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lammps/bench/log.22Jun07.rhodo.scaled.liberty.8
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log.22Jun07.rhodo.scaled.liberty.8
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LAMMPS (22 June 2007)
# 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)
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
orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 109.088)
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 = 139.074 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -202846.6035 KinEng = 171558.6503 Temp = 299.0288
PotEng = -374405.2538 E_bond = 20303.9521 E_angle = 87370.9937
E_dihed = 41694.2920 E_impro = 1708.0927 E_vdwl = -18462.9073
E_coul = 1630560.5366 E_long = -2137580.2135 Press = -142.0456
Volume = 2463960.2680
---------------- Step 50 ----- CPU = 74.8537 (sec) ----------------
TotEng = -202633.5610 KinEng = 172010.7811 Temp = 299.8169
PotEng = -374644.3420 E_bond = 19774.3302 E_angle = 86693.4128
E_dihed = 41917.7989 E_impro = 1817.0662 E_vdwl = -15943.3555
E_coul = 1628731.3465 E_long = -2137634.9412 Press = 238.5780
Volume = 2464254.6355
---------------- Step 100 ----- CPU = 155.1037 (sec) ----------------
TotEng = -202315.0204 KinEng = 172724.9944 Temp = 301.0618
PotEng = -375040.0148 E_bond = 20545.2484 E_angle = 86257.2003
E_dihed = 41587.6129 E_impro = 1733.5368 E_vdwl = -15186.8930
E_coul = 1627613.3289 E_long = -2137590.0491 Press = 10.9720
Volume = 2465078.7315
Loop time of 155.104 on 8 procs for 100 steps with 256000 atoms
Pair time (%) = 102.817 (66.2892)
Bond time (%) = 4.29529 (2.76929)
Kspce time (%) = 22.4796 (14.4932)
Neigh time (%) = 15.5455 (10.0226)
Comm time (%) = 2.68199 (1.72915)
Outpt time (%) = 0.00327626 (0.00211229)
Other time (%) = 7.28125 (4.69442)
FFT time (% of Kspce) = 6.0543 (26.9324)
FFT Gflps 3d 1d-only = 0.738243 7.05801
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 = 96223696
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
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