forked from lijiext/lammps
130 lines
4.7 KiB
Groff
130 lines
4.7 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 lj/sdk/coul/long 15.0
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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 1 lj9_6 0.7000 4.3210 # SO4 SO4
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pair_coeff 1 2 lj9_6 0.3830 4.4135 # SO4 CM
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pair_coeff 1 3 lj9_6 0.4050 4.4530 # SO4 CT
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pair_coeff 1 4 lj12_4 1.1000 4.1000 # SO4 SOD
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pair_coeff 1 5 lj12_4 1.1000 4.1000 # SO4 W
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pair_coeff 2 2 lj9_6 0.4200 4.5060 # CM CM
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pair_coeff 2 3 lj9_6 0.4440 4.5455 # CT CM
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pair_coeff 2 4 lj12_4 0.3400 4.4385 # SOD CM
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pair_coeff 2 5 lj12_4 0.3400 4.4385 # W CM
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pair_coeff 3 3 lj9_6 0.4690 4.5850 # CT CT
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pair_coeff 3 4 lj12_4 0.3600 4.4780 # SOD CT
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pair_coeff 3 5 lj12_4 0.3600 4.4780 # W CT
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pair_coeff 4 4 lj12_4 0.3500 4.3710 # SOD SOD
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pair_coeff 4 5 lj12_4 0.8950 4.3710 # SOD W
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pair_coeff 5 5 lj12_4 0.8950 4.3710 # W W
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kspace_style pppm/cg 0.00001
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kspace_modify order 3
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neighbor 2.0 bin
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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) = 0.0789325
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grid = 15 8 25
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stencil order = 3
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estimated absolute RMS force accuracy = 0.00275556
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estimated relative force accuracy = 8.29828e-06
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using double precision FFTs
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3d grid and FFT values/proc = 2156 840
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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 = 17
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ghost atom cutoff = 17
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binsize = 8.5, bins = 27 14 48
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/sdk/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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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) = 17.32 | 17.32 | 17.32 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 310.0934 -247030.21 2566.2036 -215551.9 -14.547393
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10 310.89138 -247061.61 2549.4854 -215525.62 -18.043512
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20 310.29287 -247017.8 2542.4491 -215544.65 -19.148631
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30 308.13371 -247024.82 2602.1061 -215693.32 -17.390902
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40 309.40426 -247058.41 2558.7402 -215651.82 -15.445066
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50 309.11317 -246753.92 2570.8603 -215362.36 -7.4232007
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60 312.52974 -246964.73 2618.8108 -215206.66 -15.23965
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70 310.11675 -246941.68 2591.8668 -215435.53 -16.153691
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80 310.48262 -247090.02 2595.0493 -215546.58 -18.080368
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90 309.60017 -247067.1 2604.6545 -215596.33 -14.583764
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100 309.7356 -247004.05 2604.8729 -215520.43 -12.78624
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Loop time of 2.45408 on 4 procs for 100 steps with 31280 atoms
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Performance: 35.207 ns/day, 0.682 hours/ns, 40.748 timesteps/s
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99.1% 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 | 2.0065 | 2.0143 | 2.0326 | 0.8 | 82.08
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Bond | 0.0084255 | 0.0086145 | 0.0088007 | 0.1 | 0.35
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Kspace | 0.033373 | 0.052041 | 0.060933 | 4.8 | 2.12
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Neigh | 0.32741 | 0.32748 | 0.32754 | 0.0 | 13.34
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Comm | 0.022403 | 0.023025 | 0.023735 | 0.4 | 0.94
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Output | 0.00060058 | 0.00086623 | 0.0016549 | 0.0 | 0.04
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Modify | 0.022533 | 0.022723 | 0.022876 | 0.1 | 0.93
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Other | | 0.005038 | | | 0.21
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Nlocal: 7820 ave 7866 max 7775 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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Nghost: 8679.75 ave 8699 max 8666 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Neighs: 838026 ave 841202 max 834819 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Total # of neighbors = 3352103
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Ave neighs/atom = 107.164
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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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Total wall time: 0:00:02
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