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/old #multi neigh_modify delay 0 #collection/interval 2 1 20 comm_modify mode multi/old vel yes #reduce/multi # 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/old/newton/tri stencil: half/multi/old/2d/tri bin: standard Per MPI rank memory allocation (min/avg/max) = 10.38 | 10.38 | 10.38 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395623 0.66837658 7200 1000 0.32273428 0 0.32263619 0.17174972 7859.8897 2000 0.12441598 0 0.12437817 0.067078155 8212.9946 3000 0.067389284 0 0.067368801 0.040425551 8336.7112 4000 0.044312733 0 0.044299264 0.028220228 8229.0658 5000 0.032702163 0 0.032692223 0.024302012 7931.1298 6000 0.025856 0 0.025848141 0.021241317 7603.5534 7000 0.021437473 0 0.021430957 0.019285494 7243.5757 8000 0.018129567 0 0.018124057 0.020738727 6877.4816 9000 0.016370159 0 0.016365184 0.020261904 6515.3445 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 11000 0.014156551 0 0.014152248 0.021324815 5815.4665 12000 0.013725406 0 0.013721235 0.021159958 5483.6304 13000 0.013215746 0 0.013211729 0.021685712 5165.4758 14000 0.012398153 0 0.012394384 0.024155434 4862.8657 15000 0.011842796 0 0.011839196 0.028503991 4577.9008 16000 0.011433182 0 0.011429706 0.033564839 4309.8792 17000 0.011166574 0 0.01116318 0.040592677 4058.9964 18000 0.01100067 0 0.010997326 0.04899206 3825.155 19000 0.010224474 0 0.010221366 0.063670337 3607.6577 20000 0.0091360558 0 0.0091332789 0.088230111 3408.5658 21000 0.0077336471 0 0.0077312964 0.11769368 3227.7002 22000 0.0060202357 0 0.0060184059 0.15272492 3064.3986 23000 0.0046705738 0 0.0046691542 0.19450723 2918.0014 24000 0.0040248311 0 0.0040236078 0.24161743 2788.4113 25000 0.0032075267 0 0.0032065518 0.28976925 2674.5604 26000 0.0021358008 0 0.0021351516 0.33635615 2574.9564 27000 0.0016902771 0 0.0016897633 0.37624261 2487.2379 28000 0.0014038216 0 0.0014033949 0.41492061 2409.2461 29000 0.00090262588 0 0.00090235152 0.45392924 2340.0308 30000 0.00049466445 0 0.0004945141 0.49295063 2279.2316 31000 0.00056998139 0 0.00056980814 0.53299532 2226.5683 32000 0.00057327032 0 0.00057309607 0.56856551 2181.7093 33000 0.00044845449 0 0.00044831818 0.59623461 2142.7574 34000 0.00059840346 0 0.00059822157 0.61758978 2107.1254 35000 0.00075311121 0 0.0007528823 0.63756791 2072.7217 36000 0.00053773653 0 0.00053757309 0.66026022 2039.1654 37000 0.00030439696 0 0.00030430444 0.69059127 2007.7901 38000 0.00034435616 0 0.00034425149 0.72166346 1980.7136 39000 0.00039692535 0 0.0003968047 0.7468036 1957.9531 40000 0.0003542502 0 0.00035414252 0.76604173 1937.3834 41000 0.0003094667 0 0.00030937263 0.78323183 1916.7027 42000 0.00027258976 0 0.0002725069 0.80315572 1895.0714 43000 0.00020659987 0 0.00020653707 0.82746098 1873.5408 44000 0.00016023865 0 0.00016018994 0.85418945 1853.8677 45000 0.00016112731 0 0.00016107833 0.87913874 1837.1144 46000 0.00016131366 0 0.00016126463 0.89921653 1822.7355 47000 0.00015754747 0 0.00015749958 0.91653641 1809.0285 48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043 49000 0.00018879338 0 0.000188736 0.95775166 1780.0323 50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442 Loop time of 74.6636 on 1 procs for 50000 steps with 3290 atoms Performance: 289297.713 tau/day, 669.671 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 | 56.696 | 56.696 | 56.696 | 0.0 | 75.93 Neigh | 2.2232 | 2.2232 | 2.2232 | 0.0 | 2.98 Comm | 6.1867 | 6.1867 | 6.1867 | 0.0 | 8.29 Output | 0.0012016 | 0.0012016 | 0.0012016 | 0.0 | 0.00 Modify | 8.432 | 8.432 | 8.432 | 0.0 | 11.29 Other | | 1.125 | | | 1.51 Nlocal: 3290.00 ave 3290 max 3290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6295.00 ave 6295 max 6295 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53729.0 ave 53729 max 53729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53729 Ave neighs/atom = 16.331003 Neighbor list builds = 348 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:01:14