forked from lijiext/lammps
146 lines
5.2 KiB
Groff
146 lines
5.2 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# coarse grained SDS surfactant monolayer
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units real
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dimension 3
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atom_style full
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processors * * 1
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pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5
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bond_style harmonic
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angle_style sdk
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special_bonds lj/coul 0.0 0.0 1.0
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read_data data.sds.gz
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orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200)
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4 by 1 by 1 MPI processor grid
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reading atoms ...
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31280 atoms
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reading velocities ...
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31280 velocities
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scanning bonds ...
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1 = 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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4096 bonds
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reading angles ...
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3072 angles
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of special neighbors
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pair_coeff 1 4 coul/long # SO4 SOD
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pair_coeff 4 4 coul/long # SOD SOD
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pair_coeff 1 1 lj/sdk lj9_6 0.7000 4.3210 # SO4 SO4
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pair_coeff 1 2 lj/sdk lj9_6 0.3830 4.4135 # SO4 CM
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pair_coeff 1 3 lj/sdk lj9_6 0.4050 4.4530 # SO4 CT
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pair_coeff 1 4 lj/sdk lj12_4 1.1000 4.1000 # SO4 SOD
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pair_coeff 1 5 lj/sdk lj12_4 1.1000 4.1000 # SO4 W
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pair_coeff 2 2 lj/sdk lj9_6 0.4200 4.5060 # CM CM
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pair_coeff 2 3 lj/sdk lj9_6 0.4440 4.5455 # CT CM
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pair_coeff 2 4 lj/sdk lj12_4 0.3400 4.4385 # SOD CM
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pair_coeff 2 5 lj/sdk lj12_4 0.3400 4.4385 # W CM
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pair_coeff 3 3 lj/sdk lj9_6 0.4690 4.5850 # CT CT
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pair_coeff 3 4 lj/sdk lj12_4 0.3600 4.4780 # SOD CT
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pair_coeff 3 5 lj/sdk lj12_4 0.3600 4.4780 # W CT
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pair_coeff 4 4 lj/sdk lj12_4 0.3500 4.3710 # SOD SOD
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pair_coeff 4 5 lj/sdk lj12_4 0.8950 4.3710 # SOD W
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pair_coeff 5 5 lj/sdk lj12_4 0.8950 4.3710 # W W
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group charged type 1 4
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2048 atoms in group charged
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atom_modify first charged
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kspace_style pppm/cg 0.00001
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kspace_modify order 3
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comm_modify mode multi
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neighbor 2.0 multi
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neigh_modify delay 4 every 2 check yes
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timestep 10.0
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fix 1 all nvt temp 310.0 310.0 100.0
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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) = 0.0416781
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grid = 8 4 12
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stencil order = 3
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estimated absolute RMS force accuracy = 0.00248777
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estimated relative force accuracy = 7.49185e-06
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using double precision FFTs
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3d grid and FFT values/proc = 525 96
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Neighbor list info ...
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update every 2 steps, delay 4 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 28.5
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ghost atom cutoff = 28.5
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binsize = 8.5, bins = 27 14 48
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair lj/sdk, perpetual
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attributes: half, newton on
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pair build: half/multi/newton
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stencil: half/multi/3d/newton
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bin: standard
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(2) pair coul/long, 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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PPPM/cg optimization cutoff: 1e-05
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Total charged atoms: 6.5%
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Min/max charged atoms/proc: 6.4% 6.7%
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Per MPI rank memory allocation (min/avg/max) = 17.48 | 17.48 | 17.48 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516
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10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262
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20 310.33025 -249325.09 2543.0138 -217847.89 -30.069751
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30 308.24273 -249331.54 2604.3227 -217987.66 -28.033129
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40 309.41339 -249363.5 2560.6727 -217954.13 -25.802838
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50 309.16857 -249071.94 2571.9117 -217674.15 -17.946457
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60 312.67237 -249288.77 2621.0185 -217515.19 -25.723545
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70 310.13623 -249262.32 2595.874 -217750.35 -26.276067
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80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924
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90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575
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100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823
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Loop time of 2.54454 on 4 procs for 100 steps with 31280 atoms
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Performance: 33.955 ns/day, 0.707 hours/ns, 39.300 timesteps/s
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98.9% 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 | 1.8639 | 1.8913 | 1.9283 | 1.8 | 74.33
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Bond | 0.0092797 | 0.0094567 | 0.0095828 | 0.1 | 0.37
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Kspace | 0.018389 | 0.056616 | 0.084424 | 10.7 | 2.23
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Neigh | 0.53553 | 0.53569 | 0.53605 | 0.0 | 21.05
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Comm | 0.023819 | 0.02433 | 0.02506 | 0.3 | 0.96
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Output | 0.00058866 | 0.00084978 | 0.0016243 | 0.0 | 0.03
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Modify | 0.021841 | 0.022059 | 0.022308 | 0.1 | 0.87
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Other | | 0.004233 | | | 0.17
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Nlocal: 7820 ave 7866 max 7774 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Nghost: 9179.5 ave 9199 max 9157 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Neighs: 850419 ave 853627 max 846921 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Total # of neighbors = 3401676
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Ave neighs/atom = 108.749
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Ave special neighs/atom = 0.458312
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Neighbor list builds = 10
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:02
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