lammps/bench/log.5Oct07.rhodo.fixed.linux.4

97 lines
3.3 KiB
Groff

LAMMPS (5 Oct 2007)
# Rhodopsin model
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 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
4 = max bonds/atom
8 = max angles/atom
18 = max dihedrals/atom
2 = max impropers/atom
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
1 by 2 by 2 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
fix 1 all shake 0.0001 5 0 m 1.0 a 232
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
fix 2 all npt 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0
special_bonds charmm
thermo 50
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector = 0.245875
grid = 24 32 30
RMS precision = 8.76365e-05
brick FFT buffer size/proc = 12180 6144 5481
Memory usage per processor = 50.2175 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25355.8260 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46800.6573 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 203820.0665 E_long = -267197.5267 Press = -142.0485
Volume = 307995.0335
---------------- Step 50 ----- CPU = 9.6422 (sec) ----------------
TotEng = -25329.9165 KinEng = 21500.9586 Temp = 299.8223
PotEng = -46830.8752 E_bond = 2471.7583 E_angle = 10836.5458
E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9667
E_coul = 203591.3235 E_long = -267204.3691 Press = 238.4820
Volume = 308031.8242
---------------- Step 100 ----- CPU = 19.4814 (sec) ----------------
TotEng = -25291.5443 KinEng = 21589.5406 Temp = 301.0576
PotEng = -46881.0849 E_bond = 2568.0538 E_angle = 10781.7478
E_dihed = 5198.3743 E_impro = 216.6829 E_vdwl = -1898.4506
E_coul = 203451.2690 E_long = -267198.7621 Press = 10.7475
Volume = 308134.7686
Loop time of 19.4821 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 12.9977 (66.7161)
Bond time (%) = 0.64311 (3.30104)
Kspce time (%) = 2.5143 (12.9057)
Neigh time (%) = 1.95058 (10.0122)
Comm time (%) = 0.480013 (2.46387)
Outpt time (%) = 0.0015353 (0.00788057)
Other time (%) = 0.894842 (4.59316)
FFT time (% of Kspce) = 0.315807 (12.5604)
FFT Gflps 3d 1d-only = 1.46568 6.19563
Nlocal: 8000 ave 8143 max 7933 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 22735.5 ave 22770 max 22697 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 3.00699e+06 ave 3.0975e+06 max 2.96494e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 12027976
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0