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lammps/examples/ASPHERE/ellipsoid/log.ellipsoid.mp.10Sep13
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LAMMPS (9 Sep 2013)
# SRD viscosity demo - ellipsoids
units lj
atom_style ellipsoid
atom_modify first big
dimension 2
# create big ellipsoidal particles
lattice sq 0.14
Lattice spacing in x,y,z = 2.67261 2.67261 2.67261
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -1.33631) to (26.7261 26.7261 1.33631)
4 by 2 by 1 MPI processor grid
create_atoms 1 region box
Created 100 atoms
set type 1 mass 1.0
100 settings made for mass
set type 1 shape 3.0 1.0 1.0
100 settings made for shape
group big type 1
100 atoms in group big
set group big quat/random 29898
100 settings made for quat/random
velocity big create 1.44 87287 loop geom
# equilibrate big particles
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve/asphere
fix 2 all enforce2d
compute rot big temp/asphere
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z # quatw quati quatj quatk
thermo_style custom step temp c_rot epair etotal press
thermo 100
run 1000
Memory usage per processor = 3.31955 Mbytes
Step Temp rot E_pair TotEng Press
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
800 2.7632972 2.9060854 -0.52075353 2.2149107 0.77106777
900 2.9905599 2.8869667 -0.49099384 2.4696604 0.6961683
1000 2.8470141 2.9005014 -0.51282121 2.3057228 0.68817475
Loop time of 0.216003 on 8 procs for 1000 steps with 100 atoms
Pair time (%) = 0.033883 (15.6863)
Neigh time (%) = 0.000561774 (0.260077)
Comm time (%) = 0.110359 (51.0913)
Outpt time (%) = 0.00236297 (1.09395)
Other time (%) = 0.0688367 (31.8684)
Nlocal: 12.5 ave 16 max 8 min
Histogram: 1 1 0 0 0 3 0 0 1 2
Nghost: 34.125 ave 42 max 28 min
Histogram: 1 0 2 2 0 1 0 1 0 1
Neighs: 46.125 ave 65 max 20 min
Histogram: 1 0 1 0 1 2 0 0 1 2
Total # of neighbors = 369
Ave neighs/atom = 3.69
Neighbor list builds = 174
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 120.0
Lattice spacing in x,y,z = 0.0912871 0.0912871 0.0912871
create_atoms 2 region plane
Created 85849 atoms
set type 2 mass 0.01
85849 settings made for mass
group small type 2
85849 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 2.0
neigh_modify one 10000
delete_atoms overlap 1.6 small big
Deleted 71060 atoms, new total = 14889
# 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 gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 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 0.0005
fix 1 big nve/asphere
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
fix 3 small viscosity 20 x y 50
fix 4 all enforce2d
# diagnostics
compute tbig big temp/asphere
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp c_rot f_2[9] 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:438)
thermo 1000
#dump 1 all custom 500 dump.ellipsoid.mp id type x y z # quatw quati quatj quatk
#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 = 14789 100
big particle diameter max/min = 3 1
SRD temperature & lamda = 1 0.1
SRD max distance & max velocity = 0.4 40
SRD grid counts: 107 107 1
SRD grid size: request, actual (xyz) = 0.25, 0.249777 0.249777 2.67261
SRD per actual grid cell = 1.92757
SRD viscosity = 0.688101
big/SRD mass density ratio = 1.37367
# of rescaled SRD velocities = 0
ave/max small velocity = 13.3093 24.3359
ave/max big velocity = 2.08028 5.05672
Memory usage per processor = 10.6335 Mbytes
Step Temp rot 2[9] 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 2.9005014 2.9005014 0 0.025582147 -0.51282121 3.8089259 0.89862319 0 0 0 0 0 0 0 0 0 0 0 0
1000 4.0772042 4.0772042 0.6709105 0.040214379 -0.08751542 5.9875189 2.7529672 14344 42 225 0 224495 98040 11449 6583 0.6709105 1320 50 0
2000 2.7438363 2.7438363 0.76662675 0.02408678 -0.50203535 3.5862807 1.751055 15904 52 228 0 516986 98040 11449 6696 0.76662675 3017 50 0
3000 4.3077081 4.3077081 0.80827675 0.039345067 -0.56039804 5.858087 1.7998404 16676 49 241 0 813000 98040 11449 6693 0.80827675 4732 50 0
4000 2.6526774 2.6526774 0.78555744 0.022082331 -0.66465108 3.2878383 1.0403545 17617 43 222 0 1127008 98040 11449 6765 0.78555744 6334 50 0
5000 2.594913 2.594913 0.82350776 0.021770968 -0.62494096 3.2414795 1.0780953 17703 57 382 0 1391570 98040 11449 6743 0.82350776 7729 50 0
6000 3.0343473 3.0343473 0.84065515 0.026658458 -0.55199962 3.9691778 1.2301173 18015 52 363 0 1676493 98040 11449 6775 0.84065515 9263 50 0
7000 3.0413763 3.0413763 0.79884495 0.026536497 -0.58063167 3.9510191 1.1147571 18292 55 458 0 1953690 98040 11449 6800 0.79884495 10658 50 0
8000 2.7812045 2.7812045 0.80159783 0.024478142 -0.49944409 3.6445506 1.3707277 18408 61 475 0 2238100 98040 11449 6833 0.80159783 12186 50 0
9000 2.7102571 2.7102571 0.82556805 0.023142083 -0.59265825 3.4456248 0.98842401 18286 61 194 0 2576779 98040 11449 6818 0.82556805 13939 50 0
10000 3.2045912 3.2045912 0.8622825 0.027989227 -0.60752488 4.167316 1.1341927 18288 50 179 0 2962819 98040 11449 6720 0.8622825 15849 50 0
11000 4.6098925 4.6098925 0.8551898 0.042356478 -0.56228382 6.306456 1.4720289 18764 62 280 0 3277277 98040 11449 6818 0.8551898 17581 50 0
12000 3.5052136 3.5052136 0.85951127 0.03109149 -0.59355628 4.6292119 1.0101413 18788 51 361 0 3618996 98040 11449 6778 0.85951127 19490 50 0
13000 3.2931183 3.2931183 0.87082756 0.030037721 -0.43442997 4.4723163 1.3509023 19082 56 519 0 3950820 98040 11449 6816 0.87082756 21387 50 0
14000 3.3837607 3.3837607 0.84668317 0.030465137 -0.50584917 4.5359543 1.3664689 19368 59 413 0 4299096 98040 11449 6788 0.84668317 23311 50 0
15000 3.9613429 3.9613429 0.88196505 0.038203107 -0.21434033 5.6880606 1.8415287 18619 61 472 0 4666678 98040 11449 6808 0.88196505 25272 50 0
16000 4.2615312 4.2615312 0.82672895 0.038879833 -0.56086323 5.7888183 1.2281404 18687 49 453 0 5016630 98040 11449 6724 0.82672895 27200 50 0
17000 3.1642486 3.1642486 0.82812979 0.028702004 -0.44128899 4.2734414 1.2224354 18918 54 385 0 5318150 98040 11449 6780 0.82812979 28796 50 0
18000 4.326255 4.326255 0.80700754 0.039935329 -0.50014888 5.9459711 1.5337863 19242 59 417 0 5620823 98040 11449 6819 0.80700754 30496 50 0
19000 4.7303091 4.7303091 0.82398378 0.043920179 -0.50888521 6.5392754 1.3695551 18896 56 276 0 5900972 98040 11449 6807 0.82398378 32209 50 0
20000 3.4002668 3.4002668 0.84006847 0.031221557 -0.41781984 4.6485777 1.1290385 18861 52 142 0 6221193 98040 11449 6816 0.84006847 33883 50 0
21000 3.8655857 3.8655857 0.85324995 0.03542669 -0.48504283 5.2746799 1.0819496 19111 53 192 0 6513564 98040 11449 6830 0.85324995 35352 50 0
22000 3.6574509 3.6574509 0.84025473 0.033965163 -0.39252882 5.0570731 1.4286148 19280 54 269 0 6824809 98040 11449 6781 0.84025473 36941 50 0
23000 4.4296219 4.4296219 0.86770551 0.041555285 -0.41297036 6.1871663 1.4156152 19160 37 435 0 7161579 98040 11449 6752 0.86770551 38716 50 0
24000 4.0435169 4.0435169 0.84111419 0.036578859 -0.57861376 5.4462264 0.96478184 19059 48 379 0 7512598 98040 11449 6797 0.84111419 40660 50 0
25000 3.8100627 3.8100627 0.84181242 0.035211679 -0.43432659 5.2426668 1.3297193 19418 54 385 0 7859647 98040 11449 6749 0.84181242 42653 50 0
26000 4.4865488 4.4865488 0.83287786 0.041526308 -0.50210571 6.182852 1.2409485 19282 51 239 0 8238637 98040 11449 6792 0.83287786 44767 50 0
27000 7.0852396 7.0852396 0.85841948 0.068172726 -0.40676992 10.150237 2.0194952 19317 56 283 0 8632769 98040 11449 6726 0.85841948 46983 50 0
28000 5.1517725 5.1517725 0.87627692 0.048475654 -0.45860096 7.2175401 1.3442212 18868 59 429 0 8971998 98040 11449 6805 0.87627692 48888 50 0
29000 3.759401 3.759401 0.85080417 0.034921423 -0.40205682 5.1994507 1.2957581 19528 51 223 0 9358797 98040 11449 6767 0.85080417 50864 50 0
30000 4.1056897 4.1056897 0.89048135 0.038239787 -0.42395586 5.6935219 1.3427608 19322 55 320 0 9714933 98040 11449 6726 0.89048135 52987 50 0
31000 3.9169919 3.9169919 0.83225664 0.036119283 -0.45851779 5.3778001 1.2227344 19378 56 183 0 10093157 98040 11449 6835 0.83225664 55203 50 0
32000 4.2947449 4.2947449 0.85282769 0.040398791 -0.38419394 6.0149759 1.4475348 18971 64 192 0 10449851 98040 11449 6788 0.85282769 57103 50 0
33000 6.3981858 6.3981858 0.8752853 0.061770539 -0.33628134 9.1970155 1.8805105 19093 65 113 0 10906186 98040 11449 6698 0.8752853 59700 50 0
34000 4.1610677 4.1610677 0.84406404 0.038747185 -0.43092244 5.7690684 1.1157695 19427 62 413 0 11309588 98040 11449 6739 0.84406404 62078 50 0
35000 4.8088073 4.8088073 0.87151511 0.045354512 -0.4122896 6.7528333 1.4394764 19376 66 434 0 11696476 98040 11449 6763 0.87151511 64175 50 0
36000 4.2921897 4.2921897 0.84488024 0.039617438 -0.49672227 5.8986404 1.1291104 19529 45 264 0 12022588 98040 11449 6795 0.84488024 65897 50 0
37000 3.7112825 3.7112825 0.8416428 0.033678706 -0.51538845 5.0144225 1.0454583 19827 69 455 0 12340474 98040 11449 6782 0.8416428 67632 50 0
38000 3.6819111 3.6819111 0.85373497 0.034285125 -0.38133519 5.1047123 1.2393947 19380 47 149 0 12643621 98040 11449 6771 0.85373497 69404 50 0
39000 4.271666 4.271666 0.87592802 0.040171423 -0.38365909 5.9811232 1.3509653 19208 53 437 0 12951773 98040 11449 6773 0.87592802 71144 50 0
40000 7.8961104 7.8961104 0.83195448 0.075474381 -0.52782399 11.237381 2.0854836 19587 54 140 0 13284474 98040 11449 6739 0.83195448 73005 50 0
41000 5.3324705 5.3324705 0.84594041 0.050595382 -0.41223462 7.5331464 1.8824 19398 60 246 0 13591740 98040 11449 6739 0.84594041 74623 50 0
42000 5.3412052 5.3412052 0.85510315 0.050390916 -0.45569229 7.5027035 1.6185323 19004 56 411 0 13943637 98040 11449 6811 0.85510315 76708 50 0
43000 4.538738 4.538738 0.84330484 0.04134934 -0.6062163 6.1565033 0.93340583 18747 55 166 0 14310076 98040 11449 6816 0.84330484 78713 50 0
44000 4.7059719 4.7059719 0.87465087 0.043139856 -0.58880485 6.4230932 1.1555897 18636 55 185 0 14663012 98040 11449 6779 0.87465087 80547 50 0
45000 4.3751196 4.3751196 0.8849121 0.039833588 -0.58810522 5.930823 1.3402888 18537 61 382 0 15031341 98040 11449 6796 0.8849121 82486 50 0
46000 3.8815029 3.8815029 0.84817481 0.034767594 -0.60689233 5.1765471 0.94880018 18642 64 807 0 15350275 98040 11449 6877 0.84817481 84256 50 0
47000 4.2821501 4.2821501 0.85615543 0.039739616 -0.46357218 5.9168314 1.2473512 19321 51 240 0 15717133 98040 11449 6744 0.85615543 86379 50 0
48000 4.8566025 4.8566025 0.88283248 0.045601238 -0.44676931 6.7895684 1.3643402 19369 64 555 0 16181209 98040 11449 6711 0.88283248 89052 50 0
49000 5.041306 5.041306 0.83860275 0.046968778 -0.51836452 6.9931814 1.2925069 19148 56 645 0 16630113 98040 11449 6767 0.83860275 91645 50 0
50000 4.017754 4.017754 0.85846415 0.037037752 -0.47190243 5.514551 1.2505985 19331 70 388 0 17084877 98040 11449 6815 0.85846415 94299 50 0
Loop time of 14.4429 on 8 procs for 50000 steps with 14889 atoms
Pair time (%) = 1.82692 (12.6493)
Neigh time (%) = 0.991614 (6.86577)
Comm time (%) = 1.32936 (9.20426)
Outpt time (%) = 0.0033724 (0.02335)
Other time (%) = 10.2916 (71.2574)
Nlocal: 1861.12 ave 1950 max 1735 min
Histogram: 1 0 1 0 1 0 1 2 1 1
Nghost: 34 ave 37 max 30 min
Histogram: 1 0 1 0 2 1 0 0 1 2
Neighs: 46.125 ave 64 max 32 min
Histogram: 1 2 0 1 1 1 0 0 1 1
Total # of neighbors = 369
Ave neighs/atom = 0.0247834
Neighbor list builds = 2575
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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