LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 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 Time spent = 0.00047946 secs 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 ${dof} compute_modify rot extra/dof 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 ${dof} compute_modify 1_temp extra/dof 357 # equilibrate to shrink box around dilute system run 2000 Neighbor list info ... 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 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair resquared, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 4.738 | 4.738 | 4.738 Mbytes Step c_rot E_pair TotEng Press Volume 0 2.2718861 0 2.394 0.04788 20000 100 1.7443419 0 1.8381003 0.035765442 20557.278 200 2.2768798 0 2.3992621 0.046544845 20618.928 300 1.8573086 0 1.9571389 0.04239709 18464.842 400 2.1706741 -2.5275641e-05 2.2873225 0.066771565 13701.864 500 2.012561 0.0079467721 2.063898 0.10816504 8501.4958 600 2.1428003 0.083982458 2.2020759 0.3340759 4786.6892 700 2.0449292 0.17309565 2.1718849 0.78086274 2774.9262 800 1.9528849 0.31804014 2.2520272 1.8059473 1826.0933 900 1.6296095 0.24347613 1.8589813 1.7120274 1518.1139 1000 1.9349826 0.13913538 2.1125467 1.3044646 1519.7133 1100 2.1040629 0.11218748 2.2384236 1.0097965 1751.5229 1200 1.7801858 0.051922127 1.8564589 0.54836207 2198.0187 1300 2.3147158 0.049339841 2.390002 0.48871848 2754.4057 1400 1.754921 0.025804182 1.785499 0.28804529 3305.8359 1500 2.3701432 0.070771258 2.4523449 0.42290556 3531.1976 1600 1.7628065 0.054682596 1.830609 0.36138713 3319.2576 1700 2.2969598 0.130209 2.454872 0.73541699 2721.9102 1800 1.8253139 0.23039663 2.0810243 1.2065009 2155.7953 1900 2.017999 0.16257657 2.1664889 1.1654021 1815.9914 2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751 Loop time of 0.513811 on 4 procs for 2000 steps with 400 atoms Performance: 672620.799 tau/day, 3892.481 timesteps/s 97.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3553 | 0.36778 | 0.37737 | 1.4 | 71.58 Neigh | 0.0039301 | 0.0040173 | 0.004127 | 0.1 | 0.78 Comm | 0.056627 | 0.065564 | 0.076112 | 3.0 | 12.76 Output | 0.00041318 | 0.00061768 | 0.0012202 | 0.0 | 0.12 Modify | 0.070257 | 0.072503 | 0.074547 | 0.6 | 14.11 Other | | 0.003331 | | | 0.65 Nlocal: 100 ave 108 max 96 min Histogram: 1 2 0 0 0 0 0 0 0 1 Nghost: 123.5 ave 125 max 122 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 471 ave 518 max 433 min Histogram: 1 0 1 0 0 1 0 0 0 1 Total # of neighbors = 1884 Ave neighs/atom = 4.71 Neighbor list builds = 177 Dangerous builds = 144 # run dynamics on dense system unfix 1 fix 1 all nve/asphere run 2000 Per MPI rank memory allocation (min/avg/max) = 4.739 | 4.739 | 4.739 Mbytes Step c_rot E_pair TotEng Press Volume 2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751 2100 2.0234333 0.11888043 2.165674 1.056689 1669.0751 2200 1.9652317 0.18018588 2.1288332 1.3191509 1669.0751 2300 1.9982484 0.1453846 2.1438911 1.2670661 1669.0751 2400 1.9752559 0.16967804 2.1177286 1.303768 1669.0751 2500 1.978203 0.16642165 2.1631435 1.2908362 1669.0751 2600 1.9587508 0.18695271 2.1506896 1.3513902 1669.0751 2700 1.9654455 0.17997218 2.1247901 1.3360492 1669.0751 2800 1.9870267 0.15716584 2.1207709 1.2045104 1669.0751 2900 1.9230662 0.22448703 2.1353571 1.4964289 1669.0751 3000 2.0042113 0.13903204 2.1149787 1.210065 1669.0751 3100 1.9543694 0.19149467 2.0984705 1.3409714 1669.0751 3200 1.9991114 0.14441984 2.1292354 1.1756471 1669.0751 3300 1.9629781 0.18246618 2.1463676 1.3162687 1669.0751 3400 1.940353 0.20630269 2.1687038 1.4952819 1669.0751 3500 1.9887413 0.15531296 2.1485274 1.2530446 1669.0751 3600 1.9732704 0.17171758 2.1755757 1.295861 1669.0751 3700 2.0072863 0.13576402 2.1212392 1.1421254 1669.0751 3800 1.9581337 0.18761851 2.1743384 1.3710796 1669.0751 3900 1.9761519 0.16864273 2.142963 1.3037308 1669.0751 4000 1.9615865 0.18390288 2.1244667 1.4179575 1669.0751 Loop time of 0.846017 on 4 procs for 2000 steps with 400 atoms Performance: 408502.313 tau/day, 2364.018 timesteps/s 97.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63647 | 0.67097 | 0.74711 | 5.4 | 79.31 Neigh | 0.0015061 | 0.0015807 | 0.0017054 | 0.2 | 0.19 Comm | 0.058258 | 0.1341 | 0.16808 | 12.1 | 15.85 Output | 0.00045156 | 0.00077933 | 0.0016997 | 0.0 | 0.09 Modify | 0.028721 | 0.029793 | 0.03152 | 0.6 | 3.52 Other | | 0.0088 | | | 1.04 Nlocal: 100 ave 106 max 97 min Histogram: 1 1 1 0 0 0 0 0 0 1 Nghost: 114 ave 117 max 111 min Histogram: 1 0 0 1 0 0 1 0 0 1 Neighs: 468 ave 528 max 431 min Histogram: 2 0 0 0 1 0 0 0 0 1 Total # of neighbors = 1872 Ave neighs/atom = 4.68 Neighbor list builds = 50 Dangerous builds = 0 Total wall time: 0:00:01