forked from lijiext/lammps
162 lines
6.3 KiB
Groff
162 lines
6.3 KiB
Groff
LAMMPS (10 Jan 2012)
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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 gayberne 1.0 3.0 1.0 4.0
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#pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
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#pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
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#pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
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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.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
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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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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 = 3.70503 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 0.700645 on 4 procs for 2000 steps with 400 atoms
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Pair time (%) = 0.315776 (45.0694)
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Neigh time (%) = 0.00318927 (0.45519)
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Comm time (%) = 0.202914 (28.961)
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Outpt time (%) = 0.0198641 (2.83512)
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Other time (%) = 0.158901 (22.6793)
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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 = 3.70587 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 1.3384026 1657.9242
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2800 1.9512215 0.15099708 2.0988078 1.2134332 1657.9242
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2900 1.9211262 0.18279165 2.0994516 1.3620722 1657.9242
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3000 1.9067873 0.19775135 2.0931298 1.4157491 1657.9242
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3100 1.9114597 0.19296344 2.1126573 1.4113468 1657.9242
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3200 1.942739 0.15998509 2.0865326 1.3075162 1657.9242
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3300 1.9111617 0.19317434 2.1216595 1.4309773 1657.9242
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3400 1.9538374 0.14833002 2.121014 1.2276232 1657.9242
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3500 1.9244329 0.17929295 2.0825158 1.3186873 1657.9242
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3600 1.9511828 0.1510749 2.1197985 1.227186 1657.9242
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3700 1.9369672 0.16601695 2.0970237 1.2813052 1657.9242
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3800 1.9418088 0.16093858 2.1231366 1.2354749 1657.9242
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3900 1.9450382 0.15761114 2.1394772 1.2392412 1657.9242
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4000 1.9350119 0.16819038 2.1142388 1.2676423 1657.9242
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Loop time of 0.718566 on 4 procs for 2000 steps with 400 atoms
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Pair time (%) = 0.588593 (81.9121)
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Neigh time (%) = 0.00123084 (0.171291)
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Comm time (%) = 0.0711493 (9.90156)
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Outpt time (%) = 0.0183669 (2.55604)
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Other time (%) = 0.0392267 (5.45902)
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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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