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 - dimer 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.dimer fix molprop NULL Molecules Reading data file ... orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5) 1 by 1 by 1 MPI processor grid reading atoms ... 200 atoms read_data CPU = 0.001 seconds set type 1 mass 1.0 Setting atom values ... 200 settings made for mass group big type 1 200 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 fix 1 big rigid molecule 100 rigid bodies with 200 atoms fix 2 all enforce2d #dump 1 all atom 10 dump.dimer.equil 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 = 27 27 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) = 5.557 | 5.557 | 5.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 3.4028231 0 0 0.83369167 -0.55065517 100 9.5167872 2.392105 0 4.7237178 2.8319556 200 13.564465 3.0352634 0 6.3585572 3.6388732 300 13.133051 4.3835112 0 7.6011086 4.060051 400 14.576837 5.5141059 0 9.0854309 4.422762 500 15.227825 6.6472106 0 10.378028 4.8598912 600 16.93219 7.454865 0 11.603251 5.2908894 700 16.573769 8.7323442 0 12.792918 5.3544684 800 17.482599 9.7221047 0 14.005341 5.6200973 900 18.548144 10.739353 0 15.283649 4.7817995 1000 18.068079 12.058417 0 16.485096 6.5773091 Loop time of 0.0511113 on 1 procs for 1000 steps with 200 atoms Performance: 8452141.519 tau/day, 19565.142 timesteps/s, 3.913 Matom-step/s 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0095507 | 0.0095507 | 0.0095507 | 0.0 | 18.69 Neigh | 0.0042239 | 0.0042239 | 0.0042239 | 0.0 | 8.26 Comm | 0.002203 | 0.002203 | 0.002203 | 0.0 | 4.31 Output | 8.8531e-05 | 8.8531e-05 | 8.8531e-05 | 0.0 | 0.17 Modify | 0.03336 | 0.03336 | 0.03336 | 0.0 | 65.27 Other | | 0.001685 | | | 3.30 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 64 ave 64 max 64 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 275 ave 275 max 275 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 275 Ave neighs/atom = 1.375 Neighbor list builds = 193 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 29929 atoms using lattice units in orthogonal box = (-9.341652 -9.341652 -0.5) to (9.341652 9.341652 0.5) create_atoms CPU = 0.007 seconds set type 2 mass 0.1 Setting atom values ... 29929 settings made for mass group small type 2 29929 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 = 14 14 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 12776 atoms, new total = 17353 # 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 100 rigid bodies with 200 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 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] 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.dimer #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 = 17153 200 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: 75 75 1 SRD grid size: request, actual (xyz) = 0.25, 0.24911072 0.24911072 1 SRD per actual grid cell = 5.544404 SRD viscosity = 0.23553122 big/SRD mass density ratio = 0.14250828 # of rescaled SRD velocities = 0 ave/max small velocity = 4.191188 7.6900178 ave/max big velocity = 2.6813242 7.1846104 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 = 18.683304, 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) = 26.77 | 26.77 | 26.77 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 6.8392143 0 0.297476 20.71529 25.810505 4.0555741 0 0 0 0 0 0 0 0 0 0 0 0 1000 1.2285566 3375 0.24673495 20.492683 21.407958 5.237464 13477 54 54 1 652 16900 5625 3375 1.1653557 0 15 0 2000 1.3561011 3395 0.24763991 20.476182 21.486477 9.2878509 13435 67 67 0 1504 16900 5625 3395 1.1651182 0 15 0 3000 1.2445369 3352 0.24713723 20.515681 21.442861 8.0289529 13186 62 63 2 2379 16900 5625 3352 1.1746721 0 15 0 4000 1.1058201 3389 0.24596239 20.51709 21.340926 10.003266 13466 66 66 0 3264 16900 5625 3389 1.1671415 0 15 0 5000 1.0584198 3407 0.24539623 20.503281 21.291804 9.1119405 13254 64 64 0 4189 16900 5625 3407 1.1687685 0 15 0 6000 1.3335611 3360 0.24737788 20.470239 21.463742 8.6885126 13281 62 62 1 5031 16900 5625 3360 1.1568996 0 15 0 7000 1.1384759 3401 0.24570869 20.47075 21.318914 9.1801119 13059 47 47 1 5878 16900 5625 3401 1.182474 0 15 0 8000 1.2982334 3397 0.24667224 20.435333 21.402517 6.5904007 13405 56 56 0 6729 16900 5625 3397 1.169017 0 24 0 9000 1.0456752 3381 0.24504517 20.482316 21.261344 10.497413 13205 81 81 2 7706 16900 5625 3381 1.1694675 0 24 0 10000 1.2222547 3394 0.24653264 20.479825 21.390405 8.7495888 13296 68 68 1 8581 16900 5625 3394 1.1613437 0 24 0 Loop time of 7.18514 on 1 procs for 10000 steps with 17353 atoms Performance: 120248.165 tau/day, 1391.761 timesteps/s, 24.151 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 | 0.14497 | 0.14497 | 0.14497 | 0.0 | 2.02 Neigh | 0.031835 | 0.031835 | 0.031835 | 0.0 | 0.44 Comm | 0.094201 | 0.094201 | 0.094201 | 0.0 | 1.31 Output | 0.00082765 | 0.00082765 | 0.00082765 | 0.0 | 0.01 Modify | 6.8507 | 6.8507 | 6.8507 | 0.0 | 95.35 Other | | 0.06259 | | | 0.87 Nlocal: 17353 ave 17353 max 17353 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1334 ave 1334 max 1334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1334 Ave neighs/atom = 0.076874316 Neighbor list builds = 500 Dangerous builds = 0 Total wall time: 0:00:07