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/old #multi neigh_modify delay 0 #multi/custom 2 1*4 5 comm_modify mode multi/old #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) = 4.404 | 4.406 | 4.410 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 -0.090814168 1.8042332 0.075557943 77825.289 4000 1.9567884 -0.072243657 1.8838981 0.072836007 90931.521 5000 2.0386455 -0.084279096 1.9536927 0.06867562 90054.581 6000 2.0816461 -0.093158646 1.9877995 0.082802397 78084.994 7000 2.0854943 -0.10553618 1.979269 0.10230351 63886.068 8000 2.0923948 -0.14072173 1.9509816 0.11775174 52590.899 9000 2.0687841 -0.15957251 1.9085279 0.14963059 44575.69 10000 2.0607467 -0.18970216 1.8703636 0.17210861 39016.271 11000 2.0538523 -0.20866031 1.8445133 0.18554787 34992.223 12000 2.0408745 -0.22276635 1.8174337 0.21228473 31794.869 13000 2.0366678 -0.24217764 1.7938171 0.22999314 29186.441 14000 2.0470314 -0.26923854 1.7771164 0.2576977 26941.432 15000 2.0262458 -0.27296827 1.7526079 0.25960813 25184.491 16000 2.0410096 -0.30940081 1.7309343 0.27842776 23619.633 17000 2.027379 -0.32411477 1.7025943 0.32102949 22231.582 18000 2.0338405 -0.34468182 1.6884866 0.3306203 21028.933 19000 2.032206 -0.36558904 1.6659454 0.33926726 19958.945 20000 2.0347643 -0.3915229 1.642569 0.33718716 19054.271 21000 2.0242901 -0.38913219 1.634489 0.38062225 18190.934 22000 2.0207557 -0.41078199 1.6093059 0.40143768 17422.03 23000 2.0069068 -0.42062708 1.5856165 0.40146954 16717.999 24000 2.0300595 -0.4536262 1.5757624 0.49229743 16097.323 25000 2.0347548 -0.47655047 1.5575319 0.46787969 15564.848 26000 2.0180789 -0.46537586 1.5520362 0.48541997 15072.597 27000 2.0150506 -0.4886202 1.5257645 0.53829749 14621.24 28000 2.0175464 -0.50951413 1.5073655 0.50140171 14253.441 29000 2.0186127 -0.53911975 1.4788258 0.52955802 13930.266 30000 2.0006844 -0.52621334 1.4738099 0.60130639 13650.051 31000 2.0179614 -0.54573939 1.4715551 0.58747508 13285.903 32000 2.0333208 -0.57431851 1.4583303 0.62631039 12894.077 33000 2.0017273 -0.57778326 1.4232825 0.61159622 12595.987 34000 2.0063025 -0.58192939 1.4237101 0.66174764 12316.964 35000 2.0174782 -0.60591394 1.4108976 0.63571024 12063.433 36000 2.025112 -0.64319133 1.3812514 0.62829458 11930.246 37000 2.0431268 -0.64342323 1.3990283 0.68038546 11651.664 38000 2.0064271 -0.63716263 1.3686014 0.72167175 11345.421 39000 2.0284014 -0.67236471 1.3553663 0.68693225 11062.293 40000 2.0181711 -0.6962559 1.3212483 0.76033095 10864.176 41000 1.9908152 -0.66607906 1.3240783 0.90250403 10812.599 42000 2.0007084 -0.68853623 1.311511 0.88096905 10627.922 43000 1.998883 -0.69053805 1.3076844 0.81765345 10469.928 44000 2.0197069 -0.72507021 1.2939693 0.87004916 10194.954 45000 2.0112835 -0.72638581 1.284233 0.99236207 9968.2662 46000 2.0195002 -0.75152677 1.2673061 0.92706763 9751.1162 47000 1.983694 -0.75006702 1.2329714 0.8945741 9652.1453 48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543 49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823 50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277 Loop time of 10.7578 on 4 procs for 50000 steps with 3026 atoms Performance: 2007847.166 tau/day, 4647.794 timesteps/s 98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3814 | 2.6878 | 2.9507 | 15.2 | 24.98 Neigh | 2.3959 | 2.6615 | 2.9677 | 16.2 | 24.74 Comm | 2.4113 | 2.9894 | 3.5621 | 29.6 | 27.79 Output | 0.00077024 | 0.00091029 | 0.0012971 | 0.0 | 0.01 Modify | 1.7966 | 1.8497 | 1.907 | 3.8 | 17.19 Other | | 0.5686 | | | 5.29 Nlocal: 756.500 ave 838 max 693 min Histogram: 2 0 0 0 0 0 0 1 0 1 Nghost: 1282.50 ave 1333 max 1216 min Histogram: 1 0 0 0 1 0 0 0 1 1 Neighs: 6426.25 ave 7350 max 5786 min Histogram: 2 0 0 0 0 1 0 0 0 1 Total # of neighbors = 25705 Ave neighs/atom = 8.4947125 Neighbor list builds = 4326 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:10