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LAMMPS (9 Sep 2013)
# 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
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 = 0.443016 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 0.0545385 on 8 procs for 1000 steps with 420 atoms
Pair time (%) = 0.00437456 (8.02105)
Neigh time (%) = 0.00148079 (2.71512)
Comm time (%) = 0.0152201 (27.9071)
Outpt time (%) = 0.000281721 (0.516555)
Other time (%) = 0.0331814 (60.8402)
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:438)
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:2759)
# 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 = 13.4256 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 17794 0.24158286 42.201127 42.564024 10.312083 10282 38 38 0 958 90440 23409 17794 0.83363455 0 69 0
2000 1.8731193 17757 0.24043583 42.165699 42.361931 8.6094692 10336 34 34 0 1779 90440 23409 17757 0.83414447 0 69 0
3000 1.2193752 17775 0.24002443 42.161704 42.289448 9.6884156 10041 43 43 0 2420 90440 23409 17775 0.84700093 0 69 0
4000 1.1297717 17824 0.23999784 42.166405 42.284762 10.426248 10121 39 39 0 3126 90440 23409 17824 0.85633304 0 69 0
5000 1.1615474 17837 0.24000689 42.164671 42.286357 9.7517646 10150 27 27 0 3852 90440 23409 17837 0.85320758 0 69 0
6000 0.90652092 17750 0.23996236 42.183542 42.278511 16.586628 9996 56 56 0 4564 90440 23409 17750 0.86506192 0 69 0
7000 0.83910042 17804 0.23978466 42.159296 42.247202 10.856698 10135 40 40 0 5229 90440 23409 17804 0.85548326 0 69 0
8000 0.99144403 17793 0.23987007 42.158385 42.262251 9.5637223 10222 32 32 0 5954 90440 23409 17793 0.86291538 0 69 0
9000 1.1109778 17818 0.2398755 42.14682 42.263208 10.917584 10423 42 42 0 6692 90440 23409 17818 0.86552775 0 69 0
10000 1.0782518 17840 0.23985498 42.146632 42.259591 8.85358 10308 36 36 0 7397 90440 23409 17840 0.86462939 0 69 0
11000 1.0268236 17833 0.23980517 42.143244 42.250816 12.172006 10254 44 44 0 8080 90440 23409 17833 0.861416 0 69 0
12000 1.060866 17842 0.23979196 42.137351 42.248489 10.419562 10353 34 34 0 8810 90440 23409 17842 0.86289215 0 69 0
13000 1.1876599 17763 0.23989166 42.141633 42.266054 7.8240476 10268 34 34 0 9525 90440 23409 17763 0.87071361 0 69 0
14000 0.95206604 17823 0.23970806 42.133967 42.233707 12.293388 10359 40 40 0 10306 90440 23409 17823 0.86909841 0 69 0
15000 1.1155458 17822 0.23974949 42.124139 42.241006 12.521383 10256 36 36 0 11029 90440 23409 17822 0.87234166 0 69 0
16000 1.1574448 17829 0.2398005 42.128737 42.249993 8.5872634 10044 38 38 0 11766 90440 23409 17829 0.87292148 0 69 0
17000 0.87868625 17815 0.23968874 42.13825 42.230303 10.488609 10092 37 37 0 12571 90440 23409 17815 0.87070803 0 69 0
18000 1.1008021 17797 0.23970316 42.117521 42.232843 8.91155 9964 31 31 0 13349 90440 23409 17797 0.87684173 0 69 0
19000 0.90843127 17832 0.23953614 42.108247 42.203416 10.681924 10353 33 33 0 14070 90440 23409 17832 0.87489631 0 69 0
20000 1.1525128 17827 0.23958362 42.091043 42.211782 10.324591 10318 42 42 0 14891 90440 23409 17827 0.87472282 0 69 0
21000 0.97088045 17831 0.23963415 42.118973 42.220685 8.9525609 10150 23 23 0 15681 90440 23409 17831 0.8744301 0 69 0
22000 0.86024198 17818 0.23946932 42.101523 42.191644 12.817308 9929 47 47 0 16514 90440 23409 17818 0.87940492 0 69 0
23000 1.0365388 17841 0.23960538 42.107025 42.215615 8.3943475 10190 36 36 0 17300 90440 23409 17841 0.88076259 0 69 0
24000 1.0134969 17828 0.23957307 42.103748 42.209924 11.013413 10329 40 40 0 18153 90440 23409 17828 0.87875237 0 69 0
25000 0.90091994 17843 0.23954136 42.109953 42.204335 13.312428 10143 45 45 0 18852 90440 23409 17843 0.87388578 0 69 0
26000 1.0221933 17846 0.23961351 42.10996 42.217047 9.2279785 10329 35 35 0 19615 90440 23409 17846 0.87558424 0 69 0
27000 0.93940255 17835 0.23950604 42.099699 42.198112 13.504134 10291 39 39 0 20431 90440 23409 17835 0.87190502 0 69 0
28000 1.0710516 17829 0.23960837 42.103937 42.216142 7.9022268 10251 35 35 0 21197 90440 23409 17829 0.87583025 0 69 0
29000 0.83696568 17783 0.23958234 42.123874 42.211556 9.8273998 10121 47 47 0 22044 90440 23409 17783 0.8820577 0 69 0
30000 1.0180681 17800 0.2396419 42.115395 42.22205 11.18041 10160 39 39 0 22803 90440 23409 17800 0.87992368 0 69 0
31000 1.233447 17832 0.23970136 42.103307 42.232526 11.388978 10169 45 45 0 23608 90440 23409 17832 0.87847887 0 69 0
32000 0.96295204 17849 0.23957991 42.110247 42.211128 12.911795 10118 41 41 0 24364 90440 23409 17849 0.87317056 0 69 0
33000 1.0254742 17836 0.23958855 42.10522 42.21265 11.197726 10202 43 43 0 25162 90440 23409 17836 0.87655301 0 69 0
34000 1.0255122 17812 0.23948733 42.087383 42.194817 10.238978 10253 42 42 0 25996 90440 23409 17812 0.87150515 0 69 0
35000 1.0719997 17824 0.23953256 42.090481 42.202785 9.1594527 10190 37 37 0 26786 90440 23409 17824 0.86960071 0 69 0
36000 0.86929827 17801 0.2394198 42.091849 42.182919 12.021567 10145 36 36 0 27586 90440 23409 17801 0.87124989 0 69 0
37000 0.9195314 17801 0.23946164 42.093958 42.19029 11.122704 10083 42 43 0 28321 90440 23409 17801 0.87692574 0 69 0
38000 0.88209926 17821 0.23936949 42.081644 42.174055 9.3732038 10239 37 37 0 29094 90440 23409 17821 0.87364127 0 69 0
39000 1.0463087 17819 0.23943558 42.076086 42.185699 11.373309 10300 44 44 0 29804 90440 23409 17819 0.87650979 0 69 0
40000 0.97425688 17807 0.2394417 42.084711 42.186776 13.415635 10171 50 50 0 30544 90440 23409 17807 0.87219589 0 69 0
41000 1.0314516 17853 0.23945459 42.080991 42.189047 9.7139261 10050 38 38 0 31307 90440 23409 17853 0.87283313 0 69 0
42000 1.0804164 17808 0.23949436 42.082868 42.196055 12.340256 10377 35 35 0 32052 90440 23409 17808 0.87185243 0 69 0
43000 1.0687043 17835 0.2394289 42.072563 42.184523 12.276278 10187 41 42 0 32870 90440 23409 17835 0.87231717 0 69 0
44000 1.0355523 17787 0.23942635 42.075587 42.184073 13.512133 10013 38 38 0 33661 90440 23409 17787 0.87400868 0 69 0
45000 1.194095 17794 0.23944632 42.062495 42.187591 10.205101 10159 30 30 0 34402 90440 23409 17794 0.8739309 0 69 0
46000 0.84466181 17796 0.23920256 42.056156 42.144644 10.087591 9986 38 38 1 35149 90440 23409 17796 0.87869701 0 69 0
47000 0.93714931 17806 0.239206 42.047072 42.14525 13.876772 10228 47 47 0 35938 90440 23409 17806 0.87830705 0 69 0
48000 0.72949249 17796 0.23910309 42.050694 42.127117 9.8468313 10017 47 47 0 36668 90440 23409 17796 0.87327264 0 69 0
49000 1.0645999 17790 0.23930769 42.051637 42.163166 7.4358626 10277 32 32 0 37413 90440 23409 17790 0.8752094 0 69 0
50000 0.83794425 17817 0.23913221 42.044463 42.132248 8.9803438 10132 31 33 0 38183 90440 23409 17817 0.87857184 0 69 0
51000 1.062864 17789 0.23932593 42.055033 42.166381 17.329071 9926 42 42 1 38978 90440 23409 17789 0.8802125 0 69 0
52000 1.1722666 17829 0.23941856 42.059892 42.1827 10.825667 10158 44 44 0 39819 90440 23409 17829 0.87723184 0 69 0
53000 1.0628181 17744 0.23938195 42.064907 42.17625 11.797173 10008 34 34 0 40601 90440 23409 17744 0.87283218 0 69 0
54000 0.99372853 17841 0.23927037 42.052486 42.156591 12.17125 10068 45 45 0 41361 90440 23409 17841 0.86254752 0 69 0
55000 0.98975398 17807 0.23931559 42.06087 42.164558 9.4176785 10050 40 40 0 42113 90440 23409 17807 0.86704764 0 69 0
56000 1.2416282 17834 0.23940795 42.050755 42.180831 10.979518 10103 32 32 0 42836 90440 23409 17834 0.87721916 0 69 0
57000 1.1624419 17798 0.23935794 42.050239 42.172019 12.160453 10291 47 47 0 43564 90440 23409 17798 0.86494273 0 69 0
58000 0.76060878 17840 0.23906489 42.040706 42.120388 10.124046 10057 41 41 0 44303 90440 23409 17840 0.87205383 0 69 0
59000 0.8928696 17800 0.23908927 42.031144 42.124683 9.5453786 10054 40 40 0 45052 90440 23409 17800 0.87434651 0 69 0
60000 0.94592548 17794 0.23911586 42.03027 42.129367 9.2638612 10243 36 36 0 45825 90440 23409 17794 0.87526045 0 69 0
61000 1.1130865 17809 0.23930525 42.046126 42.162735 10.750849 10002 35 35 0 46608 90440 23409 17809 0.8747269 0 69 0
62000 1.211348 17822 0.2392555 42.027069 42.153972 7.371417 10008 24 24 0 47366 90440 23409 17822 0.87452709 0 69 0
63000 0.80855346 17834 0.23891571 42.009398 42.094104 9.812354 10122 34 34 0 48089 90440 23409 17834 0.86767806 0 69 0
64000 1.0823604 17785 0.23907804 42.009314 42.122704 12.694543 9780 40 40 0 48834 90440 23409 17785 0.87010421 0 69 0
65000 1.1681262 17819 0.23899593 41.985863 42.108239 13.521338 9939 50 50 0 49566 90440 23409 17819 0.87537564 0 69 0
66000 1.0903421 17856 0.23903071 42.00014 42.114366 12.301665 9888 40 40 0 50342 90440 23409 17856 0.87239173 0 69 0
67000 1.118394 17844 0.23901798 41.994958 42.112123 8.8459568 9818 25 25 0 51083 90440 23409 17844 0.86584906 0 69 0
68000 0.93948628 17859 0.23892088 41.996592 42.095014 14.068409 9749 43 44 0 51827 90440 23409 17859 0.87202088 0 69 0
69000 0.990697 17820 0.2389651 41.999019 42.102807 10.194771 9842 40 40 0 52556 90440 23409 17820 0.87288445 0 69 0
70000 1.1688722 17813 0.2391014 42.004367 42.12682 8.7519297 9844 29 29 0 53315 90440 23409 17813 0.86525878 0 69 0
71000 1.1452575 17818 0.23899789 41.988604 42.108583 8.7612004 9845 40 40 0 54037 90440 23409 17818 0.86500198 0 69 0
72000 0.72969657 17836 0.23879062 41.99562 42.072064 11.153851 9829 38 38 0 54737 90440 23409 17836 0.86237278 0 69 0
73000 1.3107884 17813 0.23912958 41.994464 42.131785 10.862806 9844 40 40 0 55443 90440 23409 17813 0.86460503 0 69 0
74000 1.1126473 17809 0.23897768 41.98846 42.105023 9.663087 10106 35 35 0 56166 90440 23409 17809 0.87193847 0 69 0
75000 1.0693301 17794 0.23895603 41.989183 42.101208 8.9374157 10022 32 32 0 56941 90440 23409 17794 0.86326628 0 69 0
76000 0.74083943 17831 0.23870905 41.98008 42.057692 7.4143173 10015 37 37 0 57653 90440 23409 17831 0.86354244 0 69 0
77000 0.98084748 17842 0.23886095 41.9817 42.084455 9.4554943 9716 31 31 0 58336 90440 23409 17842 0.8620535 0 69 0
78000 0.91225901 17815 0.23882673 41.982857 42.078427 13.333677 9926 43 43 1 59053 90440 23409 17815 0.8676841 0 69 0
79000 1.1488535 17820 0.2389454 41.978979 42.099335 10.298772 9750 29 29 0 59744 90440 23409 17820 0.86385906 0 69 0
80000 0.84064371 17821 0.23872693 41.972776 42.060843 9.8779227 9978 30 30 0 60450 90440 23409 17821 0.8629371 0 69 0
81000 1.0935129 17803 0.23886127 41.969953 42.084512 7.1940139 9938 35 35 0 61155 90440 23409 17803 0.86416591 0 69 0
82000 1.0216631 17879 0.23884983 41.975465 42.082497 8.6808843 9987 36 36 0 61901 90440 23409 17879 0.87201261 0 69 0
83000 1.1155302 17808 0.23890657 41.975628 42.092493 11.387186 10066 49 49 0 62668 90440 23409 17808 0.8655501 0 69 0
84000 1.2958273 17773 0.23908145 41.987553 42.123306 11.222215 9969 44 44 0 63341 90440 23409 17773 0.86573453 0 69 0
85000 0.74628215 17829 0.23869483 41.977005 42.055187 11.073853 9949 43 43 0 64140 90440 23409 17829 0.86391947 0 69 0
86000 0.80359232 17803 0.23872195 41.97578 42.059966 9.6085498 9716 31 31 0 64837 90440 23409 17803 0.865418 0 69 0
87000 1.1098155 17802 0.23884012 41.96452 42.080786 13.693733 9576 45 45 0 65543 90440 23409 17802 0.86275585 0 69 0
88000 1.1138796 17818 0.23881314 41.95934 42.076033 11.517335 9714 36 36 0 66248 90440 23409 17818 0.85491105 0 69 0
89000 0.93926562 17840 0.2387707 41.970156 42.068555 9.6487297 9615 46 46 0 66962 90440 23409 17840 0.85885199 0 69 0
90000 1.0870662 17806 0.2388668 41.971603 42.085486 7.4390878 9564 31 31 0 67698 90440 23409 17806 0.86503288 0 69 0
91000 1.0454873 17807 0.2388344 41.970251 42.079778 12.514272 9645 46 46 1 68392 90440 23409 17807 0.86550889 0 69 0
92000 0.9113326 17794 0.23875573 41.970444 42.065917 7.9745011 9858 31 31 0 69167 90440 23409 17794 0.86294582 0 69 0
93000 0.78689269 17806 0.23871392 41.976114 42.05855 7.7081978 9499 35 35 0 69893 90440 23409 17806 0.87091194 0 69 0
94000 1.0352085 17794 0.23883458 41.971359 42.079809 14.612099 9789 43 43 0 70667 90440 23409 17794 0.87298934 0 69 0
95000 0.91726046 17789 0.2387641 41.971297 42.067391 10.210387 9513 38 38 0 71405 90440 23409 17789 0.87024642 0 69 0
96000 0.81485499 17819 0.23874488 41.97864 42.064006 11.759393 9924 42 42 0 72083 90440 23409 17819 0.87063449 0 69 0
97000 1.3260071 17811 0.23919656 42.004672 42.143587 9.8667031 9417 44 44 0 72818 90440 23409 17811 0.8655796 0 69 0
98000 1.0837996 17805 0.2389241 41.982041 42.095581 7.1836799 9975 23 23 0 73551 90440 23409 17805 0.86800841 0 69 0
99000 1.1892528 17831 0.23911593 42.004792 42.12938 9.6721123 9972 36 36 0 74319 90440 23409 17831 0.87381766 0 69 0
100000 0.85151797 17820 0.23885094 41.993485 42.082692 12.111833 9709 33 33 0 75042 90440 23409 17820 0.86631253 0 69 0
Loop time of 61.6618 on 8 procs for 100000 steps with 73999 atoms
Pair time (%) = 0.679072 (1.10128)
Neigh time (%) = 3.89789 (6.3214)
Comm time (%) = 3.42736 (5.55832)
Outpt time (%) = 0.0100309 (0.0162676)
Other time (%) = 53.6475 (87.0027)
Nlocal: 9249.88 ave 10571 max 6409 min
Histogram: 1 0 0 0 1 0 2 1 0 3
Nghost: 66.625 ave 92 max 38 min
Histogram: 1 0 2 0 0 2 0 1 0 2
Neighs: 345.875 ave 740 max 150 min
Histogram: 3 1 0 0 2 1 0 0 0 1
Total # of neighbors = 2767
Ave neighs/atom = 0.0373924
Neighbor list builds = 5000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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