LAMMPS (1 Feb 2014) # RESquared ellipsoids in LJ background fluid units lj atom_style ellipsoid dimension 2 lattice sq 0.02 Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 region box block 0 20 0 20 -0.5 0.5 create_box 2 box Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 400 atoms set group all type/fraction 2 0.1 95392 45 settings made for type/fraction set type 1 mass 1.0 355 settings made for mass set type 2 mass 1.5 45 settings made for mass set type 1 shape 1 1 1 355 settings made for shape set type 2 shape 3 1 1 45 settings made for shape set group all quat/random 18238 400 settings made for quat/random compute rot all temp/asphere group spheroid type 1 355 atoms in group spheroid variable dof equal count(spheroid)+2 compute_modify rot extra ${dof} compute_modify rot extra 357 velocity all create 2.4 87287 loop geom pair_style resquared 4.0 pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5 pair_coeff 1 2 3.0 1 1 1 1 0 0 0 pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0 neighbor 0.8 bin thermo_style custom step c_rot epair etotal press vol thermo 100 timestep 0.002 compute q all property/atom quatw quati quatj quatk #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] #dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 #dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 #dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 #dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 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 fix 2 all enforce2d compute_modify 1_temp extra ${dof} compute_modify 1_temp extra 357 # equilibrate to shrink box around dilute system run 2000 Memory usage per processor = 3.39986 Mbytes Step rot E_pair TotEng Press Volume 0 2.2718861 0 2.394 0.04788 20000 100 1.7443002 0 1.8380563 0.03576216 20558.672 200 2.2770454 0 2.3994366 0.046545139 20620.298 300 1.8573283 0 1.9571597 0.04240689 18460.771 400 2.1708604 -2.7650654e-05 2.2875165 0.066837495 13689.498 500 1.997512 0.016920625 2.0564634 0.11517748 8482.9706 600 2.0622304 0.078679437 2.0821362 0.28827312 4776.2481 700 2.1106581 0.19687916 2.326279 0.85203631 2756.4602 800 1.745752 0.29267549 1.978786 1.6290595 1832.812 900 1.7925965 0.24064027 2.0273447 1.7295568 1516.7688 1000 1.8280597 0.16642381 1.9844257 1.4314533 1517.3656 1100 2.157879 0.10561715 2.2607067 0.98795205 1744.9669 1200 1.7966771 0.057760855 1.8309261 0.54369976 2182.8259 1300 2.2982472 0.036382605 2.3348878 0.45715755 2731.1166 1400 1.7666501 0.038109497 1.7892555 0.32977405 3230.78 1500 2.3048922 0.081153096 2.376275 0.45835895 3431.9991 1600 1.8588345 0.067622658 1.9190878 0.39494686 3276.3398 1700 2.1798404 0.1400767 2.3395072 0.71093539 2829.7905 1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547 1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276 2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242 Loop time of 0.435333 on 4 procs for 2000 steps with 400 atoms Pair time (%) = 0.307563 (70.65) Neigh time (%) = 0.00319058 (0.732905) Comm time (%) = 0.0498152 (11.443) Outpt time (%) = 0.00043124 (0.0990598) Other time (%) = 0.0743331 (17.075) Nlocal: 100 ave 109 max 96 min Histogram: 2 0 1 0 0 0 0 0 0 1 Nghost: 116 ave 120 max 109 min Histogram: 1 0 0 0 0 0 1 0 0 2 Neighs: 471.5 ave 499 max 455 min Histogram: 2 0 0 0 1 0 0 0 0 1 Total # of neighbors = 1886 Ave neighs/atom = 4.715 Neighbor list builds = 179 Dangerous builds = 148 # run dynamics on dense system unfix 1 fix 1 all nve/asphere run 2000 Memory usage per processor = 3.4007 Mbytes Step rot E_pair TotEng Press Volume 2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242 2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242 2200 1.9410444 0.1617683 2.122019 1.2634696 1657.9242 2300 1.918524 0.185457 2.1121008 1.3486177 1657.9242 2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242 2500 1.8892245 0.21635014 2.1016576 1.5081781 1657.9242 2600 1.9450941 0.15744769 2.0838764 1.2106283 1657.9242 2700 1.9229729 0.18066636 2.1170012 1.3384025 1657.9242 2800 1.9512215 0.15099706 2.0988077 1.2134331 1657.9242 2900 1.9211263 0.18279161 2.0994515 1.362072 1657.9242 3000 1.9067874 0.19775131 2.0931298 1.415749 1657.9242 3100 1.9114597 0.1929634 2.1126573 1.4113467 1657.9242 3200 1.9427391 0.15998497 2.0865325 1.3075156 1657.9242 3300 1.9111628 0.19317321 2.1216596 1.4309722 1657.9242 3400 1.9538367 0.14833072 2.1210148 1.2276275 1657.9242 3500 1.9244321 0.17929374 2.0825174 1.3186878 1657.9242 3600 1.9511866 0.15107093 2.1197989 1.2271649 1657.9242 3700 1.9369592 0.16602536 2.0970215 1.2813456 1657.9242 3800 1.9418194 0.16092741 2.1231381 1.2354327 1657.9242 3900 1.9450474 0.15760145 2.1394611 1.2392217 1657.9242 4000 1.9350001 0.16820285 2.114271 1.2677094 1657.9242 Loop time of 0.68978 on 4 procs for 2000 steps with 400 atoms Pair time (%) = 0.582906 (84.5062) Neigh time (%) = 0.0012635 (0.183174) Comm time (%) = 0.0669423 (9.70488) Outpt time (%) = 0.000495672 (0.0718595) Other time (%) = 0.0381718 (5.53392) Nlocal: 100 ave 107 max 97 min Histogram: 1 2 0 0 0 0 0 0 0 1 Nghost: 117.5 ave 121 max 115 min Histogram: 1 1 0 0 0 1 0 0 0 1 Neighs: 475.75 ave 511 max 446 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 1903 Ave neighs/atom = 4.7575 Neighbor list builds = 49 Dangerous builds = 0