LAMMPS (1 Feb 2014) # GayBerne 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 gayberne 1.0 3.0 1.0 4.0 pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5 pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0 pair_coeff 2 2 1.0 1.0 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.gayberne # 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 2.1709963 -0.00050890768 2.2871782 0.066789189 13689.461 500 1.987484 -0.043660052 2.0342913 0.099199049 8475.4405 600 2.088535 -0.24318266 1.8270941 0.22391583 4674.8592 700 2.2604089 -0.73325761 1.481207 0.57184109 2507.095 800 1.8731398 -1.6161576 0.22080738 1.3049285 1420.4278 900 2.1404423 -3.0146759 -0.84039269 3.3566833 922.07169 1000 1.5927835 -4.5754144 -2.9697785 2.5493591 743.19289 1100 1.8380043 -4.8820159 -3.0604394 2.2950846 708.014 1200 2.05516 -4.5701279 -2.4718822 1.466469 753.52878 1300 2.0000364 -4.0755503 -2.031995 0.35675413 842.14053 1400 2.1055032 -3.7342781 -1.6632699 0.58193577 925.51606 1500 1.9241806 -3.582658 -1.639377 0.24973032 1006.7339 1600 2.125676 -3.4733166 -1.3572836 0.72069214 1061.1355 1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646 1800 2.1014782 -3.1254259 -1.0248797 0.9525477 1162.1817 1900 1.8977855 -3.1905908 -1.2727444 0.7315737 1191.4876 2000 2.0794708 -3.2531471 -1.2230906 0.49491309 1187.4615 Loop time of 0.247263 on 4 procs for 2000 steps with 400 atoms Pair time (%) = 0.132236 (53.4797) Neigh time (%) = 0.00340456 (1.3769) Comm time (%) = 0.0404702 (16.3672) Outpt time (%) = 0.000372708 (0.150733) Other time (%) = 0.0707802 (28.6254) Nlocal: 100 ave 113 max 79 min Histogram: 1 0 0 0 0 1 0 0 1 1 Nghost: 139.75 ave 151 max 132 min Histogram: 2 0 0 0 0 1 0 0 0 1 Neighs: 717 ave 880 max 487 min Histogram: 1 0 0 0 0 1 0 1 0 1 Total # of neighbors = 2868 Ave neighs/atom = 7.17 Neighbor list builds = 138 Dangerous builds = 80 # 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 2.0794708 -3.2531471 -1.2230906 0.49491309 1187.4615 2100 2.0350673 -3.2084761 -1.1823685 0.33981993 1187.4615 2200 1.9674878 -3.1385619 -1.1467435 1.1720132 1187.4615 2300 2.0160349 -3.191283 -1.1652127 0.98222388 1187.4615 2400 2.1323062 -3.3152814 -1.1669961 0.76099822 1187.4615 2500 2.0866909 -3.2692048 -1.1766063 0.67971376 1187.4615 2600 2.098286 -3.2774469 -1.1869922 0.90453433 1187.4615 2700 2.0482737 -3.2229412 -1.1928882 0.69426669 1187.4615 2800 1.9676254 -3.1400305 -1.1685788 0.75785389 1187.4615 2900 2.0421207 -3.2182098 -1.1866861 0.79382733 1187.4615 3000 2.1074356 -3.2870234 -1.2012809 0.18867661 1187.4615 3100 2.0466079 -3.2226774 -1.1821925 0.7048821 1187.4615 3200 2.1158976 -3.2976855 -1.1589624 0.5209376 1187.4615 3300 2.1508115 -3.3368934 -1.1793489 0.45871464 1187.4615 3400 2.1046063 -3.2881336 -1.1615171 0.71895972 1187.4615 3500 2.066052 -3.2475413 -1.1359344 0.77760912 1187.4615 3600 2.0042504 -3.1791312 -1.1647191 0.50555439 1187.4615 3700 1.9888544 -3.1596354 -1.1679759 0.4059197 1187.4615 3800 1.9919683 -3.1636959 -1.1860197 0.70259722 1187.4615 3900 2.056542 -3.2325648 -1.1700712 0.43059703 1187.4615 4000 1.9958145 -3.1666798 -1.2556316 0.87469089 1187.4615 Loop time of 0.272762 on 4 procs for 2000 steps with 400 atoms Pair time (%) = 0.159981 (58.6524) Neigh time (%) = 0.00155282 (0.569295) Comm time (%) = 0.0710112 (26.0341) Outpt time (%) = 0.000505924 (0.185482) Other time (%) = 0.0397106 (14.5587) Nlocal: 100 ave 118 max 69 min Histogram: 1 0 0 0 0 0 0 1 1 1 Nghost: 139 ave 156 max 130 min Histogram: 2 0 0 1 0 0 0 0 0 1 Neighs: 729.75 ave 951 max 409 min Histogram: 1 0 0 0 0 1 0 0 1 1 Total # of neighbors = 2919 Ave neighs/atom = 7.2975 Neighbor list builds = 47 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation