forked from lijiext/lammps
144 lines
4.8 KiB
Groff
144 lines
4.8 KiB
Groff
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LAMMPS (6 Oct 2016)
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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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orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
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1 by 2 by 2 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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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 MPI 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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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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G vector (1/distance) = 0.248593
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grid = 48 60 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0359793
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estimated relative force accuracy = 0.00010835
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using double precision FFTs
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3d grid and FFT values/proc = 41615 25920
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6 -> bins = 19 26 13
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Memory usage per processor = 96.9597 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -101425.4887 KinEng = 85779.3251 Temp = 299.0304
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PotEng = -187204.8138 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 = 827053.5824 E_long = -1080565.6077 Press = -149.0358
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Volume = 1231980.1340
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---------------- Step 50 ----- CPU = 18.1689 (sec) ----------------
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TotEng = -101320.0211 KinEng = 86003.4933 Temp = 299.8118
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PotEng = -187323.5144 E_bond = 9887.1189 E_angle = 43346.8448
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E_dihed = 20958.7108 E_impro = 908.4721 E_vdwl = -7973.4486
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E_coul = 826141.5493 E_long = -1080592.7617 Press = 238.0404
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Volume = 1232126.1814
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---------------- Step 100 ----- CPU = 37.2027 (sec) ----------------
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TotEng = -101157.9546 KinEng = 86355.7413 Temp = 301.0398
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PotEng = -187513.6959 E_bond = 10272.0456 E_angle = 43128.7018
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E_dihed = 20794.0107 E_impro = 867.0928 E_vdwl = -7587.2409
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E_coul = 825584.2416 E_long = -1080572.5474 Press = 15.1729
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Volume = 1232535.8440
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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
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99.9% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 25.431 | 25.738 | 25.984 | 4.0 | 69.18
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Bond | 1.2966 | 1.3131 | 1.3226 | 0.9 | 3.53
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Kspace | 3.7563 | 4.0123 | 4.3127 | 10.0 | 10.79
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Neigh | 4.3778 | 4.378 | 4.3782 | 0.0 | 11.77
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Comm | 0.1903 | 0.19549 | 0.20485 | 1.3 | 0.53
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Output | 0.00031805 | 0.00037521 | 0.00039601 | 0.2 | 0.00
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Modify | 1.4861 | 1.5051 | 1.5122 | 0.9 | 4.05
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Other | | 0.05992 | | | 0.16
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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 1.19991e+07 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 48112540
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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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Total wall time: 0:00:38
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