Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/examples/ASPHERE/star/log.star.10Sep13
d9b19cf6ba16lammm-devel

Last Change
Raw File

log.star.10Sep13
View Options

LAMMPS (9 Sep 2013)
# SRD diffusion demo - rigid star 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.star fix molprop NULL Molecules
orthogonal box = (-13.2934 -13.2934 -0.5) to (13.2934 13.2934 0.5)
4 by 2 by 1 MPI processor grid
270 atoms
set type 1 mass 1.0
270 settings made for mass
group big type 1
270 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
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 big rigid molecule
30 rigid bodies with 270 atoms
fix 2 all enforce2d
#dump 1 all atom 10 dump.star.equil
thermo 100
run 1000
Memory usage per processor = 2.64859 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0.24721146
100 0 3.291475 0 3.291475 0.69158089
200 0 4.6176595 0 4.6176595 0.71737945
300 0 7.0921814 0 7.0921814 1.2163497
400 0 8.3666709 0 8.3666709 0.50645957
500 0 10.630838 0 10.630838 0.72764487
600 0 12.42157 0 12.42157 1.0130599
700 0 14.349074 0 14.349074 0.74795509
800 0 16.464746 0 16.464746 1.054549
900 0 18.253108 0 18.253108 0.51551753
1000 0 20.699563 0 20.699563 1.8084662
Loop time of 0.0416153 on 8 procs for 1000 steps with 270 atoms
Pair time (%) = 0.0029633 (7.1207)
Neigh time (%) = 0.0011363 (2.73049)
Comm time (%) = 0.0124508 (29.9187)
Outpt time (%) = 0.000216633 (0.520561)
Other time (%) = 0.0248483 (59.7095)
Nlocal: 33.75 ave 42 max 22 min
Histogram: 1 0 1 0 0 2 0 1 1 2
Nghost: 23.375 ave 30 max 14 min
Histogram: 1 0 1 0 0 2 1 0 1 2
Neighs: 52.25 ave 69 max 27 min
Histogram: 1 0 1 0 1 0 1 1 1 2
Total # of neighbors = 418
Ave neighs/atom = 1.54815
Neighbor list builds = 176
Dangerous builds = 0
#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 60025 atoms
set type 2 mass 0.1
60025 settings made for mass
group small type 2
60025 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 16305 atoms, new total = 43990
# 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
30 rigid bodies with 270 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 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:438)
thermo 1000
#dump 1 all atom 1000 dump.star
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
run 100000
SRD info:
SRD/big particles = 43720 270
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: 106 106 1
SRD grid size: request, actual (xyz) = 0.25, 0.250819 0.250819 1
SRD per actual grid cell = 5.55866
SRD viscosity = 0.235582
big/SRD mass density ratio = 0.144099
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
# of rescaled SRD velocities = 0
ave/max small velocity = 4.19085 7.72582
ave/max big velocity = 2.20262 5.4168
Memory usage per processor = 7.45056 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 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
1000 1.0984098 8760 0.22959363 37.227755 37.406755 4.3729461 14167 62 62 0 669 57680 11236 8760 0.95903221 0 5 0
2000 1.0937022 8791 0.22965168 37.237979 37.416212 7.8592382 14199 47 47 0 1473 57680 11236 8791 0.95561013 0 5 0
3000 1.1301744 8765 0.2296652 37.234239 37.418416 5.3554554 14104 54 54 0 2227 57680 11236 8765 0.95555673 0 66 0
4000 1.2329006 8777 0.22959864 37.206654 37.407571 5.1494579 14604 63 64 0 2969 57680 11236 8777 0.94949717 0 66 0
5000 1.3436586 8795 0.22951427 37.174858 37.393824 4.9830237 14523 57 57 0 3769 57680 11236 8795 0.94626627 0 66 0
6000 0.96282041 8788 0.2292679 37.196781 37.353685 9.3973109 14421 62 62 0 4513 57680 11236 8788 0.95152148 0 66 0
7000 0.89525926 8774 0.22909802 37.180113 37.326007 8.4919264 14263 54 54 0 5313 57680 11236 8774 0.94362657 0 66 0
8000 1.3407703 8787 0.22948792 37.171035 37.389531 6.3302799 14065 49 50 0 6028 57680 11236 8787 0.94436375 0 66 0
9000 0.89298676 8784 0.22897425 37.160318 37.305842 13.249825 14496 65 65 0 6784 57680 11236 8784 0.94156932 0 66 0
10000 1.5075857 8760 0.22964883 37.170068 37.415749 7.706417 14096 59 59 0 7527 57680 11236 8760 0.94760815 0 66 0
11000 1.0507595 8786 0.22915291 37.163716 37.334951 8.0764539 14302 54 54 0 8226 57680 11236 8786 0.93676874 0 66 0
12000 1.3608191 8795 0.22938389 37.150819 37.372582 2.2906149 14425 51 51 0 8956 57680 11236 8795 0.94320409 0 66 0
13000 1.1201602 8776 0.22932315 37.180142 37.362687 10.481998 14229 55 55 0 9648 57680 11236 8776 0.9397721 0 66 0
14000 1.0716401 8784 0.22905315 37.144059 37.318697 10.138958 14141 62 62 0 10352 57680 11236 8784 0.93554357 0 66 0
15000 1.1025268 8756 0.22896359 37.124434 37.304105 7.6249828 14017 64 64 0 11073 57680 11236 8756 0.9430112 0 66 0
16000 1.2846996 8791 0.22918958 37.131566 37.340925 11.973123 14082 61 61 0 11827 57680 11236 8791 0.93833228 0 66 0
17000 1.1023602 8737 0.2290447 37.137676 37.31732 7.2599397 14077 70 70 0 12530 57680 11236 8737 0.94839589 0 66 0
18000 1.1254832 8791 0.22887219 37.105801 37.289213 7.7429889 14028 67 67 0 13240 57680 11236 8791 0.93873361 0 66 0
19000 1.0356983 8772 0.22904086 37.147914 37.316694 4.5522757 14010 66 66 0 13931 57680 11236 8772 0.93790841 0 66 0
20000 0.71316343 8764 0.22873892 37.151281 37.2675 10.416168 14258 60 60 0 14615 57680 11236 8764 0.95207188 0 66 0
21000 1.2373277 8776 0.22921948 37.144157 37.345796 4.5997765 14160 43 43 0 15364 57680 11236 8776 0.94242444 0 66 0
22000 1.0036835 8717 0.22912507 37.166851 37.330414 9.6600309 14147 49 49 0 16148 57680 11236 8717 0.94673443 0 66 0
23000 1.2216081 8747 0.22929851 37.159594 37.358671 7.9846293 13938 71 71 0 16835 57680 11236 8747 0.94804999 0 66 0
24000 1.0032568 8793 0.22911586 37.16542 37.328913 0.60601362 14202 73 73 1 17576 57680 11236 8793 0.9414152 0 66 0
25000 0.94965 8781 0.22909875 37.171368 37.326126 6.6584192 14261 59 59 0 18287 57680 11236 8781 0.93110924 0 66 0
26000 1.4038862 8770 0.22955552 37.171764 37.400545 6.9399909 14168 53 53 0 18961 57680 11236 8770 0.94165291 0 66 0
27000 1.0373393 8771 0.22927442 37.1857 37.354748 10.125555 13921 59 59 0 19684 57680 11236 8771 0.94374269 0 66 0
28000 1.0969388 8771 0.22909362 37.146529 37.32529 6.7985501 13965 58 58 0 20453 57680 11236 8771 0.94053206 0 66 0
29000 1.2684633 8750 0.22920667 37.136996 37.343709 9.8044908 14008 63 63 0 21157 57680 11236 8750 0.94469514 0 66 0
30000 1.0723854 8771 0.22897873 37.131813 37.306572 7.2792401 14057 58 58 0 21801 57680 11236 8771 0.92857754 0 66 0
31000 0.82971683 8763 0.22857114 37.104952 37.240165 7.7873396 13798 55 55 1 22447 57680 11236 8763 0.93260855 0 66 0
32000 1.1854057 8768 0.22894391 37.107721 37.300898 4.2769411 13933 61 62 0 23177 57680 11236 8768 0.94159224 0 66 0
33000 1.0436865 8772 0.22886047 37.117222 37.287304 6.2761906 13923 54 54 0 23961 57680 11236 8772 0.93663695 0 66 0
34000 1.2387476 8768 0.229117 37.12723 37.3291 11.376966 14008 55 56 0 24671 57680 11236 8768 0.94134637 0 66 0
35000 1.1827221 8777 0.22892611 37.105258 37.297998 2.5334458 14032 46 46 0 25359 57680 11236 8777 0.94278115 0 66 0
36000 1.0401004 8786 0.22881254 37.109997 37.279495 10.60278 14096 59 59 0 26064 57680 11236 8786 0.93296672 0 66 0
37000 1.0984228 8766 0.22869539 37.081405 37.260407 6.8054601 13808 69 69 0 26726 57680 11236 8766 0.93400815 0 66 0
38000 1.0364646 8774 0.22857543 37.071959 37.240864 7.1036604 13800 63 63 0 27340 57680 11236 8774 0.93085761 0 66 0
39000 0.81230064 8747 0.22852596 37.100428 37.232803 3.2521293 13917 52 52 0 28006 57680 11236 8747 0.92853969 0 66 0
40000 1.1721059 8805 0.2288046 37.087192 37.278202 3.0925306 14118 65 65 0 28641 57680 11236 8805 0.93248575 0 66 0
41000 1.3273673 8777 0.22903004 37.098619 37.314931 4.5511385 13847 60 60 0 29306 57680 11236 8777 0.93520024 0 66 0
42000 1.1052507 8745 0.22888354 37.110948 37.291063 9.2630606 13743 55 55 0 29968 57680 11236 8745 0.93879074 0 66 0
43000 0.98143573 8767 0.22866451 37.095439 37.255377 10.836032 14161 50 50 1 30636 57680 11236 8767 0.94242574 0 66 0
44000 1.3073559 8766 0.22888363 37.078026 37.291077 7.1037959 13988 64 64 0 31356 57680 11236 8766 0.93251181 0 66 0
45000 1.1193942 8794 0.22872075 37.082121 37.264541 10.640442 14106 64 64 0 32030 57680 11236 8794 0.92767399 0 66 0
46000 0.97836443 8770 0.22871232 37.10373 37.263167 7.1768889 13999 46 46 0 32724 57680 11236 8770 0.92348771 0 66 0
47000 0.87384342 8766 0.22838593 37.067584 37.209988 8.2743957 13966 59 59 1 33415 57680 11236 8766 0.94605663 0 66 0
48000 1.1247625 8737 0.22881404 37.096444 37.279739 7.4933665 13890 58 58 0 34188 57680 11236 8737 0.94564485 0 66 0
49000 0.97549128 8760 0.22903868 37.15737 37.316339 9.212114 13731 61 61 3 35188 57680 11236 8760 0.94181244 0 264 0
50000 0.84795594 8792 0.22864062 37.113299 37.251484 4.554655 14066 45 45 0 35891 57680 11236 8792 0.9394553 0 264 0
51000 1.2748335 8793 0.22896977 37.097361 37.305111 9.6671568 13935 65 65 0 36612 57680 11236 8793 0.93487065 0 264 0
52000 1.0805373 8810 0.2285793 37.065407 37.241495 6.8776416 13980 67 67 0 37272 57680 11236 8810 0.9367572 0 264 0
53000 1.130649 8761 0.22862734 37.065067 37.249321 2.7290713 13926 49 49 0 37929 57680 11236 8761 0.93655185 0 264 0
54000 1.0591847 8785 0.22882065 37.108209 37.280816 6.3873447 13895 50 50 0 38580 57680 11236 8785 0.93515717 0 264 0
55000 1.0652496 8787 0.22845918 37.048328 37.221924 8.4260372 13975 45 45 0 39233 57680 11236 8787 0.94125089 0 264 0
56000 0.98336412 8817 0.22838409 37.049438 37.20969 5.2198817 14164 53 53 0 39880 57680 11236 8817 0.93411507 0 264 0
57000 0.75643143 8772 0.22818592 37.054132 37.177402 6.3608331 13531 46 46 0 40586 57680 11236 8772 0.93676316 0 264 0
58000 0.96052993 8787 0.22863449 37.093956 37.250486 5.3118075 13591 69 69 0 41316 57680 11236 8787 0.94694416 0 264 0
59000 1.192266 8791 0.22843725 37.024055 37.21835 8.4075315 13670 69 69 0 42042 57680 11236 8791 0.93074428 0 264 0
60000 0.86528129 8763 0.22838246 37.068415 37.209423 12.614127 13944 56 56 0 42742 57680 11236 8763 0.93980863 0 264 0
61000 0.98392057 8781 0.22850911 37.069716 37.230059 4.1196257 13833 55 55 0 43466 57680 11236 8781 0.94055519 0 264 0
62000 0.86377638 8769 0.22825891 37.048531 37.189294 7.5952438 13732 55 55 0 44157 57680 11236 8769 0.93273238 0 264 0
63000 1.1345544 8753 0.2285473 37.05139 37.23628 8.4944082 13829 39 39 1 44853 57680 11236 8753 0.93637828 0 264 0
64000 1.3052001 8761 0.22872188 37.052025 37.264725 8.1141027 13693 56 56 0 45476 57680 11236 8761 0.92802715 0 264 0
65000 0.96041617 8760 0.22837135 37.051102 37.207614 8.9305096 13696 47 47 0 46161 57680 11236 8760 0.93690077 0 264 0
66000 1.2667968 8773 0.22874931 37.062752 37.269193 7.0070038 13795 53 53 0 46873 57680 11236 8773 0.93548723 0 264 0
67000 1.1041556 8805 0.22867835 37.077695 37.257632 10.315126 13719 53 53 0 47611 57680 11236 8805 0.93398934 0 264 0
68000 1.0634591 8756 0.22833079 37.027701 37.201005 11.004387 13805 52 52 0 48261 57680 11236 8756 0.93907878 0 264 0
69000 1.0634356 8759 0.22836391 37.033101 37.206402 7.8960556 13846 60 60 0 48930 57680 11236 8759 0.9387394 0 264 0
70000 0.78705939 8797 0.22815713 37.044451 37.172712 5.2268623 13886 55 55 1 49637 57680 11236 8797 0.94420106 0 264 0
71000 1.262646 8796 0.22836767 37.001249 37.207013 4.2192091 13984 55 55 0 50380 57680 11236 8796 0.93354313 0 264 0
72000 0.89288469 8767 0.22793751 36.991423 37.13693 7.5274353 13402 48 48 0 51044 57680 11236 8767 0.93651002 0 264 0
73000 0.99805643 8785 0.22794231 36.975066 37.137712 8.1692078 13647 61 61 0 51713 57680 11236 8785 0.92710476 0 264 0
74000 1.1316546 8797 0.22823421 37.000852 37.18527 8.475577 13702 70 70 0 52408 57680 11236 8797 0.93300949 0 264 0
75000 1.3589973 8782 0.22842134 36.994292 37.215758 5.4899759 13846 62 62 0 53038 57680 11236 8782 0.92968164 0 264 0
76000 0.98311155 8765 0.22810013 37.003215 37.163426 5.8491632 13396 50 50 0 53737 57680 11236 8765 0.9332015 0 264 0
77000 0.93588923 8768 0.22812976 37.015736 37.168252 6.1482719 13419 41 41 0 54440 57680 11236 8768 0.94649087 0 264 0
78000 1.0726273 8763 0.22814803 36.996431 37.171229 3.7413229 13652 53 53 0 55122 57680 11236 8763 0.93732834 0 264 0
79000 1.1142622 8747 0.22823701 37.004143 37.185727 5.3431863 13752 52 52 0 55788 57680 11236 8747 0.94102654 0 264 0
80000 1.1877489 8777 0.22804997 36.961694 37.155253 7.5892699 13821 65 65 1 56474 57680 11236 8777 0.9388659 0 264 0
81000 1.5174205 8789 0.22848952 36.979583 37.226866 8.2338826 13400 58 58 0 57138 57680 11236 8789 0.93859931 0 264 0
82000 1.011418 8763 0.22816534 37.009225 37.174048 5.9285277 13389 53 53 0 57882 57680 11236 8763 0.94017606 0 264 0
83000 1.048045 8774 0.22802349 36.980145 37.150938 1.7682458 13617 62 62 0 58587 57680 11236 8774 0.93181775 0 264 0
84000 1.0416932 8791 0.22815029 37.00184 37.171598 1.6650384 13546 60 60 0 59277 57680 11236 8791 0.93336422 0 264 0
85000 0.9808074 8785 0.22805209 36.995762 37.155597 5.3853011 13847 58 58 0 59941 57680 11236 8785 0.93675898 0 264 0
86000 0.94845236 8741 0.22819508 37.024332 37.178894 9.0236195 13483 53 53 0 60569 57680 11236 8741 0.94106832 0 264 0
87000 0.91367557 8761 0.22814468 37.021789 37.170684 2.0373865 13627 46 46 0 61240 57680 11236 8761 0.93526035 0 264 0
88000 1.1199914 8786 0.22824582 37.004644 37.187161 12.508533 13835 61 61 0 61903 57680 11236 8786 0.93075967 0 264 0
89000 1.1170348 8766 0.2282638 37.008056 37.190092 3.3612922 13599 53 53 0 62539 57680 11236 8766 0.93937123 0 264 0
90000 0.80168936 8787 0.22787344 36.995845 37.126491 5.447793 14009 70 70 0 63231 57680 11236 8787 0.92972768 0 264 0
91000 0.9278704 8748 0.22800786 36.997183 37.148392 6.9490954 13577 51 51 0 63973 57680 11236 8748 0.93217751 0 264 0
92000 0.89936733 8761 0.22813535 37.0226 37.169164 2.7999912 13491 55 55 0 64685 57680 11236 8761 0.93392714 0 264 0
93000 0.97509746 8750 0.22824406 37.027971 37.186875 7.5849958 13569 62 62 0 65443 57680 11236 8750 0.94168102 0 264 0
94000 1.1704849 8741 0.22814395 36.979819 37.170565 7.3998451 13706 71 71 0 66141 57680 11236 8741 0.94474366 0 264 0
95000 0.82884583 8779 0.22780742 36.980663 37.115734 4.1939749 13606 60 60 0 66881 57680 11236 8779 0.93030745 0 264 0
96000 1.1004846 8783 0.22820868 37.001772 37.18111 9.7475128 13650 50 50 0 67644 57680 11236 8783 0.93134822 0 264 0
97000 0.88396347 8767 0.22799895 37.002887 37.146941 1.417848 13564 54 54 0 68384 57680 11236 8767 0.93526241 0 264 0
98000 1.0540322 8782 0.22821568 37.010483 37.182251 6.0103183 13539 51 51 0 69056 57680 11236 8782 0.94045268 0 264 0
99000 0.87480326 8776 0.22814014 37.027383 37.169944 9.727466 13663 45 45 0 69714 57680 11236 8776 0.92949266 0 264 0
100000 1.0188288 8799 0.22832221 37.033577 37.199608 5.6127459 13731 57 57 1 70429 57680 11236 8799 0.92271662 0 264 0
Loop time of 40.6233 on 8 procs for 100000 steps with 43990 atoms
Pair time (%) = 0.442836 (1.0901)
Neigh time (%) = 2.10093 (5.17173)
Comm time (%) = 2.34834 (5.78077)
Outpt time (%) = 0.00742877 (0.0182869)
Other time (%) = 35.7238 (87.9391)
Nlocal: 5498.75 ave 6220 max 4960 min
Histogram: 1 1 2 0 0 2 1 0 0 1
Nghost: 57.25 ave 82 max 41 min
Histogram: 1 1 1 1 2 1 0 0 0 1
Neighs: 214.5 ave 270 max 148 min
Histogram: 1 0 1 0 2 1 0 1 1 1
Total # of neighbors = 1716
Ave neighs/atom = 0.0390089
Neighbor list builds = 5001
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
c4science · Help