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) 2 by 2 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) = 10.09 | 10.10 | 10.10 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395623 0.66837658 7200 1000 0.32605303 0 0.32595393 0.17341558 7862.5037 2000 0.12631567 0 0.12627728 0.069188881 8216.7174 3000 0.069373812 0 0.069352726 0.040740832 8344.2982 4000 0.045084633 0 0.045070929 0.029328609 8239.3656 5000 0.032681746 0 0.032671813 0.025416741 7943.7831 6000 0.026301239 0 0.026293245 0.021418793 7617.8426 7000 0.021666723 0 0.021660138 0.018961011 7255.9338 8000 0.018141337 0 0.018135823 0.019306113 6887.4963 9000 0.015922309 0 0.015917469 0.020033398 6524.016 10000 0.014744547 0 0.014740066 0.020959503 6168.1945 11000 0.013872852 0 0.013868636 0.021708943 5823.3153 12000 0.013321594 0 0.013317545 0.02332141 5491.4979 13000 0.01269964 0 0.012695779 0.024796428 5174.6263 14000 0.01227055 0 0.012266821 0.027785072 4873.4516 15000 0.012120508 0 0.012116824 0.029656636 4588.8603 16000 0.011612027 0 0.011608498 0.034695109 4320.4674 17000 0.011216697 0 0.011213288 0.042746966 4069.4275 18000 0.010950166 0 0.010946838 0.053528994 3835.5439 19000 0.010887635 0 0.010884325 0.069684492 3619.562 20000 0.010563449 0 0.010560238 0.08654561 3420.2636 21000 0.0092336323 0 0.0092308257 0.11286068 3237.1408 22000 0.006929086 0 0.0069269799 0.15018917 3072.0438 23000 0.0052239156 0 0.0052223277 0.19067193 2924.441 24000 0.0044210081 0 0.0044196644 0.23908686 2793.2426 25000 0.0034916086 0 0.0034905473 0.29112824 2678.7912 26000 0.002549072 0 0.0025482972 0.33567824 2579.3738 27000 0.0020890726 0 0.0020884377 0.37328514 2491.0502 28000 0.001772982 0 0.0017724431 0.41079958 2411.9111 29000 0.001127719 0 0.0011273762 0.44752241 2341.1888 30000 0.00053266563 0 0.00053250373 0.48791815 2278.5611 31000 0.00050278646 0 0.00050263364 0.52896525 2224.5328 32000 0.00051880956 0 0.00051865187 0.56884574 2178.6674 33000 0.00054908167 0 0.00054891477 0.6016387 2140.3696 34000 0.00075213884 0 0.00075191023 0.62070188 2106.6504 35000 0.00081295162 0 0.00081270452 0.63492031 2073.0077 36000 0.00056699821 0 0.00056682587 0.65608409 2038.3251 37000 0.0003540723 0 0.00035396468 0.68803919 2005.497 38000 0.00031139738 0 0.00031130273 0.72103717 1977.7345 39000 0.00034087822 0 0.00034077461 0.74697975 1954.8979 40000 0.00035452426 0 0.0003544165 0.76682035 1934.5695 41000 0.00030882258 0 0.00030872871 0.78390763 1914.3326 42000 0.00025492799 0 0.00025485051 0.80439795 1893.1474 43000 0.00021545017 0 0.00021538468 0.82803644 1872.073 44000 0.00017293257 0 0.00017288 0.85436769 1852.6548 45000 0.00014097725 0 0.0001409344 0.8796181 1836.0087 46000 0.0001139199 0 0.00011388527 0.90006173 1821.7977 47000 0.00012678598 0 0.00012674745 0.90876359 1808.4913 48000 0.00013796773 0 0.00013792579 0.93661523 1793.8082 49000 0.00014723144 0 0.00014718669 0.95869417 1779.1875 50000 0.00013610653 0 0.00013606516 0.97777198 1765.3247 Loop time of 17.7405 on 4 procs for 50000 steps with 3290 atoms Performance: 1217551.996 tau/day, 2818.407 timesteps/s 100.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.6629 | 9.6168 | 12.444 | 76.6 | 54.21 Neigh | 0.049771 | 0.055182 | 0.06133 | 2.0 | 0.31 Comm | 1.7883 | 4.6306 | 7.6179 | 111.5 | 26.10 Output | 0.00085342 | 0.0010606 | 0.0015425 | 0.9 | 0.01 Modify | 2.7244 | 2.895 | 3.0436 | 8.2 | 16.32 Other | | 0.5419 | | | 3.05 Nlocal: 822.500 ave 897 max 779 min Histogram: 1 1 0 1 0 0 0 0 0 1 Nghost: 190.500 ave 211 max 179 min Histogram: 2 0 0 1 0 0 0 0 0 1 Neighs: 6665.75 ave 7329 max 6104 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 26663 Ave neighs/atom = 8.1042553 Neighbor list builds = 342 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:17