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 - rigid star particles units lj atom_style sphere atom_modify map array first big dimension 2 # read in clusters of rigid bodies fix molprop all property/atom mol ghost yes read_data data.star fix molprop NULL Molecules Reading data file ... orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5) 2 by 2 by 1 MPI processor grid reading atoms ... 270 atoms read_data CPU = 0.001 seconds set type 1 mass 1.0 Setting atom values ... 270 settings made for mass group big type 1 270 atoms in group big velocity big create 1.44 87287 loop geom # equilibrate big particles pair_style soft 1.12 pair_coeff 1 1 0.0 pair_coeff 2 2 0.0 0.0 pair_coeff 1 2 0.0 0.0 variable prefactor equal ramp(0,60) fix soft all adapt 1 pair soft a * * v_prefactor neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 big rigid molecule 30 rigid bodies with 270 atoms fix 2 all enforce2d #dump 1 all atom 10 dump.star.equil compute tbig all temp/sphere thermo_modify temp tbig thermo 100 run 1000 Generated 0 of 1 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 = 1.42 ghost atom cutoff = 1.42 binsize = 0.71, bins = 38 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair soft, 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) = 5.554 | 5.554 | 5.555 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.3101488 0 0 0.21350573 0.32876464 100 5.0954142 3.291475 0 4.1218387 1.0087565 200 13.041252 4.6176595 0 6.7429006 1.5291618 300 11.912727 7.0921814 0 9.0335147 1.9578844 400 17.60886 8.3666709 0 11.236263 1.602563 500 16.786375 10.630838 0 13.366396 1.7725508 600 18.470347 12.42157 0 15.431552 2.1627885 700 19.39794 14.349074 0 17.510219 1.9554238 800 19.082984 16.464746 0 19.574566 2.2424126 900 20.702091 18.253108 0 21.626782 1.8041661 1000 18.299191 20.699563 0 23.681654 2.9475408 Loop time of 0.0312248 on 4 procs for 1000 steps with 270 atoms Performance: 13835169.963 tau/day, 32025.856 timesteps/s, 8.647 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 | 0.0026978 | 0.0031211 | 0.0033489 | 0.5 | 10.00 Neigh | 0.0011292 | 0.0013054 | 0.0014446 | 0.3 | 4.18 Comm | 0.010095 | 0.010474 | 0.010975 | 0.3 | 33.54 Output | 0.00019592 | 0.00021948 | 0.00027642 | 0.0 | 0.70 Modify | 0.013333 | 0.013668 | 0.013952 | 0.2 | 43.77 Other | | 0.002437 | | | 7.80 Nlocal: 67.5 ave 80 max 54 min Histogram: 1 1 0 0 0 0 0 0 1 1 Nghost: 29.75 ave 33 max 26 min Histogram: 1 0 0 0 1 0 0 1 0 1 Neighs: 104.5 ave 135 max 72 min Histogram: 1 0 0 1 0 0 0 1 0 1 Total # of neighbors = 418 Ave neighs/atom = 1.5481481 Neighbor list builds = 176 Dangerous builds = 0 #undump 1 unfix soft 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 85.0 Lattice spacing in x,y,z = 0.10846523 0.10846523 0.10846523 create_atoms 2 region plane Created 60025 atoms using lattice units in orthogonal box = (-13.293404 -13.293404 -0.5) to (13.293404 13.293404 0.5) create_atoms CPU = 0.003 seconds set type 2 mass 0.1 Setting atom values ... 60025 settings made for mass group small type 2 60025 atoms in group small velocity small create 1.0 593849 loop geom # delete overlaps # must set 1-2 cutoff to non-zero value pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 pair_coeff 2 2 0.0 1.0 0.0 pair_coeff 1 2 0.0 1.0 0.5 delete_atoms overlap 0.5 small big System init for delete_atoms ... Generated 0 of 1 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 = 19 19 1 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 16305 atoms, new total = 43990 # 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 2.5 pair_coeff 1 1 1.0 1.0 pair_coeff 2 2 0.0 1.0 0.0 pair_coeff 1 2 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 rigid molecule 30 rigid bodies with 270 atoms fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes fix 3 all enforce2d # diagnostics uncompute tbig 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] f_2[12] WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904) 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.star #dump 1 all image 1000 image.*.jpg type type zoom 1.6 #dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2 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 0 of 1 mixed pair_coeff terms from geometric mixing rule SRD info: SRD/big particles = 43720 270 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: 106 106 1 SRD grid size: request, actual (xyz) = 0.25, 0.25081894 0.25081894 1 SRD per actual grid cell = 5.5586635 SRD viscosity = 0.23558168 big/SRD mass density ratio = 0.14409881 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 = 4.1908497 7.725824 ave/max big velocity = 2.202625 5.4167964 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 = 26.586808, 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) = 14.19 | 14.19 | 14.2 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] f_2[12] 0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0 1000 1.4057114 8217 0.22974151 37.20177 37.430849 11.548865 14197 56 57 0 682 42436 11236 8217 1.0187465 0 3 0 2000 1.0468288 8223 0.22932205 37.191914 37.362508 4.8322766 14185 60 60 0 1452 42436 11236 8223 1.0271433 0 64 0 3000 0.89541606 8240 0.22921893 37.199787 37.345707 9.7555289 14770 60 60 0 2175 42436 11236 8240 1.0157844 0 64 0 4000 1.021344 8222 0.22920858 37.177579 37.344021 6.2834235 14480 50 50 0 2951 42436 11236 8222 1.0130315 0 64 0 5000 1.045809 8222 0.2294309 37.209813 37.380241 2.8847497 14109 59 60 0 3667 42436 11236 8222 1.0126872 0 64 0 6000 1.1527336 8227 0.22933212 37.176296 37.364149 5.4760843 14597 42 42 0 4418 42436 11236 8227 1.0188272 0 64 0 7000 1.1799559 8216 0.22941075 37.18467 37.376959 10.243848 14281 57 57 0 5154 42436 11236 8216 1.0063617 0 64 0 8000 1.1913762 8188 0.22940126 37.181263 37.375413 5.7338518 14497 47 47 0 5878 42436 11236 8188 1.0076169 0 64 0 9000 1.0587094 8230 0.22928172 37.183406 37.355936 5.7323116 14267 62 62 0 6550 42436 11236 8230 1.0108237 0 64 0 10000 1.0359117 8165 0.22944086 37.21305 37.381865 9.4246373 14016 52 52 0 7246 42436 11236 8165 1.0147132 0 64 0 Loop time of 6.61179 on 4 procs for 10000 steps with 43990 atoms Performance: 130675.562 tau/day, 1512.449 timesteps/s, 66.533 Matom-step/s 99.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041077 | 0.059027 | 0.07409 | 4.8 | 0.89 Neigh | 0.015706 | 0.017829 | 0.019903 | 1.1 | 0.27 Comm | 0.23742 | 0.25326 | 0.26722 | 2.1 | 3.83 Output | 0.00073333 | 0.00077549 | 0.00084859 | 0.0 | 0.01 Modify | 6.1477 | 6.174 | 6.2149 | 1.0 | 93.38 Other | | 0.1069 | | | 1.62 Nlocal: 10997.5 ave 11924 max 10204 min Histogram: 1 0 1 0 0 1 0 0 0 1 Nghost: 64.25 ave 71 max 56 min Histogram: 1 0 0 1 0 0 0 0 1 1 Neighs: 395.5 ave 497 max 271 min Histogram: 1 0 0 0 0 1 1 0 0 1 Total # of neighbors = 1582 Ave neighs/atom = 0.035962719 Neighbor list builds = 500 Dangerous builds = 0 Total wall time: 0:00:07