LAMMPS (27 May 2021) using 1 OpenMP thread(s) per MPI task # SRD diffusion demo - rigid box 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.box fix molprop NULL Molecules Reading data file ... orthogonal box = (-19.144690 -19.144690 -0.50000000) to (19.144690 19.144690 0.50000000) 1 by 1 by 1 MPI processor grid reading atoms ... 420 atoms read_data CPU = 0.002 seconds set type 1 mass 1.0 Setting atom values ... 420 settings made for mass group big type 1 420 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 420 atoms fix 2 all enforce2d #dump 1 all atom 10 dump.box.equil compute tbig all temp/sphere thermo_modify temp tbig thermo 100 run 1000 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 = 54 54 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) = 5.570 | 5.570 | 5.570 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.4252596 0 0 0.14931291 -8.727261 100 4.7699234 3.4203218 0 3.9200281 0.63667047 200 14.850064 5.3315601 0 6.8872811 0.71533738 300 21.249889 7.2094878 0 9.4356667 1.0710181 400 24.551027 9.2008598 0 11.772872 1.0133205 500 23.999755 11.562353 0 14.076613 1.3275867 600 25.022182 13.731564 0 16.352935 1.0236907 700 26.601942 15.850142 0 18.637012 0.80166569 800 24.154216 18.395444 0 20.925886 1.7521839 900 27.3897 20.3322 0 23.201597 0.65472411 1000 27.381112 22.600716 0 25.469214 0.69152692 Loop time of 0.0920079 on 1 procs for 1000 steps with 420 atoms Performance: 4695251.138 tau/day, 10868.637 timesteps/s 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.029557 | 0.029557 | 0.029557 | 0.0 | 32.12 Neigh | 0.011621 | 0.011621 | 0.011621 | 0.0 | 12.63 Comm | 0.0041208 | 0.0041208 | 0.0041208 | 0.0 | 4.48 Output | 0.00034363 | 0.00034363 | 0.00034363 | 0.0 | 0.37 Modify | 0.042122 | 0.042122 | 0.042122 | 0.0 | 45.78 Other | | 0.004243 | | | 4.61 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 84.0000 ave 84 max 84 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 562.000 ave 562 max 562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 562 Ave neighs/atom = 1.3380952 Neighbor list builds = 158 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 124609 atoms create_atoms CPU = 0.042 seconds set type 2 mass 0.1 Setting atom values ... 124609 settings made for mass group small type 2 124609 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 1.0 delete_atoms overlap 1.0 small big System init for delete_atoms ... 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 = 28 28 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:308) Deleted 51030 atoms, new total = 73999 # 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 420 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:689) thermo_modify temp tbig WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:483) thermo 1000 #dump 1 all atom 1000 dump.box #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 = {P.{\,}J.~in{\,}'t~Veld 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 = {Comp.~Phys.~Comm.}, year = 2008, volume = 179, pages = {320--329} } @article{Stratford2018, author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin}, title = {Implementation of multi-level contact detection in LAMMPS}, year = {2018} } @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} } - fix srd command: @Article{Petersen10, author = {M. K. Petersen, J. B. Lechman, S. J. Plimpton, G. S. Grest, P. J. in 't Veld, P. R. Schunk}, title = {Mesoscale Hydrodynamics via Stochastic Rotation Dynamics: Comparison with Lennard-Jones Fluid}, journal = {J.~Chem.~Phys.}, year = 2010, volume = 132, pages = {174106} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE SRD info: SRD/big particles = 73579 420 big particle diameter max/min = 1.0000000 1.0000000 SRD temperature & lamda = 1.0000000 0.063245553 SRD max distance & max velocity = 0.25298221 12.649111 SRD grid counts: 153 153 1 SRD grid size: request, actual (xyz) = 0.25000000, 0.25025738 0.25025738 1.0000000 SRD per actual grid cell = 4.0557326 SRD viscosity = 0.22929663 big/SRD mass density ratio = 0.19661407 WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2845) # of rescaled SRD velocities = 0 ave/max small velocity = 4.1966772 7.7276214 ave/max big velocity = 2.1275716 5.8359099 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 = 38.289379, 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/newton stencil: half/multi/2d bin: multi Per MPI rank memory allocation (min/avg/max) = 75.37 | 75.37 | 75.37 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 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0 1000 3.7986429 16232 0.24173874 42.193535 42.591488 10.849557 10086 45 45 0 1004 51984 23409 16232 0.91196906 0 5 0 2000 1.4227624 16312 0.24027816 42.185099 42.334151 11.114609 10229 28 28 0 1829 51984 23409 16312 0.91266737 0 5 0 3000 1.2870561 16338 0.24012829 42.172911 42.307746 9.1532934 10247 29 29 0 2474 51984 23409 16338 0.92249481 0 5 0 4000 0.99207377 16354 0.23996323 42.174734 42.278665 13.010306 10390 42 42 0 3137 51984 23409 16354 0.93252257 0 5 0 5000 1.2778672 16234 0.24012389 42.1731 42.306972 11.375628 10158 39 39 0 3802 51984 23409 16234 0.93405963 0 7 0 6000 0.92241679 16273 0.23984728 42.161601 42.258235 9.4164757 10190 34 35 0 4514 51984 23409 16273 0.94347665 0 7 0 7000 1.4747828 16291 0.24015741 42.158375 42.312876 11.273642 10208 40 40 0 5231 51984 23409 16291 0.94315382 0 7 0 8000 1.143932 16385 0.23997671 42.1612 42.28104 11.518583 10409 31 31 0 5954 51984 23409 16385 0.94024078 0 7 0 9000 1.123729 16298 0.23981793 42.135341 42.253065 14.210625 10067 51 51 0 6654 51984 23409 16298 0.9463894 0 7 0 10000 1.0362924 16356 0.23977465 42.136875 42.245439 10.19621 10227 33 34 0 7437 51984 23409 16356 0.94188712 0 7 0 Loop time of 41.8379 on 1 procs for 10000 steps with 73999 atoms Performance: 20651.124 tau/day, 239.018 timesteps/s 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44984 | 0.44984 | 0.44984 | 0.0 | 1.08 Neigh | 0.11618 | 0.11618 | 0.11618 | 0.0 | 0.28 Comm | 0.4757 | 0.4757 | 0.4757 | 0.0 | 1.14 Output | 0.0035887 | 0.0035887 | 0.0035887 | 0.0 | 0.01 Modify | 40.52 | 40.52 | 40.52 | 0.0 | 96.85 Other | | 0.2722 | | | 0.65 Nlocal: 73999.0 ave 73999 max 73999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 135.000 ave 135 max 135 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2407.00 ave 2407 max 2407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 2407 Ave neighs/atom = 0.032527467 Neighbor list builds = 500 Dangerous builds = 0 Total wall time: 0:00:45