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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7497 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2012-01-10 01:54:14 +00:00
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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 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 = 0.245952
grid = 48 64 60
stencil order = 5
RMS precision = 8.7421e-05
using double precision FFTs
brick FFT buffer size/proc = 237705 184320 40365
Memory usage per processor = 757.714 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157025.0401 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15767.5754 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
E_coul = 1894235.3907 E_long = -2130427.5409 Press = 9562.2425
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 36.8336 (sec) ----------------
TotEng = -233301.4802 KinEng = 123222.6026 Temp = 214.7785
PotEng = -356524.0828 E_bond = 13098.4631 E_angle = 56766.9481
E_dihed = 45556.8121 E_impro = 1313.9420 E_vdwl = -40863.8988
E_coul = 1705023.3608 E_long = -2137419.7102 Press = -1634.3633
Volume = 2522232.7977
---------------- Step 200 ----- CPU = 72.2618 (sec) ----------------
TotEng = -308340.6857 KinEng = 108944.3257 Temp = 189.8913
PotEng = -417285.0114 E_bond = 9579.0680 E_angle = 47373.8383
E_dihed = 39847.6180 E_impro = 967.6100 E_vdwl = -23634.8218
E_coul = 1646565.2623 E_long = -2137983.5863 Press = -1185.9778
Volume = 2554683.5150
Loop time of 72.2618 on 1 procs for 200 steps with 256000 atoms
Pair time (%) = 10.1078 (13.9878)
Bond time (%) = 29.9182 (41.4025)
Kspce time (%) = 7.29844 (10.1)
Neigh time (%) = 1.64225 (2.27264)
Comm time (%) = 0.614946 (0.850997)
Outpt time (%) = 0.00137877 (0.00190803)
Other time (%) = 22.6787 (31.3841)
FFT time (% of Kspce) = 5.23688 (71.7535)
FFT Gflps 3d (1d only) = 1.70695 3.00498
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 161678 ave 161678 max 161678 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