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LAMMPS (1 Feb 2014)
# SRD diffusion 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 0.0221665 on 8 procs for 1000 steps with 100 atoms
Pair time (%) = 0.000323534 (1.45957)
Neigh time (%) = 0.000274181 (1.23692)
Comm time (%) = 0.0146933 (66.2864)
Outpt time (%) = 2.864e-05 (0.129204)
Other time (%) = 0.00684676 (30.8879)
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 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 1000 dump.poly
#dump 1 all image 1000 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 100000
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 0.84607633 3934 0.0065245151 0.058016014 1.3186697 4.2649214 7470 26 26 0 665 36480 5329 3934 0.95810956 0 2
2000 0.86586785 3944 0.0045898954 -0.36247933 0.92766376 2.1563866 7786 30 30 0 1374 36480 5329 3944 1.0799777 0 49
3000 0.78968677 4001 0.00417319 -0.33318986 0.84344343 1.9302042 7957 34 34 0 2129 36480 5329 4001 1.1247747 0 49
4000 0.7110667 4005 0.0031642256 -0.41996775 0.63952164 1.9679689 8188 24 24 0 2925 36480 5329 4005 1.1345941 0 49
5000 0.80379425 4052 0.0038912991 -0.41118297 0.78647047 1.6851034 8326 30 30 0 3794 36480 5329 4052 1.1310774 0 49
6000 0.96927432 4048 0.0054656969 -0.33954674 1.104672 1.8976158 8380 23 23 0 4643 36480 5329 4048 1.1861264 0 49
7000 0.75821666 4050 0.0036201309 -0.39807817 0.73166465 1.6087451 8450 51 51 0 5699 36480 5329 4050 1.1664119 0 49
8000 0.8712338 4035 0.0047243103 -0.343308 0.95483036 1.4707918 8458 42 42 0 6974 36480 5329 4035 1.1947807 0 91
9000 0.87995969 4048 0.0042778416 -0.44654537 0.86459457 1.5567027 8379 36 36 0 7965 36480 5329 4048 1.1675384 0 91
10000 0.83009098 4053 0.0042178709 -0.38436167 0.85247389 1.9119485 8373 34 34 0 8952 36480 5329 4053 1.1933986 0 91
11000 0.73595909 4015 0.0037439098 -0.33989742 0.75668162 1.6495307 8333 22 22 0 9983 36480 5329 4015 1.1959519 0 91
12000 0.84043443 4034 0.0041823741 -0.40694768 0.84529962 1.5115578 8566 31 31 0 11023 36480 5329 4034 1.2064988 0 91
13000 0.64253331 4044 0.0034868675 -0.25264383 0.7047308 1.739124 8528 31 31 0 12101 36480 5329 4044 1.1912336 0 91
14000 0.99330171 4042 0.0055047339 -0.36745778 1.1125618 1.8215191 8548 36 36 0 13098 36480 5329 4042 1.1819124 0 91
15000 0.90379859 4049 0.0049047446 -0.35536197 0.99129793 1.7159536 8459 37 37 0 14130 36480 5329 4049 1.1806762 0 91
16000 0.87446498 4034 0.0053318245 -0.22533777 1.0776151 2.0239395 8690 33 33 0 15176 36480 5329 4034 1.1912858 0 91
17000 0.95733995 4035 0.0053759665 -0.33989994 1.0865366 1.6243881 8518 27 27 0 16147 36480 5329 4035 1.2074487 0 91
18000 1.03543 4032 0.0052946469 -0.47268961 1.0701011 1.5444562 8464 28 28 0 17230 36480 5329 4032 1.1959755 0 91
19000 0.75997582 4051 0.0034371936 -0.43767278 0.6946912 1.4209137 8436 39 39 0 18276 36480 5329 4051 1.182461 0 91
20000 0.89615234 4037 0.0048910458 -0.34673773 0.98852926 1.5843879 8433 28 28 0 19275 36480 5329 4037 1.1850673 0 91
21000 0.85849578 4063 0.0044978314 -0.37010201 0.9090567 1.5445809 8504 40 40 0 20278 36480 5329 4063 1.1931031 0 91
22000 0.79050471 4066 0.0038260812 -0.40456274 0.77328927 1.6214277 8463 44 44 0 21287 36480 5329 4066 1.1948824 0 91
23000 0.89563532 4026 0.0051030186 -0.30312555 1.0313711 1.4848223 8548 35 35 0 22422 36480 5329 4026 1.1975081 0 91
24000 0.83528717 4036 0.0043136275 -0.37275064 0.87182725 1.5504059 8527 34 34 0 23404 36480 5329 4036 1.1755463 0 91
25000 0.64179358 4022 0.0035185741 -0.24513342 0.71113901 1.7238889 8452 47 47 0 24522 36480 5329 4022 1.2066339 0 91
26000 0.86710098 4028 0.0046099591 -0.36026164 0.93171883 1.4255297 8734 33 33 0 25524 36480 5329 4028 1.2001233 0 91
27000 0.8327003 4054 0.0045323379 -0.32469262 0.91603082 1.2654649 8468 34 34 0 26520 36480 5329 4054 1.1814901 0 91
28000 0.84396759 4049 0.0042805934 -0.39236096 0.86515074 1.2929473 8536 37 37 0 27657 36480 5329 4049 1.1897647 0 91
29000 0.77639299 4052 0.0038143413 -0.38590904 0.77091652 1.3627099 8637 36 36 0 28773 36480 5329 4052 1.1858017 0 91
30000 0.69994805 4046 0.0034430868 -0.34704032 0.69588228 1.5351247 8704 46 46 0 29818 36480 5329 4046 1.1724555 0 91
31000 0.73907898 4039 0.003034759 -0.48787254 0.61335514 1.2291035 8486 29 29 0 30848 36480 5329 4039 1.2063852 0 91
32000 0.84649298 4052 0.0044326201 -0.36539769 0.89587685 1.4591662 8513 28 28 0 31917 36480 5329 4052 1.1917883 0 91
33000 0.7188891 4031 0.0033440675 -0.39527528 0.67586949 1.2495703 8800 37 37 0 32938 36480 5329 4031 1.191087 0 91
34000 0.93588921 4054 0.0054112843 -0.30080024 1.0936747 1.3650172 8585 33 33 0 33913 36480 5329 4054 1.1840415 0 91
35000 0.86446961 4039 0.0053251497 -0.21179371 1.076266 1.3791947 8607 22 22 0 34865 36480 5329 4039 1.1916342 0 91
36000 0.90510006 4011 0.0054168442 -0.2538007 1.0947984 1.5747653 8479 31 31 0 35842 36480 5329 4011 1.1760305 0 91
37000 0.95332175 4058 0.0055020495 -0.30843018 1.1120192 1.4326924 8512 29 29 0 36751 36480 5329 4058 1.180738 0 91
38000 0.71413841 4043 0.0038380378 -0.2883604 0.77570582 1.4283837 8611 39 39 0 37689 36480 5329 4043 1.1693806 0 91
39000 0.81161335 4064 0.0044323475 -0.31348213 0.89582176 1.4378305 8697 28 28 0 38696 36480 5329 4064 1.1987209 0 91
40000 0.8294437 4062 0.0051262098 -0.19981285 1.0360583 1.6010501 8559 31 31 0 39743 36480 5329 4062 1.2092371 0 91
41000 0.79325147 4079 0.0045273868 -0.26691453 0.91503015 1.4080428 8775 53 53 0 40806 36480 5329 4079 1.1989619 0 91
42000 0.95693891 4027 0.005623893 -0.28919396 1.136645 1.5334192 8509 34 34 0 41793 36480 5329 4027 1.1931035 0 91
43000 0.66458435 4029 0.0035902162 -0.26461209 0.72561859 1.4253918 8559 44 44 0 42768 36480 5329 4029 1.2111853 0 91
44000 0.84442459 4022 0.0050980388 -0.22782802 1.0303646 1.4587515 8522 32 32 0 43812 36480 5329 4022 1.1943268 0 91
45000 0.96505326 4051 0.0057148128 -0.28290855 1.1550208 1.3014361 8496 32 32 0 44803 36480 5329 4051 1.1912109 0 91
46000 0.75345782 4064 0.0040245838 -0.30924351 0.81340864 1.7179797 8568 29 29 0 45795 36480 5329 4064 1.1975591 0 91
47000 0.87187806 4017 0.004406241 -0.40855293 0.89054538 1.3105257 8586 36 36 0 46822 36480 5329 4017 1.1834816 0 91
48000 0.83729235 4078 0.0045115864 -0.33572888 0.91183673 1.3856733 8513 38 38 0 47866 36480 5329 4078 1.1996374 0 91
49000 0.65112065 4048 0.0030445536 -0.35483503 0.61533473 1.2659451 8705 32 32 0 48907 36480 5329 4048 1.1907782 0 91
50000 0.82730473 4066 0.0045492584 -0.31323342 0.91945063 1.1803982 8562 41 41 0 49965 36480 5329 4066 1.1696702 0 91
51000 0.74252279 4048 0.0046741422 -0.16166808 0.94469088 1.5539445 8564 35 35 0 50948 36480 5329 4048 1.1748481 0 91
52000 0.85671386 4051 0.0058575179 -0.092640701 1.183863 1.6307333 8609 19 19 0 51894 36480 5329 4051 1.1770671 0 91
53000 0.7233951 4068 0.0043421658 -0.20026358 0.87759512 1.453924 8582 28 28 0 52893 36480 5329 4068 1.2027667 0 91
54000 0.72117217 4051 0.0040247209 -0.26111018 0.81343635 1.3496518 8679 25 25 0 53831 36480 5329 4051 1.1823115 0 91
55000 0.87940919 4044 0.0047057065 -0.35924936 0.95107033 1.240057 8559 34 34 0 54813 36480 5329 4044 1.1815144 0 91
56000 0.83192698 4044 0.0046298732 -0.30382753 0.93574367 1.547229 8441 37 37 0 55740 36480 5329 4044 1.1761232 0 91
57000 0.91043729 4058 0.0050029377 -0.34540782 1.0111437 1.4951603 8550 32 32 0 56678 36480 5329 4058 1.2024504 0 91
58000 0.97648852 4036 0.0053292287 -0.37787747 1.0770904 1.4058278 8554 31 31 0 57683 36480 5329 4036 1.1746239 0 91
59000 0.72239185 4018 0.0046615138 -0.1342253 0.94213856 1.8337414 8716 35 35 0 58640 36480 5329 4018 1.1697661 0 91
60000 0.73800253 4032 0.0037590001 -0.33989225 0.75973152 1.399426 8561 32 32 0 59593 36480 5329 4032 1.1958194 0 91
61000 0.72778603 4060 0.0042599892 -0.22341476 0.86098642 1.3778202 8541 31 31 0 60573 36480 5329 4060 1.1980875 0 91
62000 0.80350669 4044 0.0042316822 -0.34195968 0.85526529 1.4379455 8487 37 37 0 61608 36480 5329 4044 1.1942365 0 91
63000 0.90084181 4066 0.0043040273 -0.47236734 0.86988695 1.4672845 8504 32 32 0 62670 36480 5329 4066 1.1829834 0 91
64000 0.87220486 4059 0.0047840275 -0.33268544 0.9668998 1.5398216 8588 34 34 0 63605 36480 5329 4059 1.1884975 0 91
65000 0.82469157 4057 0.004405933 -0.33830733 0.89048312 1.5284565 8783 32 32 0 64693 36480 5329 4057 1.1952722 0 91
66000 0.88692288 4081 0.0047264561 -0.36625105 0.95526405 1.3151847 8745 36 36 0 65755 36480 5329 4081 1.1834684 0 91
67000 0.83322374 4031 0.0047732147 -0.27678896 0.96471442 1.5085732 8415 34 34 0 66796 36480 5329 4031 1.1969 0 91
68000 0.75375865 4020 0.0044379413 -0.22614806 0.89695233 1.6351001 8573 30 30 0 67876 36480 5329 4020 1.1911308 0 91
69000 0.91169697 4055 0.0050371842 -0.34036318 1.0180653 1.2495539 8625 20 20 0 68979 36480 5329 4055 1.1860768 0 91
70000 0.80502435 4075 0.0042565586 -0.33919322 0.86029306 1.3194042 8571 36 36 0 69947 36480 5329 4075 1.18994 0 91
71000 0.8928873 4055 0.0050586026 -0.3080079 1.0223942 1.3949364 8698 32 32 0 71037 36480 5329 4055 1.2154821 0 91
72000 0.95397384 4050 0.0052866702 -0.35293209 1.0684889 1.2950893 8613 35 35 0 72090 36480 5329 4050 1.1790804 0 91
73000 0.78742879 4053 0.004378612 -0.28830762 0.88496127 1.5168042 8624 30 30 0 73174 36480 5329 4053 1.2008591 0 91
74000 0.79498726 4046 0.0042999917 -0.31545969 0.86907133 1.3751647 8562 22 22 0 74250 36480 5329 4046 1.1921334 0 91
75000 0.88929145 4051 0.0048995187 -0.33480254 0.99024172 1.6589606 8393 33 33 0 75296 36480 5329 4051 1.1753137 0 91
76000 0.98366685 4045 0.0049217494 -0.47092883 0.99473478 1.5271346 8555 29 29 0 76301 36480 5329 4045 1.2031327 0 91
77000 0.72618119 4051 0.0035028638 -0.37404618 0.7079638 1.5178344 8565 37 37 0 77315 36480 5329 4051 1.1993308 0 91
78000 0.80445682 4028 0.003992176 -0.39178196 0.8068587 1.3682816 8624 32 32 0 78299 36480 5329 4028 1.2065456 0 91
79000 1.091703 4052 0.0063793569 -0.33730561 1.2893318 1.5717928 8677 39 39 0 79249 36480 5329 4052 1.1725194 0 91
80000 0.77212865 4052 0.0041275152 -0.31625959 0.8342121 1.5583982 8526 33 33 0 80284 36480 5329 4052 1.1981751 0 91
81000 0.80732682 4061 0.004618782 -0.26941493 0.93350203 1.5517327 8444 36 36 0 81331 36480 5329 4061 1.2095831 0 91
82000 0.80166933 4057 0.0042732734 -0.33081602 0.86367129 1.3937505 8476 29 29 0 82335 36480 5329 4057 1.2047807 0 91
83000 0.76980598 4049 0.0041331379 -0.31166241 0.83534851 1.1411979 8561 34 34 0 83375 36480 5329 4049 1.1810941 0 91
84000 0.85529188 4076 0.0046148117 -0.34168531 0.93269959 1.3284464 8664 27 27 0 84510 36480 5329 4076 1.192734 0 91
85000 0.96167157 4034 0.0053261317 -0.35642617 1.0764645 1.3195071 8557 36 36 0 85517 36480 5329 4034 1.2000123 0 91
86000 0.88130862 4047 0.0046646382 -0.37037981 0.94277003 1.3595079 8634 36 36 0 86578 36480 5329 4047 1.1654584 0 91
87000 0.68799517 4037 0.0042184867 -0.17251446 0.85259834 1.5087731 8363 40 40 0 87606 36480 5329 4037 1.1833599 0 91
88000 0.83191621 4041 0.0048307277 -0.26321678 0.97633838 1.4008912 8597 39 39 0 88490 36480 5329 4041 1.1607031 0 91
89000 0.71456519 4036 0.0039378285 -0.26882761 0.79587453 1.2251569 8397 36 36 0 89436 36480 5329 4036 1.1991362 0 91
90000 0.75198251 4048 0.0043377839 -0.24374445 0.87670949 1.4896261 8551 29 29 0 90453 36480 5329 4048 1.1899998 0 91
91000 0.83310145 4032 0.0049902932 -0.232733 1.0085882 1.4140378 8583 48 48 0 91563 36480 5329 4032 1.1953029 0 91
92000 0.8819465 4050 0.0058087956 -0.14008461 1.1740157 1.753218 8610 46 46 0 92618 36480 5329 4050 1.1972268 0 91
93000 0.76721608 4048 0.0041923848 -0.29582907 0.8473229 1.4126521 8671 32 32 0 93690 36480 5329 4048 1.2027935 0 91
94000 0.8942606 4050 0.0051973822 -0.28200539 1.0504429 1.5743434 8751 21 21 0 94750 36480 5329 4050 1.1804594 0 91
95000 0.73609582 4036 0.0035091666 -0.38754512 0.70923765 1.28494 8660 31 31 0 95713 36480 5329 4036 1.1883125 0 91
96000 0.79430429 4078 0.0043400156 -0.30635284 0.87716056 1.4351927 8600 38 38 0 96695 36480 5329 4078 1.1704833 0 91
97000 0.74817621 4044 0.0038163094 -0.34346826 0.77131429 1.255104 8377 36 36 0 97683 36480 5329 4044 1.1756023 0 91
98000 0.78160255 4048 0.0039385343 -0.36857064 0.79601716 1.5320263 8350 25 25 0 98631 36480 5329 4048 1.181196 0 91
99000 0.804448 4053 0.004503827 -0.28835905 0.91026848 1.7569548 8506 35 35 0 99687 36480 5329 4053 1.1950898 0 91
100000 0.74975993 4032 0.004263269 -0.255493 0.86164929 1.5983872 8621 33 33 0 100701 36480 5329 4032 1.1910217 0 91
Loop time of 13.4746 on 8 procs for 100000 steps with 20211 atoms
Pair time (%) = 0.0563478 (0.418178)
Neigh time (%) = 0.794382 (5.89541)
Comm time (%) = 1.23773 (9.18569)
Outpt time (%) = 0.00554895 (0.0411809)
Other time (%) = 11.3806 (84.4595)
Nlocal: 2526.38 ave 2725 max 2337 min
Histogram: 2 0 0 1 1 1 1 0 1 1
Nghost: 23.875 ave 27 max 21 min
Histogram: 1 1 0 2 0 2 0 0 0 2
Neighs: 17 ave 25 max 12 min
Histogram: 3 1 0 1 1 0 0 0 0 2
Total # of neighbors = 136
Ave neighs/atom = 0.00672901
Neighbor list builds = 5008
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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