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) 2 by 2 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) = 4.327 | 4.329 | 4.330 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 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688 3000 1.8956738 -0.090814176 1.8042332 0.075557943 77825.289 4000 1.9570462 -0.072505537 1.8838939 0.072824365 90931.708 5000 2.0376745 -0.083247829 1.9537533 0.068496975 90055.295 6000 2.0744887 -0.085395371 1.9884077 0.0821927 78070.648 7000 2.1002183 -0.11654617 1.9829781 0.10523249 63934.448 8000 2.0818325 -0.13271654 1.948428 0.11909162 52636.484 9000 2.0693987 -0.16404154 1.9046733 0.14702552 44539.609 10000 2.0667772 -0.19779488 1.8682993 0.17245383 38822.542 11000 2.0640582 -0.22114917 1.842227 0.18083079 34788.927 12000 2.0308462 -0.20353105 1.8266441 0.20640739 31706.009 13000 2.0395895 -0.24217765 1.7967378 0.21832952 29152.654 14000 2.030848 -0.2586169 1.77156 0.26577748 27068.89 15000 2.0222966 -0.27554585 1.7460825 0.2777169 25272.786 16000 2.0398867 -0.31547563 1.723737 0.27763622 23666.792 17000 2.03026 -0.32453791 1.7050512 0.28099246 22272.809 18000 2.0345512 -0.35026242 1.6836164 0.36600779 21023.172 19000 2.0242864 -0.35813231 1.6654851 0.33415432 19941.244 20000 2.0132465 -0.36563904 1.6469422 0.403365 18979.884 21000 2.0280384 -0.4075867 1.6197815 0.37205362 18152.487 22000 2.0206494 -0.40600336 1.6139782 0.42704594 17370.812 23000 2.0395761 -0.45083258 1.5880695 0.40276343 16700.427 24000 2.017203 -0.44930293 1.5672335 0.43867313 16161.79 25000 2.0191846 -0.4672218 1.5512955 0.47031215 15622.756 26000 2.0131624 -0.46436088 1.5481363 0.51717944 15141.645 27000 2.0322461 -0.50659994 1.5249745 0.49218933 14627.657 28000 2.0169304 -0.50555565 1.5107082 0.55547935 14186.079 29000 2.024656 -0.52258414 1.5014028 0.59125812 13759.99 30000 2.0153725 -0.53585947 1.478847 0.57235811 13384.355 31000 2.0163261 -0.56383766 1.4518221 0.58232057 13098.196 32000 2.0109673 -0.56784395 1.4424588 0.58282178 12831.934 33000 2.0099169 -0.57625621 1.4329964 0.65139601 12479.442 34000 2.0238152 -0.60189607 1.4212503 0.62659152 12210.628 35000 2.0359989 -0.62654733 1.4087787 0.67574446 11972.725 36000 2.0222689 -0.62880837 1.3927923 0.66602146 11690.049 37000 1.9982569 -0.62746376 1.3701328 0.71326589 11433.825 38000 1.9969836 -0.63975181 1.3565719 0.72799891 11285.497 39000 2.0071087 -0.65781805 1.3486274 0.79121297 11107.469 40000 2.0243046 -0.6881221 1.3355135 0.77519099 10943.846 41000 2.0351657 -0.70309175 1.3314014 0.68815156 10742.515 42000 2.0224788 -0.70975664 1.3120538 0.80484619 10505.657 43000 2.0123135 -0.70818545 1.3034631 0.84204556 10353.024 44000 1.999883 -0.70981202 1.2894101 0.94070546 10212.224 45000 2.0127291 -0.73338075 1.2786832 0.82095205 10109.959 46000 2.0109037 -0.75130029 1.2589389 0.88538358 9953.4822 47000 1.9879175 -0.73152019 1.2557404 0.92089629 9832.892 48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453 49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918 50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268 Loop time of 6.98615 on 4 procs for 50000 steps with 3026 atoms Performance: 3091831.080 tau/day, 7157.016 timesteps/s 99.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2795 | 2.5856 | 2.9414 | 17.4 | 37.01 Neigh | 0.62273 | 0.70156 | 0.76736 | 7.4 | 10.04 Comm | 1.0765 | 1.4945 | 1.8884 | 28.6 | 21.39 Output | 0.00076496 | 0.0008953 | 0.0012832 | 0.0 | 0.01 Modify | 1.718 | 1.7755 | 1.827 | 3.7 | 25.41 Other | | 0.4281 | | | 6.13 Nlocal: 756.500 ave 839 max 673 min Histogram: 1 0 1 0 0 0 0 1 0 1 Nghost: 292.500 ave 307 max 282 min Histogram: 2 0 0 0 0 0 1 0 0 1 Neighs: 6435.25 ave 7367 max 5493 min Histogram: 1 0 0 1 0 0 1 0 0 1 Total # of neighbors = 25741 Ave neighs/atom = 8.5066094 Neighbor list builds = 4335 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:07