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lammps/examples/ASPHERE/poly/log.poly.10Sep13
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LAMMPS (9 Sep 2013)
# 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 = 2.74744 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 0.0263424 on 8 procs for 1000 steps with 100 atoms
Pair time (%) = 0.000377953 (1.43477)
Neigh time (%) = 0.000303119 (1.15069)
Comm time (%) = 0.0153534 (58.2839)
Outpt time (%) = 3.43621e-05 (0.130444)
Other time (%) = 0.0102736 (39.0002)
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:438)
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:2759)
# 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 = 11.7296 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 0.84607636 4320 0.0065245155 0.058016042 1.3186698 4.2649215 7470 26 26 0 649 36480 5329 4320 0.87250069 0 2
2000 0.90485259 4380 0.0052749864 -0.28210286 1.0661275 2.1610016 7779 41 41 0 1285 36480 5329 4380 0.96910154 0 2
3000 0.86997866 4359 0.0051174794 -0.26197443 1.0342938 2.0552139 7976 32 32 0 2031 36480 5329 4359 1.0066773 0 2
4000 0.81799751 4386 0.004339179 -0.34182481 0.87699148 1.8252707 8228 36 36 0 2797 36480 5329 4386 1.0427782 0 2
5000 0.86406909 4378 0.005062484 -0.2642843 1.0231786 2.0027892 8402 31 31 0 3662 36480 5329 4378 1.0498595 0 2
6000 0.81122089 4390 0.0045773647 -0.28358794 0.92513119 1.6291269 8343 22 22 0 4542 36480 5329 4390 1.075211 0 2
7000 0.86048278 4374 0.0045829051 -0.35586841 0.92625094 1.787504 8229 26 26 0 5515 36480 5329 4374 1.0816492 0 2
8000 0.86834891 4381 0.0045794089 -0.36829555 0.92554432 1.6425705 8375 34 34 0 6432 36480 5329 4381 1.0734234 0 2
9000 0.85897968 4394 0.0042698244 -0.4169055 0.86297422 1.4346364 8500 30 30 0 7355 36480 5329 4394 1.087639 0 2
10000 0.70846773 4404 0.0030688471 -0.43537222 0.6202447 1.355036 8291 36 36 0 8314 36480 5329 4404 1.0788748 0 2
11000 0.79937389 4390 0.0043439579 -0.31310977 0.87795733 1.5807555 8350 27 27 0 9281 36480 5329 4390 1.0790792 0 2
12000 0.85824569 4411 0.0046841509 -0.33207234 0.94671374 1.591183 8327 37 37 0 10262 36480 5329 4411 1.0788503 0 2
13000 0.81732539 4415 0.0037450448 -0.46090383 0.756911 1.1438166 8483 26 26 0 11238 36480 5329 4415 1.0917525 0 2
14000 0.89802245 4399 0.005085064 -0.31031115 1.0277423 1.599284 8514 27 27 0 12274 36480 5329 4399 1.0749784 0 54
15000 0.68998926 4394 0.0029236972 -0.43717555 0.59090845 1.2810011 8383 45 45 0 13277 36480 5329 4394 1.0756773 0 54
16000 0.83208983 4407 0.004493664 -0.33159942 0.90821442 1.6639201 8320 28 28 0 14243 36480 5329 4407 1.090866 0 54
17000 0.70920173 4404 0.003792538 -0.29020072 0.76650986 1.475147 8517 34 34 0 15183 36480 5329 4404 1.0816438 0 54
18000 0.75974526 4395 0.003566885 -0.41111731 0.72090312 1.3301798 8506 36 36 0 16138 36480 5329 4395 1.0676888 0 54
19000 0.8732303 4409 0.0040921591 -0.47404688 0.82706627 1.3282596 8512 38 38 0 17108 36480 5329 4409 1.0864062 0 54
20000 0.74373268 4407 0.0037797876 -0.34422884 0.76393286 1.3084704 8505 30 30 0 18099 36480 5329 4407 1.0738575 0 54
21000 0.73961986 4400 0.0038147704 -0.33103034 0.77100326 1.4165508 8508 32 32 0 19164 36480 5329 4400 1.0878172 0 54
22000 0.71412304 4402 0.0033459777 -0.38778778 0.67625555 1.4732933 8571 32 32 0 20209 36480 5329 4402 1.0961455 0 54
23000 0.6485368 4391 0.0031023431 -0.33930525 0.62701457 1.2255142 8654 32 32 0 21226 36480 5329 4391 1.0955652 0 54
24000 0.62496852 4383 0.0031101939 -0.3026018 0.62860128 1.2574516 8456 40 40 0 22229 36480 5329 4383 1.1043661 0 54
25000 0.71882821 4387 0.0039504377 -0.27263108 0.79842295 1.5423115 8462 38 38 0 23302 36480 5329 4387 1.0988273 0 54
26000 0.81325766 4374 0.0046964629 -0.2625518 0.94920212 1.3027349 8469 22 22 0 24256 36480 5329 4374 1.0957156 0 54
27000 0.75769478 4404 0.0036955181 -0.38206406 0.74690116 1.2565814 8313 36 36 0 25218 36480 5329 4404 1.096358 0 54
28000 0.73180309 4400 0.003869417 -0.30833874 0.78204787 1.4692801 8537 33 33 0 26166 36480 5329 4400 1.0838456 0 54
29000 0.87301447 4404 0.0049666713 -0.29697763 1.0038139 1.4686871 8561 30 30 0 27154 36480 5329 4404 1.0950654 0 54
30000 0.90865536 4400 0.0050855318 -0.32605966 1.0278368 1.5864144 8483 20 20 0 28190 36480 5329 4400 1.0798509 0 54
31000 0.79500293 4393 0.0038246276 -0.41155888 0.77299548 1.3568346 8454 32 32 0 29155 36480 5329 4393 1.0724713 0 54
32000 0.87294832 4376 0.0054025526 -0.20878308 1.0919099 1.690247 8487 32 32 0 30185 36480 5329 4376 1.093595 0 54
33000 0.7796704 4387 0.003870468 -0.37944861 0.78226028 1.3978337 8338 28 28 0 31158 36480 5329 4387 1.0950913 0 54
34000 0.83949838 4408 0.0048589409 -0.26881205 0.98204055 1.3199495 8502 29 29 0 32212 36480 5329 4408 1.0994115 0 54
35000 0.89882881 4386 0.0046758361 -0.3942217 0.94503323 1.1627131 8500 40 40 0 33253 36480 5329 4386 1.0952495 0 54
36000 0.98891767 4388 0.0051298733 -0.43668865 1.0367987 1.3347621 8589 35 35 0 34383 36480 5329 4388 1.1028282 0 54
37000 0.78021407 4404 0.0035932812 -0.4362809 0.72623807 1.0910515 8528 35 35 0 35451 36480 5329 4404 1.0910774 0 54
38000 0.83518145 4383 0.0044236947 -0.35034742 0.89407294 1.2542227 8581 39 39 2 36623 36480 5329 4383 1.0969125 0 60
39000 0.79413048 4410 0.0045336904 -0.26695025 0.91630417 1.628798 8573 49 49 0 37739 36480 5329 4410 1.0786676 0 60
40000 0.69391266 4401 0.0035290325 -0.3206771 0.71325276 1.2434063 8722 24 24 0 38806 36480 5329 4401 1.0930726 0 60
41000 0.87777539 4405 0.0046384823 -0.37040166 0.93748366 1.3485397 8591 29 29 0 39844 36480 5329 4405 1.0934857 0 60
42000 0.88000424 4419 0.0041538556 -0.47167057 0.83953575 1.373462 8528 30 30 0 40851 36480 5329 4419 1.1058136 0 60
43000 0.80894411 4394 0.0043471883 -0.3267165 0.87861023 1.5520932 8516 34 34 0 41927 36480 5329 4394 1.0940256 0 60
44000 0.81278253 4413 0.0043670096 -0.32842965 0.88261632 1.7514988 8424 37 37 0 42979 36480 5329 4413 1.0890373 0 60
45000 0.81669704 4391 0.0042902765 -0.34977079 0.86710779 1.2720081 8603 29 29 0 43991 36480 5329 4391 1.0959104 0 60
46000 0.68105471 4415 0.0033462068 -0.33846966 0.67630186 1.3572051 8597 37 37 0 45054 36480 5329 4415 1.0831668 0 60
47000 0.74650613 4406 0.0031567817 -0.47427698 0.63801715 1.2357289 8712 37 37 0 46111 36480 5329 4406 1.0825124 0 60
48000 0.78925983 4419 0.0037255285 -0.42303057 0.75296657 1.2629704 8539 39 39 0 47063 36480 5329 4419 1.086451 0 60
49000 0.76629818 4405 0.0039711762 -0.33916987 0.80261443 1.3028869 8446 38 38 0 48085 36480 5329 4405 1.0962223 0 60
50000 0.8104353 4406 0.0041783294 -0.36306645 0.84448215 1.0644192 8664 36 36 0 49080 36480 5329 4406 1.082981 0 60
51000 0.88113764 4402 0.0051570248 -0.27060881 1.0422863 1.4386175 8624 38 38 0 50185 36480 5329 4402 1.0798375 0 60
52000 0.77033709 4389 0.0045371435 -0.23080019 0.91700207 1.4602717 8436 30 30 0 51245 36480 5329 4389 1.0931273 0 60
53000 0.81214351 4410 0.0048922416 -0.22132289 0.98877095 1.7454029 8706 29 29 0 52280 36480 5329 4410 1.0939736 0 60
54000 0.89983347 4386 0.0045215928 -0.42689275 0.91385912 1.2867976 8602 26 26 0 53359 36480 5329 4386 1.0938981 0 60
55000 0.85535843 4388 0.0045846672 -0.34787698 0.92660708 1.4863714 8630 36 36 0 54411 36480 5329 4388 1.0865711 0 60
56000 0.65511288 4409 0.0035485946 -0.25891173 0.71720646 1.4491969 8573 33 33 0 55419 36480 5329 4409 1.1167746 0 60
57000 0.82787973 4393 0.004433496 -0.33748691 0.89605388 1.3780497 8608 28 28 0 56458 36480 5329 4393 1.090579 0 60
58000 0.78199015 4411 0.0041719007 -0.32198248 0.84318285 1.5489896 8596 39 39 0 57518 36480 5329 4411 1.0950974 0 60
59000 0.83342791 4387 0.004742265 -0.2833484 0.95845919 1.5035913 8580 23 23 0 58495 36480 5329 4387 1.1044386 0 60
60000 0.92726046 4412 0.0054717726 -0.27571813 1.1059 1.5223588 8601 47 47 0 59516 36480 5329 4412 1.1053325 0 60
61000 0.71162631 4397 0.0034106311 -0.37100055 0.68932266 1.4441628 8600 35 35 0 60613 36480 5329 4397 1.1205275 0 60
62000 0.83061614 4395 0.0051751609 -0.19166627 1.0459518 1.8120796 8665 39 39 0 61539 36480 5329 4395 1.0942761 0 60
63000 0.69264654 4404 0.003733218 -0.27752266 0.75452069 1.4946754 8671 41 41 0 62499 36480 5329 4404 1.0864782 0 60
64000 0.81150665 4409 0.0044149583 -0.31683769 0.89230723 1.4495005 8498 45 45 0 63585 36480 5329 4409 1.0947081 0 60
65000 0.72188875 4415 0.0034008627 -0.38826587 0.68734836 1.3906117 8707 26 26 0 64598 36480 5329 4415 1.0867011 0 60
66000 0.66159508 4395 0.0030869268 -0.36187789 0.62389878 1.4297478 8664 32 32 0 65686 36480 5329 4395 1.0920408 0 60
67000 0.89720139 4402 0.0047549655 -0.37580398 0.96102608 1.3498224 8561 31 31 0 66668 36480 5329 4402 1.1140343 0 60
68000 0.77646005 4399 0.0044770291 -0.25207312 0.90485236 1.450115 8645 34 34 0 67762 36480 5329 4399 1.1031979 0 60
69000 0.76847183 4389 0.0046195632 -0.21136311 0.93365992 1.5393165 8663 37 37 0 68816 36480 5329 4389 1.100983 0 60
70000 0.68687373 4398 0.0036588724 -0.28394714 0.73949471 1.4069676 8686 29 29 0 69917 36480 5329 4398 1.1173713 0 60
71000 0.85660695 4405 0.0051111547 -0.24332887 1.0330155 1.5159938 8564 32 32 0 70984 36480 5329 4405 1.088877 0 60
72000 0.83851058 4378 0.0047881845 -0.2816408 0.96773997 1.3016234 8815 41 41 0 72066 36480 5329 4378 1.0903007 0 60
73000 0.9574802 4405 0.0054905849 -0.31694339 1.1097021 1.3834758 8498 39 39 0 73126 36480 5329 4405 1.0835447 0 60
74000 0.93413914 4428 0.005594213 -0.26122094 1.1306464 1.3968649 8610 36 36 0 74134 36480 5329 4428 1.0925707 0 60
75000 0.85110304 4399 0.0050214404 -0.2532602 1.0148833 1.7151794 8533 35 35 0 75226 36480 5329 4399 1.121987 0 60
76000 0.74293246 4402 0.004159075 -0.26637871 0.84059065 1.5301113 8744 45 45 0 76247 36480 5329 4402 1.0786119 0 60
77000 0.69374764 4398 0.0033526037 -0.35608924 0.67759474 1.3550134 8570 38 38 0 77323 36480 5329 4398 1.1077261 0 60
78000 0.79184739 4387 0.0041458172 -0.3419415 0.83791112 1.53132 8488 33 33 0 78545 36480 5329 4387 1.0944135 0 81
79000 0.73855485 4399 0.0040930305 -0.27320432 0.8272424 1.4930252 8590 40 40 0 79562 36480 5329 4399 1.0921682 0 81
80000 0.80000829 4407 0.0035856307 -0.46732053 0.72469182 1.4649608 8480 38 38 0 80554 36480 5329 4407 1.0866433 0 81
81000 0.75614881 4386 0.0040626682 -0.30555586 0.82110586 1.5424611 8489 32 32 0 81620 36480 5329 4386 1.1065811 0 81
82000 0.74187824 4425 0.0042618334 -0.24403944 0.86135915 1.5254143 8495 23 23 0 82648 36480 5329 4425 1.0999901 0 81
83000 0.96795247 4379 0.0056667045 -0.29695155 1.1452976 1.434689 8542 44 44 0 83674 36480 5329 4379 1.1055145 0 81
84000 0.71973336 4403 0.0038014078 -0.30410018 0.76830252 1.416144 8595 34 34 0 84706 36480 5329 4403 1.0730077 0 81
85000 0.67586077 4404 0.0039613843 -0.20639716 0.80063539 1.5423424 8573 39 39 0 85773 36480 5329 4404 1.0902847 0 81
86000 0.7824605 4400 0.0039579087 -0.36593321 0.79993293 1.2665296 8709 33 33 0 86777 36480 5329 4400 1.0796536 0 81
87000 0.80925546 4399 0.0044421598 -0.30798573 0.89780491 1.5569681 8668 36 36 0 87785 36480 5329 4399 1.0994771 0 81
88000 0.76586354 4417 0.0039373168 -0.34536557 0.7957711 1.3500605 8615 35 35 0 88859 36480 5329 4417 1.0895919 0 81
89000 0.69829963 4402 0.0031383989 -0.40616466 0.63430179 1.088111 8786 45 45 0 89860 36480 5329 4402 1.0866392 0 81
90000 0.84707532 4410 0.0049394012 -0.26383986 0.99830237 1.5746697 8414 30 30 0 90900 36480 5329 4410 1.1136544 0 81
91000 0.81479881 4391 0.0047153823 -0.26102431 0.95302592 1.4560202 8617 30 30 0 91885 36480 5329 4391 1.0909121 0 81
92000 0.67926947 4398 0.0033034611 -0.344449 0.66766252 1.235949 8439 37 37 0 92933 36480 5329 4398 1.0877594 0 81
93000 0.76411115 4388 0.0035573512 -0.41954937 0.71897625 1.1042722 8524 33 33 0 94014 36480 5329 4388 1.09172 0 81
94000 0.76881091 4402 0.0044450994 -0.24712922 0.89839904 1.4046651 8626 31 31 0 94955 36480 5329 4402 1.090443 0 81
95000 0.8089261 4372 0.0042760848 -0.34106038 0.8642395 1.4929178 8539 43 43 0 95962 36480 5329 4372 1.0761039 0 81
96000 0.7316235 4418 0.0039746747 -0.2867975 0.80332151 1.6570629 8580 34 34 0 96941 36480 5329 4418 1.0768381 0 81
97000 0.7858829 4407 0.003617173 -0.4398987 0.73106683 1.312132 8467 22 22 0 97963 36480 5329 4407 1.1078034 0 81
98000 0.72898498 4397 0.0037674527 -0.32474775 0.76143987 1.2373268 8552 33 33 0 99024 36480 5329 4397 1.1024714 0 81
99000 0.90435165 4378 0.0049764011 -0.34170354 1.0057804 1.6945983 8417 31 31 0 100116 36480 5329 4378 1.0899259 0 81
100000 0.69815567 4407 0.0036001551 -0.3126246 0.72762735 1.4724301 8502 42 42 0 101118 36480 5329 4407 1.0777306 0 81
Loop time of 15.4007 on 8 procs for 100000 steps with 20211 atoms
Pair time (%) = 0.0612983 (0.398022)
Neigh time (%) = 0.858353 (5.57346)
Comm time (%) = 1.11288 (7.22617)
Outpt time (%) = 0.00592667 (0.0384831)
Other time (%) = 13.3623 (86.7639)
Nlocal: 2526.38 ave 2618 max 2409 min
Histogram: 1 2 0 0 0 1 0 0 1 3
Nghost: 24.5 ave 28 max 21 min
Histogram: 1 0 2 0 1 1 0 2 0 1
Neighs: 17.5 ave 21 max 13 min
Histogram: 1 1 0 0 0 1 2 1 1 1
Total # of neighbors = 140
Ave neighs/atom = 0.00692692
Neighbor list builds = 5005
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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