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lammps/examples/USER/cg-cmm/sds-monolayer/log.sds-regular
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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 lj/sdk/coul/long 15.0
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 1 lj9_6 0.7000 4.3210 # SO4 SO4
pair_coeff 1 2 lj9_6 0.3830 4.4135 # SO4 CM
pair_coeff 1 3 lj9_6 0.4050 4.4530 # SO4 CT
pair_coeff 1 4 lj12_4 1.1000 4.1000 # SO4 SOD
pair_coeff 1 5 lj12_4 1.1000 4.1000 # SO4 W
pair_coeff 2 2 lj9_6 0.4200 4.5060 # CM CM
pair_coeff 2 3 lj9_6 0.4440 4.5455 # CT CM
pair_coeff 2 4 lj12_4 0.3400 4.4385 # SOD CM
pair_coeff 2 5 lj12_4 0.3400 4.4385 # W CM
pair_coeff 3 3 lj9_6 0.4690 4.5850 # CT CT
pair_coeff 3 4 lj12_4 0.3600 4.4780 # SOD CT
pair_coeff 3 5 lj12_4 0.3600 4.4780 # W CT
pair_coeff 4 4 lj12_4 0.3500 4.3710 # SOD SOD
pair_coeff 4 5 lj12_4 0.8950 4.3710 # SOD W
pair_coeff 5 5 lj12_4 0.8950 4.3710 # W W
kspace_style pppm/cg 0.00001
kspace_modify order 3
neighbor 2.0 bin
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) = 0.0789325
grid = 15 8 25
stencil order = 3
estimated absolute RMS force accuracy = 0.00275556
estimated relative force accuracy = 8.29828e-06
using double precision FFTs
3d grid and FFT values/proc = 2156 840
PPPM/cg optimization cutoff: 1e-05
Total charged atoms: 6.5%
Min/max charged atoms/proc: 6.4% 6.7%
Memory usage per processor = 8.05923 Mbytes
Step Temp E_pair E_mol TotEng Press
0 310.0934 -247030.21 2566.2036 -215551.9 -14.547393
10 310.89138 -247061.61 2549.4854 -215525.62 -18.043512
20 310.29287 -247017.8 2542.4491 -215544.65 -19.148631
30 308.13371 -247024.82 2602.1061 -215693.32 -17.390902
40 309.40426 -247058.41 2558.7402 -215651.82 -15.445066
50 309.11317 -246753.92 2570.8603 -215362.36 -7.4232007
60 312.52974 -246964.73 2618.8108 -215206.66 -15.23965
70 310.11675 -246941.68 2591.8668 -215435.53 -16.153691
80 310.48262 -247090.02 2595.0493 -215546.58 -18.080368
90 309.60017 -247067.1 2604.6545 -215596.33 -14.583764
100 309.7356 -247004.05 2604.8729 -215520.43 -12.78624
Loop time of 3.44972 on 4 procs for 100 steps with 31280 atoms
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 25.046 ns/day 0.958 hours/ns 28.988 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7883 | 2.817 | 2.8415 | 1.1 | 81.66
Bond | 0.017868 | 0.018973 | 0.020636 | 0.7 | 0.55
Kspace | 0.063881 | 0.088012 | 0.11571 | 6.2 | 2.55
Neigh | 0.42765 | 0.42828 | 0.42882 | 0.1 | 12.41
Comm | 0.043887 | 0.044575 | 0.045079 | 0.2 | 1.29
Output | 0.00072694 | 0.00096422 | 0.0016718 | 1.3 | 0.03
Modify | 0.035513 | 0.035955 | 0.036887 | 0.3 | 1.04
Other | | 0.01597 | | | 0.46
Nlocal: 7820 ave 7866 max 7775 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 8679.75 ave 8699 max 8666 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 838026 ave 841202 max 834819 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 3352103
Ave neighs/atom = 107.164
Ave special neighs/atom = 0.458312
Neighbor list builds = 10
Dangerous builds = 0
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