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LAMMPS (1 Feb 2014)
# SRD diffusion demo - rigid star 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.star fix molprop NULL Molecules
orthogonal box = (-13.2934 -13.2934 -0.5) to (13.2934 13.2934 0.5)
4 by 2 by 1 MPI processor grid
reading atoms ...
270 atoms
set type 1 mass 1.0
270 settings made for mass
group big type 1
270 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 270 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.star.equil
thermo 100
run 1000
Memory usage per processor = 2.64859 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0.24721146
100 0 3.291475 0 3.291475 0.69158089
200 0 4.6176595 0 4.6176595 0.71737945
300 0 7.0921814 0 7.0921814 1.2163497
400 0 8.3666709 0 8.3666709 0.50645957
500 0 10.630838 0 10.630838 0.72764487
600 0 12.42157 0 12.42157 1.0130599
700 0 14.349074 0 14.349074 0.74795509
800 0 16.464746 0 16.464746 1.054549
900 0 18.253108 0 18.253108 0.51551753
1000 0 20.699563 0 20.699563 1.8084662
Loop time of 0.040709 on 8 procs for 1000 steps with 270 atoms
Pair time (%) = 0.00249004 (6.11668)
Neigh time (%) = 0.000995547 (2.44552)
Comm time (%) = 0.0116902 (28.7165)
Outpt time (%) = 0.000232756 (0.571755)
Other time (%) = 0.0253005 (62.1496)
Nlocal: 33.75 ave 42 max 22 min
Histogram: 1 0 1 0 0 2 0 1 1 2
Nghost: 23.375 ave 30 max 14 min
Histogram: 1 0 1 0 0 2 1 0 1 2
Neighs: 52.25 ave 69 max 27 min
Histogram: 1 0 1 0 1 0 1 1 1 2
Total # of neighbors = 418
Ave neighs/atom = 1.54815
Neighbor list builds = 176
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 60025 atoms
set type 2 mass 0.1
60025 settings made for mass
group small type 2
60025 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 0.5
delete_atoms overlap 0.5 small big
Deleted 16305 atoms, new total = 43990
# 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 270 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.star
#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 = 43720 270
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: 106 106 1
SRD grid size: request, actual (xyz) = 0.25, 0.250819 0.250819 1
SRD per actual grid cell = 5.55866
SRD viscosity = 0.235582
big/SRD mass density ratio = 0.144099
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.19085 7.72582
ave/max big velocity = 2.20262 5.4168
Memory usage per processor = 7.83759 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 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.3155168 8201 0.22979575 37.225304 37.439685 8.9588433 14577 56 56 0 687 57680 11236 8201 1.0283377 0 5 0
2000 0.82290815 8187 0.22918912 37.206746 37.340849 6.0607727 14326 56 56 0 1524 57680 11236 8187 1.0127464 0 5 0
3000 0.99928391 8168 0.22921842 37.182777 37.345623 10.268998 14389 68 68 0 2274 57680 11236 8168 1.023497 0 5 0
4000 1.0348458 8200 0.22920437 37.174693 37.343335 9.8954805 14335 51 51 0 3047 57680 11236 8200 1.0156984 0 5 0
5000 1.1496765 8199 0.22939095 37.186379 37.373733 8.0143223 14444 74 74 0 3868 57680 11236 8199 1.0104858 0 5 0
6000 0.91767381 8225 0.2292466 37.200668 37.350215 8.6189298 14131 61 61 0 4594 57680 11236 8225 1.0147272 0 5 0
7000 0.74806752 8203 0.22888634 37.169611 37.291518 9.8613421 14121 53 53 1 5322 57680 11236 8203 1.0198289 0 19 0
8000 1.1177867 8213 0.22924801 37.168286 37.350444 7.911691 14380 62 62 0 6024 57680 11236 8213 1.0066799 0 19 0
9000 1.1258411 8209 0.22939703 37.191253 37.374723 6.7377179 14350 51 51 0 6821 57680 11236 8209 1.0081225 0 19 0
10000 1.0597344 8182 0.22919436 37.169006 37.341703 9.7769156 14372 48 48 0 7543 57680 11236 8182 1.0099373 0 19 0
11000 1.3337199 8159 0.22943046 37.162823 37.38017 6.0897666 14359 58 58 0 8245 57680 11236 8159 1.0046221 0 19 0
12000 1.0280975 8184 0.22894286 37.133186 37.300728 2.555317 14162 51 51 0 8935 57680 11236 8184 1.0010306 0 19 0
13000 1.2318533 8190 0.22921487 37.144299 37.345045 6.1739989 14285 64 64 0 9634 57680 11236 8190 1.0138112 0 19 0
14000 1.1851991 8215 0.22915708 37.142485 37.335629 7.8380175 14151 66 66 0 10407 57680 11236 8215 1.0008011 0 19 0
15000 0.89853218 8214 0.22897294 37.159201 37.305628 4.0743953 14077 61 61 0 11069 57680 11236 8214 1.0041341 0 19 0
16000 1.0295974 8176 0.22891205 37.127921 37.295708 8.7527117 14000 48 48 0 11832 57680 11236 8176 1.0089653 0 23 0
17000 1.1793664 8219 0.22906268 37.128056 37.320249 5.2583304 14268 57 57 0 12490 57680 11236 8219 1.0157079 0 23 0
18000 0.90486919 8180 0.22891008 37.147927 37.295387 4.8498125 13939 64 64 0 13154 57680 11236 8180 0.99700921 0 23 0
19000 0.81486319 8219 0.22881911 37.147773 37.280566 1.6338041 13934 59 59 1 13861 57680 11236 8219 1.0099189 0 23 0
20000 1.0146287 8180 0.22896254 37.138587 37.303934 2.1682593 14057 45 45 0 14593 57680 11236 8180 1.0009466 0 23 0
21000 1.3031463 8164 0.22920646 37.131309 37.343674 6.570906 13944 65 65 0 15323 57680 11236 8164 0.98955239 0 23 0
22000 1.1258162 8174 0.22915084 37.151147 37.334613 9.0817519 14052 56 56 0 16042 57680 11236 8174 1.0083228 0 23 0
23000 1.1421222 8217 0.22906722 37.134865 37.320989 8.0529401 14143 66 66 0 16797 57680 11236 8217 1.0111161 0 23 0
24000 0.77402445 8168 0.22883056 37.156294 37.282431 6.8609899 14258 62 62 0 17559 57680 11236 8168 1.0080535 0 23 0
25000 0.94006632 8215 0.22879533 37.123496 37.276692 3.8570839 14446 48 48 0 18267 57680 11236 8215 1.0087899 0 23 0
26000 1.2808563 8192 0.22933112 37.155253 37.363985 5.3591484 13960 54 54 1 19004 57680 11236 8192 1.0101851 0 79 0
27000 1.0266075 8171 0.22898652 37.140542 37.307841 2.9961422 14049 56 56 1 19683 57680 11236 8171 0.99950217 0 79 0
28000 0.98185838 8199 0.22867129 37.096475 37.256481 12.080529 14106 61 62 0 20417 57680 11236 8199 1.0026548 0 79 0
29000 0.96921352 8192 0.22861802 37.089856 37.247802 8.257635 13891 63 64 0 21169 57680 11236 8192 1.0128041 0 79 0
30000 1.0107665 8223 0.22866616 37.090929 37.255646 9.4280788 14021 61 61 1 21863 57680 11236 8223 1.0034994 0 79 0
31000 1.1859435 8195 0.22877222 37.079661 37.272926 7.3863353 14093 78 78 0 22480 57680 11236 8195 0.9945582 0 79 0
32000 1.2951374 8172 0.22897044 37.094161 37.30522 6.4322363 13792 52 52 0 23151 57680 11236 8172 1.0026092 0 79 0
33000 0.82899919 8176 0.22823894 37.050944 37.186041 0.60210493 13797 62 62 0 23903 57680 11236 8176 1.0051075 0 79 0
34000 0.96685714 8165 0.22828901 37.036637 37.194199 8.1409866 13837 50 50 0 24591 57680 11236 8165 1.0157895 0 79 0
35000 0.95645753 8206 0.22833008 37.045022 37.200889 8.9956195 14130 63 63 0 25340 57680 11236 8206 1.0030424 0 79 0
36000 1.2933379 8197 0.22879201 37.065383 37.27615 8.3938627 13978 80 80 0 26085 57680 11236 8197 1.0094497 0 79 0
37000 1.1511434 8176 0.22861016 37.058929 37.246523 4.9481995 13856 49 49 1 26759 57680 11236 8176 1.0063722 0 79 0
38000 0.93310274 8181 0.22837532 37.056199 37.20826 5.9575015 13949 51 51 0 27445 57680 11236 8181 1.0152607 0 79 0
39000 1.0352467 8215 0.22861437 37.078501 37.247208 9.8519532 14109 69 69 0 28245 57680 11236 8215 1.005523 0 79 0
40000 1.2696427 8193 0.22885162 37.078957 37.285862 8.4680587 13931 54 55 0 28960 57680 11236 8193 1.0014074 0 79 0
41000 1.3270531 8193 0.22909573 37.109374 37.325634 4.3731598 14115 62 62 0 29668 57680 11236 8193 1.0022493 0 79 0
42000 1.3650738 8183 0.22911257 37.105921 37.328377 6.6345101 13659 52 52 0 30400 57680 11236 8183 1.0145834 0 79 0
43000 1.0780084 8209 0.22855316 37.06156 37.237235 5.5147087 14062 52 52 0 31092 57680 11236 8209 1.0031365 0 79 0
44000 0.96146724 8193 0.22846546 37.066263 37.222946 9.7967735 13699 56 56 0 31771 57680 11236 8193 1.0072364 0 79 0
45000 1.1733618 8200 0.2286481 37.061489 37.252703 9.8058881 13967 51 52 0 32532 57680 11236 8200 1.0068663 0 79 0
46000 0.94784989 8211 0.22845052 37.066048 37.220513 5.8834756 13944 34 35 0 33213 57680 11236 8211 1.0080225 0 79 0
47000 1.2354771 8207 0.22859598 37.042876 37.244213 6.1458407 13851 56 56 0 33886 57680 11236 8207 1.0151781 0 79 0
48000 1.0834097 8164 0.22835968 37.029157 37.205712 6.7378814 13944 56 56 0 34578 57680 11236 8164 1.0128575 0 79 0
49000 0.9386786 8208 0.22837254 37.054838 37.207808 5.0809383 13618 53 53 0 35328 57680 11236 8208 1.0045622 0 79 0
50000 1.047176 8154 0.22859126 37.072791 37.243442 4.8016981 13847 55 55 0 36059 57680 11236 8154 1.0005378 0 79 0
51000 1.0943417 8222 0.22844191 37.040773 37.21911 7.9359541 13897 61 61 0 36711 57680 11236 8222 1.0036343 0 79 0
52000 1.2811259 8200 0.22871149 37.054255 37.263031 4.9958687 13744 56 56 0 37402 57680 11236 8200 1.0049188 0 79 0
53000 1.0997162 8218 0.22853173 37.05453 37.233743 4.6772882 13967 65 65 0 38082 57680 11236 8218 1.0054533 0 79 0
54000 0.97625718 8185 0.2283994 37.05309 37.212184 5.9026406 13741 69 69 0 38761 57680 11236 8185 0.99393606 0 79 0
55000 0.97919465 8192 0.22835234 37.044944 37.204516 6.8419755 13990 58 58 0 39453 57680 11236 8192 1.0103052 0 79 0
56000 0.86300824 8181 0.22842164 37.075169 37.215808 6.8288348 13751 57 57 0 40118 57680 11236 8181 0.99683099 0 79 0
57000 0.89429559 8181 0.22851743 37.085677 37.231414 9.378853 13746 72 72 0 40730 57680 11236 8181 1.0086882 0 79 0
58000 1.0853441 8172 0.22857719 37.064279 37.24115 7.4580035 13869 58 58 1 41462 57680 11236 8172 1.0092141 0 79 0
59000 1.0149632 8199 0.22868187 37.092803 37.258205 8.2913359 13720 54 54 0 42159 57680 11236 8199 1.0082738 0 79 0
60000 0.99214038 8241 0.22871146 37.101344 37.263026 7.9905647 13776 67 67 0 42858 57680 11236 8241 1.0027929 0 79 0
61000 0.95721926 8211 0.2285241 37.07651 37.232501 11.837258 13907 62 62 0 43565 57680 11236 8211 1.0201117 0 79 0
62000 1.1457294 8195 0.22866514 37.068769 37.25548 9.7934944 13796 40 40 1 44292 57680 11236 8195 1.005192 0 79 0
63000 1.1096177 8193 0.22863037 37.068989 37.249815 8.0809047 13984 54 55 0 44986 57680 11236 8193 1.0076438 0 79 0
64000 1.1643495 8168 0.22860016 37.055147 37.244893 4.7376475 13857 50 50 1 45657 57680 11236 8168 1.002011 0 79 0
65000 1.2172585 8201 0.22845803 37.023368 37.221736 8.9744616 13610 53 53 0 46295 57680 11236 8201 1.0033999 0 79 0
66000 0.99924611 8189 0.22807344 36.996237 37.159077 8.5854786 13849 49 49 0 46944 57680 11236 8189 1.015528 0 79 0
67000 1.2543542 8165 0.22831075 36.993327 37.19774 5.0081411 13906 57 58 1 47666 57680 11236 8165 1.0189753 0 79 0
68000 1.0360874 8205 0.22812149 36.99806 37.166904 2.2431831 13650 52 52 0 48363 57680 11236 8205 1.0076864 0 79 0
69000 0.69755552 8218 0.22766249 36.978446 37.092121 4.2769033 13654 51 51 0 49044 57680 11236 8218 1.009863 0 79 0
70000 0.90921994 8167 0.22796236 36.992809 37.140978 9.3555738 13927 52 52 0 49793 57680 11236 8167 1.0015807 0 79 0
71000 0.95608837 8177 0.22797832 36.987772 37.143579 8.0740708 13612 63 63 0 50464 57680 11236 8177 1.0097491 0 79 0
72000 1.0374855 8192 0.22803745 36.98414 37.153212 4.4789755 13561 52 52 0 51127 57680 11236 8192 0.99496724 0 79 0
73000 0.90636338 8214 0.22783374 36.97232 37.120024 9.3364171 13598 53 53 0 51799 57680 11236 8214 1.0078219 0 79 0
74000 1.1869638 8179 0.22834625 37.010094 37.203525 4.8292929 13771 51 51 0 52500 57680 11236 8179 0.98865277 0 79 0
75000 1.0177351 8188 0.22826506 37.024443 37.190296 5.1808505 13508 55 55 0 53183 57680 11236 8188 0.99903558 0 79 0
76000 1.062496 8230 0.22820987 37.008158 37.181305 8.1032524 13769 58 58 0 53864 57680 11236 8230 0.99397021 0 79 0
77000 0.9762027 8131 0.22831271 37.038975 37.19806 10.309798 13787 47 47 0 54553 57680 11236 8131 1.0066289 0 79 0
78000 1.0688533 8160 0.22855677 37.06364 37.237824 7.4800503 13224 58 58 0 55248 57680 11236 8160 1.0073477 0 79 0
79000 1.2598513 8151 0.22844942 37.015024 37.220333 7.4724924 13859 63 63 0 55911 57680 11236 8151 1.0065168 0 79 0
80000 1.1044575 8176 0.22834306 37.023019 37.203005 3.0142586 13579 62 62 0 56611 57680 11236 8176 1.0008704 0 79 0
81000 1.2756491 8205 0.22853748 37.026797 37.23468 6.434309 13702 52 52 0 57313 57680 11236 8205 1.0058366 0 79 0
82000 1.1276926 8193 0.22857049 37.056287 37.240059 11.825248 13621 63 63 0 58011 57680 11236 8193 1.0113537 0 79 0
83000 0.96941691 8173 0.22824759 37.029471 37.18745 2.9152799 13478 48 49 0 58712 57680 11236 8173 1.0168819 0 79 0
84000 1.0770325 8186 0.22821292 37.006285 37.181802 5.0626072 13733 60 61 0 59433 57680 11236 8186 1.0177757 0 79 0
85000 1.1959489 8175 0.2284266 37.021719 37.216615 5.3844747 13964 55 55 0 60226 57680 11236 8175 1.007371 0 79 0
86000 1.035779 8204 0.22845952 37.053185 37.221979 7.5428558 13713 64 64 0 60982 57680 11236 8204 1.0110801 0 79 0
87000 1.1878573 8204 0.22836412 37.012859 37.206436 3.1124447 13655 47 47 0 61668 57680 11236 8204 1.0034968 0 79 0
88000 0.98402924 8206 0.22815704 37.012337 37.172698 10.613422 13947 56 56 0 62325 57680 11236 8206 1.0081468 0 79 0
89000 0.83763529 8199 0.22807071 37.022127 37.158631 5.4628281 13966 50 50 0 63012 57680 11236 8199 0.99956322 0 79 0
90000 1.1976672 8187 0.22849599 37.032745 37.227921 5.5583762 13903 43 43 0 63697 57680 11236 8187 1.0047573 0 79 0
91000 0.94863742 8188 0.22818061 37.021945 37.176537 5.157692 13859 46 46 0 64382 57680 11236 8188 1.0041894 0 79 0
92000 1.2038427 8172 0.22846103 37.026042 37.222224 6.685059 13675 57 57 0 65081 57680 11236 8172 1.0036906 0 79 0
93000 0.95835618 8210 0.22828548 37.037446 37.193622 8.0038227 13826 57 58 0 65761 57680 11236 8210 1.0076646 0 79 0
94000 1.2451267 8197 0.22856138 37.035665 37.238575 3.6305666 13918 62 62 0 66462 57680 11236 8197 1.0110913 0 79 0
95000 0.82128549 8206 0.22809174 37.028218 37.162057 8.7024273 13817 44 44 0 67185 57680 11236 8206 1.0032224 0 79 0
96000 0.83473128 8199 0.22820935 37.04519 37.18122 8.1258155 14167 54 54 0 67912 57680 11236 8199 1.0035561 0 79 0
97000 0.98924493 8196 0.22847944 37.064014 37.225225 8.9964529 14039 48 51 0 68608 57680 11236 8196 1.0007515 0 79 0
98000 1.1749668 8211 0.22879851 37.085733 37.27721 7.0283734 13850 58 59 0 69305 57680 11236 8211 0.99525651 0 79 0
99000 1.3269705 8163 0.22890919 37.078994 37.295241 9.7962294 13885 63 63 0 69994 57680 11236 8163 1.011015 0 107 0
100000 1.0020436 8171 0.22867221 37.093336 37.256632 4.9455304 14102 55 56 0 70707 57680 11236 8171 1.0072865 0 107 0
Loop time of 33.9872 on 8 procs for 100000 steps with 43990 atoms
Pair time (%) = 0.379981 (1.11801)
Neigh time (%) = 2.01801 (5.93757)
Comm time (%) = 2.30255 (6.77476)
Outpt time (%) = 0.00694308 (0.0204285)
Other time (%) = 29.2797 (86.1492)
Nlocal: 5498.75 ave 6445 max 4431 min
Histogram: 1 0 0 2 1 1 0 1 1 1
Nghost: 62.5 ave 70 max 57 min
Histogram: 3 0 0 1 1 0 1 0 1 1
Neighs: 207 ave 365 max 92 min
Histogram: 1 1 1 1 2 0 1 0 0 1
Total # of neighbors = 1656
Ave neighs/atom = 0.0376449
Neighbor list builds = 5000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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