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lammps/examples/gpu/log.gpu.rhodo.9Jan12.linux.4
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log.gpu.rhodo.9Jan12.linux.4
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LAMMPS (10 Jan 2012)
# 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 = 0.245952
grid = 48 64 60
stencil order = 5
RMS precision = 8.7421e-05
using double precision FFTs
brick FFT buffer size/proc = 68635 46080 17649
Memory usage per processor = 249.821 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157025.0390 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15767.5765 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
E_coul = 1894235.3896 E_long = -2130427.5409 Press = 9562.2425
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 12.2605 (sec) ----------------
TotEng = -233301.4713 KinEng = 123222.6058 Temp = 214.7785
PotEng = -356524.0771 E_bond = 13098.4614 E_angle = 56766.9463
E_dihed = 45556.8096 E_impro = 1313.9414 E_vdwl = -40863.8548
E_coul = 1705023.3285 E_long = -2137419.7095 Press = -1634.3527
Volume = 2522232.7976
---------------- Step 200 ----- CPU = 23.7724 (sec) ----------------
TotEng = -308340.7251 KinEng = 108941.9220 Temp = 189.8871
PotEng = -417282.6471 E_bond = 9579.0415 E_angle = 47373.9551
E_dihed = 39847.5174 E_impro = 967.5823 E_vdwl = -23636.2292
E_coul = 1646568.9776 E_long = -2137983.4917 Press = -1186.1181
Volume = 2554683.4248
Loop time of 23.7725 on 4 procs for 200 steps with 256000 atoms
Pair time (%) = 4.55113 (19.1446)
Bond time (%) = 7.43137 (31.2604)
Kspce time (%) = 3.8699 (16.2789)
Neigh time (%) = 0.51208 (2.15409)
Comm time (%) = 0.544156 (2.28902)
Outpt time (%) = 0.000452995 (0.00190555)
Other time (%) = 6.86337 (28.8711)
FFT time (% of Kspce) = 1.94085 (50.1524)
FFT Gflps 3d (1d only) = 4.60577 11.8123
Nlocal: 64000 ave 64003 max 63997 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 70640.8 ave 70645 max 70636 min
Histogram: 1 0 0 0 1 0 1 0 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
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