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lammps/examples/ASPHERE/dimer/log.dimer.mp.1Feb14
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LAMMPS (1 Feb 2014)
# SRD viscosity demo - dimer 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.dimer fix molprop NULL Molecules
orthogonal box = (-9.34165 -9.34165 -0.5) to (9.34165 9.34165 0.5)
4 by 2 by 1 MPI processor grid
reading atoms ...
200 atoms
set type 1 mass 1.0
200 settings made for mass
group big type 1
200 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
fix 1 big rigid molecule
100 rigid bodies with 200 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.dimer.equil
thermo 100
run 1000
Memory usage per processor = 3.1029 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3.4028231 0 0 0.83369167 -0.55065517
100 9.5167872 2.392105 0 4.7237178 2.8319556
200 13.564465 3.0352634 0 6.3585572 3.6388732
300 13.133051 4.3835112 0 7.6011086 4.060051
400 14.584346 5.5141254 0 9.0872901 4.4231056
500 15.331515 6.6554832 0 10.411704 4.847642
600 16.953755 7.4794317 0 11.633102 5.2020696
700 16.503256 8.8572339 0 12.900532 5.6694613
800 17.006131 9.877343 0 14.043845 5.5483363
900 17.305927 11.081594 0 15.321546 6.2908201
1000 18.122491 12.126462 0 16.566472 5.7536055
Loop time of 0.0603173 on 8 procs for 1000 steps with 200 atoms
Pair time (%) = 0.00182396 (3.02395)
Neigh time (%) = 0.000557959 (0.92504)
Comm time (%) = 0.0127766 (21.1823)
Outpt time (%) = 0.000280827 (0.465583)
Other time (%) = 0.0448779 (74.4031)
Nlocal: 25 ave 30 max 20 min
Histogram: 1 0 1 1 0 0 3 1 0 1
Nghost: 28.375 ave 36 max 22 min
Histogram: 1 0 1 2 1 0 2 0 0 1
Neighs: 33.125 ave 45 max 22 min
Histogram: 1 0 2 1 0 1 1 0 1 1
Total # of neighbors = 265
Ave neighs/atom = 1.325
Neighbor list builds = 99
Dangerous builds = 96
#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 29929 atoms
set type 2 mass 0.1
29929 settings made for mass
group small type 2
29929 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 0.5
delete_atoms overlap 0.5 small big
Deleted 12759 atoms, new total = 17370
# 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
100 rigid bodies with 200 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 500 dump.dimer.mp
#dump 1 all image 500 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 50000
SRD info:
SRD/big particles = 17170 200
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: 75 75 1
SRD grid size: request, actual (xyz) = 0.25, 0.249111 0.249111 1
SRD per actual grid cell = 5.5499
SRD viscosity = 0.235551
big/SRD mass density ratio = 0.142367
# of rescaled SRD velocities = 0
ave/max small velocity = 4.20347 7.72323
ave/max big velocity = 2.64047 6.60911
Memory usage per processor = 7.0395 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 6.9744766 0 0.30175295 21.011259 26.207244 2.7219331 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.906187 3319 0.25279446 20.53509 21.955199 9.3471734 14560 77 77 9 6051 40320 5625 3319 1.2073941 0 1062 0
2000 1.6009081 3420 0.25060769 20.572601 21.765278 12.835365 13521 63 63 1 7515 40320 5625 3420 1.1621445 0 1062 0
3000 1.8288965 3342 0.25195284 20.519576 21.882104 7.1720562 13550 62 62 1 8561 40320 5625 3342 1.1411375 0 1062 0
4000 1.8940522 3383 0.25185767 20.462769 21.873838 7.3011842 13210 55 55 0 9536 40320 5625 3383 1.1541274 0 1062 0
5000 1.7848964 3377 0.25063675 20.438054 21.767801 5.7235852 13258 60 60 1 10628 40320 5625 3377 1.1401366 0 1062 0
6000 2.0436442 3393 0.2528503 20.437534 21.960048 4.3266887 13369 65 65 1 11693 40320 5625 3393 1.1363335 0 1062 0
7000 2.0248598 3377 0.25304247 20.468218 21.976738 9.1535003 13126 69 69 2 12819 40320 5625 3377 1.1556137 0 1062 0
8000 1.9627172 3397 0.25201977 20.425693 21.887917 7.9563872 13216 58 58 3 14113 40320 5625 3397 1.144738 0 1062 0
9000 2.4805409 3385 0.25688024 20.462046 22.310049 6.0178529 13031 42 42 1 15329 40320 5625 3385 1.1667813 0 1062 0
10000 2.534712 3377 0.25802283 20.520922 22.409283 5.8494568 12804 49 50 1 16835 40320 5625 3377 1.1559636 0 1062 0
11000 2.4295377 3368 0.25671703 20.485869 22.295874 7.0797587 13097 56 56 2 18180 40320 5625 3368 1.1634145 0 1062 0
12000 2.5699389 3377 0.25784825 20.479516 22.39412 10.440503 13263 63 63 5 19848 40320 5625 3377 1.1714081 0 1062 0
13000 2.5416625 3359 0.25893582 20.595038 22.488576 6.823793 12926 57 57 1 21307 40320 5625 3359 1.1478982 0 1062 0
14000 2.9400702 3353 0.26140738 20.512878 22.703231 10.592709 12848 67 67 0 22782 40320 5625 3353 1.1642018 0 1062 0
15000 2.7315042 3364 0.26050572 20.589951 22.624922 7.6633608 12640 49 49 0 24273 40320 5625 3364 1.1532394 0 1062 0
16000 2.7176527 3389 0.25840703 20.418 22.442651 8.0150175 13019 59 59 1 25970 40320 5625 3389 1.1555937 0 1062 0
17000 2.883266 3355 0.26040537 20.468173 22.616206 6.053208 12916 54 54 1 27532 40320 5625 3355 1.1363169 0 1062 0
18000 2.8072496 3369 0.26013039 20.500924 22.592325 5.7179969 12989 45 45 0 29011 40320 5625 3369 1.1341799 0 1062 0
19000 2.8007066 3372 0.2602809 20.51887 22.605396 8.9063895 12817 59 59 1 30504 40320 5625 3372 1.1253001 0 1062 0
20000 3.0147455 3352 0.26233709 20.537991 22.783977 10.01786 13099 63 63 2 32100 40320 5625 3352 1.1263738 0 1062 0
21000 2.5502874 3354 0.25762968 20.475174 22.375138 7.4525361 12917 55 55 3 33904 40320 5625 3354 1.1432482 0 1062 0
22000 2.5643661 3357 0.25754499 20.45733 22.367782 9.5567227 12893 58 58 0 35500 40320 5625 3357 1.1309581 0 1062 0
23000 2.8451307 3387 0.26090715 20.540164 22.659786 7.8308779 12735 65 65 2 37080 40320 5625 3387 1.1666359 0 1062 0
24000 2.6241046 3341 0.25916876 20.553849 22.508807 9.7905794 12815 54 54 1 38864 40320 5625 3341 1.1422596 0 1062 0
25000 2.6054468 3374 0.25897446 20.550874 22.491932 9.4099539 13094 59 59 4 40505 40320 5625 3374 1.1887482 0 1062 0
26000 3.1370949 3356 0.26301193 20.50545 22.842586 9.930938 12785 59 59 0 42126 40320 5625 3356 1.1539158 0 1062 0
27000 2.757373 3361 0.26029623 20.552484 22.606727 7.4336931 12687 59 59 2 43728 40320 5625 3361 1.1408006 0 1062 0
28000 2.9939441 3393 0.26250984 20.568491 22.79898 9.201853 12802 66 66 0 45174 40320 5625 3393 1.1429688 0 1062 0
29000 3.1611971 3376 0.26252235 20.444974 22.800066 8.2146139 13042 48 48 0 46696 40320 5625 3376 1.1370708 0 1062 0
30000 2.2624796 3374 0.25475303 20.439753 22.125301 9.3304907 13249 53 53 1 48164 40320 5625 3374 1.1062325 0 1062 0
31000 2.6864602 3393 0.2607928 20.648442 22.649855 7.6108593 13028 58 58 0 49556 40320 5625 3393 1.1154125 0 1062 0
32000 2.8404087 3377 0.26037369 20.497351 22.613455 6.9017135 13055 63 63 1 51004 40320 5625 3377 1.1320087 0 1062 0
33000 2.8467378 3365 0.26095982 20.543541 22.664361 7.194747 13306 58 58 0 52481 40320 5625 3365 1.1312548 0 1062 0
34000 3.0833296 3382 0.26259198 20.509033 22.806114 7.44833 12988 59 60 1 54049 40320 5625 3382 1.1447344 0 1062 0
35000 3.1068536 3382 0.26441995 20.650266 22.964872 9.3804156 13139 54 54 0 55749 40320 5625 3382 1.1272861 0 1062 0
36000 2.6998442 3369 0.25864735 20.452138 22.463522 6.3327985 13317 52 52 0 57348 40320 5625 3369 1.1312386 0 1062 0
37000 2.600171 3376 0.25882039 20.541424 22.478551 9.3909788 12841 57 57 0 58880 40320 5625 3376 1.1319429 0 1062 0
38000 2.3962821 3367 0.25728672 20.560122 22.345352 7.4364329 13039 66 66 0 60627 40320 5625 3367 1.1468141 0 1062 0
39000 2.8548804 3422 0.26044489 20.492753 22.619638 6.0832552 13249 50 50 0 62327 40320 5625 3422 1.1442726 0 1062 0
40000 2.7721124 3375 0.25927374 20.452701 22.517924 10.368128 13197 55 55 1 63903 40320 5625 3375 1.140807 0 1062 0
41000 3.0463159 3378 0.26123216 20.418508 22.688013 10.179554 13030 64 64 0 65629 40320 5625 3378 1.1277894 0 1062 0
42000 2.9625288 3388 0.26205988 20.552817 22.759901 8.8326646 12958 64 64 0 67242 40320 5625 3388 1.159201 0 1062 0
43000 2.7524867 3347 0.2592403 20.464417 22.51502 10.30221 12815 65 65 2 68734 40320 5625 3347 1.1444123 0 1062 0
44000 2.8779981 3354 0.26009923 20.44551 22.589618 12.127509 12743 67 67 3 70309 40320 5625 3354 1.1467915 0 1062 0
45000 2.7833999 3365 0.25968205 20.479753 22.553386 8.6942365 12909 46 47 0 71846 40320 5625 3365 1.1480348 0 1062 0
46000 2.6564678 3370 0.25935897 20.546258 22.525327 9.2618375 12923 61 61 1 73491 40320 5625 3370 1.1528284 0 1062 0
47000 2.821625 3414 0.25999655 20.47859 22.5807 7.5359036 12861 55 55 2 75201 40320 5625 3414 1.1395745 0 1062 0
48000 2.9301623 3351 0.26139433 20.519127 22.702098 9.5177842 13037 49 49 2 76819 40320 5625 3351 1.1472505 0 1062 0
49000 2.528824 3390 0.25834586 20.553364 22.437338 8.953785 13127 49 49 0 78450 40320 5625 3390 1.1495903 0 1062 0
50000 3.0054471 3375 0.261046 20.432787 22.671845 7.9749959 13089 56 56 2 80717 40320 5625 3375 1.1574724 0 1062 0
Loop time of 10.5055 on 8 procs for 50000 steps with 17370 atoms
Pair time (%) = 0.156617 (1.49081)
Neigh time (%) = 0.556925 (5.30126)
Comm time (%) = 0.902042 (8.58637)
Outpt time (%) = 0.00305247 (0.0290559)
Other time (%) = 8.88688 (84.5925)
Nlocal: 2171.25 ave 2567 max 1849 min
Histogram: 2 0 0 1 1 2 1 0 0 1
Nghost: 62.625 ave 71 max 57 min
Histogram: 2 0 1 0 2 2 0 0 0 1
Neighs: 168.25 ave 232 max 120 min
Histogram: 1 0 1 2 2 1 0 0 0 1
Total # of neighbors = 1346
Ave neighs/atom = 0.0774899
Neighbor list builds = 2599
Dangerous builds = 17
Please see the log.cite file for references relevant to this simulation
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