 2 0 0 0 0 0 0 0 0 0
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Nghost: 3912 ave 3920 max 3904 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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Neighbor list builds = 25
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Dangerous builds = 25
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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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 1 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 lj-melt-potential.py 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) = 3.247 | 3.247 | 3.247 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.6275257 -4.7224992 0 -2.281821 5.9567365
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50 1.6454666 -4.7497515 0 -2.2821686 5.8729175
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100 1.6512008 -4.7582693 0 -2.2820874 5.8090548
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150 1.6537193 -4.7627023 0 -2.2827434 5.8177704
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200 1.6258731 -4.7205017 0 -2.2823017 5.952511
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250 1.6370862 -4.7373176 0 -2.2823022 5.925807
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Loop time of 33.0043 on 2 procs for 250 steps with 4000 atoms
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Performance: 3272.302 tau/day, 7.575 timesteps/s
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31.8% CPU use with 2 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 | 31.676 | 32.248 | 32.819 | 10.1 | 97.71
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Neigh | 0.12725 | 0.12751 | 0.12778 | 0.1 | 0.39
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Comm | 0.038764 | 0.60973 | 1.1807 | 73.1 | 1.85
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Output | 0.000359 | 0.000424 | 0.000489 | 0.0 | 0.00
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Modify | 0.015441 | 0.01555 | 0.01566 | 0.1 | 0.05
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Other | | 0.003519 | | | 0.01
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Nlocal: 2000 ave 2004 max 1996 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 3923.5 ave 3927 max 3920 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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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: 0:01:42
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