forked from lijiext/lammps
161 lines
6.3 KiB
Groff
161 lines
6.3 KiB
Groff
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LAMMPS (1 Feb 2014)
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# RESquared ellipsoids in LJ background fluid
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units lj
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atom_style ellipsoid
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dimension 2
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lattice sq 0.02
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Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
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region box block 0 20 0 20 -0.5 0.5
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create_box 2 box
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Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
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2 by 2 by 1 MPI processor grid
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create_atoms 1 box
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Created 400 atoms
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set group all type/fraction 2 0.1 95392
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45 settings made for type/fraction
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set type 1 mass 1.0
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355 settings made for mass
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set type 2 mass 1.5
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45 settings made for mass
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set type 1 shape 1 1 1
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355 settings made for shape
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set type 2 shape 3 1 1
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45 settings made for shape
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set group all quat/random 18238
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400 settings made for quat/random
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compute rot all temp/asphere
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group spheroid type 1
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355 atoms in group spheroid
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variable dof equal count(spheroid)+2
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compute_modify rot extra ${dof}
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compute_modify rot extra 357
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velocity all create 2.4 87287 loop geom
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pair_style resquared 4.0
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pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
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pair_coeff 1 2 3.0 1 1 1 1 0 0 0
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pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
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neighbor 0.8 bin
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thermo_style custom step c_rot epair etotal press vol
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thermo 100
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timestep 0.002
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compute q all property/atom quatw quati quatj quatk
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#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
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#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
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#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
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#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
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#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
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fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
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fix 2 all enforce2d
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compute_modify 1_temp extra ${dof}
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compute_modify 1_temp extra 357
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# equilibrate to shrink box around dilute system
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run 2000
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Memory usage per processor = 3.39986 Mbytes
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Step rot E_pair TotEng Press Volume
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0 2.2718861 0 2.394 0.04788 20000
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100 1.7443002 0 1.8380563 0.03576216 20558.672
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200 2.2770454 0 2.3994366 0.046545139 20620.298
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300 1.8573283 0 1.9571597 0.04240689 18460.771
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400 2.1708604 -2.7650654e-05 2.2875165 0.066837495 13689.498
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500 1.997512 0.016920625 2.0564634 0.11517748 8482.9706
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600 2.0622304 0.078679437 2.0821362 0.28827312 4776.2481
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700 2.1106581 0.19687916 2.326279 0.85203631 2756.4602
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800 1.745752 0.29267549 1.978786 1.6290595 1832.812
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900 1.7925965 0.24064027 2.0273447 1.7295568 1516.7688
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1000 1.8280597 0.16642381 1.9844257 1.4314533 1517.3656
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1100 2.157879 0.10561715 2.2607067 0.98795205 1744.9669
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1200 1.7966771 0.057760855 1.8309261 0.54369976 2182.8259
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1300 2.2982472 0.036382605 2.3348878 0.45715755 2731.1166
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1400 1.7666501 0.038109497 1.7892555 0.32977405 3230.78
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1500 2.3048922 0.081153096 2.376275 0.45835895 3431.9991
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1600 1.8588345 0.067622658 1.9190878 0.39494686 3276.3398
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1700 2.1798404 0.1400767 2.3395072 0.71093539 2829.7905
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1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547
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1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276
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2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
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Loop time of 0.435333 on 4 procs for 2000 steps with 400 atoms
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Pair time (%) = 0.307563 (70.65)
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Neigh time (%) = 0.00319058 (0.732905)
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Comm time (%) = 0.0498152 (11.443)
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Outpt time (%) = 0.00043124 (0.0990598)
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Other time (%) = 0.0743331 (17.075)
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Nlocal: 100 ave 109 max 96 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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Nghost: 116 ave 120 max 109 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Neighs: 471.5 ave 499 max 455 min
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Histogram: 2 0 0 0 1 0 0 0 0 1
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Total # of neighbors = 1886
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Ave neighs/atom = 4.715
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Neighbor list builds = 179
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Dangerous builds = 148
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# run dynamics on dense system
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unfix 1
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fix 1 all nve/asphere
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run 2000
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Memory usage per processor = 3.4007 Mbytes
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Step rot E_pair TotEng Press Volume
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2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
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2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242
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2200 1.9410444 0.1617683 2.122019 1.2634696 1657.9242
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2300 1.918524 0.185457 2.1121008 1.3486177 1657.9242
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2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242
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2500 1.8892245 0.21635014 2.1016576 1.5081781 1657.9242
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2600 1.9450941 0.15744769 2.0838764 1.2106283 1657.9242
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2700 1.9229729 0.18066636 2.1170012 1.3384025 1657.9242
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2800 1.9512215 0.15099706 2.0988077 1.2134331 1657.9242
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2900 1.9211263 0.18279161 2.0994515 1.362072 1657.9242
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3000 1.9067874 0.19775131 2.0931298 1.415749 1657.9242
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3100 1.9114597 0.1929634 2.1126573 1.4113467 1657.9242
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3200 1.9427391 0.15998497 2.0865325 1.3075156 1657.9242
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3300 1.9111628 0.19317321 2.1216596 1.4309722 1657.9242
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3400 1.9538367 0.14833072 2.1210148 1.2276275 1657.9242
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3500 1.9244321 0.17929374 2.0825174 1.3186878 1657.9242
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3600 1.9511866 0.15107093 2.1197989 1.2271649 1657.9242
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3700 1.9369592 0.16602536 2.0970215 1.2813456 1657.9242
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3800 1.9418194 0.16092741 2.1231381 1.2354327 1657.9242
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3900 1.9450474 0.15760145 2.1394611 1.2392217 1657.9242
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4000 1.9350001 0.16820285 2.114271 1.2677094 1657.9242
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Loop time of 0.68978 on 4 procs for 2000 steps with 400 atoms
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Pair time (%) = 0.582906 (84.5062)
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Neigh time (%) = 0.0012635 (0.183174)
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Comm time (%) = 0.0669423 (9.70488)
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Outpt time (%) = 0.000495672 (0.0718595)
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Other time (%) = 0.0381718 (5.53392)
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Nlocal: 100 ave 107 max 97 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Nghost: 117.5 ave 121 max 115 min
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Histogram: 1 1 0 0 0 1 0 0 0 1
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Neighs: 475.75 ave 511 max 446 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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Total # of neighbors = 1903
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Ave neighs/atom = 4.7575
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Neighbor list builds = 49
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Dangerous builds = 0
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