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LAMMPS (1 Feb 2014)
# SRD viscosity demo - poydisperse spheres
units lj
atom_style sphere
atom_modify first big
dimension 2
# create big particles with 3 different types and diameters
lattice sq 0.3
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region box block 0 10 0 10 -0.5 0.5
create_box 4 box
Created orthogonal box = (0 0 -0.912871) to (18.2574 18.2574 0.912871)
2 by 4 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
group big type 1
100 atoms in group big
set group big type/fraction 2 0.33 394895
35 settings made for type/fraction
set group big type/fraction 3 0.5 989894
57 settings made for type/fraction
group big type 2 3
100 atoms in group big
set type 1*3 mass 1.0
100 settings made for mass
velocity big create 1.44 87287 loop geom
# equilibrate big particles, repulsive only to prevent aggregation
pair_style lj/cut 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 0.0 1.0 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
#dump 1 all atom 10 dump.poly.equil
run 1000
Memory usage per processor = 2.7472 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.16013916 0 1.2654608 1.1298975
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
Loop time of 0.0173425 on 8 procs for 1000 steps with 100 atoms
Pair time (%) = 0.00033614 (1.93825)
Neigh time (%) = 0.000266045 (1.53407)
Comm time (%) = 0.0115004 (66.3132)
Outpt time (%) = 2.78056e-05 (0.160332)
Other time (%) = 0.00521213 (30.0541)
Nlocal: 12.5 ave 18 max 10 min
Histogram: 1 3 1 1 0 1 0 0 0 1
Nghost: 27.75 ave 31 max 24 min
Histogram: 1 0 1 0 2 2 0 0 0 2
Neighs: 19 ave 30 max 16 min
Histogram: 4 1 2 0 0 0 0 0 0 1
Total # of neighbors = 152
Ave neighs/atom = 1.52
Neighbor list builds = 115
Dangerous builds = 0
#undump 1
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 250.0
Lattice spacing in x,y,z = 0.0632456 0.0632456 0.0632456
create_atoms 4 region plane
Created 83521 atoms
set type 4 mass 0.1
83521 settings made for mass
group small type 4
83521 atoms in group small
velocity small create 1.0 593849 loop geom
# delete overlaps
# must set *-4 cutoffs to non-zero values
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
pair_coeff 2 2 1.0 2.0
pair_coeff 3 3 1.0 1.5
pair_coeff 1 4 0.0 1.0 0.5
pair_coeff 2 4 0.0 1.0 1.0
pair_coeff 3 4 0.0 1.0 0.75
delete_atoms overlap 1.0 small big
Deleted 63410 atoms, new total = 20211
# 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 1.12
pair_coeff 1 1 1.0 1.0 1.12
pair_coeff 2 2 1.0 2.0 2.24
pair_coeff 3 3 1.0 1.5 1.68
pair_coeff 4 4 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 nve
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
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]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
thermo 1000
#dump 1 all atom 500 dump.poly.mp
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
run 50000
SRD info:
SRD/big particles = 20111 100
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: 73 73 1
SRD grid size: request, actual (xyz) = 0.25, 0.250102 0.250102 1.82574
SRD per actual grid cell = 4.93717
SRD viscosity = 0.23322
big/SRD mass density ratio = 0.161311
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.19344 7.74495
ave/max big velocity = 1.43991 3.5724
Memory usage per processor = 11.8633 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]
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
1000 0.76223471 3964 0.0058318994 0.042955471 1.1786852 3.9611295 7412 29 29 0 611 36480 5329 3964 0.97424113 0 1
2000 0.83394503 3951 0.0050432506 -0.22328672 1.0192914 2.7492771 7829 30 30 0 1225 36480 5329 3951 1.0832295 0 3
3000 0.86856945 3991 0.0048205728 -0.31988251 0.97428597 2.4105317 7961 34 34 0 2000 36480 5329 3991 1.1243219 0 6
4000 0.88106888 4009 0.0066731082 0.035909261 1.3487019 3.025346 8002 33 33 0 2895 36480 5329 4009 1.1359575 0 6
5000 1.0764198 4036 0.0070136315 -0.18634051 1.4175251 2.7617336 8117 36 36 0 3808 36480 5329 4036 1.1147743 0 6
6000 1.0433139 4004 0.0059532709 -0.35132214 1.2032156 2.3597383 8004 23 23 0 4845 36480 5329 4004 1.1192873 0 6
7000 1.1551053 4026 0.0074766715 -0.20999681 1.5111101 2.280806 8269 36 36 0 5873 36480 5329 4026 1.1704244 0 6
8000 1.2222713 4008 0.0078175708 -0.24117508 1.5800092 1.967726 8218 33 33 0 7077 36480 5329 4008 1.1496529 0 6
9000 1.2240884 4012 0.0081583857 -0.17500037 1.6488913 2.3684675 8502 27 27 0 8359 36480 5329 4012 1.1664455 0 6
10000 1.2071315 4035 0.0073838443 -0.30627724 1.4923488 2.124366 8376 33 33 0 9778 36480 5329 4035 1.1942304 0 6
11000 1.1694272 4036 0.0077950192 -0.16699527 1.5754513 2.4203067 8623 40 40 0 11210 36480 5329 4036 1.1802896 0 42
12000 1.0911561 4044 0.0074117515 -0.12783343 1.4979891 2.4859591 8490 30 30 0 12647 36480 5329 4044 1.171701 0 42
13000 1.3535072 4023 0.0091503262 -0.16735325 1.8493724 2.7718999 8320 33 33 0 14082 36480 5329 4023 1.1841757 0 42
14000 1.4191753 4043 0.0095368758 -0.18707328 1.927498 2.8442438 8422 25 25 0 15462 36480 5329 4043 1.1567854 0 42
15000 1.703769 4053 0.010892787 -0.33707457 2.2015412 2.4160876 8123 34 34 0 16985 36480 5329 4053 1.1875794 0 42
16000 1.4270161 4032 0.010142553 -0.076342616 2.0499114 2.9568071 8360 34 34 0 18487 36480 5329 4032 1.164586 0 42
17000 1.2267528 4013 0.0080642511 -0.19799584 1.6298658 2.5084784 8477 27 27 0 20101 36480 5329 4013 1.1529604 0 42
18000 1.4228586 4050 0.01009573 -0.079611446 2.0404479 2.8013833 8519 33 33 0 21633 36480 5329 4050 1.1549291 0 42
19000 1.3041379 4040 0.0082901927 -0.26763462 1.6755308 1.9403854 8483 30 30 0 23194 36480 5329 4040 1.1592747 0 42
20000 1.3837406 4030 0.0092446911 -0.19332904 1.8684445 2.4550531 8425 25 25 0 24761 36480 5329 4030 1.1757648 0 42
21000 1.7882552 4031 0.012076007 -0.22381856 2.4406817 2.4206092 8581 40 40 0 26371 36480 5329 4031 1.1591574 0 42
22000 1.5079803 4015 0.010373742 -0.15025377 2.0966369 2.6321039 8383 33 33 0 27989 36480 5329 4015 1.1495522 0 42
23000 1.3835348 4044 0.0087922321 -0.28446888 1.776998 2.2729548 8441 30 30 0 29575 36480 5329 4044 1.1616377 0 42
24000 1.5854836 4044 0.0099174248 -0.35795983 2.0044107 2.2250073 8462 35 35 0 31298 36480 5329 4044 1.1796851 0 42
25000 1.5314412 4062 0.010880793 -0.082730301 2.1991171 2.6858232 8473 28 28 0 33079 36480 5329 4062 1.1726593 0 54
26000 1.2896316 4070 0.0090198232 -0.098554631 1.8229965 2.3437649 8453 40 40 0 34816 36480 5329 4070 1.1764482 0 54
27000 1.6956611 4035 0.012064024 -0.088275024 2.43826 2.8138661 8380 32 32 0 36453 36480 5329 4035 1.1622504 0 54
28000 1.3560979 4043 0.0088193796 -0.23810107 1.7824848 2.1799536 8611 30 30 0 38202 36480 5329 4043 1.1681248 0 54
29000 1.5837646 4029 0.010790526 -0.17893612 2.1808731 2.3116753 8480 26 26 0 39846 36480 5329 4029 1.1774511 0 54
30000 1.6549448 4035 0.01137773 -0.16631482 2.2995529 2.6236656 8637 30 30 0 41461 36480 5329 4035 1.1538405 0 54
31000 1.445315 4050 0.01013447 -0.1052417 2.0482777 2.4440312 8504 38 38 0 43099 36480 5329 4050 1.1690375 0 54
32000 1.5572315 4037 0.010828477 -0.13173155 2.1885434 2.5911192 8453 30 30 0 44760 36480 5329 4037 1.1612147 0 54
33000 2.018109 4068 0.013467519 -0.28506208 2.7219203 2.5784978 8701 40 40 0 46462 36480 5329 4068 1.1727186 0 54
34000 1.2455134 4066 0.0083640288 -0.16536113 1.6904539 2.3054829 8428 32 32 0 48055 36480 5329 4066 1.1712016 0 54
35000 1.6248596 4012 0.011213824 -0.15461501 2.2664259 2.8697537 8453 31 31 0 49658 36480 5329 4012 1.1693962 0 54
36000 1.5485873 4039 0.01112737 -0.058442367 2.2489527 3.0386676 8529 42 42 0 51330 36480 5329 4039 1.1750818 0 54
37000 1.5561543 4024 0.011313246 -0.032149816 2.2865202 2.7583779 8484 45 45 0 52981 36480 5329 4024 1.1613247 0 54
38000 1.5174762 4043 0.010120957 -0.21549294 2.0455467 2.2489655 8528 37 37 0 54637 36480 5329 4043 1.1692017 0 54
39000 1.5936544 4045 0.010946409 -0.16216642 2.2123787 2.7579117 8460 35 35 0 56452 36480 5329 4045 1.1670575 0 54
40000 1.7884514 4051 0.011913021 -0.2570519 2.4077408 2.494169 8539 37 37 0 58163 36480 5329 4051 1.1744075 0 54
41000 1.4173685 4042 0.0096196931 -0.16764288 1.9442362 1.9949409 8511 42 42 0 59967 36480 5329 4042 1.1747318 0 54
42000 1.4946304 4055 0.0098254549 -0.24117659 1.9858227 1.9958514 8395 39 39 0 61697 36480 5329 4055 1.1745062 0 54
43000 1.6486882 4041 0.011190255 -0.19488288 2.2616625 2.2173122 8473 28 28 0 63447 36480 5329 4041 1.1631975 0 54
44000 1.7473914 4055 0.011743128 -0.23020951 2.3734036 2.3913609 8421 30 30 0 65095 36480 5329 4055 1.1567659 0 54
45000 1.7826681 4027 0.011993913 -0.23208563 2.4240898 2.4582759 8539 35 35 0 66749 36480 5329 4027 1.1513285 0 54
46000 1.3988187 4049 0.0091738733 -0.23010838 1.8541315 2.3866226 8447 38 38 0 68459 36480 5329 4049 1.1728215 0 54
47000 1.8402398 4064 0.01271321 -0.17249031 2.569467 2.7748374 8524 33 33 0 70139 36480 5329 4064 1.1555276 0 54
48000 1.5634287 4042 0.011047794 -0.096639164 2.2328696 2.7173437 8561 33 33 0 71923 36480 5329 4042 1.177462 0 54
49000 1.789207 4058 0.012453079 -0.14902655 2.5168918 2.9310418 8545 38 38 0 73721 36480 5329 4058 1.1581934 0 54
50000 1.3475703 4010 0.0092484369 -0.13867816 1.8692016 2.1619389 8664 32 32 0 75439 36480 5329 4010 1.1589691 0 54
Loop time of 6.84 on 8 procs for 50000 steps with 20211 atoms
Pair time (%) = 0.0295508 (0.432029)
Neigh time (%) = 0.400359 (5.8532)
Comm time (%) = 0.622996 (9.10813)
Outpt time (%) = 0.00241029 (0.0352382)
Other time (%) = 5.78468 (84.5714)
Nlocal: 2526.38 ave 2651 max 2342 min
Histogram: 1 0 0 2 1 0 0 1 1 2
Nghost: 24.5 ave 27 max 23 min
Histogram: 1 0 4 0 0 2 0 0 0 1
Neighs: 17.375 ave 24 max 13 min
Histogram: 2 2 0 1 1 0 0 0 0 2
Total # of neighbors = 139
Ave neighs/atom = 0.00687744
Neighbor list builds = 2502
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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