Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/examples/srd/log.15May15.srd.mixture.g++.4
07f62aea1a51lammm-devel

Last Change
Raw File

log.15May15.srd.mixture.g++.4
View Options

LAMMPS (30 Apr 2015)
# 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 2.8
Memory usage per processor = 3.60121 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 0.0145814 on 4 procs for 1000 steps with 100 atoms
Pair time (%) = 0.0021292 (14.6021)
Neigh time (%) = 0.000770807 (5.28622)
Comm time (%) = 0.00848264 (58.1742)
Outpt time (%) = 2.12789e-05 (0.145931)
Other time (%) = 0.00317752 (21.7916)
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
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 2.8
WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:277)
Deleted 6700 atoms, new total = 14716
# SRD run
reset_timestep 0
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
comm_modify mode 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:445)
thermo 100
#dump 1 all atom 250 dump.srd.mixture
#dump 2 all image 250 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 4 adiam 1 1 adiam 2 0.2
#dump 3 all movie 250 movie.mpg type type zoom 1.6
#dump_modify 3 pad 4 adiam 1 1 adiam 2 0.2
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:2884)
# of rescaled SRD velocities = 0
ave/max small velocity = 13.2944 24.262
ave/max big velocity = 1.69284 5.10989
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 2.8
Memory usage per processor = 5.3246 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 0.0030633093 -0.93959598 0.4507966 0.78900119 7464 99 99 0 17 22500 3005 1.028131 0
200 1.1569383 3969 0.0010543995 -0.99020352 0.15516543 0.50132981 7393 82 82 0 43 22500 2996 1.014347 0
300 0.97802835 3969 -0.00019991154 -0.99766705 -0.029418982 0.35789515 7411 90 90 0 84 22500 3001 1.0213725 0
400 1.0992982 3969 0.00055034756 -1.007316 0.080989146 0.35177983 7443 78 78 0 107 22500 2993 1.0451641 0
500 1.0436705 3969 -7.4779704e-05 -1.0442384 -0.011004581 0.15132448 7504 94 94 0 141 22500 3007 1.0236992 0
600 1.0216461 3969 -0.00032426678 -1.0591487 -0.047719099 0.2200765 7508 111 111 0 179 22500 3007 1.0304838 0
700 1.1491339 3969 0.0012328743 -0.95621278 0.18142978 0.80670059 7448 95 95 0 201 22500 2978 1.0099113 0
800 1.0332166 3969 -0.00040684239 -1.0827554 -0.059870926 0.35939225 7453 113 113 0 235 22500 3024 1.0141565 0
900 1.0652211 3969 -6.1337025e-06 -1.0554715 -0.00090263566 0.51460169 7447 97 97 0 259 22500 2982 1.0192735 0
1000 0.92834993 3969 -0.00067681883 -1.0186671 -0.09960066 0.738738 7328 78 78 0 286 22500 2999 1.023841 0
1100 1.0386338 3969 -0.00018904027 -1.0560666 -0.027819166 0.57129719 7449 96 96 0 325 22500 3012 1.0373885 0
1200 0.92218024 3969 -0.00077989365 -1.0277276 -0.11476915 0.48613467 7507 100 100 0 355 22500 3003 1.0254889 0
1300 1.1835318 3969 0.00096836748 -1.0291915 0.14250496 0.62935386 7439 92 92 0 384 22500 2993 1.0289037 0
1400 1.0895805 3969 0.00022072203 -1.0462033 0.032481455 0.49130771 7492 80 80 0 426 22500 3005 1.0083895 0
1500 1.0713283 3969 0.00042008247 -0.99879571 0.061819337 0.63979877 7498 87 87 0 457 22500 3000 1.0009934 0
1600 0.97815063 3969 -0.0005425653 -1.048213 -0.079843909 0.3604669 7533 105 105 0 492 22500 3004 1.0375508 0
1700 1.1626991 3969 0.00048969594 -1.0790084 0.072063654 0.36261544 7493 87 87 0 519 22500 3014 1.0151507 0
1800 0.91077626 3969 -0.001205934 -1.0791337 -0.17746525 0.14204132 7553 77 77 0 554 22500 3001 1.0393648 0
1900 1.073632 3969 0.00048053229 -0.99218055 0.070715131 0.56468311 7660 96 96 0 579 22500 2990 1.0071005 0
2000 1.0516743 3969 -0.00020689596 -1.0716044 -0.03044681 0.28030578 7561 96 96 0 631 22500 3020 1.0222307 0
2100 1.141885 3969 0.00040167415 -1.0713558 0.059110368 0.32604475 7569 69 69 0 662 22500 2968 1.0125404 0
2200 1.2228391 3969 0.0010327668 -1.0586288 0.15198196 0.36038619 7572 86 86 0 691 22500 2979 1.0235277 0
2300 1.1087892 3969 0.00043721167 -1.0333612 0.06434007 0.39699935 7512 68 68 0 716 22500 3022 1.0515275 0
2400 1.0637949 3969 0.00033715078 -1.0035418 0.049615108 0.47092535 7508 82 82 0 742 22500 2997 1.0295291 0
2500 1.0345185 3969 0.00023374535 -0.98977538 0.034397966 0.57463578 7514 89 89 0 778 22500 2986 1.0252443 0
2600 1.1040438 3969 0.00024293233 -1.0572534 0.035749922 0.38043986 7543 82 82 0 811 22500 2995 1.0181075 0
2700 0.96252159 3969 -0.00081483156 -1.072807 -0.11991061 0.2771083 7555 97 97 0 842 22500 2990 1.0125575 0
2800 0.98730039 3969 -0.00037330307 -1.0323627 -0.05493528 0.57796755 7359 88 88 0 866 22500 2981 1.0187945 0
2900 1.056508 3969 0.0003868833 -0.98900914 0.056933747 0.63280739 7485 84 84 0 906 22500 3009 1.0260952 0
3000 0.97367876 3969 -0.0002599408 -1.0021949 -0.038252888 0.66404419 7424 99 99 0 951 22500 2998 1.0143644 0
3100 0.97186052 3969 -0.00084858744 -1.08702 -0.12487813 0.33835871 7502 88 88 0 983 22500 3016 1.0292976 0
3200 0.97992936 3969 -0.0006672966 -1.0683294 -0.098199368 0.45138198 7326 72 72 0 1026 22500 3005 1.023367 0
3300 0.96722828 3969 -0.00034604616 -1.0084802 -0.050924152 0.58525322 7383 70 70 0 1053 22500 2986 1.034213 0
3400 1.1202892 3969 0.00043227098 -1.0454733 0.063612998 0.43718189 7364 85 85 0 1087 22500 2995 1.0158362 0
3500 0.79750662 3969 -0.0014948003 -1.0095064 -0.21997481 0.41132937 7511 90 90 0 1116 22500 2993 1.0182386 0
3600 1.0491778 3969 -0.00010433247 -1.0540396 -0.015353567 0.42315074 7489 95 95 0 1144 22500 2999 1.020922 0
3700 0.9610381 3969 -0.00021690291 -0.98334715 -0.031919432 0.55752687 7496 80 80 0 1172 22500 3019 1.0303605 0
3800 0.76471906 3969 -0.0017426239 -1.0135164 -0.25644453 0.32180761 7518 89 89 0 1213 22500 3008 1.0419804 0
3900 1.086591 3969 0.00018698809 -1.0482079 0.027517167 0.26073092 7462 98 98 0 1246 22500 3005 1.0261112 0
4000 0.82619819 3969 -0.0014452395 -1.0306176 -0.21268144 0.14915039 7545 98 98 0 1287 22500 3008 1.0352711 0
4100 0.95064219 3969 -0.00053545528 -1.0199334 -0.0787976 0.39089361 7572 85 85 0 1318 22500 3001 1.0372179 0
4200 0.90370321 3969 -0.0007185822 -1.0004127 -0.10574656 0.47384816 7460 61 61 0 1355 22500 2998 1.012362 0
4300 0.97729216 3969 -0.00029144098 -1.0104077 -0.042888455 0.46030155 7533 70 70 0 1388 22500 3007 1.0223284 0
4400 1.0140429 3969 4.720814e-06 -1.0032078 0.00069471498 0.55984871 7501 88 88 0 1412 22500 2995 1.0285533 0
4500 1.0498677 3969 0.00022703142 -1.0059591 0.033409944 0.61932234 7461 82 82 0 1442 22500 2994 1.0292131 0
4600 0.90182406 3969 -0.00092157839 -1.0284253 -0.13561948 0.59198635 7499 73 73 0 1483 22500 3020 1.0159894 0
4700 1.0138009 3969 -0.00028404538 -1.045463 -0.041800118 0.53428422 7407 78 78 0 1507 22500 3011 1.0058816 0
4800 1.0506575 3969 -0.00043345499 -1.1039381 -0.063787236 0.30643257 7543 87 87 0 1524 22500 2995 1.0210242 0
4900 1.1479137 3969 -0.00019383126 -1.1649587 -0.028524208 0.28842185 7416 91 91 0 1557 22500 2988 1.0063463 0
5000 0.9092746 3969 -0.00087214131 -1.0285262 -0.12834432 0.76635862 7389 85 85 0 1589 22500 3000 1.0157079 0
Loop time of 0.858493 on 4 procs for 5000 steps with 14716 atoms
Pair time (%) = 0.0114868 (1.33802)
Neigh time (%) = 0.0539718 (6.28681)
Comm time (%) = 0.0641824 (7.47617)
Outpt time (%) = 0.00263882 (0.307378)
Other time (%) = 0.726213 (84.5916)
Nlocal: 3679 ave 4013 max 3459 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 48.25 ave 54 max 44 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 117 ave 136 max 87 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 468
Ave neighs/atom = 0.0318021
Neighbor list builds = 250
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
c4science · Help