LAMMPS (1 Feb 2014) # 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 read_data data.box fix molprop NULL Molecules orthogonal box = (-19.1447 -19.1447 -0.5) to (19.1447 19.1447 0.5) 4 by 2 by 1 MPI processor grid reading atoms ... 420 atoms set type 1 mass 1.0 420 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 thermo 100 run 1000 Memory usage per processor = 0.443012 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 0 0 0 -8.770036 100 0 3.4203218 0 3.4203218 0.49351517 200 0 5.3315601 0 5.3315601 0.26965614 300 0 7.2094878 0 7.2094878 0.43326479 400 0 9.2008598 0 9.2008598 0.27649318 500 0 11.562353 0 11.562353 0.60730421 600 0 13.731564 0 13.731564 0.27272312 700 0 15.850142 0 15.850142 0.0032862218 800 0 18.395444 0 18.395444 1.0272658 900 0 20.3322 0 20.3322 -0.16729762 1000 0 22.600716 0 22.600716 -0.13023705 Loop time of 0.0534293 on 8 procs for 1000 steps with 420 atoms Pair time (%) = 0.00388658 (7.27425) Neigh time (%) = 0.0012759 (2.38801) Comm time (%) = 0.0151907 (28.4315) Outpt time (%) = 0.000330567 (0.618701) Other time (%) = 0.0327455 (61.2876) Nlocal: 52.5 ave 67 max 35 min Histogram: 1 1 1 0 1 0 0 1 1 2 Nghost: 30.625 ave 41 max 17 min Histogram: 1 0 0 1 1 1 2 0 1 1 Neighs: 70.25 ave 90 max 44 min Histogram: 2 0 0 1 1 0 1 0 0 3 Total # of neighbors = 562 Ave neighs/atom = 1.3381 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 = 0.108465 0.108465 0.108465 create_atoms 2 region plane Created 124609 atoms set type 2 mass 0.1 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 Deleted 51030 atoms, new total = 73999 # SRD run reset_timestep 0 neighbor 0.3 bin neigh_modify delay 0 every 1 check yes communicate 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 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 (../thermo.cpp:439) 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 100000 SRD info: SRD/big particles = 73579 420 big particle diameter max/min = 1 1 SRD temperature & lamda = 1 0.0632456 SRD max distance & max velocity = 0.252982 12.6491 SRD grid counts: 153 153 1 SRD grid size: request, actual (xyz) = 0.25, 0.250257 0.250257 1 SRD per actual grid cell = 4.05573 SRD viscosity = 0.229297 big/SRD mass density ratio = 0.196614 WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875) # of rescaled SRD velocities = 0 ave/max small velocity = 4.19668 7.72762 ave/max big velocity = 2.12757 5.83591 Memory usage per processor = 14.2707 Mbytes Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 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 3.4640099 16291 0.24158286 42.201127 42.564024 10.312083 10282 38 38 0 957 90440 23409 16291 0.91054529 0 69 0 2000 1.4820124 16228 0.24022248 42.169082 42.324341 9.5969069 10066 30 30 0 1726 90440 23409 16228 0.91140743 0 69 0 3000 1.3797075 16198 0.24017061 42.170661 42.315202 11.093574 10151 43 43 0 2410 90440 23409 16198 0.91909014 0 69 0 4000 1.3403741 16287 0.24014493 42.170257 42.310677 10.101336 10172 38 38 0 3094 90440 23409 16287 0.92752333 0 69 0 5000 1.0444432 16295 0.2399965 42.175108 42.284525 9.5498999 10375 26 26 0 3799 90440 23409 16295 0.93506273 0 69 0 6000 0.78295352 16299 0.2398933 42.184319 42.266343 9.535916 10090 37 37 0 4563 90440 23409 16299 0.93041308 0 69 0 7000 1.1675613 16333 0.24006565 42.174393 42.296709 11.594065 10426 37 37 0 5266 90440 23409 16333 0.94031182 0 69 0 8000 1.1343357 16302 0.24001364 42.168711 42.287546 9.8091173 9979 39 39 0 5993 90440 23409 16302 0.94116994 0 69 0 9000 1.4165164 16306 0.24010969 42.156072 42.304469 10.736953 10191 38 39 1 6683 90440 23409 16306 0.93957787 0 69 0 10000 0.63657628 16306 0.23958347 42.145066 42.211755 6.3923231 10115 37 37 0 7409 90440 23409 16306 0.9420945 0 69 0 11000 0.9421837 16286 0.23976832 42.145619 42.244324 9.9611184 10079 45 45 0 8122 90440 23409 16286 0.94240902 0 69 0 12000 0.9735159 16295 0.23980202 42.148274 42.250262 11.862106 10345 36 36 0 8854 90440 23409 16295 0.94994179 0 69 0 13000 0.93356977 16392 0.23970059 42.134589 42.232391 11.29915 10321 41 41 0 9607 90440 23409 16392 0.94747955 0 69 0 14000 1.0596151 16306 0.2397451 42.129226 42.240233 12.305503 10075 37 37 0 10323 90440 23409 16306 0.94857373 0 69 0 15000 1.4275311 16285 0.23986502 42.11181 42.261361 8.6785032 9963 43 43 0 11054 90440 23409 16285 0.95130035 0 69 0 16000 1.1798179 16367 0.23973717 42.115236 42.238836 9.7201163 10138 38 38 0 11785 90440 23409 16367 0.94838949 0 69 0 17000 1.2809316 16368 0.23978706 42.113433 42.247626 7.4568393 10239 31 31 0 12545 90440 23409 16368 0.94818482 0 69 0 18000 1.0552359 16355 0.23962676 42.108834 42.219382 11.024507 10270 39 39 0 13350 90440 23409 16355 0.94825339 0 69 0 19000 1.1373204 16343 0.23964456 42.103371 42.222519 9.1505749 10245 37 37 0 14198 90440 23409 16343 0.94776971 0 69 0 20000 0.89607862 16295 0.23962161 42.1246 42.218475 8.377591 10173 48 48 0 14985 90440 23409 16295 0.95836326 0 69 0 21000 0.93823225 16323 0.23958542 42.113808 42.212099 9.9128627 10398 39 39 0 15722 90440 23409 16323 0.94732512 0 69 0 22000 1.0132051 16270 0.23958637 42.106121 42.212267 12.521464 10414 37 37 1 16538 90440 23409 16270 0.94611956 0 69 0 23000 1.2399208 16420 0.2396696 42.097034 42.226931 9.1607507 10169 32 32 0 17263 90440 23409 16420 0.95141771 0 69 0 24000 1.2359103 16395 0.23957354 42.080529 42.210006 10.051289 10225 34 34 1 18057 90440 23409 16395 0.95487046 0 69 0 25000 0.96280337 16322 0.23944374 42.086271 42.187136 11.818136 10183 40 40 0 18818 90440 23409 16322 0.95691179 0 69 0 26000 0.83139747 16344 0.23940306 42.09287 42.179968 10.844701 10090 38 38 0 19555 90440 23409 16344 0.95332651 0 69 0 27000 1.107274 16270 0.23949948 42.080957 42.196957 14.435937 10028 46 46 0 20355 90440 23409 16270 0.95321506 0 69 0 28000 1.0892583 16399 0.23938721 42.063064 42.177177 9.3768225 10011 38 38 0 21195 90440 23409 16399 0.95935372 0 69 0 29000 1.1099534 16320 0.23940855 42.064655 42.180936 8.8044985 9919 34 34 0 22020 90440 23409 16320 0.95465302 0 69 0 30000 1.0119272 16302 0.23934223 42.06324 42.169252 12.13721 10160 47 47 0 22750 90440 23409 16302 0.94922806 0 69 0 31000 0.9567755 16335 0.23916982 42.038642 42.138875 8.3903033 10007 30 30 0 23497 90440 23409 16335 0.95223124 0 69 0 32000 0.86048362 16291 0.23910468 42.037252 42.127398 11.646647 10347 41 41 0 24266 90440 23409 16291 0.95484469 0 69 0 33000 1.1129645 16284 0.23928206 42.042053 42.15865 9.0389494 9909 33 33 0 25073 90440 23409 16284 0.96246044 0 69 0 34000 1.0741874 16303 0.23920774 42.033022 42.145556 12.710332 10125 35 35 0 25845 90440 23409 16303 0.95343962 0 69 0 35000 0.87606515 16293 0.23916564 42.046361 42.138139 13.784203 10044 42 42 0 26569 90440 23409 16293 0.95827172 0 69 0 36000 0.8268686 16315 0.23912916 42.045087 42.131712 13.474499 10240 43 44 0 27324 90440 23409 16315 0.9539089 0 69 0 37000 1.1732368 16336 0.23930076 42.039035 42.161945 8.7392785 9996 34 34 0 28094 90440 23409 16336 0.95672234 0 69 0 38000 1.089263 16323 0.2391967 42.029498 42.143611 9.464664 10104 39 39 0 28856 90440 23409 16323 0.95362271 0 69 0 39000 1.06444 16335 0.23919427 42.03167 42.143183 10.036973 9961 36 36 0 29607 90440 23409 16335 0.95464483 0 69 0 40000 1.1390869 16376 0.23927054 42.037288 42.156621 9.8133871 10206 38 38 0 30409 90440 23409 16376 0.95191201 0 69 0 41000 0.76020035 16347 0.23906101 42.040064 42.119704 10.826738 10406 41 41 0 31195 90440 23409 16347 0.94685002 0 69 0 42000 1.3087439 16311 0.23945151 42.051398 42.188505 11.375199 10219 45 45 0 31938 90440 23409 16311 0.95326292 0 69 0 43000 0.98306175 16313 0.23923796 42.047893 42.15088 10.536429 10269 47 47 0 32660 90440 23409 16313 0.94791465 0 69 0 44000 1.1067947 16299 0.23929754 42.045427 42.161377 10.366386 10166 33 33 0 33471 90440 23409 16299 0.9520033 0 69 0 45000 1.1754605 16269 0.2394174 42.059352 42.182496 7.898603 9985 37 37 0 34245 90440 23409 16269 0.95500544 0 69 0 46000 0.93860976 16272 0.23926541 42.057387 42.155717 11.566786 10108 35 35 0 35050 90440 23409 16272 0.95183186 0 69 0 47000 1.3576761 16315 0.23942 42.040721 42.182954 10.037574 9902 33 33 0 35807 90440 23409 16315 0.95525561 0 69 0 48000 1.3465813 16308 0.23938501 42.035719 42.176789 8.9584586 9830 33 33 0 36625 90440 23409 16308 0.95044669 0 69 0 49000 0.93823974 16340 0.23917669 42.041793 42.140085 10.474409 9930 35 35 0 37393 90440 23409 16340 0.94869206 0 69 0 50000 1.0643183 16332 0.23923523 42.0389 42.1504 8.9372951 9886 43 43 0 38182 90440 23409 16332 0.94865149 0 69 0 51000 0.87518396 16310 0.23914944 42.043598 42.135284 11.284535 9695 40 40 0 38995 90440 23409 16310 0.9560088 0 69 0 52000 1.1910982 16336 0.23929054 42.035364 42.160145 12.437325 9961 44 44 0 39787 90440 23409 16336 0.95735399 0 69 0 53000 1.0023949 16384 0.23923896 42.046043 42.151056 10.386358 9859 36 36 0 40569 90440 23409 16384 0.95693245 0 69 0 54000 0.98715708 16261 0.23921241 42.042962 42.146379 9.9941499 10027 35 35 0 41343 90440 23409 16261 0.951038 0 69 0 55000 1.0004435 16299 0.23914811 42.030241 42.135049 12.345206 9830 47 48 0 42056 90440 23409 16299 0.95562154 0 69 0 56000 1.0479458 16296 0.23914874 42.025377 42.135162 11.587952 9801 39 39 0 42915 90440 23409 16296 0.94868699 0 69 0 57000 0.94369119 16319 0.23902076 42.013749 42.112612 10.195934 9764 46 46 0 43652 90440 23409 16319 0.95438171 0 69 0 58000 1.1549569 16347 0.23924582 42.031269 42.152265 9.511812 9910 41 41 0 44366 90440 23409 16347 0.9484367 0 69 0 59000 0.81453047 16402 0.23895926 42.016445 42.101776 10.359564 9967 46 46 0 45115 90440 23409 16402 0.95256147 0 69 0 60000 0.9253868 16360 0.23897085 42.006873 42.103818 12.308731 9839 44 44 0 45872 90440 23409 16360 0.95753176 0 69 0 61000 0.95173279 16298 0.23908799 42.024752 42.124457 10.985428 9848 45 45 0 46621 90440 23409 16298 0.95937218 0 69 0 62000 1.0168886 16273 0.23910318 42.020603 42.127134 13.493586 9842 41 41 0 47356 90440 23409 16273 0.95720763 0 69 0 63000 0.59853847 16306 0.23888991 42.026854 42.089558 11.654045 10030 47 47 0 48152 90440 23409 16306 0.95164201 0 69 0 64000 0.88165231 16295 0.23904152 42.023907 42.11627 8.6017877 9808 31 31 0 48944 90440 23409 16295 0.95791125 0 69 0 65000 0.83089386 16306 0.23895929 42.014736 42.101782 11.57787 10042 51 51 0 49729 90440 23409 16306 0.95848466 0 69 0 66000 1.1172469 16324 0.23919188 42.025716 42.142761 11.423941 9802 55 55 0 50498 90440 23409 16324 0.94666759 0 69 0 67000 0.97470955 16356 0.23903681 42.013327 42.11544 11.345125 10043 40 40 0 51251 90440 23409 16356 0.95264876 0 69 0 68000 0.90592443 16274 0.23906764 42.025966 42.120872 11.050097 9782 44 44 0 52009 90440 23409 16274 0.95334971 0 69 0 69000 1.0820724 16352 0.23920813 42.032265 42.145625 11.892518 9803 43 43 0 52800 90440 23409 16352 0.95290952 0 69 0 70000 1.0413192 16301 0.23929529 42.051891 42.160982 13.193444 9847 48 48 0 53595 90440 23409 16301 0.95613844 0 69 0 71000 0.95433723 16430 0.23919345 42.04306 42.143038 12.116035 9898 46 46 0 54350 90440 23409 16430 0.95532726 0 69 0 72000 0.80923962 16318 0.23909626 42.041137 42.125915 10.240888 9800 37 37 0 55133 90440 23409 16318 0.95196829 0 69 0 73000 0.93773964 16330 0.23920083 42.046099 42.144338 13.100955 9780 37 37 0 55931 90440 23409 16330 0.95075325 0 69 0 74000 1.0547823 16296 0.23913003 42.021364 42.131865 12.215247 10308 45 45 0 56705 90440 23409 16296 0.95515593 0 69 0 75000 0.74939607 16287 0.23910386 42.048745 42.127253 10.270685 10092 43 43 0 57457 90440 23409 16287 0.95365363 0 69 0 76000 0.95221448 16326 0.23921923 42.047825 42.147581 10.33549 10191 47 47 0 58254 90440 23409 16326 0.95389896 0 69 0 77000 0.94854568 16249 0.23925669 42.054809 42.15418 10.317964 10055 35 35 1 59026 90440 23409 16249 0.95716276 0 69 0 78000 1.2663624 16282 0.23949043 42.062695 42.195362 10.496265 9893 41 41 0 59780 90440 23409 16282 0.94847998 0 69 0 79000 0.98933199 16264 0.2392933 42.056987 42.160631 12.876564 9946 41 41 0 60518 90440 23409 16264 0.95354593 0 69 0 80000 0.8212992 16341 0.23927469 42.07131 42.157351 8.5608431 9838 40 40 0 61296 90440 23409 16341 0.95234534 0 69 0 81000 0.98231967 16339 0.23928757 42.056712 42.159622 11.491156 10104 37 38 0 62061 90440 23409 16339 0.94886686 0 69 0 82000 0.99158973 16299 0.23925843 42.050607 42.154488 9.4538952 10047 37 37 0 62852 90440 23409 16299 0.95656275 0 69 0 83000 1.2341517 16344 0.239348 42.040977 42.170269 10.524371 9784 37 37 0 63608 90440 23409 16344 0.94780456 0 69 0 84000 1.1753084 16288 0.23928447 42.035947 42.159074 9.1748883 9831 37 37 0 64314 90440 23409 16288 0.94217045 0 69 0 85000 0.84912682 16310 0.23915288 42.046935 42.135891 11.43337 9890 42 42 0 64992 90440 23409 16310 0.9423407 0 69 0 86000 0.88939653 16275 0.23909757 42.032971 42.126146 12.34417 9961 46 46 0 65677 90440 23409 16275 0.93887016 0 69 0 87000 1.1303842 16248 0.23922093 42.029458 42.147879 11.934641 9945 47 47 0 66417 90440 23409 16248 0.93840688 0 69 0 88000 1.2294052 16326 0.23916023 42.00839 42.137185 9.7233305 9838 35 36 0 67149 90440 23409 16326 0.94945034 0 69 0 89000 1.0455638 16345 0.23918575 42.032147 42.141682 8.6325214 9871 35 35 0 67855 90440 23409 16345 0.94891424 0 69 0 90000 0.79047982 16288 0.23897011 42.020876 42.103688 10.271997 10053 45 45 0 68551 90440 23409 16288 0.94963234 0 69 0 91000 0.85451256 16320 0.23898107 42.016098 42.105619 12.567859 10053 42 42 0 69246 90440 23409 16320 0.9506585 0 69 0 92000 1.1082033 16363 0.23917252 42.023254 42.139351 11.730554 9858 46 46 0 70046 90440 23409 16363 0.95352701 0 69 0 93000 0.90368051 16312 0.23897927 42.010631 42.105303 10.70167 9793 37 37 0 70824 90440 23409 16312 0.95992717 0 69 0 94000 0.95749706 16350 0.23909592 42.025545 42.125855 10.174353 9970 42 42 0 71646 90440 23409 16350 0.95082103 0 69 0 95000 0.90723392 16298 0.23898239 42.010809 42.105853 11.561525 9938 33 33 0 72414 90440 23409 16298 0.94768554 0 69 0 96000 1.0249944 16288 0.23910408 42.019912 42.127292 10.755062 9945 38 38 0 73184 90440 23409 16288 0.94637131 0 69 0 97000 0.96263604 16339 0.23911151 42.027754 42.128601 9.9303923 9816 36 36 0 73853 90440 23409 16339 0.94851816 0 69 0 98000 0.93105892 16301 0.23897506 42.00702 42.10456 12.088691 9933 39 39 0 74604 90440 23409 16301 0.94785265 0 69 0 99000 1.2448977 16286 0.23920972 42.015487 42.145905 11.565661 10001 51 51 0 75328 90440 23409 16286 0.9483854 0 69 0 100000 0.95492648 16337 0.23919603 42.043453 42.143492 11.223512 9793 32 32 0 76045 90440 23409 16337 0.95143273 0 69 0 Loop time of 51.3335 on 8 procs for 100000 steps with 73999 atoms Pair time (%) = 0.586967 (1.14344) Neigh time (%) = 3.95145 (7.69761) Comm time (%) = 2.97199 (5.78957) Outpt time (%) = 0.0085291 (0.0166151) Other time (%) = 43.8145 (85.3528) Nlocal: 9249.88 ave 10642 max 7533 min Histogram: 1 0 0 1 1 1 2 0 1 1 Nghost: 57.375 ave 89 max 34 min Histogram: 1 2 0 1 1 0 2 0 0 1 Neighs: 335.875 ave 616 max 209 min Histogram: 2 1 0 3 1 0 0 0 0 1 Total # of neighbors = 2687 Ave neighs/atom = 0.0363113 Neighbor list builds = 5000 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation