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 = 0.063 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) = 10.20 | 10.20 | 10.20 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 0.01637016 0 0.016365184 0.020261904 6515.3445 10000 0.01500918 0 0.015004618 0.020551803 6160.4475 11000 0.014156553 0 0.01415225 0.021324818 5815.4665 12000 0.013725412 0 0.01372124 0.021159958 5483.6304 13000 0.013215733 0 0.013211716 0.021685624 5165.4758 14000 0.012398179 0 0.012394411 0.024155572 4862.8657 15000 0.01184269 0 0.01183909 0.028504106 4577.901 16000 0.01143291 0 0.011429435 0.033564204 4309.88 17000 0.011166204 0 0.01116281 0.040588854 4058.9972 18000 0.011000875 0 0.010997532 0.048998904 3825.1569 19000 0.010225905 0 0.010222797 0.063669588 3607.6622 20000 0.0091390255 0 0.0091362477 0.088165402 3408.567 21000 0.0077382041 0 0.0077358521 0.11770474 3227.6936 22000 0.00601731 0 0.0060154811 0.15261994 3064.3873 23000 0.0046667591 0 0.0046653407 0.19453819 2917.9782 24000 0.0040425749 0 0.0040413461 0.24145833 2788.3897 25000 0.0031933217 0 0.0031923511 0.28989713 2674.5164 26000 0.0021138997 0 0.0021132571 0.33598673 2574.9312 27000 0.001700508 0 0.0016999912 0.37665013 2487.1626 28000 0.0014434246 0 0.0014429859 0.41572163 2409.327 29000 0.00089885063 0 0.00089857742 0.453431 2340.2313 30000 0.00048556478 0 0.00048541719 0.49176025 2279.2155 31000 0.00058130972 0 0.00058113303 0.53236818 2226.2349 32000 0.00057749847 0 0.00057732294 0.5691506 2181.2738 33000 0.00044719326 0 0.00044705733 0.59696179 2142.571 34000 0.00060924828 0 0.0006090631 0.61735036 2107.1282 35000 0.00077419805 0 0.00077396273 0.63696098 2072.6008 36000 0.00055752003 0 0.00055735057 0.65981842 2038.8242 37000 0.00031402452 0 0.00031392907 0.69018949 2007.3235 38000 0.00034969879 0 0.0003495925 0.72155053 1980.1706 39000 0.00041434197 0 0.00041421603 0.74680715 1957.3838 40000 0.00037229243 0 0.00037217927 0.76581686 1936.8034 41000 0.00031028842 0 0.00031019411 0.78321059 1916.1108 42000 0.00026623668 0 0.00026615575 0.80267329 1894.4649 43000 0.00020543723 0 0.00020537479 0.82714001 1872.7672 44000 0.0001563321 0 0.00015628458 0.85496396 1853.0284 45000 0.00014981713 0 0.00014977159 0.87924842 1836.4755 46000 0.00015641585 0 0.00015636831 0.89896936 1822.1989 47000 0.00016004701 0 0.00015999837 0.91661933 1808.4606 48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258 49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032 50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534 Loop time of 30.1448 on 4 procs for 50000 steps with 3290 atoms Performance: 716540.413 tau/day, 1658.658 timesteps/s 90.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.7565 | 12.704 | 16.036 | 89.8 | 42.14 Neigh | 0.4494 | 0.56436 | 0.66263 | 11.8 | 1.87 Comm | 9.5962 | 12.989 | 17.006 | 90.8 | 43.09 Output | 0.00088467 | 0.0011022 | 0.0015811 | 0.9 | 0.00 Modify | 2.9732 | 3.0944 | 3.2463 | 7.0 | 10.27 Other | | 0.7918 | | | 2.63 Nlocal: 822.500 ave 859 max 785 min Histogram: 1 0 1 0 0 0 0 0 1 1 Nghost: 3049.75 ave 3089 max 2999 min Histogram: 1 0 0 1 0 0 0 0 0 2 Neighs: 13440.5 ave 14459 max 11964 min Histogram: 1 0 0 0 0 1 0 0 1 1 Total # of neighbors = 53762 Ave neighs/atom = 16.341033 Neighbor list builds = 348 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:30