LAMMPS (7 Dec 2015) # initialisation units lj atom_style hybrid ellipsoid molecular # bring in configuration read_data example.dat orthogonal box = (0.117 0.0165 0) to (30.117 30.0165 30) 1 by 2 by 2 MPI processor grid reading atoms ... 250 atoms scanning bonds ... 4 = max bonds/atom 250 ellipsoids reading bonds ... 500 bonds 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 48 = max # of 1-4 neighbors 4 = max # of special neighbors set type 1 shape 0.9 0.9 0.9 50 settings made for shape set type 2 shape 1.0 1.89 0.88 200 settings made for shape set type 1 mass 1.0 50 settings made for mass set type 2 mass 6.36 200 settings made for mass group core type 1 50 atoms in group core group int type 2 200 atoms in group int # pair styles pair_style gayberne 1 1 5 5.0 pair_coeff 1 2 1 1 0 0 0 0 0 0 1.5 pair_coeff 1 1 0.1 1 1 1 1 1 1 1 1.5 pair_coeff 2 2 10 1 1 0.01 0.01 1 0.01 0.01 # settings neighbor 2.0 bin neigh_modify exclude molecule all compute rottemp all temp/asphere dof all compute angmom all property/atom angmomx angmomy angmomz compute vel all property/atom vx vy vz compute mass all property/atom mass fix rigid all rigid/small molecule langevin 1.0 1.0 1.0 56489 50 rigid bodies with 250 atoms 0.760329 = max distance from body owner to body atom compute rigke all ke/rigid rigid compute rigrot all erotate/rigid rigid variable rigtotke equal (c_rigke+c_rigrot)/count(all) compute ase all erotate/asphere compute ket all ke variable asphke equal (c_ase+c_ket)/count(all) thermo_style custom step c_rottemp ke v_asphke f_rigid v_rigtotke thermo_modify temp rottemp thermo 5000 timestep 0.03 run 200000 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 = 7 ghost atom cutoff = 7 binsize = 3.5 -> bins = 9 9 9 Memory usage per processor = 10.8389 Mbytes Step rottemp KinEng asphke rigid rigtotke 0 0 0 0 0 0 5000 1.2937622 0.76849476 0.76849476 0.87544783 0.5252687 10000 1.4637964 0.86949504 0.86949504 1.0137549 0.60825294 15000 1.7147031 1.0185336 1.0185336 1.119243 0.67154577 20000 1.4223061 0.84484984 0.84484984 0.94318198 0.56590919 25000 1.6799196 0.99787227 0.99787227 1.1528 0.69168002 30000 1.5161027 0.90056498 0.90056498 1.0041741 0.60250447 35000 1.5356179 0.91215703 0.91215703 1.0119621 0.60717729 40000 1.5026772 0.89259027 0.89259027 0.990333 0.5941998 45000 1.6846935 1.0007079 1.0007079 1.1053279 0.66319676 50000 1.4641112 0.86968204 0.86968204 1.0154397 0.60926385 55000 1.6644895 0.98870674 0.98870674 1.1351893 0.68111357 60000 1.802864 1.0709012 1.0709012 1.1539442 0.69236652 65000 1.5391011 0.91422604 0.91422604 1.0310837 0.6186502 70000 1.5296237 0.90859648 0.90859648 1.0444539 0.62667235 75000 1.5482653 0.91966958 0.91966958 1.0476378 0.62858268 80000 1.5556524 0.92405751 0.92405751 1.0970443 0.6582266 85000 1.6701492 0.99206861 0.99206861 1.0854304 0.65125826 90000 1.3655784 0.81115357 0.81115357 0.90603025 0.54361815 95000 1.2778851 0.75906372 0.75906372 0.88844158 0.53306495 100000 1.5924345 0.94590609 0.94590609 1.060828 0.63649678 105000 1.4904101 0.88530359 0.88530359 1.0351581 0.62109488 110000 1.5594761 0.92632882 0.92632882 1.0523325 0.63139951 115000 1.6067532 0.95441142 0.95441142 1.0366233 0.62197395 120000 1.618451 0.96135991 0.96135991 1.0961408 0.65768451 125000 1.401101 0.83225399 0.83225399 0.93999709 0.56399825 130000 1.3023195 0.77357778 0.77357778 0.87432376 0.52459425 135000 1.6412556 0.97490584 0.97490584 1.1443435 0.68660612 140000 1.2991778 0.77171159 0.77171159 0.90422751 0.54253651 145000 1.631247 0.9689607 0.9689607 1.0803248 0.64819487 150000 1.4242435 0.84600062 0.84600062 0.96648073 0.57988844 155000 1.4348726 0.8523143 0.8523143 0.98428401 0.59057041 160000 1.4142475 0.84006304 0.84006304 0.96011661 0.57606997 165000 1.5271841 0.90714733 0.90714733 1.025249 0.61514942 170000 1.4050544 0.83460229 0.83460229 0.92923525 0.55754115 175000 1.4876893 0.88368744 0.88368744 1.035082 0.62104921 180000 1.3689332 0.81314634 0.81314634 0.90010783 0.5400647 185000 1.3447613 0.79878819 0.79878819 0.85747982 0.51448789 190000 1.5092084 0.8964698 0.8964698 1.0241151 0.61446905 195000 1.508221 0.8958833 0.8958833 1.0101253 0.60607517 200000 1.3081934 0.7770669 0.7770669 0.90358252 0.54214951 Loop time of 41.7575 on 4 procs for 200000 steps with 250 atoms Performance: 12414548.877 tau/day, 4789.564 timesteps/s 99.9% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.423 | 17.647 | 24.788 | 155.9 | 42.26 Bond | 0.0066202 | 0.0075659 | 0.0084503 | 1.0 | 0.02 Neigh | 0.12333 | 0.19694 | 0.26565 | 15.0 | 0.47 Comm | 10.38 | 17.657 | 25.009 | 158.9 | 42.28 Output | 0.001174 | 0.0013273 | 0.0016904 | 0.6 | 0.00 Modify | 5.2623 | 5.5489 | 5.8674 | 11.3 | 13.29 Other | | 0.6996 | | | 1.68 Nlocal: 62.5 ave 73 max 57 min Histogram: 1 2 0 0 0 0 0 0 0 1 Nghost: 235 ave 245 max 228 min Histogram: 1 1 0 0 0 1 0 0 0 1 Neighs: 319.75 ave 431 max 198 min Histogram: 1 0 0 1 0 0 0 1 0 1 Total # of neighbors = 1279 Ave neighs/atom = 5.116 Ave special neighs/atom = 4 Neighbor list builds = 4655 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:41