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lammps/examples/accelerate/log.rhodo.1Feb14.gpu.1
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log.rhodo.1Feb14.gpu.1
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LAMMPS (1 Feb 2014)
# 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
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
18 = max angles/atom
scanning dihedrals ...
40 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
27723 bonds
reading angles ...
40467 angles
reading dihedrals ...
56829 dihedrals
reading impropers ...
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 = 157024.0504 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15768.5651 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6323
E_coul = 1894295.6635 E_long = -2130488.8032 Press = 9562.1557
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 36.3779 (sec) ----------------
TotEng = -233301.6813 KinEng = 123222.9259 Temp = 214.7790
PotEng = -356524.6072 E_bond = 13098.4672 E_angle = 56766.9111
E_dihed = 45556.8240 E_impro = 1313.9378 E_vdwl = -40863.9278
E_coul = 1705084.7672 E_long = -2137481.5867 Press = -1634.3912
Volume = 2522232.6302
---------------- Step 200 ----- CPU = 70.7784 (sec) ----------------
TotEng = -308342.0030 KinEng = 108937.4160 Temp = 189.8792
PotEng = -417279.4189 E_bond = 9579.0134 E_angle = 47373.6274
E_dihed = 39847.4817 E_impro = 967.6755 E_vdwl = -23635.2960
E_coul = 1646633.4711 E_long = -2138045.3918 Press = -1185.9327
Volume = 2554683.1533
Loop time of 70.7784 on 1 procs for 200 steps with 256000 atoms
Pair time (%) = 10.0374 (14.1815)
Bond time (%) = 27.2471 (38.4963)
Kspce time (%) = 7.19169 (10.1608)
Neigh time (%) = 5.43951 (7.68527)
Comm time (%) = 0.681534 (0.962912)
Outpt time (%) = 0.00139809 (0.0019753)
Other time (%) = 20.1798 (28.5112)
FFT time (% of Kspce) = 5.17983 (72.0253)
FFT Gflps 3d (1d only) = 1.72575 2.95071
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 161662 ave 161662 max 161662 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
Please see the log.cite file for references relevant to this simulation
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