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Steve Plimpton
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LAMMPS (6 Oct 2016)
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# 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 ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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
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Memory usage per processor = 96.9597 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
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E_coul = 827053.5824 E_long = -1080565.6077 Press = -149.0358
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---------------- Step 50 ----- CPU = 18.1689 (sec) ----------------
TotEng = -101320.0211 KinEng = 86003.4933 Temp = 299.8118
PotEng = -187323.5144 E_bond = 9887.1189 E_angle = 43346.8448
E_dihed = 20958.7108 E_impro = 908.4721 E_vdwl = -7973.4486
E_coul = 826141.5493 E_long = -1080592.7617 Press = 238.0404
Volume = 1232126.1814
---------------- Step 100 ----- CPU = 37.2027 (sec) ----------------
TotEng = -101157.9546 KinEng = 86355.7413 Temp = 301.0398
PotEng = -187513.6959 E_bond = 10272.0456 E_angle = 43128.7018
E_dihed = 20794.0107 E_impro = 867.0928 E_vdwl = -7587.2409
E_coul = 825584.2416 E_long = -1080572.5474 Press = 15.1729
Volume = 1232535.8440
Loop time of 37.2028 on 4 procs for 100 steps with 128000 atoms
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Performance: 0.464 ns/day, 51.671 hours/ns, 2.688 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
---------------------------------------------------------------
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Pair | 25.431 | 25.738 | 25.984 | 4.0 | 69.18
Bond | 1.2966 | 1.3131 | 1.3226 | 0.9 | 3.53
Kspace | 3.7563 | 4.0123 | 4.3127 | 10.0 | 10.79
Neigh | 4.3778 | 4.378 | 4.3782 | 0.0 | 11.77
Comm | 0.1903 | 0.19549 | 0.20485 | 1.3 | 0.53
Output | 0.00031805 | 0.00037521 | 0.00039601 | 0.2 | 0.00
Modify | 1.4861 | 1.5051 | 1.5122 | 0.9 | 4.05
Other | | 0.05992 | | | 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
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Neighs: 1.20281e+07 ave 1.20572e+07 max 1.19991e+07 min
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Total # of neighbors = 48112540
Ave neighs/atom = 375.879
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
Steve Plimpton
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Total wall time: 0:00:38