LAMMPS (15 Feb 2016) # 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) 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 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 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.8 ghost atom cutoff = 4.8 binsize = 2.4 -> bins = 59 59 3 Memory usage per processor = 4.17878 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 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499 500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241 600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723 700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757 800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943 900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585 1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058 1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608 1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358 1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014 1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144 1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855 1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472 1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401 1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099 1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587 Loop time of 1.79538 on 1 procs for 2000 steps with 400 atoms Performance: 192494.490 tau/day, 1113.973 timesteps/s 99.8% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.582 | 1.582 | 1.582 | 0.0 | 88.12 Neigh | 0.013545 | 0.013545 | 0.013545 | 0.0 | 0.75 Comm | 0.0087712 | 0.0087712 | 0.0087712 | 0.0 | 0.49 Output | 0.00034428 | 0.00034428 | 0.00034428 | 0.0 | 0.02 Modify | 0.18736 | 0.18736 | 0.18736 | 0.0 | 10.44 Other | | 0.003359 | | | 0.19 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 216 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1929 ave 1929 max 1929 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1929 Ave neighs/atom = 4.8225 Neighbor list builds = 177 Dangerous builds = 146 # run dynamics on dense system unfix 1 fix 1 all nve/asphere run 2000 Memory usage per processor = 4.18079 Mbytes Step rot E_pair TotEng Press Volume 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587 2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587 2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587 2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587 2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587 2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587 2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587 2700 1.9608664 0.18459944 2.1483889 1.3461095 1654.9587 2800 2.005755 0.13729992 2.1214078 1.1596182 1654.9587 2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587 3000 1.9606374 0.18480425 2.1301691 1.3280548 1654.9587 3100 1.9824235 0.16187644 2.1284432 1.2590072 1654.9587 3200 1.9389485 0.20774117 2.106322 1.4587341 1654.9587 3300 1.9849309 0.15929459 2.1301897 1.2415172 1654.9587 3400 1.9596863 0.18578944 2.1215072 1.3738214 1654.9587 3500 1.9671171 0.17804546 2.0934254 1.3147204 1654.9587 3600 1.9702641 0.17471582 2.1569255 1.3331099 1654.9587 3700 1.9103961 0.23792935 2.1305401 1.5832203 1654.9587 3800 1.9129619 0.23512654 2.1445946 1.5657403 1654.9587 3900 1.9868018 0.15725404 2.1658135 1.2582197 1654.9587 4000 2.0058784 0.13726837 2.1534352 1.1351359 1654.9587 Loop time of 3.05676 on 1 procs for 2000 steps with 400 atoms Performance: 113061.044 tau/day, 654.288 timesteps/s 99.8% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9201 | 2.9201 | 2.9201 | 0.0 | 95.53 Neigh | 0.0051684 | 0.0051684 | 0.0051684 | 0.0 | 0.17 Comm | 0.011668 | 0.011668 | 0.011668 | 0.0 | 0.38 Output | 0.00038481 | 0.00038481 | 0.00038481 | 0.0 | 0.01 Modify | 0.1134 | 0.1134 | 0.1134 | 0.0 | 3.71 Other | | 0.00608 | | | 0.20 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 204 ave 204 max 204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1857 ave 1857 max 1857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1857 Ave neighs/atom = 4.6425 Neighbor list builds = 48 Dangerous builds = 0 Total wall time: 0:00:04