update example outputs
This commit is contained in:
Axel Kohlmeyer
146
examples/python/log.4May17.pair_python_long.g++.4
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146
examples/python/log.4May17.pair_python_long.g++.4
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LAMMPS (4 May 2017)
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using 1 OpenMP thread(s) per MPI task
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units real
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atom_style full
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read_data data.spce
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orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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4500 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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3000 bonds
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reading angles ...
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1500 angles
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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pair_style python 12.0
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pair_coeff * * py_pot.LJCutSPCE OW HW
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bond_style harmonic
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angle_style harmonic
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dihedral_style none
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improper_style none
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bond_coeff 1 1000.00 1.000
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angle_coeff 1 100.0 109.47
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special_bonds lj/coul 0.0 0.0 1.0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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2 = max # of special neighbors
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neighbor 2.0 bin
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fix 1 all shake 0.0001 20 0 b 1 a 1
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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1500 = # of frozen angles
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fix 2 all nvt temp 300.0 300.0 100.0
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# create only lj/cut table for the oxygen atoms from python
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shell rm -f spce.table
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WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
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WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285)
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pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
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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 = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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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/newton
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stencil: half/bin/3d/newton
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bin: standard
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# switch to tabulated potential with long-range coulomb as overlay
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pair_style hybrid/overlay coul/long 12.0 table linear 2000
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kspace_style pppm 1.0e-6
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pair_coeff * * coul/long
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pair_coeff 1 1 table spce.table OW-OW
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thermo 10
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run 100
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PPPM initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
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G vector (1/distance) = 0.279652
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grid = 40 40 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000394674
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estimated relative force accuracy = 1.18855e-06
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using double precision FFTs
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3d grid and FFT values/proc = 34263 16000
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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 = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 6 6 6
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair coul/long, 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/newton
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bin: standard
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(2) pair table, perpetual, skip from (1)
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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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Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.45 | 13.45 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -16690.032 0 -16690.032 -1268.9538
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10 120.58553 -17767.504 0 -16689.536 -4063.8589
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20 136.11736 -17882.557 0 -16665.742 -5124.6758
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30 137.00764 -17872.318 0 -16647.545 -5337.2022
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40 153.38868 -17999.269 0 -16628.059 -5213.6001
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50 167.70342 -18103.06 0 -16603.883 -4460.6632
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60 163.07134 -18034.856 0 -16577.088 -3285.0037
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70 169.59286 -18064.636 0 -16548.57 -2606.407
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80 182.92893 -18153.499 0 -16518.215 -2385.5152
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90 191.2793 -18195.356 0 -16485.425 -2235.3701
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100 194.68587 -18192.458 0 -16452.073 -1948.3746
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Loop time of 2.36748 on 4 procs for 100 steps with 4500 atoms
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Performance: 3.649 ns/day, 6.576 hours/ns, 42.239 timesteps/s
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99.4% 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 | 1.5309 | 1.5977 | 1.6926 | 4.7 | 67.49
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Bond | 9.9182e-05 | 0.00012749 | 0.00016403 | 0.0 | 0.01
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Kspace | 0.52158 | 0.61232 | 0.67676 | 7.3 | 25.86
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Neigh | 0.066937 | 0.06702 | 0.067093 | 0.0 | 2.83
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Comm | 0.035882 | 0.039862 | 0.042244 | 1.2 | 1.68
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Output | 0.0004003 | 0.00044602 | 0.00057578 | 0.0 | 0.02
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Modify | 0.046088 | 0.046227 | 0.046315 | 0.0 | 1.95
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Other | | 0.003775 | | | 0.16
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Nlocal: 1125 ave 1154 max 1092 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Nghost: 12256.2 ave 12296 max 12213 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Neighs: 650442 ave 678831 max 626373 min
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Histogram: 1 0 0 0 2 0 0 0 0 1
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Total # of neighbors = 2601769
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Ave neighs/atom = 578.171
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Ave special neighs/atom = 2
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Neighbor list builds = 3
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Dangerous builds = 0
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shell rm spce.table
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Total wall time: 0:00:02
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