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lammps/bench/log.9Jan09.rhodo.scaled.linux.4
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LAMMPS (9 Jan 2009)
# Rhodopsin model
variable x index 1
variable y index 1
variable z index 1
units real
neigh_modify delay 5 every 1
atom_style full
atom_modify map hash
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
4 = max bonds/atom
8 = max angles/atom
18 = max dihedrals/atom
2 = max impropers/atom
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
1 by 2 by 2 processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 1
orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
2 by 2 by 1 processor grid
128000 atoms
110892 bonds
161868 angles
227316 dihedrals
4136 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
6468 = # of size 2 clusters
14532 = # of size 3 clusters
2988 = # of size 4 clusters
16932 = # of frozen angles
fix 2 all npt 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0
special_bonds charmm
thermo 50
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector = 0.248586
grid = 48 60 36
stencil order = 5
RMS precision = 7.66425e-05
brick FFT buffer size/proc = 41615 25920 12915
Memory usage per processor = 130.497 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -101425.4928 KinEng = 85779.3251 Temp = 299.0304
PotEng = -187204.8179 E_bond = 10151.9760 E_angle = 43685.4968
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4538
E_coul = 827025.3455 E_long = -1080537.3748 Press = -142.3110
Volume = 1231980.1340
---------------- Step 50 ----- CPU = 36.7780 (sec) ----------------
TotEng = -101320.2392 KinEng = 86003.4766 Temp = 299.8118
PotEng = -187323.7158 E_bond = 9887.1093 E_angle = 43346.7930
E_dihed = 20958.7048 E_impro = 908.4715 E_vdwl = -7973.4918
E_coul = 826113.2245 E_long = -1080564.5270 Press = 237.9865
Volume = 1232126.6400
---------------- Step 100 ----- CPU = 75.0375 (sec) ----------------
TotEng = -101158.0378 KinEng = 86355.6419 Temp = 301.0394
PotEng = -187513.6797 E_bond = 10272.0762 E_angle = 43128.6553
E_dihed = 20793.9769 E_impro = 867.0831 E_vdwl = -7586.7842
E_coul = 825555.6424 E_long = -1080544.3294 Press = 15.1826
Volume = 1232536.8037
Loop time of 75.038 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 51.8107 (69.0459)
Bond time (%) = 2.73268 (3.64172)
Kspce time (%) = 8.13185 (10.837)
Neigh time (%) = 7.95464 (10.6008)
Comm time (%) = 0.946348 (1.26116)
Outpt time (%) = 0.00172728 (0.00230188)
Other time (%) = 3.46009 (4.61111)
FFT time (% of Kspce) = 1.69206 (20.8078)
FFT Gflps 3d (1d only) = 1.41532 6.11725
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 47957 ave 47957 max 47957 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 48112464
Ave neighs/atom = 375.879
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
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