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LAMMPS (1 Feb 2014)
# 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
reading atoms ...
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 = 0.443012 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 0.0540034 on 8 procs for 1000 steps with 420 atoms
Pair time (%) = 0.00388333 (7.1909)
Neigh time (%) = 0.0012731 (2.35743)
Comm time (%) = 0.0160792 (29.7743)
Outpt time (%) = 0.000274509 (0.508318)
Other time (%) = 0.0324934 (60.169)
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:439)
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:2875)
# 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 = 14.2707 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 16229 0.24126663 42.1935 42.508307 10.275827 10158 39 39 0 970 90440 23409 16229 0.90908897 0 5 0
2000 2.1454941 16282 0.24068985 42.18192 42.406686 8.3551805 10114 39 39 0 1766 90440 23409 16282 0.91411077 0 5 0
3000 1.7194781 16297 0.24043991 42.182513 42.362649 9.0500757 10293 35 35 0 2454 90440 23409 16297 0.91613392 0 5 0
4000 1.9700398 16189 0.24063155 42.190029 42.396415 11.380017 10043 27 28 0 3083 90440 23409 16189 0.92535621 0 5 0
5000 2.2262815 16301 0.24071918 42.178625 42.411854 10.059361 10169 29 29 0 3730 90440 23409 16301 0.92861813 0 5 0
6000 2.2291507 16232 0.24063671 42.163793 42.397323 7.276142 9899 40 40 0 4445 90440 23409 16232 0.93275834 0 5 0
7000 2.7841984 16212 0.2407729 42.129641 42.421319 10.838996 10144 39 39 0 5148 90440 23409 16212 0.93329636 0 5 0
8000 3.1799279 16294 0.24102189 42.132053 42.465189 9.3204165 10068 31 31 0 5897 90440 23409 16294 0.93229671 0 5 0
9000 3.6101913 16308 0.24126974 42.130646 42.508857 9.9117415 10113 30 30 0 6716 90440 23409 16308 0.93107227 0 5 0
10000 4.1022731 16319 0.24161934 42.140689 42.570451 9.8799373 10205 34 34 0 7480 90440 23409 16319 0.92489062 0 5 0
11000 4.2790298 16269 0.2417129 42.138657 42.586936 10.14836 10002 37 37 2 8283 90440 23409 16269 0.92331323 0 10 0
12000 4.4299614 16323 0.24179577 42.137445 42.601537 11.786696 10068 37 37 1 9085 90440 23409 16323 0.93507414 0 10 0
13000 4.1451629 16263 0.24166347 42.143972 42.578227 7.5907603 9931 27 27 0 9967 90440 23409 16263 0.93269278 0 10 0
14000 5.0478037 16299 0.24222245 42.147894 42.676711 9.616107 10010 39 39 0 10856 90440 23409 16299 0.93132197 0 10 0
15000 4.9761523 16318 0.24208522 42.131222 42.652533 10.028283 10181 45 45 0 11744 90440 23409 16318 0.92914494 0 10 0
16000 5.0281695 16300 0.24209471 42.127445 42.654206 13.025657 10410 38 38 0 12657 90440 23409 16300 0.9322983 0 10 0
17000 6.0553511 16294 0.24278108 42.140765 42.775135 8.3971756 9898 31 31 0 13606 90440 23409 16294 0.93207864 0 10 0
18000 5.8870865 16349 0.24261355 42.128876 42.745619 9.4579631 9872 33 33 0 14510 90440 23409 16349 0.92911772 0 10 0
19000 6.19767 16260 0.2425369 42.082834 42.732114 10.497489 10068 37 37 0 15478 90440 23409 16260 0.9258668 0 10 0
20000 5.0588231 16330 0.24187554 42.085618 42.61559 9.3582625 9935 35 35 0 16470 90440 23409 16330 0.92639501 0 10 0
21000 6.4272357 16337 0.24285051 42.11404 42.78737 11.339789 9973 38 38 0 17363 90440 23409 16337 0.91830732 0 10 0
22000 6.3660195 16301 0.24257121 42.071243 42.738159 10.340724 9855 41 41 0 18300 90440 23409 16301 0.92735973 0 13 0
23000 5.9141967 16265 0.24245321 42.097787 42.71737 10.888473 9874 46 46 0 19294 90440 23409 16265 0.92958577 0 13 0
24000 7.3326392 16305 0.24333743 42.104977 42.873159 8.159204 9831 32 32 0 20337 90440 23409 16305 0.92498949 0 13 0
25000 7.8712498 16317 0.24365329 42.104202 42.928809 13.3861 10107 51 52 0 21343 90440 23409 16317 0.92093733 0 13 0
26000 7.6909446 16302 0.24354679 42.104327 42.910045 9.3626418 10101 45 45 0 22390 90440 23409 16302 0.91881953 0 13 0
27000 7.7525711 16296 0.24366541 42.11877 42.930944 9.3545743 9869 31 31 0 23458 90440 23409 16296 0.92276633 0 13 0
28000 7.8688635 16287 0.24363999 42.102109 42.926466 9.6143934 10023 37 37 0 24515 90440 23409 16287 0.92561111 0 13 0
29000 8.1116441 16298 0.24396496 42.13393 42.983722 9.8457785 10018 37 37 0 25571 90440 23409 16298 0.92896968 0 13 0
30000 7.5432306 16233 0.24356273 42.12261 42.912853 10.484741 9978 33 33 0 26714 90440 23409 16233 0.92084331 0 13 0
31000 7.9849131 16251 0.24395097 42.144741 42.981256 8.728219 9926 36 36 0 27794 90440 23409 16251 0.91985968 0 13 0
32000 8.8200827 16255 0.24461412 42.174088 43.098096 9.4477224 10118 31 31 0 28911 90440 23409 16255 0.92764378 0 13 0
33000 9.0462578 16266 0.24476502 42.176979 43.124682 9.0256529 9948 41 41 0 30010 90440 23409 16266 0.92496675 0 13 0
34000 11.115911 16273 0.24591951 42.163566 43.32809 10.89006 10013 35 35 1 31155 90440 23409 16273 0.9209011 0 59 0
35000 9.5287387 16348 0.24494148 42.157524 43.155772 9.1589486 10058 33 33 0 32262 90440 23409 16348 0.91852697 0 59 0
36000 8.6525285 16271 0.24454224 42.178976 43.085431 9.6115865 9936 39 39 0 33447 90440 23409 16271 0.91738637 0 59 0
37000 9.3244405 16237 0.24490339 42.172216 43.149062 11.766374 10057 49 49 0 34660 90440 23409 16237 0.92209291 0 59 0
38000 9.2952308 16272 0.24496591 42.186292 43.160078 9.5173055 10039 32 32 1 35916 90440 23409 16272 0.91915422 0 59 0
39000 10.12307 16312 0.24550971 42.195376 43.255888 10.678168 9989 43 43 1 37116 90440 23409 16312 0.92499805 0 59 0
40000 11.051307 16266 0.24606279 42.195578 43.353334 10.078073 9867 37 37 0 38363 90440 23409 16266 0.9229677 0 59 0
41000 10.400692 16313 0.24566631 42.193882 43.283479 9.2181368 10040 39 39 0 39612 90440 23409 16313 0.92195363 0 59 0
42000 9.0646248 16277 0.24487452 42.194348 43.143975 8.2531891 10173 37 37 0 40821 90440 23409 16277 0.91941681 0 59 0
43000 9.8646504 16258 0.24532194 42.189366 43.222806 10.34072 10037 37 37 0 42068 90440 23409 16258 0.91264623 0 59 0
44000 10.441846 16296 0.24553053 42.165649 43.259556 12.147264 10299 31 31 0 43277 90440 23409 16296 0.91599514 0 59 0
45000 10.458302 16261 0.24544296 42.148496 43.244128 8.8999271 10208 26 26 0 44492 90440 23409 16261 0.91716968 0 59 0
46000 10.117248 16269 0.24511999 42.127322 43.187224 9.0053892 10132 36 36 0 45691 90440 23409 16269 0.91327538 0 59 0
47000 9.6094606 16247 0.24494761 42.150148 43.156854 11.844069 9936 43 43 0 46930 90440 23409 16247 0.91513796 0 59 0
48000 12.544005 16250 0.24661869 42.137144 43.451278 14.420938 9999 43 43 0 48233 90440 23409 16250 0.91642267 0 59 0
49000 11.948168 16257 0.24628573 42.140902 43.392614 8.653163 10093 38 38 0 49517 90440 23409 16257 0.90604463 0 59 0
50000 12.315254 16233 0.2466687 42.16992 43.460089 9.1125366 10050 39 39 0 50806 90440 23409 16233 0.90490961 0 59 0
51000 11.364234 16265 0.24609762 42.168932 43.359471 9.8694192 9860 37 37 0 52074 90440 23409 16265 0.909623 0 59 0
52000 10.627787 16231 0.24578998 42.191882 43.305269 10.869196 9877 33 33 0 53420 90440 23409 16231 0.90981484 0 59 0
53000 11.809423 16261 0.24656286 42.204263 43.441441 13.38992 9828 39 39 0 54766 90440 23409 16261 0.90710704 0 59 0
54000 10.63283 16251 0.24554697 42.148537 43.262453 10.181102 10098 29 29 0 56085 90440 23409 16251 0.90800902 0 59 0
55000 10.803075 16254 0.24562954 42.145251 43.277002 7.9856721 9964 26 26 0 57451 90440 23409 16254 0.90786888 0 59 0
56000 10.844803 16274 0.2458735 42.183861 43.319983 9.9407901 10031 36 36 0 58695 90440 23409 16274 0.89847818 0 59 0
57000 10.623373 16218 0.24574768 42.184891 43.297816 12.015798 9792 43 43 0 60012 90440 23409 16218 0.90944412 0 59 0
58000 10.679964 16262 0.24583434 42.194231 43.313084 11.651504 9776 45 45 0 61295 90440 23409 16262 0.90511687 0 59 0
59000 10.35931 16278 0.24567475 42.199706 43.284967 10.599471 10069 30 30 1 62506 90440 23409 16278 0.90064789 0 59 0
60000 12.034078 16208 0.24677506 42.218115 43.478828 10.511331 9936 31 31 0 63825 90440 23409 16208 0.90250225 0 59 0
61000 11.915856 16208 0.24666669 42.211407 43.459734 11.982448 10227 34 34 0 65189 90440 23409 16208 0.90006711 0 59 0
62000 11.388719 16269 0.24635856 42.212341 43.405445 8.4867265 9991 29 29 0 66502 90440 23409 16269 0.90418592 0 59 0
63000 10.513272 16243 0.24593174 42.228854 43.330244 9.2843187 10133 39 39 0 67836 90440 23409 16243 0.91282932 0 59 0
64000 11.465761 16203 0.24638806 42.209467 43.410642 8.8736184 10023 38 39 0 69216 90440 23409 16203 0.90742452 0 59 0
65000 9.9798452 16292 0.24547666 42.204557 43.250064 12.475112 9766 36 36 0 70559 90440 23409 16292 0.90921789 0 59 0
66000 12.184131 16177 0.2468175 42.209872 43.486305 8.4442171 10049 33 33 0 71851 90440 23409 16177 0.90771921 0 59 0
67000 11.845593 16250 0.24645726 42.181869 43.422835 8.2359478 9678 33 33 0 73241 90440 23409 16250 0.9069606 0 59 0
68000 10.616202 16220 0.2456631 42.17074 43.282913 7.6844013 9954 28 28 0 74707 90440 23409 16220 0.90830051 0 59 0
69000 11.708481 16174 0.246425 42.190549 43.417152 9.6601201 10019 34 34 0 76143 90440 23409 16174 0.90853993 0 59 0
70000 13.149115 16175 0.24730865 42.195313 43.57284 7.8721271 9794 31 31 0 77520 90440 23409 16175 0.90460472 0 59 0
71000 12.420743 16210 0.24676949 42.176626 43.477846 10.370102 9886 36 36 0 78901 90440 23409 16210 0.90567986 0 59 0
72000 13.424842 16222 0.24726211 42.158228 43.56464 10.837461 9892 36 36 0 80221 90440 23409 16222 0.90896224 0 59 0
73000 12.983985 16177 0.2470467 42.16646 43.526687 7.3246122 9975 31 31 0 81578 90440 23409 16177 0.90172487 0 59 0
74000 11.873207 16217 0.24644792 42.177329 43.421189 11.257297 9937 40 40 0 83004 90440 23409 16217 0.9069376 0 59 0
75000 11.719883 16219 0.24631358 42.169723 43.397521 8.2731229 10281 28 28 0 84503 90440 23409 16219 0.90087971 0 59 0
76000 11.648725 16220 0.24633978 42.181793 43.402136 11.364684 9961 31 31 0 85910 90440 23409 16220 0.90445518 0 59 0
77000 11.315159 16169 0.24618794 42.189986 43.375384 10.639734 9853 35 35 0 87272 90440 23409 16169 0.90967681 0 59 0
78000 11.026923 16262 0.2459278 42.17435 43.329551 9.3461335 10068 36 36 0 88765 90440 23409 16262 0.90250223 0 59 0
79000 11.923316 16205 0.24657893 42.195162 43.444272 8.3200696 9914 29 29 1 90167 90440 23409 16205 0.89792511 0 59 0
80000 12.28723 16233 0.246793 42.194756 43.481989 9.8594414 9898 41 41 0 91543 90440 23409 16233 0.89920018 0 59 0
81000 12.657271 16252 0.24700788 42.193847 43.519847 9.5478351 10045 38 38 0 92888 90440 23409 16252 0.90032559 0 59 0
82000 10.415047 16249 0.24563975 42.1877 43.2788 8.4502786 9729 30 30 0 94355 90440 23409 16249 0.90516702 0 59 0
83000 13.038087 16237 0.24718282 42.184776 43.550671 10.813181 9834 48 48 0 95792 90440 23409 16237 0.90160106 0 59 0
84000 11.994728 16253 0.24664911 42.200046 43.456637 10.907779 9632 48 48 0 97203 90440 23409 16253 0.90075335 0 59 0
85000 11.560331 16253 0.24626448 42.177788 43.38887 9.8019244 9637 27 27 0 98581 90440 23409 16253 0.90204694 0 59 0
86000 12.294346 16214 0.2466302 42.165325 43.453305 8.4731319 9776 30 30 1 100022 90440 23409 16214 0.8976977 0 59 0
87000 11.439691 16227 0.24593937 42.133145 43.331589 11.138197 9408 35 35 0 101446 90440 23409 16227 0.90678956 0 59 0
88000 12.269451 16218 0.24642733 42.132191 43.417562 9.2022903 9627 28 28 0 102882 90440 23409 16218 0.89354177 0 59 0
89000 11.630085 16281 0.24612243 42.145453 43.363843 9.4906584 9713 45 45 0 104390 90440 23409 16281 0.90416008 0 59 0
90000 12.068036 16226 0.24636746 42.142743 43.407014 13.55402 9721 30 30 1 105786 90440 23409 16226 0.90693102 0 59 0
91000 11.423374 16180 0.24593187 42.133533 43.330267 11.12182 9490 33 33 0 107319 90440 23409 16180 0.89908597 0 59 0
92000 11.759782 16253 0.24594059 42.099827 43.331804 8.5785997 9808 36 37 0 108822 90440 23409 16253 0.90323757 0 59 0
93000 12.860286 16203 0.24670999 42.120094 43.467362 9.7352723 9342 32 32 0 110320 90440 23409 16203 0.89837993 0 59 0
94000 12.65067 16201 0.24650827 42.106515 43.431823 11.726981 9708 37 37 0 111721 90440 23409 16201 0.90153973 0 59 0
95000 12.938398 16301 0.2467405 42.117288 43.472739 13.229664 9490 42 42 0 113106 90440 23409 16301 0.89222858 0 59 0
96000 13.125 16243 0.24672164 42.094416 43.469416 11.492955 9666 43 43 0 114441 90440 23409 16243 0.89369219 0 59 0
97000 14.779601 16270 0.24775001 42.102263 43.650602 9.7132418 9517 31 31 0 115831 90440 23409 16270 0.88854614 0 59 0
98000 15.427308 16254 0.24808383 42.093224 43.709418 11.821283 9510 36 37 0 117263 90440 23409 16254 0.88982996 0 59 0
99000 16.212104 16248 0.24846852 42.078784 43.777195 10.786344 9807 37 37 0 118659 90440 23409 16248 0.89136464 0 59 0
100000 15.896 16229 0.24841013 42.101613 43.766908 10.836017 9640 28 28 0 120081 90440 23409 16229 0.90018614 0 59 0
Loop time of 53.3125 on 8 procs for 100000 steps with 73999 atoms
Pair time (%) = 0.559711 (1.04987)
Neigh time (%) = 3.94754 (7.40453)
Comm time (%) = 3.46588 (6.50106)
Outpt time (%) = 0.00787139 (0.0147646)
Other time (%) = 45.3315 (85.0298)
Nlocal: 9249.88 ave 10477 max 8359 min
Histogram: 1 2 1 1 0 1 0 0 0 2
Nghost: 54 ave 65 max 45 min
Histogram: 2 1 0 0 1 1 0 2 0 1
Neighs: 316.875 ave 387 max 170 min
Histogram: 1 0 0 0 1 0 0 4 0 2
Total # of neighbors = 2535
Ave neighs/atom = 0.0342572
Neighbor list builds = 5000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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