Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/examples/gpu/log.gpu.rhodo.18Feb13.linux.4
2eeae0aade06lammm-devel

Last Change
Raw File

log.gpu.rhodo.18Feb13.linux.4
View Options

LAMMPS (18 Feb 2013)
# Rhodopsin model
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long/gpu 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm/gpu 1e-4
read_data data.rhodo
4 = max bonds/atom
18 = max angles/atom
40 = max dihedrals/atom
4 = max impropers/atom
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
1 by 2 by 2 MPI 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 -36.2676) to (82.5 115.5 108.797)
1 by 2 by 2 MPI 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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 100
thermo_style multi
timestep 2.0
run 200
PPPM initialization ...
G vector (1/distance) = 0.245959
grid = 48 64 60
stencil order = 5
estimated absolute RMS force accuracy = 0.0410392
estimated relative force accuracy = 0.000123588
using double precision FFTs
3d grid and FFT values/proc = 68635 46080
Memory usage per processor = 250.358 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157024.0492 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15768.5663 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
E_coul = 1894295.6622 E_long = -2130488.8032 Press = 9562.1554
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 12.1280 (sec) ----------------
TotEng = -233301.6590 KinEng = 123222.8183 Temp = 214.7789
PotEng = -356524.4772 E_bond = 13098.4683 E_angle = 56766.9228
E_dihed = 45556.8211 E_impro = 1313.9369 E_vdwl = -40863.9000
E_coul = 1705084.8591 E_long = -2137481.5855 Press = -1634.3808
Volume = 2522232.6313
---------------- Step 200 ----- CPU = 23.3169 (sec) ----------------
TotEng = -308342.2597 KinEng = 108936.8553 Temp = 189.8783
PotEng = -417279.1150 E_bond = 9579.0042 E_angle = 47373.6037
E_dihed = 39847.3737 E_impro = 967.6451 E_vdwl = -23631.6382
E_coul = 1646630.1738 E_long = -2138045.2773 Press = -1185.5491
Volume = 2554682.9808
Loop time of 23.3169 on 4 procs for 200 steps with 256000 atoms
Pair time (%) = 4.29395 (18.4156)
Bond time (%) = 6.57406 (28.1944)
Kspce time (%) = 4.75311 (20.3848)
Neigh time (%) = 1.32057 (5.66359)
Comm time (%) = 0.555436 (2.38212)
Outpt time (%) = 0.000431776 (0.00185177)
Other time (%) = 5.81936 (24.9577)
FFT time (% of Kspce) = 1.78333 (37.5192)
FFT Gflps 3d (1d only) = 5.0126 11.639
Nlocal: 64000 ave 64003 max 63997 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 70636.8 ave 70640 max 70632 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 7.43187
Neighbor list builds = 31
Dangerous builds = 12
c4science · Help