forked from lijiext/lammps
119 lines
3.7 KiB
Groff
119 lines
3.7 KiB
Groff
LAMMPS (27 Mar 2011)
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# Rhodopsin model
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variable x index 1
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variable y index 1
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variable z index 1
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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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atom_modify map hash
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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 8.0 10.0
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pair_modify mix arithmetic
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kspace_style pppm 1e-4
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read_data data.rhodo
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4 = max bonds/atom
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8 = max angles/atom
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18 = max dihedrals/atom
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2 = max impropers/atom
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orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
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1 by 2 by 2 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 1
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orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
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2 by 2 by 1 processor grid
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128000 atoms
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110892 bonds
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161868 angles
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227316 dihedrals
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4136 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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6468 = # of size 2 clusters
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14532 = # of size 3 clusters
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2988 = # of size 4 clusters
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16932 = # 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 50
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thermo_style multi
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timestep 2.0
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run 100
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PPPM initialization ...
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G vector = 0.248586
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grid = 48 60 36
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stencil order = 5
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RMS precision = 7.66425e-05
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brick FFT buffer size/proc = 41615 25920 12915
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Memory usage per processor = 146.135 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -101425.4825 KinEng = 85779.3251 Temp = 299.0304
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PotEng = -187204.8077 E_bond = 10151.9760 E_angle = 43685.4968
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E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537
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E_coul = 827025.3556 E_long = -1080537.3748 Press = -142.3084
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Volume = 1231980.1340
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---------------- Step 50 ----- CPU = 32.8194 (sec) ----------------
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TotEng = -101320.2611 KinEng = 86003.4849 Temp = 299.8118
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PotEng = -187323.7460 E_bond = 9887.1072 E_angle = 43346.7920
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E_dihed = 20958.7034 E_impro = 908.4715 E_vdwl = -7973.4456
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E_coul = 826113.1533 E_long = -1080564.5278 Press = 238.0165
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Volume = 1232126.1854
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---------------- Step 100 ----- CPU = 66.9547 (sec) ----------------
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TotEng = -101158.1519 KinEng = 86355.6231 Temp = 301.0394
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PotEng = -187513.7749 E_bond = 10272.0700 E_angle = 43128.6453
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E_dihed = 20793.9768 E_impro = 867.0826 E_vdwl = -7586.7196
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E_coul = 825555.5006 E_long = -1080544.3306 Press = 15.2192
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Volume = 1232535.8453
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Loop time of 66.9548 on 4 procs for 100 steps with 128000 atoms
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Pair time (%) = 45.779 (68.373)
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Bond time (%) = 2.87439 (4.29303)
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Kspce time (%) = 7.5089 (11.2149)
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Neigh time (%) = 6.52016 (9.73816)
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Comm time (%) = 0.765243 (1.14293)
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Outpt time (%) = 0.000411808 (0.000615055)
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Other time (%) = 3.50669 (5.2374)
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FFT time (% of Kspce) = 1.17001 (15.5816)
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FFT Gflps 3d (1d only) = 2.04683 6.15771
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 47957 ave 47957 max 47957 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 48112468
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Ave neighs/atom = 375.879
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Ave special neighs/atom = 7.43187
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Neighbor list builds = 11
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Dangerous builds = 0
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