Homec4science
Diffusion lammps (lammm-master) Browse

lammps/bench/log.5Oct07.rhodo.scaled.linux.4
befd8fee68bblammm-master

Last Change
Raw File

log.5Oct07.rhodo.scaled.linux.4
View Options

LAMMPS (5 Oct 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)
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 = 0.246338
grid = 45 60 36
RMS precision = 8.56639e-05
brick FFT buffer size/proc = 40180 24840 17220
Memory usage per processor = 137.911 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -101423.5112 KinEng = 85779.3251 Temp = 299.0304
PotEng = -187202.8364 E_bond = 10151.9760 E_angle = 43685.4968
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4538
E_coul = 817284.2513 E_long = -1070794.2991 Press = -141.9925
Volume = 1231980.1340
---------------- Step 50 ----- CPU = 38.9431 (sec) ----------------
TotEng = -101316.6996 KinEng = 86004.2667 Temp = 299.8145
PotEng = -187320.9663 E_bond = 9887.1225 E_angle = 43346.5775
E_dihed = 20958.7139 E_impro = 908.4248 E_vdwl = -7973.9399
E_coul = 816372.0088 E_long = -1070819.8739 Press = 238.0995
Volume = 1232127.0570
---------------- Step 100 ----- CPU = 79.6546 (sec) ----------------
TotEng = -101158.1182 KinEng = 86360.5576 Temp = 301.0566
PotEng = -187518.6758 E_bond = 10272.2506 E_angle = 43128.8182
E_dihed = 20794.4833 E_impro = 867.0824 E_vdwl = -7591.0566
E_coul = 815810.2886 E_long = -1070800.5424 Press = 13.1624
Volume = 1232538.4006
Loop time of 79.6554 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 54.0019 (67.7944)
Bond time (%) = 2.60068 (3.26491)
Kspce time (%) = 9.92803 (12.4637)
Neigh time (%) = 8.09826 (10.1666)
Comm time (%) = 1.17806 (1.47895)
Outpt time (%) = 0.00191575 (0.00240505)
Other time (%) = 3.84657 (4.82902)
FFT time (% of Kspce) = 1.57698 (15.8841)
FFT Gflps 3d 1d-only = 1.41574 5.85277
Nlocal: 32000 ave 32001 max 31999 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 47957.5 ave 47959 max 47956 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.2028e+07 ave 1.20576e+07 max 1.19984e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 48112030
Ave neighs/atom = 375.875
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
c4science · Help