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lammps/examples/ASPHERE/box/log.box.1Feb14
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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
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