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) 2 by 2 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) = 5.553 | 5.553 | 5.553 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 6.5773093 Loop time of 0.0424792 on 4 procs for 1000 steps with 200 atoms Performance: 10169676.521 tau/day, 23540.918 timesteps/s, 4.708 Matom-step/s 98.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0022758 | 0.0023448 | 0.002442 | 0.1 | 5.52 Neigh | 0.0011082 | 0.0011236 | 0.0011582 | 0.1 | 2.64 Comm | 0.0099484 | 0.010092 | 0.010247 | 0.1 | 23.76 Output | 9.551e-05 | 0.00010604 | 0.00013381 | 0.0 | 0.25 Modify | 0.026025 | 0.026222 | 0.026405 | 0.1 | 61.73 Other | | 0.00259 | | | 6.10 Nlocal: 50 ave 55 max 47 min Histogram: 2 0 0 0 0 1 0 0 0 1 Nghost: 33.75 ave 38 max 32 min Histogram: 2 1 0 0 0 0 0 0 0 1 Neighs: 68.75 ave 77 max 64 min Histogram: 2 0 0 1 0 0 0 0 0 1 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 = 0.002 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 7.1846103 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) = 13.2 | 13.21 | 13.22 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 4.0555746 0 0 0 0 0 0 0 0 0 0 0 0 1000 1.1648085 3389 0.24643931 20.514525 21.382307 5.5927686 13390 59 59 0 1015 28224 5625 3389 1.1513276 0 111 0 2000 1.1870311 3385 0.24701637 20.548037 21.432375 5.9269821 13271 57 57 2 1878 28224 5625 3385 1.1619099 0 111 0 3000 1.1362839 3365 0.24577276 20.477942 21.324474 5.1621045 13244 59 60 1 2778 28224 5625 3365 1.1807679 0 111 0 4000 1.3023748 3390 0.24679509 20.442907 21.413176 5.6127077 13413 65 65 1 3705 28224 5625 3390 1.1726946 0 111 0 5000 1.195496 3387 0.2458055 20.43667 21.327314 6.1843476 13248 51 51 1 4638 28224 5625 3387 1.1730279 0 111 0 6000 1.2389419 3387 0.24546635 20.374876 21.297888 5.5909826 13184 54 54 1 5494 28224 5625 3387 1.1859134 0 111 0 7000 1.2068912 3378 0.24564722 20.414447 21.313581 8.5604547 13188 57 57 1 6428 28224 5625 3378 1.1499181 0 111 0 8000 1.1014154 3374 0.24514746 20.449665 21.270219 7.3483529 13179 63 63 0 7591 28224 5625 3374 1.1769322 0 121 0 9000 1.356464 3388 0.24749513 20.463349 21.473915 7.6809833 13138 50 50 2 8485 28224 5625 3388 1.1448659 0 121 0 10000 1.1632951 3402 0.24560819 20.44354 21.310195 9.5738599 13323 64 67 0 9304 28224 5625 3402 1.1550136 0 121 0 Loop time of 2.47185 on 4 procs for 10000 steps with 17353 atoms Performance: 349536.432 tau/day, 4045.561 timesteps/s, 70.203 Matom-step/s 99.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.037524 | 0.039903 | 0.042215 | 1.1 | 1.61 Neigh | 0.01053 | 0.010805 | 0.011068 | 0.2 | 0.44 Comm | 0.14536 | 0.14822 | 0.15102 | 0.6 | 6.00 Output | 0.00051847 | 0.00054674 | 0.0006272 | 0.0 | 0.02 Modify | 2.2276 | 2.2334 | 2.2381 | 0.3 | 90.35 Other | | 0.03895 | | | 1.58 Nlocal: 4338.25 ave 4488 max 4277 min Histogram: 2 1 0 0 0 0 0 0 0 1 Nghost: 76.75 ave 85 max 69 min Histogram: 2 0 0 0 0 0 0 0 1 1 Neighs: 331.25 ave 355 max 306 min Histogram: 1 0 0 1 0 0 1 0 0 1 Total # of neighbors = 1325 Ave neighs/atom = 0.076355673 Neighbor list builds = 507 Dangerous builds = 0 Total wall time: 0:00:02