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 viscosity 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 0.0311841 on 4 procs for 1000 steps with 270 atoms Performance: 13853197.664 tau/day, 32067.587 timesteps/s, 8.658 Matom-step/s 97.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0027957 | 0.0031644 | 0.0035219 | 0.5 | 10.15 Neigh | 0.001171 | 0.0012862 | 0.0014036 | 0.3 | 4.12 Comm | 0.0099068 | 0.010544 | 0.011053 | 0.4 | 33.81 Output | 0.00014281 | 0.00016091 | 0.00020823 | 0.0 | 0.52 Modify | 0.013319 | 0.013618 | 0.014047 | 0.2 | 43.67 Other | | 0.002411 | | | 7.73 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 small viscosity 10 x y 50 fix 4 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.mp #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 1.3506473 8186 0.22968182 37.201018 37.421123 5.6398923 14572 54 54 0 654 42436 11236 8186 1.0228728 0 3 0 2000 0.99412905 8212 0.22952823 37.234094 37.3961 8.5863689 14257 69 69 0 1394 42436 11236 8212 1.0206297 0 12 0 3000 1.4469134 8192 0.22970951 37.189841 37.425634 8.0408437 14439 53 53 0 2178 42436 11236 8192 1.0121272 0 12 0 4000 1.6112802 8172 0.2303679 37.270324 37.532903 8.3379947 14098 57 57 0 2992 42436 11236 8172 1.0171443 0 12 0 5000 2.0436283 8191 0.23016186 37.166298 37.499334 7.1370191 14030 49 49 0 3804 42436 11236 8191 1.0054513 0 12 0 6000 2.2894073 8184 0.2303867 37.162878 37.535967 7.6496143 13970 50 50 0 4662 42436 11236 8184 1.0084738 0 12 0 7000 2.1640822 8183 0.23045121 37.193812 37.546477 7.1526683 13926 56 57 0 5445 42436 11236 8183 1.0046108 0 15 0 8000 2.8851243 8199 0.23121762 37.201176 37.671344 9.1644504 13849 58 58 0 6237 42436 11236 8199 1.0081629 0 15 0 9000 2.6422092 8180 0.23070839 37.157795 37.588377 2.4816571 13651 70 70 0 7007 42436 11236 8180 1.0089869 0 15 0 10000 2.7121051 8189 0.23087145 37.172972 37.614945 11.176036 13901 63 64 0 7845 42436 11236 8189 1.0023484 0 15 0 Loop time of 6.56969 on 4 procs for 10000 steps with 43990 atoms Performance: 131513.146 tau/day, 1522.143 timesteps/s, 66.959 Matom-step/s 99.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.037869 | 0.059232 | 0.073664 | 5.4 | 0.90 Neigh | 0.015688 | 0.017835 | 0.019891 | 1.1 | 0.27 Comm | 0.22905 | 0.24375 | 0.26098 | 2.3 | 3.71 Output | 0.00069058 | 0.00071614 | 0.00078869 | 0.0 | 0.01 Modify | 6.1124 | 6.1385 | 6.1881 | 1.2 | 93.44 Other | | 0.1096 | | | 1.67 Nlocal: 10997.5 ave 12305 max 10259 min Histogram: 1 1 0 1 0 0 0 0 0 1 Nghost: 58.25 ave 73 max 48 min Histogram: 1 0 1 0 1 0 0 0 0 1 Neighs: 402.75 ave 520 max 207 min Histogram: 1 0 0 0 0 0 0 2 0 1 Total # of neighbors = 1611 Ave neighs/atom = 0.03662196 Neighbor list builds = 500 Dangerous builds = 0 Total wall time: 0:00:06