diff --git a/examples/ASPHERE/tri/in.tri.srd b/examples/ASPHERE/tri/in.tri.srd index 9bfc9d7b65..7878b9ecc2 100644 --- a/examples/ASPHERE/tri/in.tri.srd +++ b/examples/ASPHERE/tri/in.tri.srd @@ -2,7 +2,7 @@ units lj atom_style tri -atom_modify first big +atom_modify first big map yes read_data data.tri.srd @@ -52,12 +52,12 @@ pair_coeff 1 2 0.0 1.0 0.0 timestep 0.001 -fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398 -fix 2 small srd 20 big 1.0 0.25 49894 & +fix 1 big rigid/small molecule #langevin 1.0 1.0 0.1 12398 +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 + overlap yes collision noslip inside ignore -fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6 +fix 3 all deform 1 x scale 0.8 y scale 0.8 z scale 0.8 # diagnostics @@ -73,8 +73,8 @@ compute 2 all ke compute 3 all pe variable toteng equal (c_1+c_2+c_3)/atoms -thermo 1000 -thermo_style custom step f_1 c_tsmall f_2[9] temp press +thermo 100 +thermo_style custom step f_1 c_tsmall temp press f_2[9] f_2[4] thermo_modify temp tbig compute 10 all property/atom corner1x corner1y corner1z & @@ -93,9 +93,9 @@ unfix 3 change_box all triclinic -fix 2 small srd 20 big 1.0 0.25 49894 & +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 + 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 & diff --git a/examples/ASPHERE/tri/log.15Aug23.tri.srd.g++.8 b/examples/ASPHERE/tri/log.15Aug23.tri.srd.g++.8 new file mode 100644 index 0000000000..6103a5c9c9 --- /dev/null +++ b/examples/ASPHERE/tri/log.15Aug23.tri.srd.g++.8 @@ -0,0 +1,812 @@ +LAMMPS (2 Aug 2023 - Development - patch_2Aug2023-114-gdad8081d55-modified) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:537) +# 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) + 2 by 2 by 2 MPI processor grid + reading atoms ... + 1500 atoms + 1500 triangles + read_data CPU = 0.007 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 = 0.002 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 (../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 (../thermo.cpp:527) + +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 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 +WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:71) +WARNING: Using fix srd with box deformation but no SRD thermostat (../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 (../fix_srd.cpp:2805) +WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826) +WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828) + # 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/newton + stencil: half/multi/3d + bin: multi +Per MPI rank memory allocation (min/avg/max) = 125.9 | 126.4 | 126.7 Mbytes + Step f_1 c_tsmall Temp Press f_2[9] f_2[4] + 0 0 1.4401779 0 -0.15917996 0 0 + 100 0.36662911 1.1475389 0.24585067 1.0290503 1.1382325 18 + 200 0.73133134 1.0558153 0.49986673 0.73932383 1.049638 34 + 300 1.1229361 1.0218621 0.82641583 0.7589689 1.0205369 40 + 400 1.5826262 0.99541508 1.2201293 0.69171726 0.99190857 52 + 500 1.8834563 0.99351667 1.4778822 1.0147794 1.0005581 63 + 600 2.4225372 0.98954834 1.8740966 1.1362893 0.99760042 61 + 700 3.0172772 0.99153625 2.3351502 1.3284877 0.98731355 39 + 800 3.5307913 1.0012521 2.6477224 1.1404922 0.9846605 52 + 900 3.757064 0.99743944 2.7220653 1.4078087 0.97538456 55 + 1000 4.3165268 1.002214 3.055501 1.2252972 0.99123745 63 + 1100 4.2796945 1.0075233 3.1022956 1.1893685 1.0139864 69 + 1200 4.3719315 1.0037271 3.0054509 1.3886162 1.002661 64 + 1300 4.5628012 0.99368316 3.2690604 1.3621012 0.9810568 56 + 1400 4.6954389 0.99365088 3.1940001 1.8485712 0.99571089 71 + 1500 5.0270163 0.99455258 3.4120396 1.5992539 0.98294263 77 + 1600 5.5897797 1.0021621 3.647347 1.7796904 0.98967622 66 + 1700 5.5330194 1.0130853 3.6407996 1.8005429 1.0068955 62 + 1800 5.3606928 1.0090284 3.5863618 1.3308757 1.0214092 59 + 1900 5.6086195 1.0071865 3.7427101 1.5296314 0.99886937 55 + 2000 5.3726474 1.0064207 3.603621 1.9473142 0.99999816 54 + 2100 5.836183 1.0124553 3.7321841 1.7889397 1.0188986 59 + 2200 5.5090061 1.0113832 3.5884963 1.6617781 1.0071583 59 + 2300 5.4011211 1.0095947 3.520406 1.8937582 0.99689983 61 + 2400 5.2219281 1.0053246 3.3699458 1.7231672 0.99899754 59 + 2500 5.7695275 1.0141459 3.6211469 1.7767598 1.0143133 65 + 2600 5.4206253 1.0182828 3.521774 2.0800518 1.0081603 70 + 2700 5.1401099 1.0085209 3.4200563 2.4019836 1.0107652 59 + 2800 6.5420721 1.0159876 4.1996904 1.863842 1.0160738 61 + 2900 5.9082962 1.0106921 3.7223419 2.0586998 1.0073885 67 + 3000 5.6556123 1.0099021 3.6768976 1.921987 1.0068962 76 + 3100 5.2913762 1.0008567 3.4103831 1.9831969 0.99187526 80 + 3200 5.1032361 0.99756662 3.1967156 2.2448433 0.99743574 93 + 3300 5.2622386 1.0024934 3.3325614 2.0078097 1.0047789 86 + 3400 5.1247527 0.99810102 3.1363556 1.8907269 0.98936508 82 + 3500 4.9424333 1.0009344 3.2153968 1.9002728 0.99161849 71 + 3600 5.1243735 1.0037377 3.3117313 2.1267438 1.0078943 65 + 3700 5.5045819 1.0006119 3.5686193 2.3466538 0.99876164 68 + 3800 5.5355384 1.0022639 3.6701457 2.0383269 1.0008683 76 + 3900 6.4915796 1.0137733 4.3225864 2.6996933 1.0064787 79 + 4000 6.6631737 1.0236248 4.3057163 2.6352666 1.0255232 75 + 4100 6.2999507 1.0263876 4.0101385 2.5479077 1.0168303 79 + 4200 6.7902489 1.0247392 4.4616158 2.4926177 1.0191403 91 + 4300 6.505908 1.0182073 4.0675428 2.168754 1.0177101 74 + 4400 5.9554283 1.0115938 3.5787297 2.9258144 1.0133896 72 + 4500 6.2276609 1.0202416 3.8211204 2.5308249 1.0174385 74 + 4600 6.0485727 1.0195757 3.8217434 2.6421797 1.0201441 78 + 4700 6.511063 1.0220764 3.933486 2.8591093 1.0147269 83 + 4800 6.9478172 1.0106414 4.345402 3.3257663 1.00469 85 + 4900 6.7547045 1.0211842 4.1874576 3.6503845 1.022873 94 + 5000 7.2603949 1.0234313 4.5393985 3.4667806 1.0222306 105 + 5100 7.1899652 1.0256566 4.5421834 3.8137207 1.0317242 99 + 5200 7.1960739 1.026746 4.4288606 3.5523675 1.0242269 97 + 5300 7.1294458 1.017883 4.5799808 3.3917274 1.0145317 99 + 5400 6.2810892 1.0291953 4.0109229 2.8604571 1.0289438 97 + 5500 6.15246 1.0288734 3.8714587 3.2760394 1.0210757 89 + 5600 6.5860526 1.0192882 4.0272883 3.3124298 1.0096258 93 + 5700 7.0296116 1.0097293 4.2652722 3.6049788 1.012463 82 + 5800 6.8372302 1.0140065 4.2205065 4.3686183 1.0088542 93 + 5900 7.8887098 1.0090612 4.9724078 4.457317 1.0045137 92 + 6000 10.120663 1.0312443 6.3025192 4.72018 1.0374722 91 + 6100 9.1318265 1.0304199 5.7084296 4.244548 1.0259056 97 + 6200 8.9758903 1.0295285 5.1842704 4.870955 1.0178851 95 + 6300 9.0088218 1.022484 5.3742805 5.1554352 1.0138365 101 + 6400 10.470322 1.0287848 6.4602103 4.5461489 1.0335978 105 + 6500 11.100779 1.0347405 6.9630121 4.9840664 1.0339044 99 + 6600 10.139333 1.0476079 6.4284839 4.5523893 1.0433517 104 + 6700 8.9706766 1.0386262 5.8387485 4.247024 1.0408151 101 + 6800 7.7799532 1.0362651 4.9946283 4.6093924 1.0274763 102 + 6900 8.0866551 1.0337743 4.9942769 4.1679939 1.0454805 102 + 7000 8.0224277 1.0193598 4.9380527 3.9173115 1.0185001 109 + 7100 7.8361001 1.0211143 4.872673 5.3471479 1.024779 110 + 7200 7.8542147 1.0057183 4.8666653 4.668317 0.99980296 122 + 7300 7.9313852 1.0159181 5.0062527 4.1410294 1.0195705 114 + 7400 7.2769846 1.0155245 4.6349779 4.9138895 1.0005886 119 + 7500 7.5974523 1.0196295 4.7918247 4.2525935 1.0211412 124 + 7600 6.7835063 1.0203187 4.2674694 4.9251624 1.0218296 113 + 7700 6.4039017 1.0119494 4.1086667 5.5240525 1.0078246 118 + 7800 7.0715134 1.0149015 4.2450776 4.8796778 1.0164737 125 + 7900 6.3626535 1.02294 4.202778 4.482164 1.0235878 136 + 8000 6.2423869 1.0212553 4.0460303 5.2753307 1.0124884 132 + 8100 6.550891 1.0223318 4.2993545 5.2634985 1.0163244 143 + 8200 6.9122202 1.008347 4.3551124 5.4108909 1.0084913 142 + 8300 6.9104634 1.0103936 4.4622206 5.6762373 0.99559355 143 + 8400 6.4918879 1.0084381 4.1050732 5.8389788 1.0036021 135 + 8500 7.4377218 1.0216662 4.5229841 5.5431311 1.0260799 123 + 8600 7.572198 1.0228381 4.9058913 7.1028185 1.0015164 116 + 8700 8.204675 1.03457 5.2231696 6.4790244 1.0214635 132 + 8800 8.3118914 1.0381333 5.1795799 6.7437722 1.0290086 132 + 8900 8.2559198 1.0268665 5.218352 7.2191395 1.019804 138 + 9000 8.0403128 1.0339414 4.9310394 6.4942331 1.041527 156 + 9100 7.1773079 1.0397062 4.4993688 7.0272109 1.0388012 167 + 9200 7.1793935 1.0373589 4.3481663 7.4894459 1.0078785 157 + 9300 8.3705146 1.0248112 5.1036971 8.2173072 1.010168 156 + 9400 9.4935002 1.0252907 5.7846951 9.7466018 1.028941 170 + 9500 9.5208037 1.0371093 5.9635099 7.6444933 1.022673 165 + 9600 8.9992217 1.0292895 5.6224192 8.8071452 1.0101362 169 + 9700 8.682661 1.0422224 5.3997636 8.6827834 1.0337928 149 + 9800 7.6191562 1.0350948 4.7198842 8.6125595 1.0300395 151 + 9900 8.0910913 1.0319432 4.8843183 7.9013334 1.0272495 167 + 10000 7.4438347 1.0186098 4.7184985 8.999795 0.99762661 177 +Loop time of 162.325 on 8 procs for 10000 steps with 16271 atoms + +Performance: 5322.658 tau/day, 61.605 timesteps/s, 1.002 Matom-step/s +99.3% CPU use with 8 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 33.647 | 64.106 | 79.639 | 169.5 | 39.49 +Neigh | 0.30808 | 0.44033 | 0.50863 | 9.8 | 0.27 +Comm | 26.611 | 43.438 | 74.998 | 215.7 | 26.76 +Output | 0.0072573 | 0.0087791 | 0.0097993 | 0.9 | 0.01 +Modify | 53.171 | 54.121 | 55.362 | 12.3 | 33.34 +Other | | 0.2104 | | | 0.13 + +Nlocal: 2033.88 ave 2601 max 1413 min +Histogram: 1 2 0 0 0 0 2 1 1 1 +Nghost: 1647.25 ave 1714 max 1617 min +Histogram: 4 0 1 0 0 1 1 0 0 1 +Neighs: 12482.8 ave 17009 max 8679 min +Histogram: 1 1 1 0 1 1 2 0 0 1 + +Total # of neighbors = 99862 +Ave neighs/atom = 6.1374224 +Neighbor list builds = 562 +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 40000 +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 (../fix_srd.cpp:2805) +WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2826) +WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2828) + # of rescaled SRD velocities = 1 + ave/max small velocity = 16.14994 40 + ave/max big velocity = 1.6952661 5.2200074 +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/newton/tri + stencil: half/multi/3d/tri + bin: multi +Per MPI rank memory allocation (min/avg/max) = 106.9 | 107.5 | 107.7 Mbytes + Step f_1 c_tsmall Temp Press f_2[9] f_2[4] + 10000 7.4438347 1.0189789 4.7184481 7.9505614 0 0 + 10100 7.0770142 1.0021471 4.4491455 6.606701 1 141 + 10200 6.7628072 1.002308 4.152988 8.5190386 1 125 + 10300 6.5333319 1.0007472 4.1295404 8.2341747 1 109 + 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27 + 42700 13.986613 1.001458 8.5544184 10.765136 1 29 + 42800 13.240256 1.0027899 8.2014429 10.506497 1 32 + 42900 12.784336 1.0001406 8.0823431 12.258209 1 33 + 43000 13.374145 1.0012996 8.4207155 10.32817 1 31 + 43100 13.142334 1.0022503 8.5908808 10.152205 1 32 + 43200 12.669284 1.0018944 7.8511966 10.580104 1 32 + 43300 13.155032 1.001144 8.0337768 10.6652 1 39 + 43400 12.155928 1.0019472 7.5886584 11.234772 1 35 + 43500 12.385603 1.0007639 7.8865245 9.3868914 1 32 + 43600 12.236179 1.0027456 7.7521353 10.456701 1 42 + 43700 11.49535 1.0008758 7.3633144 8.8490079 1 40 + 43800 11.469157 1.0015845 7.0035577 10.594522 1 41 + 43900 11.228266 1.0013014 7.0137223 8.0653711 1 38 + 44000 10.56742 1.0016631 6.6908938 8.1094154 1 35 + 44100 9.8964699 1.0008351 6.3550438 8.6578181 1 36 + 44200 9.041539 1.0019541 5.6721401 8.6518043 1 38 + 44300 9.0767434 1.0034191 5.7446596 8.3838528 1 38 + 44400 9.2299608 1.0019526 5.7117964 8.3106491 1 37 + 44500 9.458981 1.0030409 5.7612138 7.7679755 1 37 + 44600 8.9611997 1.0014848 5.6490756 6.9224078 1 37 + 44700 8.0853184 1.0018894 5.2288749 8.0910912 1 32 + 44800 7.9999755 1.0015853 4.8088312 7.1854304 1 30 + 44900 7.6598023 1.0009751 4.6690664 7.1999858 1 28 + 45000 7.4939315 1.0010307 4.8119666 7.9615769 1 26 + 45100 7.4690079 0.99913423 4.9704428 7.6026835 1 32 + 45200 7.7001199 1.001626 4.9315953 7.4926686 1 25 + 45300 7.8794405 1.0011648 4.8624857 8.0804457 1 26 + 45400 7.493909 1.0016257 4.7631808 8.0330626 1 26 + 45500 7.5963141 1.0005825 4.7220659 7.0971298 1 23 + 45600 7.9028612 1.0017008 4.9561022 8.440428 1 23 + 45700 7.2285584 1.0006033 4.5521456 9.385579 1 23 + 45800 7.5687284 1.0024318 4.8557498 8.3052658 1 23 + 45900 7.8938604 1.0013937 5.1393944 5.5323667 1 26 + 46000 8.318466 1.0020803 5.4761811 8.2227801 1 25 + 46100 7.9169512 1.0024598 5.0406355 8.64365 1 27 + 46200 7.5535458 1.0016318 4.8010133 9.370726 1 26 + 46300 7.8926896 1.0001525 5.18463 7.9830196 1 27 + 46400 7.487145 1.002671 4.7718312 8.300134 1 29 + 46500 7.3564658 1.0006114 4.6762189 7.34947 1 26 + 46600 7.2261291 1.0005569 4.4751221 6.5847138 1 27 + 46700 7.2943203 1.0020164 4.3335327 7.7296507 1 25 + 46800 8.5849411 1.0014634 5.4501531 9.0933014 1 25 + 46900 10.176752 1.0023799 6.0456779 9.4050423 1 16 + 47000 9.1913098 1.0029076 5.7577256 9.1826215 1 22 + 47100 9.5479771 1.0022102 6.1100973 8.9440056 1 28 + 47200 9.9944172 1.0004924 6.3649417 9.1507264 1 25 + 47300 9.3543283 1.0013246 6.0873147 10.41657 1 24 + 47400 8.594101 1.0020068 5.6864295 9.2388304 1 24 + 47500 9.3191964 1.002411 6.0537511 9.3506828 1 23 + 47600 8.1615734 1.001364 5.3757905 10.303962 1 30 + 47700 8.3615046 1.0003075 5.2727936 9.3162209 1 32 + 47800 8.3566467 1.0026031 5.4379524 7.7644422 1 33 + 47900 8.4062556 1.0006471 5.3098736 8.0181121 1 33 + 48000 8.2233307 1.0012304 4.9650027 9.2644288 1 34 + 48100 8.4495256 1.000088 4.9940422 10.01023 1 27 + 48200 8.8068097 1.0014275 5.4732649 8.410093 1 31 + 48300 8.0008187 1.0017459 4.7732764 9.25726 1 27 + 48400 7.7242529 1.0026909 4.9084505 8.7147295 1 30 + 48500 8.3752816 1.001333 5.1071228 8.2267308 1 32 + 48600 9.0777805 1.0019328 5.7331841 9.6679383 1 29 + 48700 9.3623061 1.0001767 5.7117062 8.396895 1 25 + 48800 8.1186637 1.0013185 5.2697427 8.6058372 1 27 + 48900 7.3685497 1.0007173 4.6097553 7.8047228 1 24 + 49000 7.1661421 1.0023152 4.5389038 8.8759552 1 22 + 49100 6.9857144 1.0016394 4.6489319 8.2022359 1 24 + 49200 6.7160336 1.0018413 4.2488082 8.3393245 1 25 + 49300 7.9703755 1.0010628 5.2328567 7.968278 1 28 + 49400 8.2628465 1.0010877 5.2292977 8.0196533 1 27 + 49500 8.1436558 1.0015175 5.0344712 8.0712037 1 30 + 49600 8.5182498 1.0021589 5.1029028 8.6869789 1 28 + 49700 8.3604444 1.0015016 5.0333696 9.4861656 1 25 + 49800 7.336335 1.0020055 4.6365173 8.7210022 1 30 + 49900 7.432996 1.0016415 4.7090587 8.7033033 1 29 + 50000 7.4937053 1.001014 4.7212573 9.0890363 1 29 +Loop time of 999.576 on 8 procs for 40000 steps with 16271 atoms + +Performance: 3457.466 tau/day, 40.017 timesteps/s, 651.116 katom-step/s +99.3% CPU use with 8 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 293.48 | 403.7 | 545.29 | 357.5 | 40.39 +Neigh | 2.4176 | 3.2721 | 3.8303 | 25.2 | 0.33 +Comm | 163.58 | 305.88 | 419.83 | 416.7 | 30.60 +Output | 0.032483 | 0.034794 | 0.040514 | 1.2 | 0.00 +Modify | 281.15 | 285.67 | 293.8 | 24.3 | 28.58 +Other | | 1.023 | | | 0.10 + +Nlocal: 2033.88 ave 2657 max 1198 min +Histogram: 2 0 0 0 0 2 1 0 1 2 +Nghost: 1628.12 ave 1719 max 1569 min +Histogram: 2 0 1 1 2 1 0 0 0 1 +Neighs: 13566 ave 18212 max 8488 min +Histogram: 1 0 0 1 2 1 2 0 0 1 + +Total # of neighbors = 108528 +Ave neighs/atom = 6.6700264 +Neighbor list builds = 2447 +Dangerous builds = 2 +Total wall time: 0:19:22 diff --git a/examples/ASPHERE/tri/log.1Feb14.tri.srd.g++.8 b/examples/ASPHERE/tri/log.1Feb14.tri.srd.g++.8 deleted file mode 100644 index 135eecb1e5..0000000000 --- a/examples/ASPHERE/tri/log.1Feb14.tri.srd.g++.8 +++ /dev/null @@ -1,243 +0,0 @@ -LAMMPS (1 Feb 2014) -# Aspherical shear demo - 3d triangle boxes, solvated by SRD particles - -units lj -atom_style tri -atom_modify first big - -read_data data.tri.srd - orthogonal box = (-8.43734 -8.43734 -8.43734) to (8.43734 8.43734 8.43734) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 1500 atoms - 1500 triangles - -# add small particles as hi density lattice - -lattice sc 0.4 -Lattice spacing in x,y,z = 1.35721 1.35721 1.35721 -region box block INF INF INF INF INF INF -lattice sc 20.0 -Lattice spacing in x,y,z = 0.368403 0.368403 0.368403 -create_atoms 2 region box -Created 91125 atoms - -group big type 1 -1500 atoms in group big -group small type 2 -91125 atoms in group small -set group small mass 0.01 - 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 -Deleted 76354 atoms, new total = 16271 - -# SRD run - -reset_timestep 0 - -velocity small create 1.44 87287 loop geom - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes -neigh_modify exclude molecule big include big - -communicate 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 molecule #langevin 1.0 1.0 0.1 12398 -125 rigid bodies with 1500 atoms -fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip - -fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6 - -# 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 1 big erotate/asphere -compute 2 all ke -compute 3 all pe -variable toteng equal (c_1+c_2+c_3)/atoms - -thermo 1000 -thermo_style custom step f_1 c_tsmall f_2[9] temp press -thermo_modify temp tbig -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439) - -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 10000 -WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385) -SRD info: - SRD/big particles = 14771 1500 - big particle diameter max/min = 1.46014 0.436602 - SRD temperature & lamda = 1 0.2 - SRD max distance & max velocity = 0.8 40 - SRD grid counts: 67 67 67 - SRD grid size: request, actual (xyz) = 0.25, 0.251861 0.251861 0.251861 - SRD per actual grid cell = 0.0647662 - SRD viscosity = -1.09837 - big/SRD mass density ratio = 24.668 -WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853) -WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875) -WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877) - # of rescaled SRD velocities = 0 - ave/max small velocity = 19.9708 35.1504 - ave/max big velocity = 0 0 -WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76) -Memory usage per processor = 116.135 Mbytes -Step 1 tsmall 2[9] Temp Press - 0 0 1.4405441 0 0 -0.15917996 - 1000 1.0535509 1.1241378 1.1224038 0 0.15526438 - 2000 2.4635987 1.0240667 0.94231519 0 0.011069846 - 3000 3.1093028 1.0070585 1.0176028 0 0.34124888 - 4000 2.9524179 1.0101774 1.0311733 0 -0.22118101 - 5000 2.9175438 1.0109144 1.0284445 0 0.1839507 - 6000 3.3200928 0.99108983 0.95968219 0 1.0229339 - 7000 3.3020156 0.99661428 0.98000621 0 2.3333851 - 8000 4.1500999 0.99129645 0.99723707 0 4.3054414 - 9000 6.537028 1.0074533 1.0251098 0 18.782913 - 10000 16.233245 1.0145766 1.0219787 0 147.83787 -Loop time of 228.558 on 8 procs for 10000 steps with 16271 atoms - -Pair time (%) = 145.018 (63.4492) -Neigh time (%) = 32.6283 (14.2757) -Comm time (%) = 43.3283 (18.9572) -Outpt time (%) = 0.000848889 (0.00037141) -Other time (%) = 7.58254 (3.31755) - -Nlocal: 2033.88 ave 2092 max 1902 min -Histogram: 1 0 0 0 1 1 0 1 1 3 -Nghost: 2805 ave 2855 max 2751 min -Histogram: 1 0 2 1 0 0 0 2 1 1 -Neighs: 30026.5 ave 38700 max 24367 min -Histogram: 1 0 2 1 3 0 0 0 0 1 - -Total # of neighbors = 240212 -Ave neighs/atom = 14.7632 -Neighbor list builds = 501 -Dangerous builds = 0 - -#undump 1 -#undump 2 -unfix 3 - -change_box all triclinic - triclinic box = (-5.0624 -5.0624 -5.0624) to (5.0624 5.0624 5.0624) with tilt (0 0 0) - -fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes - -#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 40000 -SRD info: - SRD/big particles = 14771 1500 - big particle diameter max/min = 1.46014 0.436602 - SRD temperature & lamda = 1 0.2 - SRD max distance & max velocity = 0.8 40 - SRD grid counts: 40 40 40 - SRD grid size: request, actual (xyz) = 0.25, 0.25312 0.25312 0.25312 - SRD per actual grid cell = -1.93929 - SRD viscosity = -0.36972 - big/SRD mass density ratio = -0.836253 -WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2853) -WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875) -WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877) - # of rescaled SRD velocities = 1 - ave/max small velocity = 16.0639 40 - ave/max big velocity = 2.05735 6.73052 -Memory usage per processor = 65.2471 Mbytes -Step 1 tsmall 2[9] Temp Press - 10000 16.233245 1.0144194 0 0 146.27032 - 11000 17.301043 1.0619209 1 0 84.226323 - 12000 13.481177 1.063945 1 0 80.42834 - 13000 12.616615 1.0536125 1 0 68.365053 - 14000 12.16592 1.0581344 1 0 59.709941 - 15000 10.811557 1.0650453 1 0 59.869798 - 16000 9.9303081 1.0641012 1 0 59.289126 - 17000 10.452639 1.0589904 1 0 52.680235 - 18000 9.2488947 1.0556713 1 0 51.044123 - 19000 8.7179788 1.0566791 1 0 50.927924 - 20000 7.8641299 1.0668891 1 0 53.961014 - 21000 8.4333975 1.0628003 1 0 54.677068 - 22000 8.554623 1.0591872 1 0 51.784737 - 23000 7.895462 1.0598512 1 0 53.26885 - 24000 7.7014869 1.055569 1 0 54.236941 - 25000 7.508138 1.0581539 1 0 53.297709 - 26000 8.0707381 1.0586451 1 0 51.411341 - 27000 8.224223 1.0585509 1 0 52.775784 - 28000 8.8720461 1.0648837 1 0 49.681447 - 29000 8.503895 1.0538278 1 0 52.478556 - 30000 8.2272425 1.0625583 1 0 52.795709 - 31000 8.4626161 1.0599557 1 0 52.905343 - 32000 7.7410527 1.0587681 1 0 57.464472 - 33000 7.2765481 1.0677531 1 0 59.46728 - 34000 7.036016 1.0640728 1 0 60.636828 - 35000 8.497203 1.0577458 1 0 55.257312 - 36000 8.9218761 1.0585038 1 0 55.668201 - 37000 8.0469115 1.0561193 1 0 58.711565 - 38000 8.6456966 1.0663818 1 0 53.691658 - 39000 8.566667 1.0616928 1 0 52.866468 - 40000 7.7081259 1.0577046 1 0 54.105829 - 41000 7.4051952 1.0570277 1 0 56.094997 - 42000 7.331432 1.0632261 1 0 55.661067 - 43000 7.5587053 1.0602077 1 0 54.30762 - 44000 7.4521497 1.0594391 1 0 52.993548 - 45000 7.6234559 1.0641992 1 0 53.352202 - 46000 8.0659693 1.0609367 1 0 50.302682 - 47000 7.5227882 1.0563543 1 0 50.43551 - 48000 8.0798684 1.0628968 1 0 48.419201 - 49000 7.130784 1.0594143 1 0 50.656081 - 50000 7.3219268 1.0608236 1 0 54.808358 -Loop time of 1651.84 on 8 procs for 40000 steps with 16271 atoms - -Pair time (%) = 1232.76 (74.6296) -Neigh time (%) = 171.893 (10.4061) -Comm time (%) = 193.625 (11.7218) -Outpt time (%) = 0.00338289 (0.000204795) -Other time (%) = 53.5578 (3.24231) - -Nlocal: 2033.88 ave 2229 max 1953 min -Histogram: 2 1 2 2 0 0 0 0 0 1 -Nghost: 2757.88 ave 2810 max 2692 min -Histogram: 1 1 1 0 1 0 0 1 1 2 -Neighs: 30098.6 ave 37369 max 25592 min -Histogram: 1 3 0 1 0 1 1 0 0 1 - -Total # of neighbors = 240789 -Ave neighs/atom = 14.7987 -Neighbor list builds = 2007 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index 74f9ea8241..86be5bab67 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -2645,7 +2645,6 @@ void FixSRD::parameterize() if (radius && radius[i] > 0.0) { double r = radfactor * radius[i]; volbig += 4.0 / 3.0 * MY_PI * r * r * r; - ; } else if (ellipsoid && ellipsoid[i] >= 0) { double *shape = ebonus[ellipsoid[i]].shape; volbig += 4.0 / 3.0 * MY_PI * shape[0] * shape[1] * shape[2] * radfactor * radfactor * @@ -2658,7 +2657,7 @@ void FixSRD::parameterize() MathExtra::sub3(c2, c1, c2mc1); MathExtra::sub3(c3, c1, c3mc1); MathExtra::cross3(c2mc1, c3mc1, cross); - volbig += 0.5 * MathExtra::len3(cross); + volbig += 0.5 * MathExtra::len3(cross) * WIDTH; } } } else {