forked from lijiext/lammps
update log files for pair style python examples
This commit is contained in:
Axel Kohlmeyer
parent
96f0a82aa5
commit
13e16dc3f1
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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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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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1 by 1 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 python 12.0 coul/long 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 potentials.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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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 = 103823 64000
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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 python, perpetual, skip from (2)
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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 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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Per MPI rank memory allocation (min/avg/max) = 41.05 | 41.05 | 41.05 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 63.3145 on 1 procs for 100 steps with 4500 atoms
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Performance: 0.136 ns/day, 175.874 hours/ns, 1.579 timesteps/s
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86.0% CPU use with 1 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 | 61.815 | 61.815 | 61.815 | 0.0 | 97.63
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Bond | 0.000132 | 0.000132 | 0.000132 | 0.0 | 0.00
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Kspace | 1.2226 | 1.2226 | 1.2226 | 0.0 | 1.93
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Neigh | 0.21684 | 0.21684 | 0.21684 | 0.0 | 0.34
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Comm | 0.015175 | 0.015175 | 0.015175 | 0.0 | 0.02
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Output | 0.000405 | 0.000405 | 0.000405 | 0.0 | 0.00
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Modify | 0.040088 | 0.040088 | 0.040088 | 0.0 | 0.06
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Other | | 0.003896 | | | 0.01
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Nlocal: 4500 ave 4500 max 4500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 21216 ave 21216 max 21216 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.44594e+06 ave 1.44594e+06 max 1.44594e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1445935
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Ave neighs/atom = 321.319
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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: 0:01:05
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@ -0,0 +1,123 @@
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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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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 python 12.0 coul/long 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 potentials.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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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 python, perpetual, skip from (2)
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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 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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Per MPI rank memory allocation (min/avg/max) = 14.59 | 14.59 | 14.59 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 29.6024 on 4 procs for 100 steps with 4500 atoms
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Performance: 0.292 ns/day, 82.229 hours/ns, 3.378 timesteps/s
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52.5% 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 | 26.631 | 27.507 | 28.649 | 14.3 | 92.92
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Bond | 0.00021 | 0.00022675 | 0.000248 | 0.0 | 0.00
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Kspace | 0.72315 | 1.8708 | 2.7365 | 54.7 | 6.32
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Neigh | 0.10667 | 0.1067 | 0.10674 | 0.0 | 0.36
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Comm | 0.045357 | 0.054035 | 0.064607 | 3.6 | 0.18
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Output | 0.000424 | 0.00086625 | 0.002189 | 0.0 | 0.00
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Modify | 0.056602 | 0.056667 | 0.056763 | 0.0 | 0.19
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Other | | 0.006337 | | | 0.02
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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: 361484 ave 376583 max 347969 min
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Histogram: 1 0 0 0 2 0 0 0 0 1
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Total # of neighbors = 1445935
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Ave neighs/atom = 321.319
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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: 0:00:30
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