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) 1 by 1 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) = 4.174 | 4.174 | 4.174 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 0.00622873 on 1 procs for 1000 steps with 100 atoms Performance: 69356032.450 tau/day, 160546.371 timesteps/s, 16.055 Matom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0015709 | 0.0015709 | 0.0015709 | 0.0 | 25.22 Neigh | 0.0014016 | 0.0014016 | 0.0014016 | 0.0 | 22.50 Comm | 0.0012066 | 0.0012066 | 0.0012066 | 0.0 | 19.37 Output | 6.169e-06 | 6.169e-06 | 6.169e-06 | 0.0 | 0.10 Modify | 0.0013508 | 0.0013508 | 0.0013508 | 0.0 | 21.69 Other | | 0.0006926 | | | 11.12 Nlocal: 100 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 60 ave 60 max 60 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 152 ave 152 max 152 min Histogram: 1 0 0 0 0 0 0 0 0 0 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 = 0.016 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) = 42 | 42 | 42 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 1.0181191 3924 0.0076572255 0.030604433 1.5476019 3.7992573 7242 26 26 0 635 15876 5329 3924 0.98110339 0 3 2000 0.69783736 3992 0.0027817464 -0.47755891 0.56221876 1.9887267 7740 34 34 1 1186 15876 5329 3992 1.0611575 0 24 3000 0.89084297 3981 0.004323119 -0.45361044 0.87374558 1.7342893 7775 24 24 0 1923 15876 5329 3981 1.1207371 0 24 4000 0.84391846 4036 0.0045581483 -0.33619115 0.92124735 1.8456288 8060 43 43 0 2734 15876 5329 4036 1.1481354 0 24 5000 0.69548234 4056 0.0030033315 -0.42926535 0.60700333 1.6113509 8260 33 33 0 3638 15876 5329 4056 1.148749 0 24 6000 0.71729125 4023 0.0035318938 -0.35493291 0.71383106 1.673491 8224 29 29 0 4528 15876 5329 4023 1.1602572 0 24 7000 0.90145513 4032 0.0047423524 -0.38469129 0.95847685 1.7537778 8382 31 31 0 5395 15876 5329 4032 1.1543513 0 24 8000 0.6739295 4026 0.0029910322 -0.39963744 0.60451751 1.646528 8409 35 35 0 6293 15876 5329 4026 1.1540519 0 24 9000 0.80563959 4041 0.0042947965 -0.33238166 0.86802133 1.6597032 8429 29 29 0 7164 15876 5329 4041 1.1880521 0 24 10000 0.90407954 4022 0.0046865656 -0.39987673 0.94720178 1.445708 8349 30 30 0 8189 15876 5329 4022 1.171667 0 24 Loop time of 5.64963 on 1 procs for 10000 steps with 20211 atoms Performance: 152930.340 tau/day, 1770.027 timesteps/s, 35.774 Matom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.019832 | 0.019832 | 0.019832 | 0.0 | 0.35 Neigh | 0.020738 | 0.020738 | 0.020738 | 0.0 | 0.37 Comm | 0.056875 | 0.056875 | 0.056875 | 0.0 | 1.01 Output | 0.00083247 | 0.00083247 | 0.00083247 | 0.0 | 0.01 Modify | 5.4828 | 5.4828 | 5.4828 | 0.0 | 97.05 Other | | 0.06854 | | | 1.21 Nlocal: 20211 ave 20211 max 20211 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 49 ave 49 max 49 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160 Ave neighs/atom = 0.0079164811 Neighbor list builds = 500 Dangerous builds = 0 Total wall time: 0:00:11