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lammps/bench/log.1Oct06.rhodo.lmp.scaled.liberty.8
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log.1Oct06.rhodo.lmp.scaled.liberty.8
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LAMMPS (1 Oct 2006)
# 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
2 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 2
2 by 2 by 2 processor grid
256000 atoms
221784 bonds
323736 angles
454632 dihedrals
8272 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
12936 = # of size 2 clusters
29064 = # of size 3 clusters
5976 = # of size 4 clusters
33864 = # 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 = 0.245875
grid = 48 64 60
RMS precision = 8.76365e-05
brick FFT buffer size/proc = 37555 24576 11655
Memory usage per processor = 140.353 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -202846.4560 KinEng = 171558.6298 Temp = 299.0311
PotEng = -374405.0858 E_bond = 20303.9521 E_angle = 87370.9937
E_dihed = 41694.2920 E_impro = 1708.0927 E_vdwl = -18462.9073
E_coul = 1630559.9965 E_long = -2137579.5054 Press = -142.0854
Volume = 2463960.2680
---------------- Step 50 ----- CPU = 80.3339 (sec) ----------------
TotEng = -202634.6400 KinEng = 172010.0889 Temp = 299.8180
PotEng = -374644.7289 E_bond = 19774.2719 E_angle = 86693.1834
E_dihed = 41917.7603 E_impro = 1817.0606 E_vdwl = -15943.4739
E_coul = 1628730.7042 E_long = -2137634.2354 Press = 238.6347
Volume = 2464254.6396
---------------- Step 100 ----- CPU = 165.2014 (sec) ----------------
TotEng = -202318.7870 KinEng = 172723.1177 Temp = 301.0609
PotEng = -375041.9047 E_bond = 20545.0687 E_angle = 86256.5048
E_dihed = 41587.4799 E_impro = 1733.5220 E_vdwl = -15187.0971
E_coul = 1627611.9671 E_long = -2137589.3501 Press = 10.9015
Volume = 2465078.6410
Loop time of 165.202 on 8 procs for 100 steps with 256000 atoms
Pair time (%) = 109.485 (66.2732)
Bond time (%) = 4.55416 (2.75672)
Kspce time (%) = 26.1207 (15.8114)
Neigh time (%) = 14.7538 (8.93074)
Comm time (%) = 2.72842 (1.65156)
Outpt time (%) = 0.00508916 (0.00308057)
Other time (%) = 7.55527 (4.57335)
FFT time (% of Kspce) = 6.32901 (24.2299)
FFT Gflps 3d 1d-only = 0.7062 7.01015
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Nghost: 47962 ave 47962 max 47962 min
Histogram: 8 0 0 0 0 0 0 0 0 0
Neighs: 1.2028e+07 ave 1.2057e+07 max 1.19989e+07 min
Histogram: 4 0 0 0 0 0 0 0 0 4
Total # of neighbors = 96223728
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
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