forked from lijiext/lammps
110 lines
3.6 KiB
Groff
110 lines
3.6 KiB
Groff
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LAMMPS (1 Feb 2014)
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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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orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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32000 atoms
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reading velocities ...
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32000 velocities
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scanning bonds ...
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4 = max bonds/atom
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scanning angles ...
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8 = max angles/atom
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scanning dihedrals ...
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18 = max dihedrals/atom
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scanning impropers ...
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2 = max impropers/atom
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reading bonds ...
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27723 bonds
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reading angles ...
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40467 angles
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reading dihedrals ...
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56829 dihedrals
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reading impropers ...
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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 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 (1/distance) = 0.248835
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grid = 25 32 32
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0355478
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estimated relative force accuracy = 0.000107051
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using double precision FFTs
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3d grid and FFT values/proc = 41070 25600
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Memory usage per processor = 139.238 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
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PotEng = -46801.0377 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 = 207025.8927 E_long = -270403.7333 Press = -142.6035
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Volume = 307995.0335
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---------------- Step 50 ----- CPU = 17.8100 (sec) ----------------
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TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230
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PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975
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E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754
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E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701
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Volume = 308031.5639
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---------------- Step 100 ----- CPU = 36.2348 (sec) ----------------
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TotEng = -25290.7592 KinEng = 21592.0117 Temp = 301.0920
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PotEng = -46882.7709 E_bond = 2567.9807 E_angle = 10781.9408
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E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783
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E_coul = 206659.2327 E_long = -270404.9733 Press = 6.9960
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Volume = 308133.9888
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Loop time of 36.2348 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 26.0418 (71.8696)
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Bond time (%) = 1.26644 (3.4951)
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Kspce time (%) = 3.24933 (8.96742)
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Neigh time (%) = 4.47968 (12.3629)
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Comm time (%) = 0.0700378 (0.193289)
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Outpt time (%) = 0.000230074 (0.000634953)
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Other time (%) = 1.12729 (3.11108)
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FFT time (% of Kspce) = 0.276809 (8.51896)
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FFT Gflps 3d (1d only) = 1.87746 3.23903
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Nlocal: 32000 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 47958 ave 47958 max 47958 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 12028107
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Ave neighs/atom = 375.878
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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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