LAMMPS (10 Jan 2012) # 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) 1 by 1 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 #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.gayberne id type x y z c_q[1] c_q[2] c_q[3] c_q[4] #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] 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 = 3.71598 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 0.95254771 1162.1817 1900 1.8977855 -3.1905908 -1.2727444 0.73157369 1191.4876 2000 2.0794708 -3.253147 -1.2230906 0.4949131 1187.4615 Loop time of 0.744775 on 1 procs for 2000 steps with 400 atoms Pair time (%) = 0.5056 (67.8863) Neigh time (%) = 0.0121155 (1.62673) Comm time (%) = 0.0133355 (1.79054) Outpt time (%) = 0.0179069 (2.40434) Other time (%) = 0.195817 (26.2921) Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 232 ave 232 max 232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2868 ave 2868 max 2868 min Histogram: 1 0 0 0 0 0 0 0 0 0 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 = 3.72613 Mbytes Step rot E_pair TotEng Press Volume 2000 2.0794708 -3.253147 -1.2230906 0.4949131 1187.4615 2100 2.0350673 -3.2084761 -1.1823685 0.33981976 1187.4615 2200 1.9674878 -3.1385619 -1.1467435 1.1720135 1187.4615 2300 2.0160349 -3.191283 -1.1652127 0.98222385 1187.4615 2400 2.1323063 -3.3152815 -1.1669962 0.76099867 1187.4615 2500 2.0866912 -3.269205 -1.176606 0.67971578 1187.4615 2600 2.0982825 -3.2774432 -1.1869918 0.90454676 1187.4615 2700 2.0482779 -3.2229456 -1.1928884 0.69425859 1187.4615 2800 1.9676351 -3.1400429 -1.1685864 0.7577946 1187.4615 2900 2.0421413 -3.2182319 -1.1866955 0.79375204 1187.4615 3000 2.1074018 -3.2869882 -1.2013002 0.18882145 1187.4615 3100 2.0467315 -3.2228162 -1.1821143 0.70508986 1187.4615 3200 2.1165018 -3.2983333 -1.1590455 0.5195734 1187.4615 3300 2.1523232 -3.3384994 -1.1803176 0.45229381 1187.4615 3400 2.0966131 -3.2797219 -1.1608863 0.75030508 1187.4615 3500 2.0623035 -3.2433952 -1.1409405 0.78443505 1187.4615 3600 2.0110509 -3.1874756 -1.1629634 0.54103399 1187.4615 3700 2.0105927 -3.1835726 -1.1894401 0.27445727 1187.4615 3800 1.9528229 -3.1230718 -1.1908005 0.53926039 1187.4615 3900 2.0657038 -3.2420623 -1.1608259 0.56113492 1187.4615 4000 2.0354627 -3.2069944 -1.2073941 0.5668484 1187.4615 Loop time of 0.780395 on 1 procs for 2000 steps with 400 atoms Pair time (%) = 0.622527 (79.7707) Neigh time (%) = 0.00560331 (0.71801) Comm time (%) = 0.0139475 (1.78723) Outpt time (%) = 0.0179484 (2.29991) Other time (%) = 0.120369 (15.4241) Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 222 ave 222 max 222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2914 ave 2914 max 2914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2914 Ave neighs/atom = 7.285 Neighbor list builds = 47 Dangerous builds = 0