forked from lijiext/lammps
139 lines
4.6 KiB
Groff
139 lines
4.6 KiB
Groff
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 hybrid/overlay coul/cut 12.0 python 12.0
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pair_coeff * * coul/cut
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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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# create combined lj/coul table for all atom types
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# generate tabulated potential from python variant
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pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472
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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/cut, 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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pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236
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pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236
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# switch to tabulated potential
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pair_style table linear 2000 pppm
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pair_coeff 1 1 spce.table OW-OW
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pair_coeff 1 2 spce.table OW-HW
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pair_coeff 2 2 spce.table HW-HW
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thermo 10
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run 100
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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 table, 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) = 9.962 | 9.963 | 9.963 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -18284.922 0 -18284.922 -2080.7739
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10 146.83806 -19552.072 0 -18239.421 -4865.31
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20 183.15761 -18706.872 0 -17069.543 -4865.6695
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30 205.96203 -18901.541 0 -17060.354 -4454.8634
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40 241.62768 -18323.117 0 -16163.099 -3269.1475
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50 265.98384 -19883.562 0 -17505.813 -2788.5194
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60 274.01897 -21320.575 0 -18870.996 -2387.0708
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70 288.7601 -19849.269 0 -17267.913 -1235.818
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80 300.64724 -20958.602 0 -18270.981 -1714.7988
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90 304.19113 -21580.4 0 -18861.099 -2144.1614
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100 304.22027 -21239.014 0 -18519.452 -2092.6759
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Loop time of 1.7361 on 4 procs for 100 steps with 4500 atoms
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Performance: 4.977 ns/day, 4.823 hours/ns, 57.600 timesteps/s
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99.2% 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 | 1.4424 | 1.5149 | 1.6066 | 5.3 | 87.26
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Bond | 8.9407e-05 | 0.00010258 | 0.00012374 | 0.0 | 0.01
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Neigh | 0.064205 | 0.064241 | 0.064295 | 0.0 | 3.70
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Comm | 0.023643 | 0.1155 | 0.18821 | 19.2 | 6.65
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Output | 0.00038004 | 0.00042355 | 0.00054145 | 0.0 | 0.02
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Modify | 0.037507 | 0.037787 | 0.038042 | 0.1 | 2.18
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Other | | 0.003148 | | | 0.18
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Nlocal: 1125 ave 1162 max 1098 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Nghost: 12267.8 ave 12302 max 12238 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Neighs: 649416 ave 681458 max 630541 min
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Histogram: 1 0 2 0 0 0 0 0 0 1
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Total # of neighbors = 2597662
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Ave neighs/atom = 577.258
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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: 0:00:01
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