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lammps/bench/log.1Feb14.rhodo.fixed.linux.1
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LAMMPS (1 Feb 2014)
# 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
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
8 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
2 = 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
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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 50
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector (1/distance) = 0.248835
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.0355478
estimated relative force accuracy = 0.000107051
using double precision FFTs
3d grid and FFT values/proc = 41070 25600
Memory usage per processor = 139.238 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035
Volume = 307995.0335
---------------- Step 50 ----- CPU = 17.8100 (sec) ----------------
TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230
PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975
E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754
E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701
Volume = 308031.5639
---------------- Step 100 ----- CPU = 36.2348 (sec) ----------------
TotEng = -25290.7592 KinEng = 21592.0117 Temp = 301.0920
PotEng = -46882.7709 E_bond = 2567.9807 E_angle = 10781.9408
E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783
E_coul = 206659.2327 E_long = -270404.9733 Press = 6.9960
Volume = 308133.9888
Loop time of 36.2348 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 26.0418 (71.8696)
Bond time (%) = 1.26644 (3.4951)
Kspce time (%) = 3.24933 (8.96742)
Neigh time (%) = 4.47968 (12.3629)
Comm time (%) = 0.0700378 (0.193289)
Outpt time (%) = 0.000230074 (0.000634953)
Other time (%) = 1.12729 (3.11108)
FFT time (% of Kspce) = 0.276809 (8.51896)
FFT Gflps 3d (1d only) = 1.87746 3.23903
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 47958 ave 47958 max 47958 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12028107
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
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