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lammps/examples/gpu/log.gpu.rhodo.18Feb13.linux.1
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log.gpu.rhodo.18Feb13.linux.1
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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 1 by 1 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 1 by 1 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 = 237705 184320
Memory usage per processor = 760.048 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157024.0524 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15768.5631 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
E_coul = 1894295.6653 E_long = -2130488.8032 Press = 9562.1554
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 36.9731 (sec) ----------------
TotEng = -233301.5647 KinEng = 123222.8702 Temp = 214.7790
PotEng = -356524.4350 E_bond = 13098.4680 E_angle = 56766.9162
E_dihed = 45556.8237 E_impro = 1313.9365 E_vdwl = -40863.9296
E_coul = 1705084.9441 E_long = -2137481.5939 Press = -1634.3724
Volume = 2522232.6324
---------------- Step 200 ----- CPU = 71.7796 (sec) ----------------
TotEng = -308341.5902 KinEng = 108937.0512 Temp = 189.8786
PotEng = -417278.6414 E_bond = 9579.0189 E_angle = 47373.5018
E_dihed = 39847.3805 E_impro = 967.6494 E_vdwl = -23632.3384
E_coul = 1646631.2737 E_long = -2138045.1272 Press = -1185.5582
Volume = 2554682.9557
Loop time of 71.7796 on 1 procs for 200 steps with 256000 atoms
Pair time (%) = 10.4771 (14.5962)
Bond time (%) = 27.3962 (38.1671)
Kspce time (%) = 7.23529 (10.0799)
Neigh time (%) = 5.6228 (7.83343)
Comm time (%) = 0.678451 (0.945186)
Outpt time (%) = 0.001441 (0.00200754)
Other time (%) = 20.3683 (28.3762)
FFT time (% of Kspce) = 5.21147 (72.0284)
FFT Gflps 3d (1d only) = 1.71528 2.99119
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 161665 ave 161665 max 161665 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 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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