forked from lijiext/lammps
122 lines
3.8 KiB
Groff
122 lines
3.8 KiB
Groff
LAMMPS (10 Jan 2012)
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# Rhodopsin model
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newton off
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package gpu force/neigh 0 1 1
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variable x index 2
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variable y index 2
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variable z index 2
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units real
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neigh_modify delay 5 every 1
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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pair_style lj/charmm/coul/long/gpu 8.0 10.0
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pair_modify mix arithmetic
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kspace_style pppm/gpu 1e-4
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read_data data.rhodo
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4 = max bonds/atom
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18 = max angles/atom
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40 = max dihedrals/atom
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4 = max impropers/atom
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orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
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1 by 2 by 2 MPI processor grid
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32000 atoms
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32000 velocities
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27723 bonds
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40467 angles
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56829 dihedrals
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1034 impropers
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4 = max # of 1-2 neighbors
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12 = max # of 1-3 neighbors
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24 = max # of 1-4 neighbors
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26 = max # of special neighbors
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replicate $x $y $z
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replicate 2 $y $z
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replicate 2 2 $z
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replicate 2 2 2
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orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
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1 by 2 by 2 MPI processor grid
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256000 atoms
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221784 bonds
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323736 angles
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454632 dihedrals
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8272 impropers
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4 = max # of 1-2 neighbors
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12 = max # of 1-3 neighbors
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24 = max # of 1-4 neighbors
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26 = max # of special neighbors
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fix 1 all shake 0.0001 5 0 m 1.0 a 232
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12936 = # of size 2 clusters
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29064 = # of size 3 clusters
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5976 = # of size 4 clusters
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33864 = # of frozen angles
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fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
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special_bonds charmm
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thermo 100
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thermo_style multi
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timestep 2.0
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run 200
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PPPM initialization ...
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G vector = 0.245952
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grid = 48 64 60
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stencil order = 5
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RMS precision = 8.7421e-05
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using double precision FFTs
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brick FFT buffer size/proc = 68635 46080 17649
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Memory usage per processor = 249.821 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = 157025.0390 KinEng = 172792.6155 Temp = 301.1796
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PotEng = -15767.5765 E_bond = 28164.9917 E_angle = 117224.0742
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E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
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E_coul = 1894235.3896 E_long = -2130427.5409 Press = 9562.2425
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Volume = 2457390.7959
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---------------- Step 100 ----- CPU = 12.2605 (sec) ----------------
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TotEng = -233301.4713 KinEng = 123222.6058 Temp = 214.7785
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PotEng = -356524.0771 E_bond = 13098.4614 E_angle = 56766.9463
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E_dihed = 45556.8096 E_impro = 1313.9414 E_vdwl = -40863.8548
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E_coul = 1705023.3285 E_long = -2137419.7095 Press = -1634.3527
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Volume = 2522232.7976
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---------------- Step 200 ----- CPU = 23.7724 (sec) ----------------
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TotEng = -308340.7251 KinEng = 108941.9220 Temp = 189.8871
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PotEng = -417282.6471 E_bond = 9579.0415 E_angle = 47373.9551
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E_dihed = 39847.5174 E_impro = 967.5823 E_vdwl = -23636.2292
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E_coul = 1646568.9776 E_long = -2137983.4917 Press = -1186.1181
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Volume = 2554683.4248
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Loop time of 23.7725 on 4 procs for 200 steps with 256000 atoms
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Pair time (%) = 4.55113 (19.1446)
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Bond time (%) = 7.43137 (31.2604)
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Kspce time (%) = 3.8699 (16.2789)
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Neigh time (%) = 0.51208 (2.15409)
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Comm time (%) = 0.544156 (2.28902)
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Outpt time (%) = 0.000452995 (0.00190555)
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Other time (%) = 6.86337 (28.8711)
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FFT time (% of Kspce) = 1.94085 (50.1524)
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FFT Gflps 3d (1d only) = 4.60577 11.8123
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Nlocal: 64000 ave 64003 max 63997 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Nghost: 70640.8 ave 70645 max 70636 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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Ave special neighs/atom = 7.43187
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Neighbor list builds = 31
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Dangerous builds = 12
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