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 # Aspherical shear demo - 3d triangle boxes, solvated by SRD particles units lj atom_style tri atom_modify first big map yes read_data data.tri.srd Reading data file ... orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405) 1 by 1 by 1 MPI processor grid reading atoms ... 1500 atoms 1500 triangles read_data CPU = 0.013 seconds # add small particles as hi density lattice lattice sc 0.4 Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088 region box block INF INF INF INF INF INF lattice sc 20.0 Lattice spacing in x,y,z = 0.36840315 0.36840315 0.36840315 create_atoms 2 region box Created 91125 atoms using lattice units in orthogonal box = (-8.4373405 -8.4373405 -8.4373405) to (8.4373405 8.4373405 8.4373405) create_atoms CPU = 0.014 seconds group big type 1 1500 atoms in group big group small type 2 91125 atoms in group small set group small mass 0.01 Setting atom values ... 91125 settings made for mass # delete overlaps # must set 1-2 cutoff to non-zero value pair_style lj/cut 1.5 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 delete_atoms overlap 1.5 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 = 1.8 ghost atom cutoff = 1.8 binsize = 0.9, bins = 19 19 19 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/3d bin: standard (2) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:312) Deleted 76354 atoms, new total = 16271 # SRD run reset_timestep 0 velocity small create 1.44 87287 loop geom neighbor 0.3 multi neigh_modify delay 0 every 1 check yes neigh_modify exclude molecule/intra big include big comm_modify mode multi group big vel yes neigh_modify include big # no pairwise interactions with small particles pair_style tri/lj 3.5 pair_coeff 1 1 0.1 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/small molecule #langevin 1.0 1.0 0.1 12398 create bodies CPU = 0.000 seconds 125 rigid bodies with 1500 atoms 1.8601881 = max distance from body owner to body atom fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip inside ignore fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8 # diagnostics compute tsmall small temp/deform compute tbig big temp variable pebig equal pe*atoms/count(big) variable ebig equal etotal*atoms/count(big) compute_modify tbig extra/dof -4500 compute 1 big erotate/asphere compute 2 all ke compute 3 all pe variable toteng equal (c_1+c_2+c_3)/atoms thermo 100 thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4] thermo_modify temp tbig WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:530) compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z #dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz #dump 2 all custom 500 dump1.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9] run 1000 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 WARNING: Using compute temp/deform with inconsistent fix deform remap option (src/compute_temp_deform.cpp:71) WARNING: Using fix srd with box deformation but no SRD thermostat (src/SRD/fix_srd.cpp:405) SRD info: SRD/big particles = 14771 1500 big particle diameter max/min = 2.9202881 0.87320391 SRD temperature & lamda = 1 0.2 SRD max distance & max velocity = 0.8 40 SRD grid counts: 17 17 17 SRD grid size: request, actual (xyz) = 1, 0.99262829 0.99262829 0.99262829 SRD per actual grid cell = -3.9971745 SRD viscosity = -34.162587 big/SRD mass density ratio = -3.3753691 WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809) WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830) WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832) # of rescaled SRD velocities = 0 ave/max small velocity = 19.970837 35.150443 ave/max big velocity = 0 0 Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.8 ghost atom cutoff = 3.8 binsize = 16.874681, bins = 1 1 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair tri/lj, perpetual attributes: half, newton on pair build: half/multi/atomonly/newton stencil: half/multi/3d bin: multi Per MPI rank memory allocation (min/avg/max) = 381.8 | 381.8 | 381.8 Mbytes Step f_1 c_tsmall Temp Press f_2[9] f_2[4] 0 0 1.4502537 0 -0.15976045 0 0 100 0.41802172 1.152223 0.27557714 1.0421065 1.1470081 283 200 0.79710339 1.0669332 0.5813323 0.97699684 1.0361619 534 300 1.3739181 1.0275476 1.0869716 0.81001536 1.0211312 658 400 1.9355117 1.0155457 1.5813236 1.7798798 0.99354559 831 500 2.8557382 1.0005021 2.267698 3.3903849 0.98597972 927 600 4.7851916 1.0156689 3.730334 2.838776 0.99140534 1053 700 5.3647697 1.0176657 3.9593121 5.1189107 0.9972029 1218 800 8.23688 1.0268086 5.899689 6.8199153 0.99310516 1349 900 9.9330758 1.0356047 7.0260595 7.2596589 0.98360014 1607 1000 9.8719995 1.043178 6.9903792 10.05101 1.0045416 1805 Loop time of 79.2664 on 1 procs for 1000 steps with 16271 atoms Performance: 1089.995 tau/day, 12.616 timesteps/s, 205.270 katom-step/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 | 57.961 | 57.961 | 57.961 | 0.0 | 73.12 Neigh | 0.34589 | 0.34589 | 0.34589 | 0.0 | 0.44 Comm | 0.28615 | 0.28615 | 0.28615 | 0.0 | 0.36 Output | 0.0022784 | 0.0022784 | 0.0022784 | 0.0 | 0.00 Modify | 20.644 | 20.644 | 20.644 | 0.0 | 26.04 Other | | 0.02724 | | | 0.03 Nlocal: 16271 ave 16271 max 16271 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4612 ave 4612 max 4612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99463 ave 99463 max 99463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99463 Ave neighs/atom = 6.1129003 Neighbor list builds = 72 Dangerous builds = 0 #undump 1 #undump 2 unfix 3 change_box all triclinic Changing box ... triclinic box = (-6.7498724 -6.7498724 -6.7498724) to (6.7498724 6.7498724 6.7498724) with tilt (0 0 0) fix 2 small srd 20 big 1.0 1.0 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes inside ignore #dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz #dump 2 all custom 500 dump2.tri.srd id type # c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] # c_10[7] c_10[8] c_10[9] fix 3 all deform 1 xy erate 0.05 units box remap v run 2000 Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule SRD info: SRD/big particles = 14771 1500 big particle diameter max/min = 2.9202881 0.87320391 SRD temperature & lamda = 1 0.2 SRD max distance & max velocity = 0.8 40 SRD grid counts: 13 13 13 SRD grid size: request, actual (xyz) = 1, 1.0384419 1.0384419 1.0384419 SRD per actual grid cell = -2.775698 SRD viscosity = -12.180602 big/SRD mass density ratio = -5.5653033 WARNING: SRD bin size for fix srd differs from user request (src/SRD/fix_srd.cpp:2809) WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2830) WARNING: Fix srd viscosity < 0.0 due to low SRD density (src/SRD/fix_srd.cpp:2832) # of rescaled SRD velocities = 3 ave/max small velocity = 16.23763 40 ave/max big velocity = 1.9825234 5.257255 Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.8 ghost atom cutoff = 3.8 binsize = 13.499745, bins = 1 1 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair tri/lj, perpetual attributes: half, newton on pair build: half/multi/atomonly/newton/tri stencil: half/multi/3d/tri bin: multi Per MPI rank memory allocation (min/avg/max) = 278.4 | 278.4 | 278.4 Mbytes Step f_1 c_tsmall Temp Press f_2[9] f_2[4] 1000 9.8719995 1.0317167 6.98982 4.0948969 0 0 1100 7.6460335 1.0028444 5.2446585 6.6348814 1 1320 1200 6.2789381 1.0012003 4.5257435 6.3278972 1 1024 1300 5.5060209 1.002182 3.7063549 7.0004503 1 794 1400 5.4107119 1.002291 3.594515 7.9511695 1 621 1500 5.072582 1.0001037 3.2501353 8.6993671 1 503 1600 4.7912016 0.99982803 3.1208274 6.464157 1 416 1700 4.5518848 1.0030059 2.9084074 6.3278992 1 346 1800 4.368682 1.000831 2.807184 6.7382017 1 282 1900 4.458655 1.0012568 2.7966515 6.0124309 1 246 2000 4.1256128 1.0004032 2.763649 6.3707442 1 208 2100 3.7040346 1.0004125 2.4398152 5.4213931 1 181 2200 4.2347861 1.002625 2.6206986 6.6832437 1 151 2300 4.254984 1.0028871 2.6794167 7.1661525 1 127 2400 4.1017692 1.0028508 2.6371178 8.388599 1 105 2500 3.9285571 1.0002888 2.5002741 6.0806187 1 95 2600 3.6239964 1.0012152 2.2573993 6.7863124 1 80 2700 3.4085702 1.0023974 2.1179914 6.7351139 1 68 2800 3.1399303 1.0005349 2.0163219 6.4502765 1 61 2900 3.1277562 1.0004013 2.0453134 6.6485498 1 51 3000 3.0737732 1.0022962 1.997382 6.797214 1 44 Loop time of 206.387 on 1 procs for 2000 steps with 16271 atoms Performance: 837.264 tau/day, 9.691 timesteps/s, 157.675 katom-step/s 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 173.6 | 173.6 | 173.6 | 0.0 | 84.12 Neigh | 1.0077 | 1.0077 | 1.0077 | 0.0 | 0.49 Comm | 0.58656 | 0.58656 | 0.58656 | 0.0 | 0.28 Output | 0.0042824 | 0.0042824 | 0.0042824 | 0.0 | 0.00 Modify | 31.128 | 31.128 | 31.128 | 0.0 | 15.08 Other | | 0.05664 | | | 0.03 Nlocal: 16271 ave 16271 max 16271 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4521 ave 4521 max 4521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94777 ave 94777 max 94777 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94777 Ave neighs/atom = 5.8249032 Neighbor list builds = 100 Dangerous builds = 0 Total wall time: 0:04:47