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lammps/bench/log.15Feb16.rhodo.scaled.icc.4
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LAMMPS (15 Feb 2016)
# Rhodopsin model
variable x index 1
variable y index 1
variable z index 1
units real
neigh_modify delay 5 every 1
atom_style full
atom_modify map hash
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 2 by 2 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
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 1
orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
2 by 2 by 1 MPI processor grid
128000 atoms
110892 bonds
161868 angles
227316 dihedrals
4136 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
6468 = # of size 2 clusters
14532 = # of size 3 clusters
2988 = # of size 4 clusters
16932 = # 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) = 0.248593
grid = 48 60 36
stencil order = 5
estimated absolute RMS force accuracy = 0.0359793
estimated relative force accuracy = 0.00010835
using double precision FFTs
3d grid and FFT values/proc = 41615 25920
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 19 26 13
Memory usage per processor = 95.5339 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -101425.4887 KinEng = 85779.3251 Temp = 299.0304
PotEng = -187204.8138 E_bond = 10151.9760 E_angle = 43685.4968
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537
E_coul = 827053.5824 E_long = -1080565.6077 Press = -142.3092
Volume = 1231980.1340
---------------- Step 50 ----- CPU = 18.7806 (sec) ----------------
TotEng = -101320.2677 KinEng = 86003.4837 Temp = 299.8118
PotEng = -187323.7514 E_bond = 9887.1072 E_angle = 43346.7922
E_dihed = 20958.7032 E_impro = 908.4715 E_vdwl = -7973.4457
E_coul = 826141.3831 E_long = -1080592.7629 Press = 238.0161
Volume = 1232126.1855
---------------- Step 100 ----- CPU = 38.3684 (sec) ----------------
TotEng = -101158.1849 KinEng = 86355.6149 Temp = 301.0393
PotEng = -187513.7998 E_bond = 10272.0693 E_angle = 43128.6454
E_dihed = 20793.9759 E_impro = 867.0826 E_vdwl = -7586.7186
E_coul = 825583.7122 E_long = -1080572.5667 Press = 15.2151
Volume = 1232535.8423
Loop time of 38.3684 on 4 procs for 100 steps with 128000 atoms
Performance: 0.450 ns/day, 53.289 hours/ns, 2.606 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 26.205 | 26.538 | 26.911 | 5.0 | 69.17
Bond | 1.298 | 1.3125 | 1.3277 | 1.0 | 3.42
Kspace | 3.7099 | 4.0992 | 4.4422 | 13.3 | 10.68
Neigh | 4.6137 | 4.6144 | 4.615 | 0.0 | 12.03
Comm | 0.21398 | 0.21992 | 0.22886 | 1.2 | 0.57
Output | 0.00030518 | 0.00031543 | 0.00033307 | 0.1 | 0.00
Modify | 1.5066 | 1.5232 | 1.5388 | 1.0 | 3.97
Other | | 0.06051 | | | 0.16
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 47957 ave 47957 max 47957 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 48112472
Ave neighs/atom = 375.879
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:39
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