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 - ellipsoids units lj atom_style ellipsoid atom_modify first big dimension 2 # create big ellipsoidal particles lattice sq 0.14 Lattice spacing in x,y,z = 2.6726124 2.6726124 2.6726124 region box block 0 10 0 10 -0.5 0.5 create_box 2 box Created orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062) 1 by 1 by 1 MPI processor grid create_atoms 1 region box Created 100 atoms using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062) create_atoms CPU = 0.000 seconds set type 1 mass 1.0 Setting atom values ... 100 settings made for mass set type 1 shape 3.0 1.0 1.0 Setting atom values ... 100 settings made for shape group big type 1 100 atoms in group big set group big quat/random 29898 Setting atom values ... 100 settings made for quat/random velocity big create 1.44 87287 loop geom # equilibrate big particles pair_style gayberne 1.0 3.0 1.0 4.0 pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1 pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0 pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0 neighbor 0.3 bin neigh_modify delay 0 every 1 check yes fix 1 big nve/asphere fix 2 all enforce2d compute rot big temp/asphere compute 0 all property/atom quatw quati quatj quatk shapex shapey shapez #dump 1 all custom 10 dump.ellipsoid.equil id type x y z c_0[*] #dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez thermo_style custom step temp c_rot epair etotal press thermo 100 run 1000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - pair gayberne command: doi:10.1063/1.3058435 @Article{Brown09, author = {W. M. Brown and M. K. Petersen and S. J. Plimpton and G. S. Grest}, title = {Liquid Crystal Nanodroplets in Solution}, journal = {J.~Chem.\ Phys.}, year = 2009, volume = 130, number = 4, pages = {044901} } 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 Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 binsize = 2.15, bins = 13 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair gayberne, 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) = 4.611 | 4.611 | 4.611 Mbytes Step Temp c_rot E_pair TotEng Press 0 1.44 0.95677852 2.7038078 4.1294078 10.518912 100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874 200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886 300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788 400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964 500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908 600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508 700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889 800 2.7632972 2.9060854 -0.52075351 2.2149107 0.7710678 900 2.9905597 2.8869667 -0.49099378 2.4696603 0.69616841 1000 2.8470138 2.9005012 -0.51282088 2.3057228 0.68817567 Loop time of 0.192844 on 1 procs for 1000 steps with 100 atoms Performance: 2240155.241 tau/day, 5185.545 timesteps/s, 518.554 katom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17225 | 0.17225 | 0.17225 | 0.0 | 89.32 Neigh | 0.0025614 | 0.0025614 | 0.0025614 | 0.0 | 1.33 Comm | 0.0024746 | 0.0024746 | 0.0024746 | 0.0 | 1.28 Output | 0.0001406 | 0.0001406 | 0.0001406 | 0.0 | 0.07 Modify | 0.014112 | 0.014112 | 0.014112 | 0.0 | 7.32 Other | | 0.001306 | | | 0.68 Nlocal: 100 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 77 ave 77 max 77 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 369 ave 369 max 369 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369 Ave neighs/atom = 3.69 Neighbor list builds = 174 Dangerous builds = 0 #undump 1 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 120.0 Lattice spacing in x,y,z = 0.091287093 0.091287093 0.091287093 create_atoms 2 region plane Created 85849 atoms using lattice units in orthogonal box = (0 0 -1.3363062) to (26.726124 26.726124 1.3363062) create_atoms CPU = 0.015 seconds set type 2 mass 0.01 Setting atom values ... 85849 settings made for mass group small type 2 85849 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 2.0 neigh_modify one 10000 delete_atoms overlap 1.6 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: 10000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4, bins = 20 20 2 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 71060 atoms, new total = 14889 # 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 gayberne 1.0 3.0 1.0 4.0 pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1 pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0 pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 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 0.0005 fix 1 big nve/asphere fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50 fix 3 small viscosity 20 x y 50 fix 4 all enforce2d # diagnostics compute tbig big temp/asphere variable pebig equal pe*atoms/count(big) variable ebig equal etotal*atoms/count(big) thermo_style custom step temp c_rot f_2[9] 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 custom 500 dump.ellipsoid id type x y z c_0[*] #dump_modify 1 colname c_0[1] quatw colname c_0[2] quati colname c_0[3] quatj colname c_0[4] quatk # colname c_0[5] shapex colname c_0[6] shapey colname c_0[7] shapez #dump 1 all image 500 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 = 14789 100 big particle diameter max/min = 3 1 SRD temperature & lamda = 1 0.1 SRD max distance & max velocity = 0.4 40 SRD grid counts: 107 107 1 SRD grid size: request, actual (xyz) = 0.25, 0.24977686 0.24977686 2.6726124 SRD per actual grid cell = 1.9275711 SRD viscosity = 0.68810145 big/SRD mass density ratio = 1.3736715 # of rescaled SRD velocities = 0 ave/max small velocity = 13.30933 24.335888 ave/max big velocity = 2.0802836 5.05672 Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 10000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 binsize = 26.726124, bins = 1 1 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair gayberne, 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) = 43.23 | 43.23 | 43.23 Mbytes Step Temp c_rot f_2[9] 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 2.9005012 2.9005012 0 0.025582147 -0.51282088 3.8089259 0.8986241 0 0 0 0 0 0 0 0 0 0 0 0 1000 2.3102693 2.3102693 0.82371999 0.019779507 -0.49733043 2.9449709 1.9807143 13954 30 30 0 277 38416 11449 4255 0.82371999 15 50 0 2000 1.5312119 1.5312119 0.90846884 0.008532096 -1.011162 1.2703438 0.58038663 14523 37 37 0 439 38416 11449 4257 0.90846884 20 50 0 3000 1.3603443 1.3603443 0.95241399 0.0085403252 -0.75534393 1.271569 1.2262133 14864 34 35 0 599 38416 11449 4287 0.95241399 20 50 0 4000 2.2408861 2.2408861 0.99089404 0.016876315 -0.82620566 2.5127146 1.2664088 15457 35 35 0 809 38416 11449 4272 0.99089404 21 50 0 5000 1.7110067 1.7110067 0.99729333 0.011146301 -0.88982716 1.6595728 0.97334407 15555 36 36 0 1026 38416 11449 4324 0.99729333 24 50 0 6000 1.684666 1.684666 1.0235606 0.009751253 -1.0582882 1.4518641 0.62435255 15752 45 46 0 1256 38416 11449 4303 1.0235606 24 50 0 7000 2.1142261 2.1142261 1.0160206 0.014786886 -0.94857757 2.2016194 0.7761903 16144 30 30 0 1492 38416 11449 4401 1.0160206 27 50 0 8000 2.5622926 2.5622926 1.0125365 0.019933518 -0.84991443 2.9679015 0.93716383 16302 43 43 0 1720 38416 11449 4346 1.0125365 27 50 0 9000 2.6593623 2.6593623 1.0110535 0.020725053 -0.87669675 3.0857531 0.97818336 16856 44 44 0 2000 38416 11449 4298 1.0110535 30 50 0 10000 2.7567851 2.7567851 1.0379053 0.021598993 -0.8917358 3.2158741 0.74950846 16770 50 53 0 2284 38416 11449 4316 1.0379053 30 50 0 Loop time of 9.02679 on 1 procs for 10000 steps with 14889 atoms Performance: 47857.551 tau/day, 1107.814 timesteps/s, 16.494 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 | 1.8454 | 1.8454 | 1.8454 | 0.0 | 20.44 Neigh | 0.018708 | 0.018708 | 0.018708 | 0.0 | 0.21 Comm | 0.059853 | 0.059853 | 0.059853 | 0.0 | 0.66 Output | 0.00081453 | 0.00081453 | 0.00081453 | 0.0 | 0.01 Modify | 7.0469 | 7.0469 | 7.0469 | 0.0 | 78.07 Other | | 0.05507 | | | 0.61 Nlocal: 14889 ave 14889 max 14889 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 75 ave 75 max 75 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 382 ave 382 max 382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 382 Ave neighs/atom = 0.025656525 Neighbor list builds = 500 Dangerous builds = 0 Total wall time: 0:00:11