Homec4science
Diffusion lammps (master) Browse

lammps/bench/log.28Mar11.rhodo.scaled.linux.4
a1978f660a7dmaster

Last Change
Raw File

log.28Mar11.rhodo.scaled.linux.4
View Options

LAMMPS (27 Mar 2011)
# 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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
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 = 146.135 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -101425.4825 KinEng = 85779.3251 Temp = 299.0304
PotEng = -187204.8077 E_bond = 10151.9760 E_angle = 43685.4968
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537
E_coul = 827025.3556 E_long = -1080537.3748 Press = -142.3084
Volume = 1231980.1340
---------------- Step 50 ----- CPU = 32.8194 (sec) ----------------
TotEng = -101320.2611 KinEng = 86003.4849 Temp = 299.8118
PotEng = -187323.7460 E_bond = 9887.1072 E_angle = 43346.7920
E_dihed = 20958.7034 E_impro = 908.4715 E_vdwl = -7973.4456
E_coul = 826113.1533 E_long = -1080564.5278 Press = 238.0165
Volume = 1232126.1854
---------------- Step 100 ----- CPU = 66.9547 (sec) ----------------
TotEng = -101158.1519 KinEng = 86355.6231 Temp = 301.0394
PotEng = -187513.7749 E_bond = 10272.0700 E_angle = 43128.6453
E_dihed = 20793.9768 E_impro = 867.0826 E_vdwl = -7586.7196
E_coul = 825555.5006 E_long = -1080544.3306 Press = 15.2192
Volume = 1232535.8453
Loop time of 66.9548 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 45.779 (68.373)
Bond time (%) = 2.87439 (4.29303)
Kspce time (%) = 7.5089 (11.2149)
Neigh time (%) = 6.52016 (9.73816)
Comm time (%) = 0.765243 (1.14293)
Outpt time (%) = 0.000411808 (0.000615055)
Other time (%) = 3.50669 (5.2374)
FFT time (% of Kspce) = 1.17001 (15.5816)
FFT Gflps 3d (1d only) = 2.04683 6.15771
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 = 48112468
Ave neighs/atom = 375.879
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
c4science · Help