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lammps/examples/ASPHERE/box/log.box.mp.10Sep13
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LAMMPS (9 Sep 2013)
# SRD viscosity 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 0.0532217 on 8 procs for 1000 steps with 420 atoms
Pair time (%) = 0.00440922 (8.28463)
Neigh time (%) = 0.00149104 (2.80156)
Comm time (%) = 0.0167182 (31.4124)
Outpt time (%) = 0.000243604 (0.457716)
Other time (%) = 0.0303596 (57.0437)
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 small viscosity 10 x y 50
fix 4 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.mp
#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 3.0049838 17777 0.24126663 42.1935 42.508307 10.275827 10158 39 39 0 969 90440 23409 17777 0.82992658 0 5 0
2000 2.0594027 17777 0.24067675 42.188632 42.404379 11.627774 10292 36 36 0 1771 90440 23409 17777 0.83080952 0 5 0
3000 2.4040501 17797 0.24079277 42.172967 42.42482 10.156226 10095 36 36 0 2459 90440 23409 17797 0.83998735 0 5 0
4000 2.2632838 17786 0.24072895 42.17647 42.413576 8.3000432 10226 39 39 0 3110 90440 23409 17786 0.84926739 0 11 0
5000 2.1615321 17771 0.2406319 42.17003 42.396476 12.614305 10146 42 42 0 3839 90440 23409 17771 0.84253705 0 12 0
6000 2.3404925 17788 0.24071728 42.166325 42.41152 8.4651458 10135 26 26 1 4611 90440 23409 17788 0.85083081 0 12 0
7000 2.7255145 17818 0.24092294 42.162224 42.447755 11.46372 10080 38 38 0 5374 90440 23409 17818 0.85293665 0 12 0
8000 3.365919 17803 0.24133267 42.167324 42.519944 9.3928156 9855 37 37 0 6193 90440 23409 17803 0.86064998 0 12 0
9000 3.9996052 17822 0.24169619 42.164986 42.583992 11.684546 10254 45 45 0 7098 90440 23409 17822 0.85610583 0 12 0
10000 3.7140801 17805 0.24148598 42.157861 42.546956 9.1699669 10100 26 26 0 7937 90440 23409 17805 0.85065679 0 12 0
11000 4.3731562 17827 0.24205487 42.189047 42.647187 9.2341771 10070 41 41 0 8764 90440 23409 17827 0.85807862 0 12 0
12000 4.1186516 17820 0.24193208 42.194074 42.625552 11.406041 10255 39 39 0 9655 90440 23409 17820 0.85643788 0 12 0
13000 4.762793 17824 0.24236854 42.203492 42.702451 12.157288 10474 47 47 1 10593 90440 23409 17824 0.85306532 0 12 0
14000 4.5224167 17792 0.24219742 42.198524 42.672301 7.1302951 10288 23 23 0 11429 90440 23409 17792 0.86236239 0 12 0
15000 5.1569684 17782 0.24264166 42.210318 42.750572 10.214491 10093 33 33 0 12370 90440 23409 17782 0.86348982 0 12 0
16000 6.5556642 17850 0.24347578 42.210751 42.897534 11.002602 10037 40 40 0 13271 90440 23409 17850 0.85200011 0 12 0
17000 5.5387674 17824 0.24266758 42.174887 42.755139 10.385285 10397 36 36 0 14175 90440 23409 17824 0.85533339 0 12 0
18000 5.6130858 17801 0.24266531 42.166701 42.754738 9.2072479 10173 31 31 0 15091 90440 23409 17801 0.85880719 0 12 0
19000 6.3690838 17731 0.24305026 42.155324 42.822562 11.000565 9904 35 35 0 16055 90440 23409 17731 0.8568314 0 12 0
20000 6.5345137 17804 0.24301313 42.131453 42.816021 8.6244348 10271 39 39 0 17065 90440 23409 17804 0.86184074 0 12 0
21000 7.8000849 17796 0.24367166 42.114894 42.932046 10.5203 10324 34 34 0 18083 90440 23409 17796 0.85189595 0 12 0
22000 7.2889302 17808 0.24348814 42.13611 42.899712 12.592106 10316 40 40 0 19144 90440 23409 17808 0.8551435 0 12 0
23000 8.0622172 17796 0.24398439 42.142531 42.987144 10.997293 10207 44 44 0 20246 90440 23409 17796 0.85458036 0 12 0
24000 9.1284316 17847 0.24461098 42.141231 43.097543 14.324353 10266 39 39 0 21367 90440 23409 17847 0.84705694 0 12 0
25000 9.0312955 17813 0.24455129 42.140891 43.087027 9.8503895 10026 38 38 0 22521 90440 23409 17813 0.84644311 0 12 0
26000 9.4732213 17795 0.24480929 42.140049 43.132482 7.2348444 10154 30 30 1 23615 90440 23409 17795 0.85372054 0 12 0
27000 9.8524378 17798 0.24513826 42.158283 43.190443 8.8910315 9894 27 27 0 24683 90440 23409 17798 0.84368629 0 12 0
28000 9.839534 17794 0.24506721 42.147117 43.177925 8.6536124 9936 36 36 0 25855 90440 23409 17794 0.85902123 0 20 0
29000 9.8880033 17788 0.24525763 42.175588 43.211474 12.57859 10393 54 54 0 26999 90440 23409 17788 0.8525183 0 20 0
30000 9.9944497 17784 0.24531874 42.175204 43.222242 7.6191563 10160 30 30 0 28150 90440 23409 17784 0.8525876 0 20 0
31000 9.4091213 17817 0.24497685 42.176287 43.162004 9.447269 10174 37 37 0 29298 90440 23409 17817 0.85820536 0 20 0
32000 9.8338203 17830 0.24533925 42.195645 43.225855 10.392617 10157 41 41 0 30497 90440 23409 17830 0.84673558 0 20 0
33000 10.170531 17841 0.24537715 42.167048 43.232533 9.4789613 10317 30 30 0 31653 90440 23409 17841 0.84189893 0 20 0
34000 9.3223103 17813 0.24482667 42.158922 43.135545 11.041395 10308 42 42 0 32824 90440 23409 17813 0.84966151 0 20 0
35000 10.3926 17793 0.24553346 42.171325 43.260073 9.9878588 10055 46 46 0 34035 90440 23409 17793 0.84654238 0 20 0
36000 9.0321397 17754 0.24478751 42.182421 43.128645 9.8056393 10047 34 34 0 35216 90440 23409 17754 0.84780342 0 20 0
37000 10.558279 17810 0.2457091 42.184913 43.291018 10.775504 10226 32 32 0 36453 90440 23409 17810 0.84924776 0 20 0
38000 10.020575 17810 0.2455366 42.210852 43.260627 9.1515261 10348 37 37 0 37802 90440 23409 17810 0.84427762 0 20 0
39000 9.9512554 17827 0.24554005 42.218721 43.261233 9.2917714 10326 33 33 0 39048 90440 23409 17827 0.84214883 0 20 0
40000 9.8735348 17774 0.24552032 42.223387 43.257758 11.642544 10168 29 29 0 40364 90440 23409 17774 0.84500349 0 20 0
41000 10.365156 17804 0.24566955 42.198177 43.284051 11.008578 10300 42 42 0 41686 90440 23409 17804 0.84403351 0 20 0
42000 10.226635 17818 0.24555953 42.193305 43.264667 9.4647805 10114 31 31 0 42984 90440 23409 17818 0.84572892 0 20 0
43000 9.8210408 17796 0.24514315 42.162435 43.191305 11.789151 10485 49 49 0 44223 90440 23409 17796 0.84076768 0 20 0
44000 7.9254401 17772 0.24398374 42.156747 42.987031 10.041925 10224 32 33 0 45547 90440 23409 17772 0.8483164 0 20 0
45000 8.5724312 17801 0.24441451 42.164862 43.062926 10.851835 10248 45 45 0 46831 90440 23409 17801 0.84635099 0 20 0
46000 9.5815129 17740 0.24508371 42.177055 43.180832 8.5573763 9951 29 29 1 48174 90440 23409 17740 0.84142197 0 20 0
47000 9.2724336 17815 0.24490579 42.178087 43.149485 10.749442 10324 41 41 0 49494 90440 23409 17815 0.84305403 0 20 0
48000 9.8698295 17829 0.2453373 42.19153 43.225512 10.992529 10010 44 44 0 50894 90440 23409 17829 0.84635867 0 20 0
49000 9.8650214 17775 0.24527147 42.180435 43.213913 9.9258034 10084 40 40 0 52221 90440 23409 17775 0.83690751 0 20 0
50000 11.52467 17800 0.24636922 42.199977 43.407323 9.5477158 10105 32 32 0 53667 90440 23409 17800 0.84402538 0 20 0
51000 9.5447655 17779 0.24527025 42.213771 43.213698 9.7717222 9994 39 39 1 54997 90440 23409 17779 0.83802916 0 20 0
52000 9.9738008 17814 0.24545383 42.201169 43.246043 9.9256895 10405 27 27 0 56351 90440 23409 17814 0.84021845 0 20 0
53000 10.294974 17805 0.24553341 42.181543 43.260064 10.07833 10251 43 43 0 57678 90440 23409 17805 0.83588955 0 20 0
54000 11.00851 17818 0.24588587 42.16889 43.322163 10.905345 10010 38 38 0 59118 90440 23409 17818 0.83044357 0 20 0
55000 12.200856 17797 0.24645934 42.145016 43.423201 10.929419 10103 45 45 0 60512 90440 23409 17797 0.83533437 0 20 0
56000 10.240644 17782 0.24544908 42.172377 43.245207 12.311462 9968 39 39 0 61888 90440 23409 17782 0.8334708 0 20 0
57000 11.858526 17799 0.24642127 42.174172 43.416493 11.602562 9675 44 44 0 63241 90440 23409 17799 0.83579075 0 20 0
58000 9.9579114 17781 0.24522905 42.16323 43.206439 9.8939621 9920 47 47 0 64565 90440 23409 17781 0.83252812 0 20 0
59000 9.4966125 17793 0.24495112 42.162588 43.157471 10.243383 9951 39 39 1 65879 90440 23409 17793 0.82795782 0 20 0
60000 9.3889539 17763 0.24483753 42.153854 43.137459 6.7498755 9893 26 26 0 67171 90440 23409 17763 0.83255788 0 98 0
61000 9.8219129 17760 0.24497944 42.133499 43.162462 10.026948 10063 39 39 0 68464 90440 23409 17760 0.83382901 0 98 0
62000 8.9772784 17744 0.24430051 42.102364 43.042841 6.7992672 9830 31 31 0 69793 90440 23409 17744 0.83040933 0 98 0
63000 9.4555226 17778 0.2446845 42.119917 43.110495 9.3613489 9507 33 33 0 71025 90440 23409 17778 0.81990914 0 98 0
64000 10.822236 17791 0.24553255 42.126154 43.259912 10.978102 9950 44 44 0 72302 90440 23409 17791 0.8205428 0 98 0
65000 10.643375 17749 0.24553889 42.146009 43.261029 9.8170035 9751 33 33 0 73657 90440 23409 17749 0.81737668 0 98 0
66000 10.65446 17802 0.24577045 42.185645 43.301827 10.068015 9838 38 38 0 74926 90440 23409 17802 0.82017685 0 98 0
67000 11.320004 17810 0.24637556 42.222536 43.408441 13.28653 9779 39 39 0 76258 90440 23409 17810 0.82794931 0 98 0
68000 11.235171 17769 0.2461615 42.193708 43.370726 11.789643 9847 37 37 0 77534 90440 23409 17769 0.81709561 0 98 0
69000 10.833468 17779 0.2459244 42.194017 43.328952 9.0530182 9896 39 39 0 78894 90440 23409 17779 0.82041697 0 98 0
70000 11.565202 17794 0.24641358 42.203546 43.415139 6.0770107 9643 29 29 0 80167 90440 23409 17794 0.82167076 0 98 0
71000 11.125212 17790 0.24620537 42.212956 43.378454 14.351282 9877 38 38 1 81552 90440 23409 17790 0.82508123 0 98 0
72000 12.644174 17763 0.24699557 42.193051 43.517679 10.531064 9953 42 42 0 82972 90440 23409 17763 0.82933853 0 98 0
73000 12.165673 17828 0.24657837 42.169674 43.444173 11.982241 10132 39 39 0 84372 90440 23409 17828 0.82853038 0 98 0
74000 13.565669 17790 0.24748187 42.182194 43.60336 11.810898 9964 32 32 0 85794 90440 23409 17790 0.83238035 0 98 0
75000 13.850885 17779 0.24764619 42.181266 43.632311 11.595796 9829 40 40 0 87294 90440 23409 17779 0.82452835 0 98 0
76000 13.730794 17774 0.24760357 42.186337 43.624801 10.314049 9977 39 39 0 88621 90440 23409 17774 0.82554866 0 98 0
77000 14.2192 17789 0.24787267 42.182584 43.672214 9.9780185 9834 32 32 0 90146 90440 23409 17789 0.82713865 0 98 0
78000 14.316206 17801 0.24800412 42.19558 43.695373 8.3314161 10132 38 39 0 91616 90440 23409 17801 0.82824877 0 98 0
79000 13.703006 17815 0.24778437 42.221104 43.656656 8.1390498 10001 35 35 0 93114 90440 23409 17815 0.82396879 0 98 0
80000 14.21882 17804 0.24812482 42.227048 43.716639 9.0164253 9950 41 41 0 94643 90440 23409 17804 0.83049102 0 98 0
81000 13.61083 17812 0.24765862 42.208604 43.634501 8.7498353 10205 30 30 0 96165 90440 23409 17812 0.83215993 0 98 0
82000 14.24814 17780 0.24806178 42.212871 43.705533 8.9596483 9898 33 33 0 97690 90440 23409 17780 0.82682824 0 98 0
83000 13.18484 17803 0.24743025 42.212995 43.594264 12.116538 9833 39 39 0 99222 90440 23409 17803 0.82225356 0 98 0
84000 12.665093 17787 0.24718115 42.223556 43.550375 7.0430872 9857 33 33 0 100749 90440 23409 17787 0.8216466 0 98 0
85000 12.22937 17748 0.24700172 42.23759 43.518762 14.858066 9924 35 35 0 102174 90440 23409 17748 0.82012834 0 98 0
86000 11.637126 17741 0.24648333 42.208301 43.427429 8.8309049 10034 38 38 0 103545 90440 23409 17741 0.82310449 0 98 0
87000 13.172172 17780 0.24761541 42.246946 43.626888 11.997785 9793 34 34 0 105003 90440 23409 17780 0.8231062 0 98 0
88000 13.867288 17774 0.2478372 42.213201 43.665964 13.008322 9930 45 45 0 106424 90440 23409 17774 0.81835323 0 98 0
89000 14.409874 17792 0.24817672 42.216177 43.725783 8.9017208 9873 33 33 0 107941 90440 23409 17792 0.812681 0 98 0
90000 14.175277 17745 0.24802753 42.21447 43.699499 7.8889612 9838 37 37 0 109384 90440 23409 17745 0.82045281 0 98 0
91000 13.80886 17809 0.24773522 42.201354 43.647996 10.153291 10077 34 34 0 110836 90440 23409 17809 0.8142495 0 98 0
92000 14.391083 17743 0.24814425 42.212425 43.720062 12.167713 9928 28 28 0 112372 90440 23409 17743 0.82301567 0 98 0
93000 13.425843 17771 0.24744975 42.191184 43.597701 10.962936 9854 29 29 0 113801 90440 23409 17771 0.81953388 0 98 0
94000 12.969876 17828 0.24733041 42.217925 43.576674 10.432208 10160 32 32 1 115320 90440 23409 17828 0.81861088 0 98 0
95000 13.550396 17812 0.24762509 42.209027 43.628593 9.1923817 10139 27 27 0 116845 90440 23409 17812 0.82254819 0 98 0
96000 14.303773 17807 0.24819751 42.230956 43.729446 8.2304906 9666 33 33 0 118316 90440 23409 17807 0.82304543 0 98 0
97000 14.027408 17825 0.24788054 42.204061 43.673599 11.160576 10211 43 43 0 119812 90440 23409 17825 0.82817945 0 98 0
98000 14.515459 17805 0.24814196 42.198993 43.71966 13.355885 10078 43 43 0 121293 90440 23409 17805 0.82291353 0 98 0
99000 13.502344 17774 0.24757651 42.205502 43.620034 9.1790624 9865 31 31 0 122780 90440 23409 17774 0.8281067 0 98 0
100000 14.173632 17761 0.24801238 42.211971 43.696828 10.204956 9866 35 35 0 124297 90440 23409 17761 0.83321256 0 98 0
Loop time of 62.3427 on 8 procs for 100000 steps with 73999 atoms
Pair time (%) = 0.637287 (1.02223)
Neigh time (%) = 3.81362 (6.11719)
Comm time (%) = 3.39013 (5.4379)
Outpt time (%) = 0.010035 (0.0160965)
Other time (%) = 54.4916 (87.4066)
Nlocal: 9249.88 ave 11502 max 7978 min
Histogram: 1 2 2 0 1 0 0 1 0 1
Nghost: 53 ave 68 max 41 min
Histogram: 3 0 0 0 0 3 0 0 1 1
Neighs: 288.625 ave 518 max 152 min
Histogram: 2 1 1 1 1 0 0 1 0 1
Total # of neighbors = 2309
Ave neighs/atom = 0.0312031
Neighbor list builds = 5000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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