240 lines
17 KiB
Plaintext
240 lines
17 KiB
Plaintext
LAMMPS (9 Sep 2013)
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# SRD viscosity demo - poydisperse spheres
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units lj
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atom_style sphere
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atom_modify first big
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dimension 2
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# create big particles with 3 different types and diameters
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lattice sq 0.3
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Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
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region box block 0 10 0 10 -0.5 0.5
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create_box 4 box
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Created orthogonal box = (0 0 -0.912871) to (18.2574 18.2574 0.912871)
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2 by 4 by 1 MPI processor grid
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create_atoms 1 region box
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Created 100 atoms
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group big type 1
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100 atoms in group big
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set group big type/fraction 2 0.33 394895
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35 settings made for type/fraction
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set group big type/fraction 3 0.5 989894
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57 settings made for type/fraction
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group big type 2 3
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100 atoms in group big
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set type 1*3 mass 1.0
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100 settings made for mass
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velocity big create 1.44 87287 loop geom
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# equilibrate big particles, repulsive only to prevent aggregation
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pair_style lj/cut 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 0.0 1.0 0.0
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 big nve
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fix 2 all enforce2d
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#dump 1 all atom 10 dump.poly.equil
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run 1000
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Memory usage per processor = 2.74744 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -0.16013916 0 1.2654608 1.1298975
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1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
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Loop time of 0.0171109 on 8 procs for 1000 steps with 100 atoms
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Pair time (%) = 0.000367314 (2.14666)
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Neigh time (%) = 0.000303924 (1.7762)
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Comm time (%) = 0.0108245 (63.2607)
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Outpt time (%) = 4.13954e-05 (0.241924)
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Other time (%) = 0.00557381 (32.5745)
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Nlocal: 12.5 ave 18 max 10 min
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Histogram: 1 3 1 1 0 1 0 0 0 1
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Nghost: 27.75 ave 31 max 24 min
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Histogram: 1 0 1 0 2 2 0 0 0 2
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Neighs: 19 ave 30 max 16 min
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Histogram: 4 1 2 0 0 0 0 0 0 1
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Total # of neighbors = 152
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Ave neighs/atom = 1.52
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Neighbor list builds = 115
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Dangerous builds = 0
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#undump 1
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unfix 1
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unfix 2
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# add small particles as hi density lattice
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region plane block INF INF INF INF -0.001 0.001 units box
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lattice sq 250.0
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Lattice spacing in x,y,z = 0.0632456 0.0632456 0.0632456
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create_atoms 4 region plane
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Created 83521 atoms
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set type 4 mass 0.1
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83521 settings made for mass
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group small type 4
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83521 atoms in group small
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velocity small create 1.0 593849 loop geom
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# delete overlaps
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# must set *-4 cutoffs to non-zero values
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0
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pair_coeff 2 2 1.0 2.0
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pair_coeff 3 3 1.0 1.5
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pair_coeff 1 4 0.0 1.0 0.5
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pair_coeff 2 4 0.0 1.0 1.0
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pair_coeff 3 4 0.0 1.0 0.75
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delete_atoms overlap 1.0 small big
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Deleted 63410 atoms, new total = 20211
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# SRD run
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reset_timestep 0
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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communicate multi group big vel yes
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neigh_modify include big
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# no pairwise interactions with small particles
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pair_style lj/cut 1.12
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pair_coeff 1 1 1.0 1.0 1.12
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pair_coeff 2 2 1.0 2.0 2.24
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pair_coeff 3 3 1.0 1.5 1.68
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pair_coeff 4 4 0.0 1.0 0.0
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# use fix SRD to push small particles out from inside big ones
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# if comment out, big particles won't see SRD particles
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timestep 0.001
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fix 1 big nve
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fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
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fix 3 small viscosity 10 x y 50
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fix 4 all enforce2d
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# diagnostics
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compute tbig big temp/sphere
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variable pebig equal pe*atoms/count(big)
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variable ebig equal etotal*atoms/count(big)
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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]
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thermo_modify temp tbig
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WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
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thermo 1000
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#dump 1 all atom 500 dump.poly.mp
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#dump 1 all image 500 image.*.jpg type type zoom 1.6
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#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
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run 50000
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SRD info:
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SRD/big particles = 20111 100
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big particle diameter max/min = 1 1
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SRD temperature & lamda = 1 0.0632456
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SRD max distance & max velocity = 0.252982 12.6491
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SRD grid counts: 73 73 1
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SRD grid size: request, actual (xyz) = 0.25, 0.250102 0.250102 1.82574
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SRD per actual grid cell = 4.93717
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SRD viscosity = 0.23322
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big/SRD mass density ratio = 0.161311
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WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
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# of rescaled SRD velocities = 0
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ave/max small velocity = 4.19344 7.74495
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ave/max big velocity = 1.43991 3.5724
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Memory usage per processor = 11.7296 Mbytes
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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]
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0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
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1000 0.76223473 4359 0.0058318998 0.042955512 1.1786853 3.9611296 7412 29 29 0 606 36480 5329 4359 0.88595821 0 1
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2000 0.90685078 4370 0.0052567627 -0.28876335 1.0624443 2.8023345 7566 38 38 0 1219 36480 5329 4370 0.98245206 0 3
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3000 0.82349169 4363 0.0040922377 -0.39992047 0.82708216 2.4033782 7677 22 22 0 2010 36480 5329 4363 0.9951035 0 3
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4000 1.0770702 4382 0.0065800011 -0.27495058 1.329884 2.9540829 8067 43 43 0 2890 36480 5329 4382 1.0247955 0 3
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5000 1.1187379 4371 0.0070884891 -0.23426486 1.4326545 2.782956 7987 34 34 0 3819 36480 5329 4371 1.0264278 0 3
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6000 1.1529648 4390 0.00804325 -0.092296355 1.6256212 2.7035637 8260 45 45 0 4906 36480 5329 4390 1.044768 0 3
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7000 1.2166621 4394 0.0084991908 -0.095055017 1.7177715 2.7964656 8289 29 29 0 6097 36480 5329 4394 1.0681058 0 3
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8000 1.0578321 4380 0.0069270677 -0.17614024 1.4000297 2.2457489 8231 32 32 0 7318 36480 5329 4380 1.0661274 0 3
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9000 1.1745002 4384 0.0080485374 -0.12331542 1.6266899 2.6780691 8348 30 30 0 8532 36480 5329 4384 1.0674998 0 3
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10000 1.2053965 4394 0.00919032 0.061414788 1.8574556 2.9760341 8315 36 36 0 9939 36480 5329 4394 1.0698008 0 3
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11000 1.2140992 4405 0.0080187349 -0.18834127 1.6206665 2.1090843 8390 38 38 0 11379 36480 5329 4405 1.0646411 0 3
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12000 1.3314891 4370 0.0085977755 -0.24622241 1.7376964 2.1024157 8371 31 31 0 12874 36480 5329 4370 1.1085934 0 3
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13000 1.7854091 4406 0.012596422 -0.11439664 2.5458629 2.8136175 8209 31 31 0 14445 36480 5329 4406 1.0656714 0 3
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14000 1.3532948 4392 0.0096486307 -0.066324512 1.9500847 2.9946734 8436 31 31 0 15853 36480 5329 4392 1.0796035 0 3
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15000 1.3652525 4406 0.0088880459 -0.23786321 1.796363 2.3354792 8476 32 32 0 17491 36480 5329 4406 1.062359 0 3
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16000 1.7207747 4397 0.010473468 -0.44716178 2.1167926 2.0550985 8412 33 33 0 18967 36480 5329 4397 1.0727867 0 3
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17000 1.4441674 4395 0.0093810416 -0.25580709 1.8960023 2.2891681 8523 25 25 0 20633 36480 5329 4395 1.0718441 0 3
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18000 1.6353203 4369 0.011239971 -0.16491671 2.2717106 2.2715018 8350 36 36 0 22227 36480 5329 4369 1.062651 0 3
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19000 1.2336121 4400 0.0078318926 -0.25517824 1.5829038 2.1478301 8506 31 31 0 23785 36480 5329 4400 1.064015 0 6
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20000 1.348169 4385 0.0093452554 -0.12000224 1.8887696 2.7793176 8501 31 31 0 25381 36480 5329 4385 1.0749601 0 6
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21000 1.2999945 4388 0.008793608 -0.15971573 1.7772761 2.2319158 8571 31 31 0 26907 36480 5329 4388 1.057039 0 6
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22000 1.4136382 4381 0.010131428 -0.058657961 2.0476629 2.9137729 8395 33 33 0 28465 36480 5329 4381 1.0483767 0 6
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23000 1.4669336 4397 0.0094913428 -0.26743576 1.9182953 2.2607135 8414 33 33 0 30174 36480 5329 4397 1.0599821 0 54
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24000 1.2402392 4393 0.0078941135 -0.25247715 1.5954793 2.1369734 8327 27 27 0 31747 36480 5329 4393 1.0756872 0 54
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25000 1.4541683 4379 0.010209747 -0.10321883 2.063492 2.540742 8397 41 41 0 33411 36480 5329 4379 1.0672776 0 54
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26000 1.3405944 4406 0.0097712528 -0.022617748 1.9748679 2.5936783 8485 41 41 0 35118 36480 5329 4406 1.0758295 0 54
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27000 1.6558588 4405 0.012177263 -0.0060829802 2.4611467 2.8707229 8422 27 27 0 36723 36480 5329 4405 1.083128 0 54
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28000 1.4410581 4387 0.0097287673 -0.18089536 1.9662812 2.2328446 8473 33 33 0 38374 36480 5329 4387 1.0974956 0 54
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29000 1.5710587 4399 0.011438826 -0.028976305 2.3119011 3.0464022 8409 36 36 0 39977 36480 5329 4399 1.0723788 0 54
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30000 1.5822758 4390 0.010254579 -0.285038 2.072553 2.4492756 8285 43 43 0 41623 36480 5329 4390 1.0800035 0 54
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31000 1.7821546 4385 0.012457185 -0.13768863 2.5177217 2.6529479 8311 26 26 0 43266 36480 5329 4385 1.0710985 0 54
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32000 1.6106571 4376 0.01150871 -0.073853599 2.3260254 2.6925206 8227 30 30 0 44806 36480 5329 4376 1.0726823 0 54
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33000 1.631601 4397 0.011271203 -0.1530625 2.2780229 2.111596 8463 40 40 0 46536 36480 5329 4397 1.0692746 0 54
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34000 1.3427275 4390 0.0092429624 -0.13256884 1.8680951 2.3330047 8481 30 30 0 48188 36480 5329 4390 1.0598242 0 54
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35000 1.8270729 4410 0.012439006 -0.20829114 2.5140475 2.4497436 8377 43 43 0 49938 36480 5329 4410 1.0639662 0 54
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36000 1.6831749 4409 0.011556546 -0.17223706 2.3356935 2.4104909 8530 38 38 0 51575 36480 5329 4409 1.0462452 0 54
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37000 1.5041928 4387 0.010868354 -0.044644177 2.1966031 2.8240213 8314 28 28 0 53275 36480 5329 4387 1.0642241 0 54
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38000 1.63922 4400 0.011191082 -0.18060817 2.2618297 2.6036583 8460 31 31 0 54863 36480 5329 4400 1.0513104 0 54
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39000 1.7856293 4402 0.01190713 -0.25403773 2.40655 2.6037177 8373 28 28 0 56511 36480 5329 4402 1.0575221 0 54
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40000 1.5627911 4395 0.010299952 -0.24683547 2.0817233 2.097953 8604 38 38 0 58065 36480 5329 4395 1.0761208 0 54
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41000 1.6374988 4391 0.011852474 -0.044369717 2.3955035 2.8099437 8581 37 37 0 59794 36480 5329 4391 1.0691616 0 54
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42000 1.5639838 4401 0.0099361957 -0.32213138 2.0082045 2.140333 8517 26 26 0 61494 36480 5329 4401 1.0551075 0 54
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43000 1.4230074 4386 0.010145789 -0.069715647 2.0505654 2.8175539 8394 35 35 0 63053 36480 5329 4386 1.0725308 0 54
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44000 1.7426342 4421 0.012394613 -0.091449657 2.5050753 3.108882 8621 22 22 3 64860 36480 5329 4421 1.0689123 0 54
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45000 1.5920362 4402 0.010869076 -0.17538493 2.196749 2.6145992 8584 33 33 0 66553 36480 5329 4402 1.0639622 0 54
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46000 1.5470871 4381 0.010652614 -0.15215985 2.1529999 2.5774405 8385 41 41 0 68217 36480 5329 4381 1.0647713 0 54
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47000 1.5733084 4394 0.010531031 -0.21580282 2.1284266 2.5415139 8473 39 39 0 70008 36480 5329 4394 1.0737587 0 54
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48000 1.6011945 4385 0.010744982 -0.21411145 2.1716683 2.6439905 8324 32 32 0 71724 36480 5329 4385 1.0697134 0 54
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49000 1.4920792 4394 0.01155316 0.11181112 2.3350091 3.2468881 8325 35 35 0 73535 36480 5329 4394 1.0606307 0 54
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50000 1.7492562 4404 0.012682847 -0.043061576 2.5633302 2.9057702 8551 24 24 0 75221 36480 5329 4404 1.0604543 0 54
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Loop time of 7.87485 on 8 procs for 50000 steps with 20211 atoms
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Pair time (%) = 0.030976 (0.393354)
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Neigh time (%) = 0.431914 (5.48473)
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Comm time (%) = 0.565844 (7.18546)
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Outpt time (%) = 0.00249878 (0.0317311)
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Other time (%) = 6.84361 (86.9047)
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Nlocal: 2526.38 ave 2659 max 2437 min
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Histogram: 1 3 0 0 1 1 0 0 1 1
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Nghost: 22.75 ave 25 max 19 min
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Histogram: 1 0 0 0 0 2 2 0 2 1
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Neighs: 16.25 ave 20 max 12 min
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Histogram: 1 0 1 1 0 1 1 2 0 1
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Total # of neighbors = 130
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Ave neighs/atom = 0.00643214
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Neighbor list builds = 2504
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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