forked from lijiext/lammps
96 lines
3.2 KiB
Groff
96 lines
3.2 KiB
Groff
LAMMPS (12 Feb 2007)
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# Rhodopsin model
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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 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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2 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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fix 1 all shake 0.0001 5 0 m 1.0 a 232
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1617 = # of size 2 clusters
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3633 = # of size 3 clusters
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747 = # of size 4 clusters
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4233 = # of frozen angles
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fix 2 all npt 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0
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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 = 0.245875
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grid = 24 32 30
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RMS precision = 8.76365e-05
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brick FFT buffer size/proc = 7140 3072 3780
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Memory usage per processor = 29.8784 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -25355.8254 KinEng = 21444.8313 Temp = 299.0397
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PotEng = -46800.6567 E_bond = 2537.9940 E_angle = 10921.3742
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E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
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E_coul = 203820.0671 E_long = -267197.5267 Press = -142.0456
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Volume = 307995.0335
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---------------- Step 50 ----- CPU = 9.4108 (sec) ----------------
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TotEng = -25329.9175 KinEng = 21500.9583 Temp = 299.8223
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PotEng = -46830.8758 E_bond = 2471.7583 E_angle = 10836.5458
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E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9669
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E_coul = 203591.3230 E_long = -267204.3691 Press = 238.4815
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Volume = 308031.8243
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---------------- Step 100 ----- CPU = 19.1853 (sec) ----------------
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TotEng = -25291.5484 KinEng = 21589.5399 Temp = 301.0576
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PotEng = -46881.0883 E_bond = 2568.0537 E_angle = 10781.7480
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E_dihed = 5198.3744 E_impro = 216.6829 E_vdwl = -1898.4511
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E_coul = 203451.2661 E_long = -267198.7623 Press = 10.7451
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Volume = 308134.7692
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Loop time of 19.1859 on 8 procs for 100 steps with 32000 atoms
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Pair time (%) = 12.5105 (65.2066)
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Bond time (%) = 0.52636 (2.74347)
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Kspce time (%) = 2.62125 (13.6624)
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Neigh time (%) = 1.56684 (8.16665)
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Comm time (%) = 0.816595 (4.25623)
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Outpt time (%) = 0.00121596 (0.00633781)
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Other time (%) = 1.14317 (5.95836)
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FFT time (% of Kspce) = 0.501384 (19.1277)
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FFT Gflps 3d 1d-only = 0.92319 7.31311
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Nlocal: 4000 ave 4083 max 3940 min
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Histogram: 2 1 0 1 2 0 0 0 1 1
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Nghost: 16028.4 ave 16084 max 15941 min
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Histogram: 1 0 0 2 0 1 0 0 2 2
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Neighs: 1.5035e+06 ave 1.55024e+06 max 1.46322e+06 min
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Histogram: 2 0 1 0 2 1 0 0 0 2
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Total # of neighbors = 12027978
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Ave neighs/atom = 375.874
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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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