LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97) using 1 OpenMP thread(s) per MPI task # Big colloid particles and small LJ particles units lj atom_style sphere dimension 2 lattice sq 0.5 Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136 region box block 0 60 0 60 -0.5 0.5 create_box 2 box Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 3600 atoms create_atoms CPU = 0.001 seconds change_box all triclinic Changing box ... triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000) # remove two spheres of small particles and add large particles in the voids region sphere1 sphere 20.0 20.0 0.0 10.0 units box region sphere2 sphere 60.0 60.0 0.0 10.0 units box delete_atoms region sphere1 Deleted 154 atoms, new total = 3446 delete_atoms region sphere2 Deleted 158 atoms, new total = 3288 create_atoms 2 single 20.0 20.0 0.0 units box Created 1 atoms create_atoms CPU = 0.000 seconds create_atoms 2 single 60.0 60.0 0.0 units box Created 1 atoms create_atoms CPU = 0.000 seconds set type 2 mass 400 Setting atom values ... 2 settings made for mass set type 1 mass 1 Setting atom values ... 3288 settings made for mass set type 2 diameter 20 Setting atom values ... 2 settings made for diameter set type 1 diameter 1 Setting atom values ... 3288 settings made for diameter velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency neighbor 1 multi #multi/old neigh_modify delay 0 collection/interval 2 1 20 comm_modify mode multi vel yes reduce/multi #multi/old # colloid potential pair_style granular pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0 fix 2 all enforce2d fix 3 all deform 1 xy erate 1e-3 #dump 1 all custom 1000 dump.granular id x y z radius #dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 #dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 #dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 thermo_style custom step temp epair etotal press vol thermo 1000 timestep 0.005 run 50000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 21 ghost atom cutoff = 21 binsize = 1, bins = 85 85 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair granular, perpetual attributes: half, newton on, size, history pair build: half/size/multi/newton/tri stencil: half/multi/2d/tri bin: multi Per MPI rank memory allocation (min/avg/max) = 10.29 | 10.29 | 10.29 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395623 0.66837658 7200 1000 0.32604952 0 0.32595042 0.17341597 7862.5013 2000 0.12631038 0 0.12627198 0.069126477 8216.6956 3000 0.069351715 0 0.069330635 0.040799593 8344.1931 4000 0.045023755 0 0.04501007 0.029184795 8239.1832 5000 0.032735149 0 0.0327252 0.025640841 7943.5691 6000 0.026205227 0 0.026197262 0.021206924 7617.6672 7000 0.02165475 0 0.021648168 0.018789365 7255.2897 8000 0.018299317 0 0.018293755 0.019272158 6887.3386 9000 0.016283763 0 0.016278813 0.020434892 6524.0274 10000 0.015148918 0 0.015144313 0.021650465 6168.4941 11000 0.014180465 0 0.014176155 0.022320009 5823.98 12000 0.013505744 0 0.013501639 0.023978674 5492.4853 13000 0.013009585 0 0.01300563 0.024391329 5175.7455 14000 0.012494373 0 0.012490576 0.027331543 4874.3212 15000 0.012057669 0 0.012054004 0.030561239 4589.518 16000 0.011510988 0 0.01150749 0.034613772 4321.1694 17000 0.011198594 0 0.01119519 0.042263536 4070.0115 18000 0.010978603 0 0.010975266 0.053637275 3836.0304 19000 0.010768789 0 0.010765516 0.069472547 3619.75 20000 0.0102256 0 0.010222492 0.085332898 3420.2738 21000 0.0089630315 0 0.0089603072 0.11199196 3236.9821 22000 0.006565581 0 0.0065635854 0.14807426 3071.3012 23000 0.0050916998 0 0.0050901522 0.1903446 2923.4162 24000 0.0040345997 0 0.0040333734 0.237983 2792.2658 25000 0.0032995328 0 0.0032985299 0.29120001 2677.7475 26000 0.0024157863 0 0.002415052 0.33851944 2578.4972 27000 0.0020664445 0 0.0020658164 0.37561848 2491.0264 28000 0.0017843883 0 0.0017838459 0.41119961 2412.3871 29000 0.0011813262 0 0.0011809672 0.44749341 2341.7208 30000 0.00063084711 0 0.00063065536 0.4879202 2279.0452 31000 0.00056027405 0 0.00056010376 0.52932126 2224.9456 32000 0.00053304715 0 0.00053288513 0.56822504 2179.1224 33000 0.00052245707 0 0.00052229826 0.60025509 2140.5345 34000 0.00073726189 0 0.0007370378 0.62001489 2106.3045 35000 0.00075804791 0 0.0007578175 0.6359631 2072.525 36000 0.00052579203 0 0.00052563222 0.65678516 2038.1907 37000 0.00036977909 0 0.0003696667 0.68784389 2005.5831 38000 0.00036252798 0 0.00036241779 0.72116044 1977.7441 39000 0.00036254566 0 0.00036243547 0.74720837 1954.9127 40000 0.00036237175 0 0.00036226161 0.76605408 1934.6006 41000 0.00032453104 0 0.00032443239 0.78424188 1914.1939 42000 0.00025394755 0 0.00025387036 0.80529272 1893.064 43000 0.00021067821 0 0.00021061418 0.82962095 1872.365 44000 0.00017927684 0 0.00017922235 0.85522899 1853.531 45000 0.0001464225 0 0.000146378 0.87925998 1837.2423 46000 0.00012922979 0 0.00012919051 0.8986549 1822.9227 47000 0.0001643557 0 0.00016430575 0.91743602 1809.0605 48000 0.00020154753 0 0.00020148627 0.93686779 1794.9227 49000 0.00017742528 0 0.00017737135 0.94988773 1780.3811 50000 0.00015150521 0 0.00015145916 0.97929588 1764.7507 Loop time of 54.9135 on 1 procs for 50000 steps with 3290 atoms Performance: 393345.914 tau/day, 910.523 timesteps/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 44.691 | 44.691 | 44.691 | 0.0 | 81.38 Neigh | 0.21653 | 0.21653 | 0.21653 | 0.0 | 0.39 Comm | 0.75388 | 0.75388 | 0.75388 | 0.0 | 1.37 Output | 0.0011999 | 0.0011999 | 0.0011999 | 0.0 | 0.00 Modify | 8.4718 | 8.4718 | 8.4718 | 0.0 | 15.43 Other | | 0.7794 | | | 1.42 Nlocal: 3290.00 ave 3290 max 3290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 525.000 ave 525 max 525 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26732.0 ave 26732 max 26732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26732 Ave neighs/atom = 8.1252280 Neighbor list builds = 342 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:54