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 0.1 Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777 region box block 0 60 0 60 -0.5 0.5 create_box 5 box Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 3600 atoms create_atoms CPU = 0.001 seconds #Roughly equally partition atoms between types 1-4 set group all type/fraction 2 0.500 23984 Setting atom values ... 1768 settings made for type/fraction set group all type/fraction 3 0.333 43684 Setting atom values ... 1255 settings made for type/fraction set group all type/fraction 4 0.250 87811 Setting atom values ... 927 settings made for type/fraction # remove two spheres of small particles and add large particles in the voids region sphere1 sphere 60.0 60.0 0.0 30.0 units box region sphere2 sphere 130.0 130.0 0.0 30.0 units box delete_atoms region sphere1 Deleted 289 atoms, new total = 3311 delete_atoms region sphere2 Deleted 287 atoms, new total = 3024 create_atoms 5 single 60.0 60.0 0.0 units box Created 1 atoms create_atoms CPU = 0.000 seconds create_atoms 5 single 130.0 130.0 0.0 units box Created 1 atoms create_atoms CPU = 0.000 seconds set type 1 mass 400 Setting atom values ... 753 settings made for mass set type 2 mass 1 Setting atom values ... 722 settings made for mass velocity all create 1.44 87287 loop geom # multi neighbor and comm for efficiency neighbor 1 multi #multi/old neigh_modify delay 0 collection/type 2 1*4 5 comm_modify mode multi reduce/multi #multi/old # colloid potential pair_style colloid 20.0 pair_coeff * * 144.0 1.0 0.0 0.0 3.0 pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0 pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0 pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0 pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0 pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0 fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 fix 2 all enforce2d #dump 1 all atom 1000 dump.colloid #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 = 31 ghost atom cutoff = 31 binsize = 2, bins = 95 95 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair colloid, perpetual attributes: half, newton on pair build: half/multi/newton stencil: half/multi/2d bin: multi Per MPI rank memory allocation (min/avg/max) = 4.385 | 4.385 | 4.385 Mbytes Step Temp E_pair TotEng Press Volume 0 1.44 0 1.4395241 0.121 36000 1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399 2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69 3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12 4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299 5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92 6000 2.0797015 -0.086800285 1.992214 0.082095164 78182.702 7000 2.0867886 -0.10960963 1.9764893 0.10103655 63990.386 8000 2.0803886 -0.12736298 1.9523381 0.12561727 52648.372 9000 2.0605661 -0.14572043 1.9141648 0.15154081 44589.764 10000 2.0636909 -0.18556771 1.8774412 0.1604707 38996.941 11000 2.0498344 -0.20303461 1.8461224 0.18295046 34927.993 12000 2.0466611 -0.2217963 1.8241884 0.23031182 31760.363 13000 2.0441824 -0.24716826 1.7963386 0.22167931 29178.226 14000 2.047513 -0.26988172 1.7769547 0.24070752 26991.372 15000 2.0154283 -0.26144354 1.7533187 0.27587713 25247.715 16000 2.0160849 -0.28106984 1.7343488 0.32297139 23703.607 17000 2.0184729 -0.31071368 1.7070922 0.29815613 22300.6 18000 2.0237288 -0.33944941 1.6836106 0.3262795 21098.856 19000 2.0329827 -0.35438937 1.6779215 0.33691952 19989.867 20000 2.021113 -0.37316841 1.6472766 0.39687648 18978.666 21000 2.0352439 -0.40857976 1.6259915 0.38632613 18146.277 22000 2.0158566 -0.41271329 1.6024771 0.41480502 17409.593 23000 2.0170409 -0.42611776 1.5902566 0.40446612 16748.968 24000 2.0108878 -0.43899286 1.5712304 0.42075035 16086.941 25000 2.0218394 -0.47012156 1.5510497 0.46655183 15460.154 26000 2.0100713 -0.47985916 1.5295479 0.45575323 15013.774 27000 2.0251738 -0.5016665 1.5228381 0.50151992 14591.521 28000 2.0062966 -0.50284394 1.5027897 0.5462034 14135.093 29000 2.0146666 -0.53126035 1.4827405 0.60379062 13725.945 30000 2.0036455 -0.53246643 1.4705169 0.56784088 13417.305 31000 2.0127662 -0.54487777 1.4672233 0.6427741 13139.392 32000 2.0221816 -0.5625554 1.4589579 0.60695012 12779.609 33000 2.024983 -0.59515221 1.4291616 0.60005385 12584.572 34000 2.0184045 -0.59033569 1.4274018 0.62519753 12355.49 35000 2.0155635 -0.61190466 1.4029927 0.71044196 12106.819 36000 2.0252503 -0.61581601 1.408765 0.68805882 11728.608 37000 2.0112487 -0.64540754 1.3651765 0.66981639 11475.772 38000 2.0147475 -0.64161981 1.3724619 0.71130901 11285.511 39000 2.0213092 -0.67174661 1.3488946 0.6969697 11044.647 40000 2.0178739 -0.67924699 1.3379601 0.77309897 10824.198 41000 1.9952353 -0.67490899 1.3196669 0.76592358 10646.649 42000 2.002415 -0.70533555 1.2964178 0.81084741 10519.804 43000 2.0211625 -0.71370366 1.3067909 0.77355048 10434.893 44000 2.0252106 -0.72635544 1.2981859 0.83770143 10132.262 45000 2.0126446 -0.75197714 1.2600024 0.88927993 9946.7842 46000 2.0431159 -0.78445975 1.257981 0.84492327 9869.8151 47000 2.0199724 -0.76967899 1.2496259 0.90977181 9653.4334 48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246 49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093 50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715 Loop time of 19.7532 on 1 procs for 50000 steps with 3026 atoms Performance: 1093493.133 tau/day, 2531.234 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 | 10.789 | 10.789 | 10.789 | 0.0 | 54.62 Neigh | 2.6848 | 2.6848 | 2.6848 | 0.0 | 13.59 Comm | 0.53244 | 0.53244 | 0.53244 | 0.0 | 2.70 Output | 0.0010482 | 0.0010482 | 0.0010482 | 0.0 | 0.01 Modify | 4.9599 | 4.9599 | 4.9599 | 0.0 | 25.11 Other | | 0.7856 | | | 3.98 Nlocal: 3026.00 ave 3026 max 3026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 584.000 ave 584 max 584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25892.0 ave 25892 max 25892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25892 Ave neighs/atom = 8.5565102 Neighbor list builds = 4330 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:19