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lammps/bench-accel/bench_gauss-diel/log.gauss-diel.1
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LAMMPS (29 Jan 2012-ICMS)
using 1 OpenMP thread(s) per MPI task
# Ionic surfactant system: S12S
units lj
dimension 3
atom_style full
read_data data.gauss-diel
1 = max bonds/atom
1 = max angles/atom
1 = max dihedrals/atom
orthogonal box = (-35 -35 -35) to (35 35 35)
1 by 1 by 1 MPI processor grid
4200 atoms
3600 bonds
3300 angles
3000 dihedrals
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
replicate 2 2 2
orthogonal box = (-35 -35 -35) to (105 105 105)
1 by 1 by 1 MPI processor grid
33600 atoms
28800 bonds
26400 angles
24000 dihedrals
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
pair_style hybrid/overlay lj/cut 3.5 coul/long 18.0 gauss/cut 3.4 coul/diel 2.5
pair_modify shift yes
dielectric 0.4255
kspace_style pppm/cg 0.00035
kspace_modify mesh 25 25 25 order 3
bond_style harmonic
angle_style harmonic
dihedral_style opls
pair_coeff 1 1 lj/cut 0.5 1.775 3.268 # HG HG
pair_coeff 1 1 coul/long # HG HG
pair_coeff 1 1 gauss/cut 0.1 2.549 0.1525
pair_coeff 1 2 lj/cut 0.31623 1.5329 1.7206 # HG CM
pair_coeff 1 3 lj/cut 0.31623 1.5329 1.7206 # HG CT
pair_coeff 1 4 lj/cut 0.05 1.75 4.375 # HG CI
pair_coeff 1 4 coul/long # HG CI
pair_coeff 1 4 gauss/cut 0.2805 1.45 0.112
pair_coeff 1 4 coul/diel 78. 1.375 0.112
pair_coeff 2 2 lj/cut 0.2000 1.2910 3.2275 # CM CM
pair_coeff 2 3 lj/cut 0.2000 1.2910 3.2275 # CM CT
pair_coeff 2 4 lj/cut 0.4472 1.1455 1.28585 # CM CI
pair_coeff 3 3 lj/cut 1.95 1.291 3.2275 # CT CT
pair_coeff 3 4 lj/cut 0.4472 1.1455 1.28585 # CT CI
pair_coeff 4 4 lj/cut 1.0 10. 1.12246 # CI CI
pair_coeff 4 4 coul/long # CI CI
bond_coeff 1 12650.0000 0.7500 # HG CM FROM TOP
bond_coeff 2 12650.0000 0.5000 # CM CM FROM TOP
bond_coeff 3 12650.0000 0.5000 # CM CM FROM TOP
bond_coeff 4 12650.0000 0.5000 # CM CM FROM TOP
bond_coeff 5 12650.0000 0.5000 # CM CM FROM TOP
bond_coeff 6 12650.0000 0.5000 # CM CM FROM TOP
bond_coeff 7 12650.0000 0.5000 # CM CM FROM TOP
bond_coeff 8 12650.0000 0.5000 # CM CM FROM TOP
bond_coeff 9 12650.0000 0.5000 # CM CM FROM TOP
bond_coeff 10 12650.0000 0.5000 # CM CM FROM TOP
bond_coeff 11 12650.0000 0.5000 # CM CM FROM TOP
bond_coeff 12 12650.0000 0.5000 # CM CT FROM TOP
angle_coeff 1 85.7600 109.5000 # HG CM CM FROM TOP
angle_coeff 2 85.7600 111.0000 # CM CM CM FROM TOP
angle_coeff 3 85.7600 111.0000 # CM CM CM FROM TOP
angle_coeff 4 85.7600 111.0000 # CM CM CM FROM TOP
angle_coeff 5 85.7600 111.0000 # CM CM CM FROM TOP
angle_coeff 6 85.7600 111.0000 # CM CM CM FROM TOP
angle_coeff 7 85.7600 111.0000 # CM CM CM FROM TOP
angle_coeff 8 85.7600 111.0000 # CM CM CM FROM TOP
angle_coeff 9 85.7600 111.0000 # CM CM CM FROM TOP
angle_coeff 10 85.7600 111.0000 # CM CM CM FROM TOP
angle_coeff 11 85.7600 111.0000 # CM CM CT FROM TOP
dihedral_coeff 1 5.7431 -2.53241 5.0742 0.0 # HG CM CM CM FROM TOP
dihedral_coeff 2 5.7431 -2.53241 5.0742 0.0 # CM CM CM CM FROM TOP
dihedral_coeff 3 5.7431 -2.53241 5.0742 0.0 # CM CM CM CM FROM TOP
dihedral_coeff 4 5.7431 -2.53241 5.0742 0.0 # CM CM CM CM FROM TOP
dihedral_coeff 5 5.7431 -2.53241 5.0742 0.0 # CM CM CM CM FROM TOP
dihedral_coeff 6 5.7431 -2.53241 5.0742 0.0 # CM CM CM CM FROM TOP
dihedral_coeff 7 5.7431 -2.53241 5.0742 0.0 # CM CM CM CM FROM TOP
dihedral_coeff 8 5.7431 -2.53241 5.0742 0.0 # CM CM CM CM FROM TOP
dihedral_coeff 9 5.7431 -2.53241 5.0742 0.0 # CM CM CM CM FROM TOP
dihedral_coeff 10 5.7431 -2.53241 5.0742 0.0 # CM CM CM CT FROM TOP
timestep 0.002
reset_timestep 0
group cions type 4
2400 atoms in group cions
group sds subtract all cions
31200 atoms in group sds
velocity all create 1. 87287 dist gaussian
neighbor 1.5 multi
neigh_modify exclude molecule sds
neigh_modify every 2 delay 4 check yes
communicate multi
fix 1 all nve/limit 0.2
fix 2 all langevin 1.0 1.0 0.05 18273
thermo_style multi
thermo 500
run 2000
PPPM initialization ...
G vector = 0.111328
grid = 25 25 25
stencil order = 3
RMS precision = 0.0003158
using single precision FFTs
brick FFT buffer size/proc = 21952 15625 4704
PPPM/cg optimization cutoff: 1e-05
Total charged atoms: 14.3%
Min/max charged atoms/proc: 14.3% 14.3%
Memory usage per processor = 36.2271 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 9.9404 KinEng = 1.5000 Temp = 1.0000
PotEng = 8.4405 E_bond = 0.0036 E_angle = 0.1237
E_dihed = 0.3185 E_impro = 0.0000 E_vdwl = 8.0100
E_coul = -0.0116 E_long = -0.0036 Press = 0.4086
---------------- Step 500 ----- CPU = 15.8884 (sec) ----------------
TotEng = 2.7559 KinEng = 1.4962 Temp = 0.9975
PotEng = 1.2598 E_bond = 0.4631 E_angle = 0.3939
E_dihed = 0.4074 E_impro = 0.0000 E_vdwl = -0.0026
E_coul = 0.0014 E_long = -0.0034 Press = -0.0002
---------------- Step 1000 ----- CPU = 31.7430 (sec) ----------------
TotEng = 2.7930 KinEng = 1.5073 Temp = 1.0049
PotEng = 1.2858 E_bond = 0.4683 E_angle = 0.3887
E_dihed = 0.4343 E_impro = 0.0000 E_vdwl = -0.0031
E_coul = 0.0011 E_long = -0.0035 Press = -0.0002
---------------- Step 1500 ----- CPU = 46.6686 (sec) ----------------
TotEng = 2.8272 KinEng = 1.5048 Temp = 1.0032
PotEng = 1.3224 E_bond = 0.4726 E_angle = 0.3969
E_dihed = 0.4598 E_impro = 0.0000 E_vdwl = -0.0040
E_coul = 0.0006 E_long = -0.0035 Press = -0.0011
---------------- Step 2000 ----- CPU = 61.5981 (sec) ----------------
TotEng = 2.8311 KinEng = 1.5020 Temp = 1.0013
PotEng = 1.3291 E_bond = 0.4641 E_angle = 0.3899
E_dihed = 0.4828 E_impro = 0.0000 E_vdwl = -0.0044
E_coul = 0.0002 E_long = -0.0035 Press = 0.0002
Loop time of 61.5982 on 1 procs (1 MPI x 1 OpenMP) for 2000 steps with 33600 atoms
Section | min time | avg time | max time |%total | #Thr
--------------------------------------------------------------
Pair | 15.49 | 15.49 | 15.49 | 25.15 | 1.0x
Bond | 29.09 | 29.09 | 29.09 | 47.23 | 1.0x
Kspace | 7.604 | 7.604 | 7.604 | 12.34 | 1.0x
Neigh | 3.961 | 3.961 | 3.961 | 6.43 | 1.0x
Comm | 0.2721 | 0.2721 | 0.2721 | 0.44 | 1.0x
Output | 0.0006061 | 0.0006061 | 0.0006061 | 0.00 | 1.0x
Modify | 4.888 | 4.888 | 4.888 | 7.93 | 1.0x
Other | | 0.2888 | | 0.47 |
FFT time (% of Kspce) = 4.25043 (55.9006)
FFT Gflps 3d (1d only) = 1.41995 1.88468
Nlocal: 33600 ave 33600 max 33600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9511 ave 9511 max 9511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 201205 ave 201205 max 201205 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 201205
Ave neighs/atom = 5.98824
Ave special neighs/atom = 4.71429
Neighbor list builds = 23
Dangerous builds = 1
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