Homec4science
Diffusion lammps (lammm-master) Browse

lammps/examples/srd/log.srd.mixture.9Jan12.linux.4
34c19302013flammm-master

Last Change
Raw File

log.srd.mixture.9Jan12.linux.4
View Options

LAMMPS (10 Jan 2012)
# 2d SRD test: big + small particles
units lj
atom_style sphere
atom_modify first big
dimension 2
# create big particles with sigma 1.0
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region box block 0 10 0 10 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569)
2 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 diameter 1.0
100 settings made for diameter
group big type 1
100 atoms in group big
velocity big create 1.44 87287 loop geom
# equilibrate big 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
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big nve
fix 2 all enforce2d
run 1000
Memory usage per processor = 2.74723 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.54272 0 0.88288 -0.041088
1000 1.8791467 -0.97185784 0 0.8884974 0.61487657
Loop time of 0.0149925 on 4 procs for 1000 steps with 100 atoms
Pair time (%) = 0.00214541 (14.3099)
Neigh time (%) = 0.000690401 (4.60498)
Comm time (%) = 0.00878567 (58.6005)
Outpt time (%) = 1.81794e-05 (0.121257)
Other time (%) = 0.00335282 (22.3634)
Nlocal: 25 ave 26 max 23 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 47 ave 48 max 46 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 114.75 ave 124 max 100 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 459
Ave neighs/atom = 4.59
Neighbor list builds = 129
Dangerous builds = 0
unfix 1
unfix 2
# add small particles as hi density lattice
lattice sq 0.4
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
region plane block 0 10 0 10 -0.001 0.001
lattice sq 85.0
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
create_atoms 2 region plane
Created 21316 atoms
set type 2 mass 0.01
21316 settings made for mass
set type 2 diameter 0.0
21316 settings made for diameter
group small type 2
21316 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 6700 atoms, new total = 14716
# 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
timestep 0.001
fix 1 big nve
fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip
fix 3 all enforce2d
# diagnostics
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
thermo_style custom step temp f_2[7] 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[8] f_2[9] f_2[10]
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:442)
thermo 100
dump 1 all atom 250 dump.srd.mixture
run 5000
SRD info:
SRD/big particles = 14616 100
big particle diameter max/min = 0.88 0.88
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 63 63 1
SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114
SRD per actual grid cell = 4.86648
SRD viscosity = 0.463448
big/SRD mass density ratio = 2.12808
WARNING: Fix srd grid size > 1/4 of big particle diameter (fix_srd.cpp:2718)
# of rescaled SRD velocities = 0
ave/max small velocity = 13.2944 24.262
ave/max big velocity = 1.69284 5.10989
Memory usage per processor = 6.32655 Mbytes
Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10]
0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487657 0 0 0 0 0 0 0 0 0
100 1.4044369 3969 0.0030633087 -0.93959598 0.45079651 0.78900114 7464 99 99 0 0 22500 3312 0.93283021 0
200 1.1569395 3969 0.0010544039 -0.99020406 0.15516608 0.50132859 7393 82 82 0 0 22500 3291 0.92342254 0
300 1.0082066 3969 1.5754289e-06 -0.99789266 0.00023184012 0.36859357 7443 90 90 0 0 22500 3298 0.93222633 0
400 1.1459472 3969 0.0010570023 -0.97893929 0.15554845 0.47616067 7327 81 81 0 0 22500 3297 0.91766446 0
500 1.0836955 3969 0.00072569678 -0.966065 0.10679354 0.49205907 7447 89 89 0 0 22500 3258 0.93553253 0
600 0.95868561 3969 -0.00031108604 -0.99487817 -0.045779421 0.3676888 7488 90 90 0 0 22500 3280 0.91061957 0
700 0.98121671 3969 -0.00022225428 -1.0041115 -0.03270694 0.3605398 7393 80 80 0 0 22500 3299 0.90992183 0
800 1.0870893 3969 0.00028589178 -1.0341466 0.042071834 0.3576364 7506 96 96 0 0 22500 3290 0.92887007 0
900 1.087553 3969 8.795578e-05 -1.0637339 0.012943573 0.28026879 7405 82 82 0 0 22500 3301 0.91599453 0
1000 1.0160539 3969 7.5618714e-05 -0.99476531 0.01112805 0.60009776 7334 88 88 0 0 22500 3296 0.92803837 0
1100 0.94619807 3969 -0.00084794884 -1.0615202 -0.12478415 0.36153566 7565 89 89 0 0 22500 3300 0.93685597 0
1200 1.2187057 3969 0.00079088888 -1.0901314 0.11638721 0.34195358 7558 94 94 0 0 22500 3281 0.92133419 0
1300 1.0297116 3969 -6.2029069e-05 -1.0285427 -0.0091281978 0.44490154 7365 76 76 0 0 22500 3273 0.92349253 0
1400 1.0723726 3969 3.8902675e-05 -1.055924 0.0057249176 0.40617642 7524 90 90 0 0 22500 3280 0.92787441 0
1500 1.0661279 3969 -0.00010841884 -1.0714216 -0.015954917 0.49701435 7285 69 69 0 0 22500 3295 0.92862687 0
1600 1.2175256 3969 0.00087968156 -1.0758964 0.12945394 0.64512981 7286 89 89 0 1 22500 3294 0.92600699 0
1700 1.1985014 3969 0.0014648642 -0.970947 0.21556942 1.0479949 7228 85 85 0 0 22500 3268 0.92256981 0
1800 1.2075839 3969 0.00072247447 -1.0891887 0.10631934 0.57872746 7449 87 87 0 0 22500 3288 0.92069976 0
1900 1.2255534 3969 0.00088656095 -1.0828315 0.13046631 0.65685308 7385 76 76 0 0 22500 3291 0.9048111 0
2000 1.291624 3969 0.0012489132 -1.0949177 0.18379006 0.54486534 7460 88 88 0 0 22500 3269 0.92086677 0
2100 1.1111637 3969 8.680692e-05 -1.0872776 0.012774506 0.54623825 7399 79 79 0 0 22500 3283 0.89787043 0
2200 1.1101509 3969 -0.00019790624 -1.1281733 -0.029123882 0.36938914 7394 80 80 0 0 22500 3289 0.92391832 0
2300 0.99008142 3969 -0.0010221939 -1.1306067 -0.15042605 0.49715741 7403 77 77 0 0 22500 3298 0.9032635 0
2400 1.1298599 3969 -0.00028442155 -1.1604168 -0.041855476 0.62622034 7213 99 99 0 0 22500 3279 0.92291152 0
2500 0.96755195 3969 -0.0013882655 -1.1621736 -0.20429715 0.53854953 7302 91 91 0 0 22500 3282 0.9169308 0
2600 0.92289325 3969 -0.0018295583 -1.1829021 -0.2692378 0.48117908 7387 114 114 0 0 22500 3292 0.90278484 0
2700 1.0556828 3969 -0.0010119543 -1.1940452 -0.14891919 0.38438637 7379 77 77 0 0 22500 3290 0.90840462 0
2800 0.96725457 3969 -0.0014988251 -1.1781491 -0.2205671 0.45335869 7311 77 77 0 0 22500 3273 0.91859555 0
2900 1.0133684 3969 -0.0012783239 -1.1913529 -0.18811815 0.47922787 7445 91 91 0 0 22500 3282 0.93217047 0
3000 0.97710883 3969 -0.0011590153 -1.1378984 -0.17056069 0.64470243 7454 90 90 0 0 22500 3294 0.90446012 0
3100 0.85234697 3969 -0.002077265 -1.1495138 -0.30569031 0.55071072 7386 95 95 0 0 22500 3276 0.90586471 0
3200 1.052911 3969 -0.00084248304 -1.1663617 -0.1239798 0.49920749 7410 84 84 0 0 22500 3298 0.94126987 0
3300 1.1427076 3969 0.00052348324 -1.0542447 0.077035793 0.97657677 7268 70 70 0 0 22500 3281 0.93981555 0
3400 1.1749571 3969 -0.00049301879 -1.2357602 -0.072552645 0.2551001 7443 77 77 0 0 22500 3296 0.92174553 0
3500 0.99448585 3969 -0.0015705474 -1.2156628 -0.23112176 0.31069295 7502 97 97 0 0 22500 3271 0.94669984 0
3600 1.0615674 3969 -0.00088670873 -1.1814398 -0.13048806 0.42774035 7386 70 70 0 0 22500 3298 0.91457914 0
3700 0.92549328 3969 -0.0018599812 -1.1899532 -0.27371483 0.36471531 7459 81 81 0 0 22500 3305 0.93382818 0
3800 0.85987993 3969 -0.0018189231 -1.1189538 -0.26767272 0.42802928 7232 75 75 0 0 22500 3304 0.91492738 0
3900 0.92111833 3969 -0.0011824977 -1.0859235 -0.17401636 0.73992354 7351 80 80 0 0 22500 3298 0.94205739 0
4000 0.91817371 3969 -0.0014469814 -1.1219298 -0.21293778 0.64725317 7478 86 86 0 0 22500 3309 0.92689567 0
4100 1.0607641 3969 -0.00061451533 -1.1405885 -0.090432076 0.54575249 7474 87 87 0 0 22500 3306 0.94825937 0
4200 1.1112883 3969 0.00012926229 -1.0811532 0.019022238 0.71771029 7527 67 67 0 1 22500 3285 0.93577595 0
4300 1.3096702 3969 0.00060322354 -1.2078031 0.088770376 0.31006723 7617 88 88 0 0 22500 3291 0.95276158 0
4400 1.2076765 3969 0.001009301 -1.047071 0.14852873 0.83105522 7355 97 97 0 0 22500 3293 0.94207048 0
4500 0.94049473 3969 -0.0011505342 -1.1004024 -0.16931262 0.46258624 7403 78 78 0 0 22500 3275 0.95198657 0
4600 0.8241741 3969 -0.0025714658 -1.1943493 -0.37841691 0.010193689 7604 99 99 0 1 22500 3287 0.94875859 0
4700 0.98678642 3969 -0.0011664864 -1.1485787 -0.17166013 0.16963181 7691 94 94 0 0 22500 3289 0.92141605 0
4800 0.97602307 3969 -0.0010910984 -1.1268289 -0.16056604 0.24433738 7547 85 85 0 0 22500 3287 0.92130755 0
4900 1.0427787 3969 -0.00050976935 -1.1073686 -0.075017657 0.30774039 7563 85 85 0 0 22500 3300 0.92864167 0
5000 1.3048873 3969 0.0015736036 -1.0602669 0.23157151 0.49881308 7529 104 104 0 0 22500 3293 0.91471093 0
Loop time of 1.185 on 4 procs for 5000 steps with 14716 atoms
Pair time (%) = 0.0118163 (0.997157)
Neigh time (%) = 0.0523425 (4.41711)
Comm time (%) = 0.077751 (6.56129)
Outpt time (%) = 0.191228 (16.1375)
Other time (%) = 0.851857 (71.887)
Nlocal: 3679 ave 4052 max 3370 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 49 ave 53 max 42 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 120.5 ave 162 max 85 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 482
Ave neighs/atom = 0.0327535
Neighbor list builds = 250
Dangerous builds = 0
c4science · Help