LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-665-g17f869bf5e) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task # SRD diffusion demo - poydisperse spheres units lj atom_style sphere atom_modify first big dimension 2 # create big particles with 3 different types and diameters lattice sq 0.3 Lattice spacing in x,y,z = 1.8257419 1.8257419 1.8257419 region box block 0 10 0 10 -0.5 0.5 create_box 4 box Created orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093) 2 by 2 by 1 MPI processor grid create_atoms 1 region box Created 100 atoms using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093) create_atoms CPU = 0.000 seconds group big type 1 100 atoms in group big set group big type/fraction 2 0.33 394895 Setting atom values ... 35 settings made for type/fraction set group big type/fraction 3 0.5 989894 Setting atom values ... 57 settings made for type/fraction group big type 2 3 100 atoms in group big set type 1*3 mass 1.0 Setting atom values ... 100 settings made for mass velocity big create 1.44 87287 loop geom # equilibrate big particles, repulsive only to prevent aggregation pair_style lj/cut 1.12 pair_coeff 1 1 1.0 1.0 1.12 pair_coeff 2 2 1.0 2.0 2.24 pair_coeff 3 3 1.0 1.5 1.68 pair_coeff 4 4 0.0 1.0 0.0 neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 big nve fix 2 all enforce2d #dump 1 all atom 10 dump.poly.equil run 1000 Generated 6 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.54 ghost atom cutoff = 2.54 binsize = 1.27, bins = 15 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -0.16013916 0 1.2654608 1.1298975 1000 1.3367862 -0.30816328 0 1.0152551 1.5440006 Loop time of 0.00891987 on 4 procs for 1000 steps with 100 atoms Performance: 48431181.463 tau/day, 112109.216 timesteps/s, 11.211 Matom-step/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 | 0.00039835 | 0.00043547 | 0.00047558 | 0.0 | 4.88 Neigh | 0.00033856 | 0.00036829 | 0.00038548 | 0.0 | 4.13 Comm | 0.0065535 | 0.0065882 | 0.0066353 | 0.0 | 73.86 Output | 1.0991e-05 | 1.2359e-05 | 1.4677e-05 | 0.0 | 0.14 Modify | 0.00043639 | 0.00045662 | 0.00050811 | 0.0 | 5.12 Other | | 0.001059 | | | 11.87 Nlocal: 25 ave 29 max 23 min Histogram: 2 0 0 1 0 0 0 0 0 1 Nghost: 33.75 ave 35 max 31 min Histogram: 1 0 0 0 0 0 0 1 0 2 Neighs: 38 ave 46 max 34 min Histogram: 1 2 0 0 0 0 0 0 0 1 Total # of neighbors = 152 Ave neighs/atom = 1.52 Neighbor list builds = 115 Dangerous builds = 0 #undump 1 unfix 1 unfix 2 # add small particles as hi density lattice region plane block INF INF INF INF -0.001 0.001 units box lattice sq 250.0 Lattice spacing in x,y,z = 0.063245553 0.063245553 0.063245553 create_atoms 4 region plane Created 83521 atoms using lattice units in orthogonal box = (0 0 -0.91287093) to (18.257419 18.257419 0.91287093) create_atoms CPU = 0.006 seconds set type 4 mass 0.1 Setting atom values ... 83521 settings made for mass group small type 4 83521 atoms in group small velocity small create 1.0 593849 loop geom # delete overlaps # must set *-4 cutoffs to non-zero values pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 pair_coeff 2 2 1.0 2.0 pair_coeff 3 3 1.0 1.5 pair_coeff 1 4 0.0 1.0 0.5 pair_coeff 2 4 0.0 1.0 1.0 pair_coeff 3 4 0.0 1.0 0.75 pair_coeff 4 4 0.0 1.0 0.0 delete_atoms overlap 1.0 small big System init for delete_atoms ... Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4, bins = 14 14 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/2d bin: standard (2) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d bin: standard WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312) Deleted 63410 atoms, new total = 20211 # SRD run reset_timestep 0 neighbor 0.3 multi neigh_modify delay 0 every 1 check yes comm_modify mode multi group big vel yes neigh_modify include big # no pairwise interactions with small particles pair_style lj/cut 1.12 pair_coeff 1 1 1.0 1.0 1.12 pair_coeff 2 2 1.0 2.0 2.24 pair_coeff 3 3 1.0 1.5 1.68 pair_coeff 4 4 0.0 1.0 0.0 # use fix SRD to push small particles out from inside big ones # if comment out, big particles won't see SRD particles timestep 0.001 fix 1 big nve fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore fix 3 all enforce2d # diagnostics compute tbig big temp/sphere variable pebig equal pe*atoms/count(big) variable ebig equal etotal*atoms/count(big) thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] thermo_modify temp tbig WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530) thermo 1000 #dump 1 all atom 1000 dump.poly #dump 1 all image 1000 image.*.jpg type type zoom 1.6 #dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1 run 10000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2 @Article{Intveld08, author = {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest}, title = {Accurate and Efficient Methods for Modeling Colloidal Mixtures in an Explicit Solvent using Molecular Dynamics}, journal = {Comput.\ Phys.\ Commut.}, year = 2008, volume = 179, pages = {320--329} } @article{Shire2020, author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin}, title = {{DEM} Simulations of Polydisperse Media: Efficient Contact Detection Applied to Investigate the Quasi-Static Limit}, journal = {Computational Particle Mechanics}, year = {2020} @article{Monti2022, author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, Ishan and Silbert, Leonardo E. and Grest, Gary S. and Lechman, Jeremy B.}, title = {Large-scale frictionless jamming with power-law particle size distributions}, journal = {Phys. Rev. E}, volume = {106} issue = {3} year = {2022} } - fix srd command: doi:10.1063/1.3419070 @Article{Petersen10, author = {M. K. Petersen and J. B. Lechman and S. J. Plimpton and G. S. Grest and in 't Veld, P. J. and P. R. Schunk}, title = {Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with {L}ennard-{J}ones Fluid}, journal = {J.~Chem.\ Phys.}, year = 2010, volume = 132, pages = 174106 } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 3 of 6 mixed pair_coeff terms from geometric mixing rule SRD info: SRD/big particles = 20111 100 big particle diameter max/min = 1 1 SRD temperature & lamda = 1 0.063245553 SRD max distance & max velocity = 0.25298221 12.649111 SRD grid counts: 73 73 1 SRD grid size: request, actual (xyz) = 0.25, 0.25010162 0.25010162 1.8257419 SRD per actual grid cell = 4.9371727 SRD viscosity = 0.23321983 big/SRD mass density ratio = 0.16131131 WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830) # of rescaled SRD velocities = 0 ave/max small velocity = 4.1934421 7.74495 ave/max big velocity = 1.4399093 3.5724039 Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.54 ghost atom cutoff = 2.54 binsize = 18.257419, bins = 1 1 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/multi/atomonly/newton stencil: half/multi/2d bin: multi Per MPI rank memory allocation (min/avg/max) = 19.17 | 19.17 | 19.18 Mbytes Step Temp f_2[8] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] 0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0 1000 0.98459665 3968 0.0086216557 0.27547381 1.7425228 4.4010488 7403 34 34 0 663 25600 5329 3968 0.98292304 0 5 2000 0.74381104 4003 0.0041077507 -0.27806095 0.8302175 2.6170187 7746 32 32 0 1272 25600 5329 4003 1.0631936 0 5 3000 0.86305095 3969 0.0048953507 -0.29654658 0.98939933 2.1215334 7834 35 35 0 1974 25600 5329 3969 1.1209619 0 5 4000 0.8262932 4022 0.0049907905 -0.2224882 1.0086887 2.079935 8196 27 27 0 2753 25600 5329 4022 1.1040604 0 5 5000 0.85908819 4038 0.0043301633 -0.40487209 0.87516931 1.7917343 8347 28 28 0 3622 25600 5329 4038 1.1575336 0 5 6000 0.8048766 4024 0.0047529981 -0.2386377 0.96062844 1.8195477 8103 26 26 0 4536 25600 5329 4024 1.1818796 0 5 7000 0.84561126 4047 0.0039459142 -0.46245206 0.79750871 1.4432235 8154 20 20 0 5483 25600 5329 4047 1.1817402 0 5 8000 0.81543891 4037 0.0037591562 -0.45524091 0.75976306 1.7501338 8377 27 27 0 6472 25600 5329 4037 1.168956 0 5 9000 0.71960112 4045 0.0035243955 -0.3598901 0.71231557 1.7333111 8440 30 30 0 7386 25600 5329 4045 1.1765277 0 5 10000 1.0831334 4043 0.0053045911 -0.54175788 1.0721109 1.7434822 8283 33 33 0 8331 25600 5329 4043 1.1696048 0 5 Loop time of 1.82855 on 4 procs for 10000 steps with 20211 atoms Performance: 472504.837 tau/day, 5468.806 timesteps/s, 110.530 Matom-step/s 99.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0057481 | 0.0069625 | 0.0087051 | 1.3 | 0.38 Neigh | 0.0067658 | 0.0070766 | 0.0076303 | 0.4 | 0.39 Comm | 0.10613 | 0.10693 | 0.10786 | 0.2 | 5.85 Output | 0.00053606 | 0.00059075 | 0.00063891 | 0.0 | 0.03 Modify | 1.6117 | 1.6525 | 1.6763 | 1.9 | 90.37 Other | | 0.05449 | | | 2.98 Nlocal: 5052.75 ave 5483 max 4509 min Histogram: 1 0 0 0 0 1 1 0 0 1 Nghost: 27 ave 28 max 26 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 39.5 ave 55 max 26 min Histogram: 1 0 0 1 0 1 0 0 0 1 Total # of neighbors = 158 Ave neighs/atom = 0.0078175251 Neighbor list builds = 500 Dangerous builds = 0 Total wall time: 0:00:03