LAMMPS (30 Nov 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:95) 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/old neigh_modify delay 0 #multi/custom 2 1*4 5 comm_modify mode multi #multi/reduce # 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/old/newton stencil: half/multi/old/2d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.611 | 5.611 | 5.611 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 -0.086800284 1.992214 0.082095164 78182.702 7000 2.086794 -0.10961479 1.9764895 0.10103993 63990.387 8000 2.082863 -0.12779588 1.9543788 0.12672452 52629.802 9000 2.0718275 -0.15189022 1.9192526 0.14728063 44541.722 10000 2.0603856 -0.18054161 1.8791631 0.16715133 38940.135 11000 2.046791 -0.20458359 1.841531 0.19532742 34907.116 12000 2.0406846 -0.2252868 1.8147234 0.2036178 31740.208 13000 2.0369763 -0.23721632 1.7990869 0.25542564 29079.901 14000 2.0376121 -0.26282517 1.7741135 0.24722118 26947.344 15000 2.0312772 -0.2851101 1.7454959 0.2801199 25180.963 16000 2.0080448 -0.28992973 1.7174515 0.30099318 23723.043 17000 2.0234993 -0.30440169 1.7184289 0.3193226 22342.977 18000 2.0216103 -0.32036933 1.7005729 0.3460322 21068.99 19000 2.0493952 -0.37711533 1.6716026 0.33804972 20013.325 20000 2.0307894 -0.38462795 1.6454903 0.37041981 19092.745 21000 2.0328577 -0.39442652 1.6377594 0.36327057 18260.298 22000 2.0325613 -0.40481002 1.6270796 0.42756691 17447.199 23000 2.0199358 -0.42175719 1.5975111 0.40948041 16768.71 24000 2.0149952 -0.43618764 1.5781417 0.45406069 16187.334 25000 2.0153221 -0.45884172 1.5558143 0.52717203 15605.577 26000 2.0099026 -0.47080566 1.5384327 0.49181459 15088.041 27000 2.0128537 -0.49799999 1.5141885 0.53907465 14590.392 28000 2.0287266 -0.53112525 1.4969309 0.59750714 14208.419 29000 2.0143609 -0.53175704 1.4819381 0.56118773 13840.642 30000 2.0235262 -0.53923416 1.4836234 0.52579997 13500.15 31000 2.0390444 -0.57976823 1.4586023 0.5760349 13082.091 32000 2.018046 -0.57797686 1.4394022 0.59127933 12761.726 33000 2.0059068 -0.57185148 1.4333925 0.58992758 12473.866 34000 1.9828456 -0.57147221 1.4107181 0.77593228 12208.869 35000 1.9900097 -0.58349168 1.4058604 0.681968 11937.285 36000 2.0271405 -0.64374859 1.382722 0.63152587 11675.264 37000 2.0032809 -0.63520712 1.3674117 0.71639384 11440.274 38000 2.0000566 -0.63941617 1.3599795 0.74099652 11235.252 39000 1.9872705 -0.64765522 1.3389586 0.7575743 11080.857 40000 2.0224403 -0.6795645 1.3422075 0.82918546 10861.905 41000 2.0137595 -0.69863075 1.3144633 0.80397759 10712.981 42000 1.9950915 -0.68892531 1.3055069 0.77631365 10632.931 43000 2.0080851 -0.70534369 1.3020778 0.82408436 10408.82 44000 2.0239806 -0.73189482 1.2914169 0.83228695 10227.18 45000 2.0019542 -0.72613202 1.2751606 0.9145618 10044.013 46000 2.0173095 -0.75370218 1.2629407 0.99791312 9837.9611 47000 1.9921201 -0.75875076 1.232711 1.0047839 9711.2083 48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933 49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165 50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069 Loop time of 29.8066 on 1 procs for 50000 steps with 3026 atoms Performance: 724671.093 tau/day, 1677.479 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 | 11.698 | 11.698 | 11.698 | 0.0 | 39.25 Neigh | 10.292 | 10.292 | 10.292 | 0.0 | 34.53 Comm | 1.405 | 1.405 | 1.405 | 0.0 | 4.71 Output | 0.11474 | 0.11474 | 0.11474 | 0.0 | 0.38 Modify | 5.3019 | 5.3019 | 5.3019 | 0.0 | 17.79 Other | | 0.9947 | | | 3.34 Nlocal: 3026.00 ave 3026 max 3026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2292.00 ave 2292 max 2292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25767.0 ave 25767 max 25767 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25767 Ave neighs/atom = 8.5152016 Neighbor list builds = 4332 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:29