forked from lijiext/lammps
130 lines
4.8 KiB
Groff
130 lines
4.8 KiB
Groff
LAMMPS (27 Nov 2018)
|
|
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)
|
|
1 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 ...
|
|
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
|
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 = 5544 3000
|
|
Neighbor list info ...
|
|
update every 2 steps, delay 4 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 17
|
|
ghost atom cutoff = 17
|
|
binsize = 8.5, bins = 27 14 48
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/sdk/coul/long, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d/newton
|
|
bin: standard
|
|
PPPM/cg optimization cutoff: 1e-05
|
|
Total charged atoms: 6.5%
|
|
Min/max charged atoms/proc: 6.5% 6.5%
|
|
Per MPI rank memory allocation (min/avg/max) = 35.36 | 35.36 | 35.36 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 9.23618 on 1 procs for 100 steps with 31280 atoms
|
|
|
|
Performance: 9.355 ns/day, 2.566 hours/ns, 10.827 timesteps/s
|
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 7.7363 | 7.7363 | 7.7363 | 0.0 | 83.76
|
|
Bond | 0.032901 | 0.032901 | 0.032901 | 0.0 | 0.36
|
|
Kspace | 0.078907 | 0.078907 | 0.078907 | 0.0 | 0.85
|
|
Neigh | 1.2706 | 1.2706 | 1.2706 | 0.0 | 13.76
|
|
Comm | 0.026005 | 0.026005 | 0.026005 | 0.0 | 0.28
|
|
Output | 0.0014131 | 0.0014131 | 0.0014131 | 0.0 | 0.02
|
|
Modify | 0.079446 | 0.079446 | 0.079446 | 0.0 | 0.86
|
|
Other | | 0.01055 | | | 0.11
|
|
|
|
Nlocal: 31280 ave 31280 max 31280 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 15812 ave 15812 max 15812 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 3.3521e+06 ave 3.3521e+06 max 3.3521e+06 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 3352103
|
|
Ave neighs/atom = 107.164
|
|
Ave special neighs/atom = 0.458312
|
|
Neighbor list builds = 10
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:09
|