update log files for peptide, peri, pour and python examples
This commit is contained in:
Axel Kohlmeyer
122
examples/python/log.27Nov18.pair_python_spce.g++.4
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122
examples/python/log.27Nov18.pair_python_spce.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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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 hybrid/overlay coul/long 12.0 python 12.0
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kspace_style pppm 1.0e-6
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pair_coeff * * coul/long
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pair_coeff * * python py_pot.LJCutSPCE OW NULL
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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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thermo 10
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/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 python, 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) = 14.64 | 14.64 | 14.64 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -16692.369 0 -16692.369 -1289.222
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10 120.56861 -17769.719 0 -16691.902 -4082.7098
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20 136.08014 -17884.591 0 -16668.109 -5140.7824
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30 136.97316 -17874.351 0 -16649.887 -5351.3571
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40 153.37285 -18001.493 0 -16630.424 -5227.0601
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50 167.70414 -18105.435 0 -16606.252 -4473.2089
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60 163.08253 -18037.29 0 -16579.422 -3295.8963
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70 169.60395 -18067.078 0 -16550.912 -2615.7026
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80 182.94811 -18155.978 0 -16520.523 -2393.3156
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90 191.29902 -18197.887 0 -16487.779 -2242.7104
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100 194.70949 -18195.021 0 -16454.425 -1955.2916
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Loop time of 4.36104 on 4 procs for 100 steps with 4500 atoms
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Performance: 1.981 ns/day, 12.114 hours/ns, 22.930 timesteps/s
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97.7% 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 | 3.5019 | 3.6105 | 3.738 | 4.4 | 82.79
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Bond | 0.00010133 | 0.00013196 | 0.00017118 | 0.0 | 0.00
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Kspace | 0.47082 | 0.59641 | 0.70417 | 10.8 | 13.68
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Neigh | 0.081036 | 0.081042 | 0.081047 | 0.0 | 1.86
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Comm | 0.030113 | 0.03092 | 0.03135 | 0.3 | 0.71
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Output | 0.00034952 | 0.00064117 | 0.001514 | 0.0 | 0.01
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Modify | 0.036583 | 0.037553 | 0.038021 | 0.3 | 0.86
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Other | | 0.00388 | | | 0.09
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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: 650440 ave 678828 max 626375 min
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Histogram: 1 0 0 0 2 0 0 0 0 1
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Total # of neighbors = 2601762
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Ave neighs/atom = 578.169
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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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Total wall time: 0:00:04
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