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lammps/examples/ASPHERE/dimer/log.dimer.10Sep13
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LAMMPS (9 Sep 2013)
# 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
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 = 3.10291 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 0.0641297 on 8 procs for 1000 steps with 200 atoms
Pair time (%) = 0.00222233 (3.46537)
Neigh time (%) = 0.000630736 (0.983532)
Comm time (%) = 0.0137274 (21.4057)
Outpt time (%) = 0.00027743 (0.432607)
Other time (%) = 0.0472718 (73.7128)
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:438)
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 = 6.81079 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 2.7219332 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.2354587 3809 0.24719873 20.548793 21.46921 7.1295283 13581 50 50 0 709 40320 5625 3809 1.0057655 0 39 0
2000 1.1883147 3812 0.24605507 20.484588 21.369883 4.6579756 13419 49 50 0 1601 40320 5625 3812 1.0536999 0 39 0
3000 1.1945015 3800 0.24698055 20.560357 21.45026 8.0187045 13398 67 67 0 2485 40320 5625 3800 1.0389278 0 39 0
4000 1.2814726 3810 0.24731813 20.524883 21.47958 7.2525742 13351 54 54 1 3331 40320 5625 3810 1.0416803 0 39 0
5000 1.2655406 3805 0.24653329 20.468588 21.411416 5.2725197 13561 54 54 2 4170 40320 5625 3805 1.0314896 0 57 0
6000 1.1591194 3774 0.24602165 20.503437 21.366981 7.6336076 13521 53 53 1 5013 40320 5625 3774 1.0519436 0 57 0
7000 1.1138313 3785 0.24577139 20.515441 21.345245 9.1512158 13365 57 57 2 5946 40320 5625 3785 1.0468342 0 57 0
8000 1.2472647 3776 0.24679288 20.504749 21.433961 9.8240373 13283 58 58 5 6956 40320 5625 3776 1.0533896 0 93 0
9000 1.3539734 3799 0.24706895 20.449228 21.457939 8.6415706 13486 52 52 0 7868 40320 5625 3799 1.0369339 0 93 0
10000 1.1240413 3790 0.2462023 20.545259 21.38267 7.9137395 13238 52 52 0 8779 40320 5625 3790 1.0438247 0 93 0
11000 1.0115706 3801 0.24396454 20.4347 21.188321 5.6596258 13397 66 66 1 9697 40320 5625 3801 1.0464352 0 93 0
12000 1.0539712 3798 0.24450261 20.449843 21.235052 8.3325065 13436 53 53 0 10590 40320 5625 3798 1.0427153 0 93 0
13000 1.2685827 3782 0.24613472 20.431707 21.376801 9.9345777 13278 67 67 1 11460 40320 5625 3782 1.0445824 0 93 0
14000 1.1149298 3804 0.24483169 20.433009 21.263632 7.4598905 13383 78 78 1 12335 40320 5625 3804 1.0459521 0 93 0
15000 1.1892144 3794 0.24570719 20.453705 21.339669 9.1494223 13335 55 55 1 13146 40320 5625 3794 1.0307813 0 93 0
16000 1.3054 3788 0.24602945 20.395135 21.367658 6.3702986 13424 47 47 0 14044 40320 5625 3788 1.0465902 0 93 0
17000 1.1646813 3805 0.24486031 20.39843 21.266118 7.7108151 13392 51 51 0 14929 40320 5625 3805 1.0213327 0 93 0
18000 1.1891201 3791 0.24554422 20.439621 21.325516 8.0653754 13192 60 60 2 15755 40320 5625 3791 1.0340398 0 93 0
19000 1.0324301 3790 0.24381204 20.405915 21.175076 6.1858385 13050 45 45 0 16724 40320 5625 3790 1.0472302 0 93 0
20000 1.3224614 3804 0.24621703 20.398715 21.383949 6.1300529 13594 54 54 1 17517 40320 5625 3804 1.030461 0 93 0
21000 1.1530445 3784 0.24518298 20.435124 21.294142 5.4852317 13275 53 54 1 18412 40320 5625 3784 1.0535382 0 93 0
22000 1.1977912 3784 0.24500736 20.386535 21.278889 6.1881822 13475 47 47 0 19198 40320 5625 3784 1.0210748 0 93 0
23000 1.2514017 3797 0.24621058 20.451095 21.383389 8.7550065 13129 46 46 2 20287 40320 5625 3797 1.0368593 0 93 0
24000 1.2176426 3810 0.2457793 20.438788 21.345932 6.9987747 13704 60 60 2 21229 40320 5625 3810 1.0454377 0 93 0
25000 1.0891735 3798 0.24446154 20.420051 21.231485 6.1085159 13065 56 56 0 22323 40320 5625 3798 1.0505581 0 120 0
26000 1.1352468 3815 0.24428891 20.370733 21.216492 6.7514766 13071 63 63 0 23082 40320 5625 3815 1.0574391 0 120 0
27000 1.2096898 3767 0.24578464 20.445177 21.346396 9.2222472 13000 62 62 0 23915 40320 5625 3767 1.0322659 0 120 0
28000 1.1822845 3810 0.24602328 20.48632 21.367122 7.6215417 13091 63 64 0 25021 40320 5625 3810 1.0109647 0 120 0
29000 1.1681651 3774 0.24483973 20.394047 21.26433 4.8780536 13234 45 45 0 25969 40320 5625 3774 1.0139235 0 120 0
30000 1.2469272 3753 0.24652211 20.481484 21.410445 7.3553052 12959 42 42 0 27355 40320 5625 3753 1.0372102 0 158 0
31000 1.6007361 3784 0.25029348 20.54544 21.737988 6.4277487 13296 65 65 4 29010 40320 5625 3784 1.0232378 0 289 0
32000 1.3008178 3782 0.24630803 20.422743 21.391852 5.1176993 13300 84 85 1 30087 40320 5625 3782 1.0396919 0 289 0
33000 1.098991 3806 0.24419427 20.389524 21.208272 7.7403219 13385 56 57 1 31020 40320 5625 3806 1.041743 0 289 0
34000 1.0690232 3788 0.24446214 20.435114 21.231537 7.5766596 13169 52 52 1 31883 40320 5625 3788 1.0361564 0 289 0
35000 1.2481706 3805 0.24604847 20.439422 21.36931 8.4852719 13287 50 50 2 32742 40320 5625 3805 1.0362327 0 289 0
36000 1.2779611 3809 0.24583215 20.398441 21.350522 4.4273482 13245 53 53 0 33581 40320 5625 3809 1.0384859 0 289 0
37000 1.1516078 3797 0.2455632 20.469216 21.327164 6.8418541 13220 56 56 0 34676 40320 5625 3797 1.0356559 0 289 0
38000 3.1966808 3804 0.26289728 20.451101 22.832629 8.6766153 13285 78 78 5 35584 40320 5625 3804 1.0212937 0 289 0
39000 1.3514672 3774 0.24773001 20.508508 21.515351 6.8562512 13267 53 54 0 37060 40320 5625 3774 1.0506286 0 289 0
40000 1.2690376 3800 0.24696212 20.503227 21.44866 7.306469 13136 48 48 1 38009 40320 5625 3800 1.0435393 0 289 0
41000 1.1629196 3815 0.24451909 20.370108 21.236483 10.994819 13294 65 65 0 38856 40320 5625 3815 1.0231193 0 289 0
42000 1.3071093 3794 0.24711438 20.488087 21.461884 11.635668 13377 63 63 0 39748 40320 5625 3794 1.0310415 0 289 0
43000 1.1790643 3814 0.24525862 20.422309 21.300712 7.4899148 13167 55 55 0 40763 40320 5625 3814 1.0643207 0 289 0
44000 1.0546224 3816 0.24416646 20.420163 21.205857 8.5184241 13383 57 57 0 41635 40320 5625 3816 1.0300963 0 289 0
45000 1.5126923 3816 0.24957769 20.548867 21.675822 7.8342626 13593 51 51 5 43135 40320 5625 3816 1.0470194 0 289 0
46000 1.1974681 3811 0.24522511 20.405687 21.297801 8.5828458 13253 58 58 0 44063 40320 5625 3811 1.0211266 0 289 0
47000 1.153913 3796 0.24546332 20.458824 21.31849 12.306291 13070 46 46 1 44904 40320 5625 3796 1.0134546 0 289 0
48000 1.0836112 3783 0.24414791 20.396955 21.204246 8.2850758 12885 57 57 1 45783 40320 5625 3783 1.0518997 0 289 0
49000 1.0541913 3804 0.24345782 20.358939 21.144312 7.5572928 13094 67 67 1 46591 40320 5625 3804 1.022045 0 289 0
50000 1.2626609 3801 0.24672175 20.487102 21.427784 9.6363068 12963 67 67 3 47434 40320 5625 3801 1.0417063 0 289 0
51000 1.1865663 3788 0.24455665 20.355754 21.239745 10.07391 13119 62 63 2 48466 40320 5625 3788 1.0503342 0 289 0
52000 1.2437795 3802 0.24570213 20.412614 21.33923 9.3613571 13065 57 57 1 49406 40320 5625 3802 1.0407195 0 289 0
53000 1.2866363 3798 0.2458415 20.39279 21.351334 9.8245291 13109 53 53 1 50265 40320 5625 3798 1.0226426 0 289 0
54000 1.2414003 3799 0.24595803 20.436612 21.361455 11.751574 13190 58 59 3 51613 40320 5625 3799 1.0357656 0 289 0
55000 1.2028463 3785 0.24595746 20.465285 21.361405 6.4299111 13186 60 61 1 52735 40320 5625 3785 1.0316105 0 289 0
56000 1.0385165 3808 0.24390301 20.409282 21.182976 6.7801109 13022 54 54 0 53622 40320 5625 3808 1.0434153 0 289 0
57000 1.0436103 3799 0.24377932 20.394745 21.172234 7.1162927 13049 50 50 0 54495 40320 5625 3799 1.0178911 0 289 0
58000 0.97106921 3795 0.24364318 20.436964 21.16041 9.022592 13286 50 50 0 55327 40320 5625 3795 1.0353873 0 289 0
59000 1.1495392 3790 0.24458585 20.385874 21.242281 9.7884887 13157 63 63 1 56179 40320 5625 3790 1.0281317 0 289 0
60000 1.188382 3781 0.24514124 20.405172 21.290516 7.3581039 12943 56 56 1 57024 40320 5625 3781 1.0596215 0 289 0
61000 1.3366984 3768 0.24662234 20.42331 21.41915 6.109315 13068 52 52 1 57921 40320 5625 3768 1.0706378 0 289 0
62000 1.1261613 3788 0.24432384 20.380535 21.219525 5.7818811 13296 54 54 0 58841 40320 5625 3788 1.0432485 0 289 0
63000 1.1620503 3831 0.24430718 20.352351 21.218079 6.6114481 13321 51 51 0 59698 40320 5625 3831 1.0438264 0 289 0
64000 1.0816323 3803 0.24367372 20.357247 21.163063 10.33086 13210 64 64 0 60543 40320 5625 3803 1.055563 0 289 0
65000 1.2024467 3790 0.24573222 20.446021 21.341844 7.3760583 12855 54 54 0 61397 40320 5625 3790 1.0581964 0 289 0
66000 1.2134054 3782 0.2459965 20.460809 21.364796 6.5901858 13015 59 61 0 62205 40320 5625 3782 1.0320373 0 289 0
67000 1.2975719 3808 0.24614477 20.410982 21.377674 9.568788 13012 56 56 1 63680 40320 5625 3808 1.0555615 0 289 0
68000 1.3311071 3811 0.24615733 20.387089 21.378764 2.2119551 13138 56 56 0 64586 40320 5625 3811 1.0417112 0 289 0
69000 1.1764971 3803 0.24501561 20.403115 21.279606 2.3580263 12903 61 61 0 65504 40320 5625 3803 1.0345172 0 289 0
70000 1.1603463 3806 0.24424231 20.347987 21.212445 5.2723227 13068 64 64 2 66386 40320 5625 3806 1.0504265 0 289 0
71000 1.151703 3802 0.24460158 20.385628 21.243647 5.9863258 12868 51 51 2 67280 40320 5625 3802 1.0323304 0 289 0
72000 1.2360087 3789 0.24540655 20.392733 21.313559 8.0678594 12835 37 37 2 68153 40320 5625 3789 1.0157807 0 289 0
73000 1.1778901 3792 0.24516585 20.415126 21.292654 8.3383517 12980 59 59 0 68917 40320 5625 3792 1.0211893 0 289 0
74000 1.1320033 3801 0.24465911 20.405302 21.248644 6.7423404 13244 63 63 0 69802 40320 5625 3801 1.0379895 0 289 0
75000 1.303095 3792 0.24597801 20.392384 21.36319 7.1605507 13290 64 64 1 70966 40320 5625 3792 1.0479027 0 289 0
76000 1.3122789 3791 0.24686821 20.462856 21.440504 5.6011815 12921 53 53 0 71853 40320 5625 3791 1.0429825 0 289 0
77000 1.1110266 3777 0.24531121 20.477563 21.305278 7.6992351 13227 59 59 1 72625 40320 5625 3777 1.0346512 0 289 0
78000 1.1423584 3788 0.24614751 20.526855 21.377912 9.1592588 12981 54 54 0 73534 40320 5625 3788 1.0394046 0 289 0
79000 1.178933 3795 0.24546662 20.440471 21.318776 5.1190336 13027 61 61 0 74357 40320 5625 3795 1.0373795 0 289 0
80000 1.2228825 3793 0.24546742 20.407798 21.318845 8.5997861 13116 61 61 2 75248 40320 5625 3793 1.0487918 0 289 0
81000 1.2539867 3795 0.24680743 20.501006 21.435226 7.7737133 13136 65 65 0 76143 40320 5625 3795 1.057414 0 289 0
82000 1.2163565 3809 0.24603827 20.462238 21.368423 8.4588097 13227 77 77 0 77052 40320 5625 3809 1.0281569 0 289 0
83000 1.1372789 3800 0.24477746 20.411649 21.258922 8.6655002 13318 53 53 1 77950 40320 5625 3800 1.052126 0 289 0
84000 1.0963118 3798 0.24395552 20.370785 21.187537 7.5285125 13298 71 72 0 78812 40320 5625 3798 1.0739334 0 289 0
85000 1.2866517 3806 0.24577005 20.386573 21.345129 9.2812098 13301 73 73 0 79713 40320 5625 3806 1.0318108 0 289 0
86000 1.191902 3776 0.24527268 20.413966 21.301932 9.1903108 13178 60 60 0 80629 40320 5625 3776 1.0473977 0 289 0
87000 1.0828531 3787 0.24432069 20.412526 21.219252 4.6934397 13047 60 60 1 81448 40320 5625 3787 1.0168512 0 289 0
88000 2.0634092 3798 0.25362055 20.489705 22.026944 8.3601433 13229 49 49 27 82676 40320 5625 3798 1.0310791 0 289 0
89000 1.1633678 3788 0.24488709 20.401735 21.268444 7.9040117 13287 49 50 1 83644 40320 5625 3788 1.0443183 0 289 0
90000 1.1834356 3790 0.24566829 20.454632 21.336291 6.8101979 13377 50 50 0 84466 40320 5625 3790 1.0426033 0 289 0
91000 1.3000933 3810 0.24590334 20.388136 21.356705 6.481335 13468 62 62 4 85683 40320 5625 3810 1.0536904 0 289 0
92000 1.282522 3775 0.24709409 20.504643 21.460122 6.0594454 13383 47 47 0 86552 40320 5625 3775 1.0455446 0 289 0
93000 1.3337412 3787 0.24688092 20.447971 21.441608 8.2151451 13298 64 64 2 87424 40320 5625 3787 1.0304143 0 289 0
94000 1.2200394 3816 0.24594726 20.45159 21.360519 5.75844 13608 48 48 2 88404 40320 5625 3816 1.0319527 0 289 0
95000 1.1162136 3804 0.24520798 20.464734 21.296313 7.9641712 13316 51 51 0 89205 40320 5625 3804 1.034941 0 289 0
96000 1.1719084 3802 0.24578082 20.472993 21.346064 5.998945 13593 59 59 0 90005 40320 5625 3802 1.0280493 0 289 0
97000 1.3506167 3794 0.24764606 20.501851 21.508061 8.7470453 13202 56 56 1 90840 40320 5625 3794 1.0235267 0 289 0
98000 1.2314111 3800 0.24699537 20.534146 21.451548 13.14846 13183 67 67 0 91659 40320 5625 3800 1.017929 0 289 0
99000 1.1466628 3796 0.24472055 20.399716 21.25398 5.5941204 13335 62 62 1 92497 40320 5625 3796 1.0247856 0 289 0
100000 1.1502546 3831 0.24457346 20.384266 21.241205 9.3619779 13566 65 65 0 93378 40320 5625 3831 1.023894 0 289 0
Loop time of 23.1526 on 8 procs for 100000 steps with 17370 atoms
Pair time (%) = 0.357818 (1.54548)
Neigh time (%) = 1.28113 (5.53343)
Comm time (%) = 1.77444 (7.66411)
Outpt time (%) = 0.00594333 (0.0256703)
Other time (%) = 19.7333 (85.2313)
Nlocal: 2171.25 ave 2686 max 1889 min
Histogram: 2 2 0 1 0 1 1 0 0 1
Nghost: 65.25 ave 68 max 60 min
Histogram: 1 0 0 1 0 1 1 0 2 2
Neighs: 171.375 ave 213 max 87 min
Histogram: 1 0 0 0 1 1 1 0 1 3
Total # of neighbors = 1371
Ave neighs/atom = 0.0789292
Neighbor list builds = 5094
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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