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lammps/examples/USER/cg-cmm/sds-monolayer/log.sds-hybrid
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log.sds-hybrid
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LAMMPS (20 Mar 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
# coarse grained SDS surfactant monolayer
units real
dimension 3
atom_style full
processors * * 1
pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5
bond_style harmonic
angle_style sdk
special_bonds lj/coul 0.0 0.0 1.0
read_data data.sds.gz
orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200)
4 by 1 by 1 MPI processor grid
reading atoms ...
31280 atoms
reading velocities ...
31280 velocities
scanning bonds ...
1 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4096 bonds
reading angles ...
3072 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
pair_coeff 1 4 coul/long # SO4 SOD
pair_coeff 4 4 coul/long # SOD SOD
pair_coeff 1 1 lj/sdk lj9_6 0.7000 4.3210 # SO4 SO4
pair_coeff 1 2 lj/sdk lj9_6 0.3830 4.4135 # SO4 CM
pair_coeff 1 3 lj/sdk lj9_6 0.4050 4.4530 # SO4 CT
pair_coeff 1 4 lj/sdk lj12_4 1.1000 4.1000 # SO4 SOD
pair_coeff 1 5 lj/sdk lj12_4 1.1000 4.1000 # SO4 W
pair_coeff 2 2 lj/sdk lj9_6 0.4200 4.5060 # CM CM
pair_coeff 2 3 lj/sdk lj9_6 0.4440 4.5455 # CT CM
pair_coeff 2 4 lj/sdk lj12_4 0.3400 4.4385 # SOD CM
pair_coeff 2 5 lj/sdk lj12_4 0.3400 4.4385 # W CM
pair_coeff 3 3 lj/sdk lj9_6 0.4690 4.5850 # CT CT
pair_coeff 3 4 lj/sdk lj12_4 0.3600 4.4780 # SOD CT
pair_coeff 3 5 lj/sdk lj12_4 0.3600 4.4780 # W CT
pair_coeff 4 4 lj/sdk lj12_4 0.3500 4.3710 # SOD SOD
pair_coeff 4 5 lj/sdk lj12_4 0.8950 4.3710 # SOD W
pair_coeff 5 5 lj/sdk lj12_4 0.8950 4.3710 # W W
group charged type 1 4
2048 atoms in group charged
atom_modify first charged
kspace_style pppm/cg 0.00001
kspace_modify order 3
communicate multi
neighbor 2.0 multi
neigh_modify delay 4 every 2 check yes
timestep 10.0
fix 1 all nvt temp 310.0 310.0 100.0
thermo 10
run 100
PPPM initialization ...
G vector (1/distance) = 0.0416781
grid = 8 4 12
stencil order = 3
estimated absolute RMS force accuracy = 0.00248777
estimated relative force accuracy = 7.49185e-06
using double precision FFTs
3d grid and FFT values/proc = 525 96
PPPM/cg optimization cutoff: 1e-05
Total charged atoms: 6.5%
Min/max charged atoms/proc: 6.4% 6.7%
Memory usage per processor = 7.66668 Mbytes
Step Temp E_pair E_mol TotEng Press
0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516
10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262
20 310.33025 -249325.09 2543.0138 -217847.89 -30.069751
30 308.24273 -249331.54 2604.3227 -217987.66 -28.033129
40 309.41339 -249363.5 2560.6727 -217954.13 -25.802838
50 309.16857 -249071.94 2571.9117 -217674.15 -17.946457
60 312.67237 -249288.77 2621.0185 -217515.19 -25.723545
70 310.13623 -249262.32 2595.874 -217750.35 -26.276067
80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924
90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575
100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823
Loop time of 4.07239 on 4 procs for 100 steps with 31280 atoms
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 21.216 ns/day 1.131 hours/ns 24.556 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.082 | 3.0928 | 3.1091 | 0.6 | 75.95
Bond | 0.021077 | 0.021421 | 0.021823 | 0.2 | 0.53
Kspace | 0.042646 | 0.058859 | 0.069797 | 4.1 | 1.45
Neigh | 0.79689 | 0.79696 | 0.79711 | 0.0 | 19.57
Comm | 0.048668 | 0.049552 | 0.050446 | 0.3 | 1.22
Output | 0.00072145 | 0.00095147 | 0.0016341 | 1.3 | 0.02
Modify | 0.034767 | 0.035175 | 0.035714 | 0.2 | 0.86
Other | | 0.01665 | | | 0.41
Nlocal: 7820 ave 7866 max 7774 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 9179.5 ave 9199 max 9157 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 850419 ave 853627 max 846921 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 3401676
Ave neighs/atom = 108.749
Ave special neighs/atom = 0.458312
Neighbor list builds = 10
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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