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LAMMPS (1 Feb 2014)
# SRD diffusion demo - dimer 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.dimer fix molprop NULL Molecules
orthogonal box = (-9.34165 -9.34165 -0.5) to (9.34165 9.34165 0.5)
4 by 2 by 1 MPI processor grid
reading atoms ...
200 atoms
set type 1 mass 1.0
200 settings made for mass
group big type 1
200 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
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.dimer.equil
thermo 100
run 1000
Memory usage per processor = 3.1029 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3.4028231 0 0 0.83369167 -0.55065517
100 9.5167872 2.392105 0 4.7237178 2.8319556
200 13.564465 3.0352634 0 6.3585572 3.6388732
300 13.133051 4.3835112 0 7.6011086 4.060051
400 14.584346 5.5141254 0 9.0872901 4.4231056
500 15.331515 6.6554832 0 10.411704 4.847642
600 16.953755 7.4794317 0 11.633102 5.2020696
700 16.503256 8.8572339 0 12.900532 5.6694613
800 17.006131 9.877343 0 14.043845 5.5483363
900 17.305927 11.081594 0 15.321546 6.2908201
1000 18.122491 12.126462 0 16.566472 5.7536055
Loop time of 0.185949 on 8 procs for 1000 steps with 200 atoms
Pair time (%) = 0.00187448 (1.00806)
Neigh time (%) = 0.000561714 (0.30208)
Comm time (%) = 0.0652371 (35.0833)
Outpt time (%) = 0.00209856 (1.12857)
Other time (%) = 0.116177 (62.4779)
Nlocal: 25 ave 30 max 20 min
Histogram: 1 0 1 1 0 0 3 1 0 1
Nghost: 28.375 ave 36 max 22 min
Histogram: 1 0 1 2 1 0 2 0 0 1
Neighs: 33.125 ave 45 max 22 min
Histogram: 1 0 2 1 0 1 1 0 1 1
Total # of neighbors = 265
Ave neighs/atom = 1.325
Neighbor list builds = 99
Dangerous builds = 96
#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 29929 atoms
set type 2 mass 0.1
29929 settings made for mass
group small type 2
29929 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 12759 atoms, new total = 17370
# 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
100 rigid bodies with 200 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.dimer
#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 = 17170 200
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: 75 75 1
SRD grid size: request, actual (xyz) = 0.25, 0.249111 0.249111 1
SRD per actual grid cell = 5.5499
SRD viscosity = 0.235551
big/SRD mass density ratio = 0.142367
# of rescaled SRD velocities = 0
ave/max small velocity = 4.20347 7.72323
ave/max big velocity = 2.64047 6.60911
Memory usage per processor = 7.0395 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 6.9744766 0 0.30175295 21.011259 26.207244 2.7219331 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.1941672 3369 0.24718395 20.578272 21.467926 9.8944086 13658 56 56 2 664 40320 5625 3369 1.1358997 0 4 0
2000 1.3247909 3390 0.24717547 20.48022 21.467189 6.5341926 13389 48 48 3 1988 40320 5625 3390 1.1814916 0 144 0
3000 1.386904 3355 0.24769415 20.478993 21.512237 6.1207029 13507 45 45 0 2871 40320 5625 3355 1.1657697 0 144 0
4000 1.1567347 3376 0.24573733 20.48052 21.342287 3.5540965 13475 46 46 0 3731 40320 5625 3376 1.1485984 0 144 0
5000 1.2565155 3376 0.24620928 20.447172 21.383276 2.5808161 13267 55 55 0 4559 40320 5625 3376 1.1778096 0 144 0
6000 1.1489985 3375 0.24520477 20.440031 21.296035 7.8204262 13362 59 59 0 5354 40320 5625 3375 1.1530517 0 144 0
7000 1.1608248 3399 0.24587989 20.489854 21.354669 7.9622779 13333 59 59 2 6254 40320 5625 3399 1.1809325 0 144 0
8000 1.1749441 3374 0.24700359 20.576929 21.452262 6.7498405 13495 64 64 0 7134 40320 5625 3374 1.1445035 0 144 0
9000 1.1285085 3405 0.24536183 20.468936 21.309675 5.8959937 13333 60 60 0 8008 40320 5625 3405 1.162836 0 144 0
10000 1.1462675 3425 0.24564758 20.480523 21.334492 7.0047543 13487 45 45 0 8967 40320 5625 3425 1.1881074 0 144 0
11000 1.2854766 3388 0.246088 20.415062 21.372742 7.8508136 13491 60 60 1 9833 40320 5625 3388 1.1698514 0 144 0
12000 1.2926536 3360 0.24602616 20.404345 21.367372 7.9286141 13142 64 64 1 11029 40320 5625 3360 1.1658039 0 161 0
13000 1.2289767 3412 0.24595657 20.44574 21.361328 2.2809592 13162 56 56 1 12018 40320 5625 3412 1.1665531 0 161 0
14000 1.3518235 3380 0.24629055 20.383226 21.390334 8.0062608 13310 59 59 7 13146 40320 5625 3380 1.1733296 0 161 0
15000 1.2971143 3355 0.24671134 20.46053 21.42688 9.7871945 12967 60 60 3 14084 40320 5625 3355 1.1703643 0 161 0
16000 1.4160948 3384 0.2478594 20.471598 21.526589 7.3141215 13123 56 56 1 14929 40320 5625 3384 1.1666782 0 161 0
17000 1.3172038 3391 0.247377 20.503375 21.484692 6.1541908 12957 54 54 0 15778 40320 5625 3391 1.1639931 0 161 0
18000 0.98748293 3369 0.2443499 20.486114 21.221789 4.0981146 13355 50 50 1 17031 40320 5625 3369 1.2083414 0 192 0
19000 1.4619261 3367 0.24867817 20.508564 21.597699 11.68547 13519 58 58 0 18334 40320 5625 3367 1.1667505 0 192 0
20000 1.44087 3391 0.24747923 20.420123 21.493571 4.0409936 13594 67 67 0 19303 40320 5625 3391 1.1869387 0 192 0
21000 1.1155365 3377 0.24474418 20.424957 21.256032 8.4985692 13423 52 52 0 20245 40320 5625 3377 1.1726608 0 192 0
22000 1.2045785 3382 0.24466159 20.351448 21.248859 7.0518674 13271 62 62 0 21128 40320 5625 3382 1.1658557 0 192 0
23000 1.2634616 3378 0.24571326 20.398918 21.340197 6.8382109 13246 61 61 1 22067 40320 5625 3378 1.170196 0 192 0
24000 1.365723 3375 0.24749053 20.477089 21.494552 5.9584152 13017 46 46 1 23017 40320 5625 3375 1.1841192 0 192 0
25000 1.1421045 3367 0.24497142 20.4249 21.275768 10.381661 13049 66 66 1 23907 40320 5625 3367 1.1856767 0 192 0
26000 1.4008939 3340 0.24678624 20.389719 21.433385 7.3799658 12971 53 53 5 24850 40320 5625 3340 1.1713233 0 192 0
27000 1.1835022 3379 0.24522732 20.416284 21.297993 7.2251705 12717 46 46 1 25723 40320 5625 3379 1.1798333 0 192 0
28000 1.0496668 3398 0.24461816 20.463086 21.245087 6.5485338 13385 60 60 0 26990 40320 5625 3398 1.1765205 0 192 0
29000 1.1779927 3453 0.24501083 20.401586 21.27919 4.8540048 13157 77 77 2 28023 40320 5625 3453 1.1741595 0 192 0
30000 1.2277637 3375 0.24554215 20.410652 21.325336 10.087705 12939 72 72 1 28855 40320 5625 3375 1.1627414 0 192 0
31000 1.1575066 3397 0.24504213 20.419566 21.281909 6.4849648 12977 66 66 0 29745 40320 5625 3397 1.1575018 0 192 0
32000 1.1752733 3381 0.2451073 20.41199 21.287569 7.2784509 12971 48 48 0 30561 40320 5625 3381 1.1790395 0 192 0
33000 1.1743895 3370 0.24485514 20.390748 21.265669 9.084299 12810 64 64 0 31342 40320 5625 3370 1.1429061 0 192 0
34000 1.2975876 3377 0.24608262 20.405573 21.372276 10.624304 12610 60 60 1 32140 40320 5625 3377 1.1685718 0 192 0
35000 1.7701252 3356 0.2497356 20.370794 21.689537 7.107766 12983 45 45 8 33862 40320 5625 3356 1.1720964 0 242 0
36000 1.2711521 3393 0.24675748 20.483878 21.430887 8.7087273 13175 60 60 0 34920 40320 5625 3393 1.1796212 0 242 0
37000 1.1140649 3373 0.24450996 20.405711 21.23569 8.0025138 12964 50 50 1 35770 40320 5625 3373 1.1772234 0 242 0
38000 1.3128798 3379 0.24583813 20.372946 21.351041 5.0554655 12939 56 56 1 36679 40320 5625 3379 1.1702949 0 242 0
39000 1.2093703 3365 0.24536578 20.409037 21.310018 5.6243735 12873 62 62 3 37511 40320 5625 3365 1.1751064 0 242 0
40000 1.2095402 3365 0.24485106 20.364207 21.265315 3.9565189 12876 54 54 1 38503 40320 5625 3365 1.1637516 0 242 0
41000 1.1146238 3350 0.24476111 20.427107 21.257502 6.5033046 12656 53 53 0 39313 40320 5625 3350 1.1553197 0 242 0
42000 1.2302245 3370 0.24452048 20.320087 21.236604 10.7363 12676 52 52 1 40108 40320 5625 3370 1.1492163 0 242 0
43000 1.2749689 3404 0.24511103 20.338041 21.287893 9.18604 13057 72 72 1 41014 40320 5625 3404 1.1572511 0 242 0
44000 1.1989211 3385 0.24450633 20.342179 21.235375 7.6714085 13086 52 53 1 41840 40320 5625 3385 1.1530041 0 242 0
45000 1.6465972 3370 0.249994 20.485264 21.711979 7.4908607 12894 58 58 7 43545 40320 5625 3370 1.1978571 0 361 0
46000 1.3082316 3412 0.24665637 20.447473 21.422106 8.9900563 13136 53 53 4 44510 40320 5625 3412 1.1686573 0 361 0
47000 1.2163258 3355 0.24493724 20.366636 21.272799 6.9309438 13020 56 56 0 45414 40320 5625 3355 1.1620943 0 361 0
48000 1.349966 3362 0.24683156 20.431596 21.437321 8.8527164 13044 64 64 1 46260 40320 5625 3362 1.1683452 0 361 0
49000 1.3903769 3347 0.24726403 20.439051 21.474881 5.9250552 13103 58 59 2 49229 40320 5625 3347 1.1924538 0 578 0
50000 1.2737918 3349 0.24563843 20.384723 21.333698 7.2419874 12892 41 41 1 50225 40320 5625 3349 1.1803233 0 578 0
51000 1.2229799 3355 0.24504936 20.371417 21.282537 8.5556146 12912 63 63 0 51096 40320 5625 3355 1.1333843 0 578 0
52000 1.2326547 3386 0.24596384 20.443632 21.361959 6.1757404 12790 66 66 1 52114 40320 5625 3386 1.1685608 0 578 0
53000 1.3695441 3389 0.24696147 20.428294 21.448604 8.7464732 12997 60 60 1 53115 40320 5625 3389 1.1631228 0 578 0
54000 1.0711204 3400 0.24322154 20.325806 21.12379 8.7228921 13005 56 56 0 53913 40320 5625 3400 1.1250986 0 578 0
55000 1.3412565 3360 0.24617922 20.381429 21.380665 6.9489559 12960 46 46 0 55249 40320 5625 3360 1.176467 0 578 0
56000 1.3910761 3355 0.2467942 20.397725 21.434077 6.6762734 12966 65 65 2 56653 40320 5625 3355 1.1715559 0 578 0
57000 1.1177307 3388 0.24424738 20.380176 21.212885 5.5073089 13153 62 62 1 57550 40320 5625 3388 1.1576307 0 578 0
58000 1.3136279 3365 0.24661231 20.439627 21.418279 9.1390284 12799 52 52 1 58366 40320 5625 3365 1.159026 0 578 0
59000 1.2667621 3374 0.24556104 20.383238 21.326976 3.4246418 13127 54 54 1 59170 40320 5625 3374 1.1461442 0 578 0
60000 1.1903121 3326 0.24492127 20.384629 21.271412 6.9439977 13078 47 47 2 60105 40320 5625 3326 1.1665886 0 578 0
61000 1.209313 3362 0.2455341 20.423699 21.324637 9.1212002 13225 61 61 4 61358 40320 5625 3362 1.1725894 0 578 0
62000 1.1720074 3366 0.24476301 20.384522 21.257667 7.7592884 13187 53 54 2 62257 40320 5625 3366 1.1599665 0 578 0
63000 1.2155508 3386 0.24486685 20.361101 21.266686 5.7864126 13090 42 42 0 63137 40320 5625 3386 1.1724234 0 578 0
64000 1.1967326 3379 0.2451834 20.402613 21.294179 4.8815049 13033 48 48 4 64152 40320 5625 3379 1.1818756 0 578 0
65000 1.1732378 3386 0.24500733 20.404824 21.278887 11.381026 12998 59 59 0 65071 40320 5625 3386 1.1625543 0 578 0
66000 1.1960739 3385 0.24407516 20.306852 21.197927 12.17249 12994 61 61 0 65941 40320 5625 3385 1.1826516 0 578 0
67000 1.3468331 3366 0.24657491 20.41164 21.415031 7.8115623 12894 62 62 1 66788 40320 5625 3366 1.1750424 0 578 0
68000 1.0742924 3369 0.24347736 20.345661 21.146009 9.5240252 13065 68 68 2 67665 40320 5625 3369 1.1561575 0 578 0
69000 1.1411254 3380 0.2450544 20.432836 21.282975 8.0392218 13134 49 49 1 68471 40320 5625 3380 1.1405485 0 578 0
70000 1.1585312 3388 0.24435206 20.358871 21.221977 7.5303626 13113 59 59 0 69320 40320 5625 3388 1.1726416 0 578 0
71000 1.3418857 3382 0.24598802 20.364355 21.36406 9.2840877 13265 68 68 0 70522 40320 5625 3382 1.1696767 0 578 0
72000 1.1547857 3388 0.24328952 20.26938 21.129695 7.9643121 13270 50 50 1 71384 40320 5625 3388 1.1647353 0 578 0
73000 1.1114283 3385 0.24397276 20.36102 21.189034 13.168935 13110 62 62 0 72335 40320 5625 3385 1.1625358 0 578 0
74000 1.6120075 3370 0.25009739 20.520013 21.720959 12.065782 12902 51 51 9 73743 40320 5625 3370 1.1873738 0 578 0
75000 1.3271087 3353 0.24600453 20.376798 21.365493 7.5902315 13076 51 51 1 74746 40320 5625 3353 1.1706259 0 578 0
76000 1.1908626 3386 0.2451628 20.405197 21.292389 6.8084086 13124 58 58 1 75702 40320 5625 3386 1.1765809 0 578 0
77000 1.042536 3391 0.24320847 20.345966 21.122655 6.4883579 12846 57 57 0 76930 40320 5625 3391 1.1769829 0 578 0
78000 1.3791243 3355 0.24628683 20.362563 21.390011 9.2397346 12897 56 56 12 78068 40320 5625 3355 1.1905167 0 578 0
79000 1.2058397 3391 0.2453076 20.406614 21.304965 9.7949819 13020 51 51 1 79065 40320 5625 3391 1.1777257 0 578 0
80000 1.0634737 3383 0.24440921 20.434652 21.22694 7.5296946 12973 61 61 2 80029 40320 5625 3383 1.1648017 0 578 0
81000 1.3768966 3373 0.24730623 20.452758 21.478546 7.1508584 13297 56 56 1 81172 40320 5625 3373 1.1740603 0 578 0
82000 1.3348382 3375 0.24680945 20.440946 21.4354 9.3251946 12822 56 56 2 82447 40320 5625 3375 1.1573749 0 578 0
83000 1.2042501 3393 0.24484972 20.368032 21.265198 7.5283729 12990 51 51 0 83344 40320 5625 3393 1.1833162 0 578 0
84000 1.1985223 3405 0.24537841 20.418216 21.311115 7.848856 13189 60 60 0 84147 40320 5625 3405 1.173911 0 578 0
85000 1.1811593 3391 0.24418657 20.32764 21.207604 8.3169438 13303 51 51 0 85022 40320 5625 3391 1.1586027 0 578 0
86000 1.2595689 3385 0.24556774 20.389179 21.327558 8.3808674 12966 56 56 1 85962 40320 5625 3385 1.1617838 0 578 0
87000 1.1419322 3356 0.24399697 20.340397 21.191137 6.8911116 13166 63 63 0 86753 40320 5625 3356 1.1729274 0 578 0
88000 1.275219 3380 0.24586129 20.403015 21.353053 6.838563 12963 56 56 0 87729 40320 5625 3380 1.1511968 0 578 0
89000 1.2794858 3366 0.24507826 20.33183 21.285047 9.3370019 12889 64 64 1 88575 40320 5625 3366 1.1660311 0 578 0
90000 1.0549593 3402 0.24289618 20.309589 21.095533 4.9944605 13076 59 59 1 89560 40320 5625 3402 1.1744335 0 578 0
91000 1.214812 3402 0.24442304 20.323106 21.228141 7.5681019 13229 44 44 1 90440 40320 5625 3402 1.1696689 0 578 0
92000 1.2019714 3374 0.24469176 20.356011 21.25148 7.6728432 13331 64 64 2 91243 40320 5625 3374 1.1678246 0 578 0
93000 1.0964004 3364 0.24364709 20.343931 21.16075 5.9650235 13086 55 55 0 92088 40320 5625 3364 1.1570838 0 578 0
94000 1.1722133 3393 0.24332541 20.259513 21.132812 7.1743779 13206 66 66 0 92858 40320 5625 3393 1.154328 0 578 0
95000 1.2413711 3373 0.24549874 20.396744 21.321566 8.131371 12967 61 61 1 93789 40320 5625 3373 1.1635681 0 578 0
96000 1.1702409 3363 0.24528289 20.430989 21.302819 11.399295 12776 63 63 0 94571 40320 5625 3363 1.1367365 0 578 0
97000 1.0696537 3368 0.242673 20.279258 21.07615 8.537175 13054 55 55 0 95403 40320 5625 3368 1.1648141 0 578 0
98000 1.1635952 3369 0.24486659 20.399785 21.266664 8.6714443 12750 70 70 0 96296 40320 5625 3369 1.1686272 0 578 0
99000 1.1286255 3397 0.24343772 20.30174 21.142566 6.7153212 12810 44 45 1 97021 40320 5625 3397 1.137818 0 578 0
100000 1.2847818 3367 0.24509282 20.329149 21.286312 8.7486629 13260 64 64 0 97855 40320 5625 3367 1.1597138 0 578 0
Loop time of 20.8136 on 8 procs for 100000 steps with 17370 atoms
Pair time (%) = 0.322913 (1.55145)
Neigh time (%) = 1.11753 (5.36921)
Comm time (%) = 1.72335 (8.27991)
Outpt time (%) = 0.00594518 (0.0285638)
Other time (%) = 17.6439 (84.7709)
Nlocal: 2171.25 ave 2428 max 1747 min
Histogram: 1 0 0 0 1 1 2 1 0 2
Nghost: 61.25 ave 69 max 54 min
Histogram: 1 1 0 1 1 1 0 2 0 1
Neighs: 175.625 ave 225 max 132 min
Histogram: 1 1 1 1 1 0 1 0 0 2
Total # of neighbors = 1405
Ave neighs/atom = 0.0808866
Neighbor list builds = 5156
Dangerous builds = 1
Please see the log.cite file for references relevant to this simulation
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