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lammps/examples/ASPHERE/star/log.star.mp.10Sep13
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log.star.mp.10Sep13
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LAMMPS (9 Sep 2013)
# SRD viscosity 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 0.0412866 on 8 procs for 1000 steps with 270 atoms
Pair time (%) = 0.00292179 (7.07684)
Neigh time (%) = 0.00114384 (2.77049)
Comm time (%) = 0.0121986 (29.5461)
Outpt time (%) = 0.000230491 (0.558271)
Other time (%) = 0.0247919 (60.0483)
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 small viscosity 10 x y 50
fix 4 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.mp
#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 1.3539178 8799 0.22973169 37.20861 37.429248 8.3072473 14385 67 67 0 702 57680 11236 8799 0.95931141 0 5 0
2000 1.2875571 8786 0.22962726 37.202411 37.412235 9.0311119 14352 63 63 0 1486 57680 11236 8786 0.95682025 0 5 0
3000 1.4635416 8800 0.22966317 37.179581 37.418084 7.6178929 14347 59 59 0 2196 57680 11236 8800 0.94729431 0 18 0
4000 1.8391551 8777 0.23015947 37.19923 37.498945 7.5387929 14212 56 56 0 2970 57680 11236 8777 0.94642004 0 18 0
5000 1.3981894 8787 0.22973225 37.201487 37.42934 10.658161 14071 73 73 0 3812 57680 11236 8787 0.93244985 0 18 0
6000 1.8148662 8786 0.2299516 37.169321 37.465077 10.11004 14154 56 56 0 4599 57680 11236 8786 0.93899702 0 18 0
7000 1.7370183 8781 0.22991739 37.176433 37.459503 7.2981594 14125 55 55 2 5380 57680 11236 8781 0.92819844 0 18 0
8000 1.9300809 8795 0.23020743 37.192227 37.506758 5.6733717 14193 51 51 0 6183 57680 11236 8795 0.92508922 0 18 0
9000 2.3407111 8779 0.23065831 37.19877 37.580219 10.534106 13966 79 79 0 7043 57680 11236 8779 0.93227329 0 18 0
10000 2.0762631 8753 0.23046098 37.209714 37.548068 6.6085525 13608 49 49 0 7866 57680 11236 8753 0.9277773 0 18 0
11000 2.5572041 8760 0.23079582 37.185893 37.602623 5.943323 14038 51 51 0 8706 57680 11236 8760 0.92846928 0 18 0
12000 3.2543217 8768 0.23146345 37.181063 37.711397 9.9600818 13725 58 58 0 9496 57680 11236 8768 0.92510656 0 18 0
13000 3.7220943 8755 0.23214107 37.215236 37.821799 5.2998459 13527 58 58 1 10369 57680 11236 8755 0.92701985 0 18 0
14000 3.1074163 8758 0.23124062 37.168698 37.675092 3.597723 13761 58 58 0 11200 57680 11236 8758 0.91892834 0 18 0
15000 4.1027548 8760 0.23230435 37.179805 37.848402 6.0772754 13862 51 51 0 12079 57680 11236 8760 0.92753237 0 18 0
16000 3.9133946 8792 0.23219659 37.193106 37.830844 4.7112711 13660 43 43 0 12960 57680 11236 8792 0.92647491 0 18 0
17000 4.0903593 8765 0.2323981 37.197098 37.863675 10.318145 13986 61 61 0 13879 57680 11236 8765 0.92733119 0 18 0
18000 3.969582 8737 0.23252501 37.237457 37.884352 6.0345677 13738 47 47 0 14857 57680 11236 8737 0.93210731 0 18 0
19000 4.9135942 8764 0.23344004 37.232701 38.033435 9.0068701 14001 46 47 0 15797 57680 11236 8764 0.92417719 0 18 0
20000 4.4990499 8726 0.23308081 37.241729 37.974907 3.4556204 14032 43 43 0 16823 57680 11236 8726 0.92968267 0 18 0
21000 3.6775519 8760 0.23209383 37.214798 37.814103 8.7361012 14249 51 51 0 17880 57680 11236 8760 0.91693857 0 18 0
22000 4.2480058 8760 0.23234702 37.163086 37.855353 9.4990008 13676 60 60 0 18840 57680 11236 8760 0.92912888 0 18 0
23000 4.0762282 8757 0.23194558 37.125675 37.789949 6.095072 13433 60 60 0 19854 57680 11236 8757 0.93403257 0 18 0
24000 3.7342162 8754 0.23149433 37.107889 37.716428 8.0963071 13528 45 45 0 20844 57680 11236 8754 0.92640554 0 18 0
25000 4.4320691 8738 0.23214598 37.100336 37.822599 2.6532327 13621 47 47 0 21927 57680 11236 8738 0.91696074 0 18 0
26000 4.739874 8795 0.2328463 37.164276 37.9367 6.0740527 13737 55 55 0 22931 57680 11236 8795 0.91601272 0 18 0
27000 4.158987 8759 0.23253846 37.208783 37.886544 7.8062033 13770 68 68 0 23891 57680 11236 8759 0.92761375 0 18 0
28000 4.5357507 8729 0.23252995 37.145997 37.885157 8.3229496 13735 62 62 0 24911 57680 11236 8729 0.91438776 0 18 0
29000 5.2763283 8757 0.23343081 37.172085 38.031931 11.607728 13345 56 56 0 25962 57680 11236 8757 0.92363255 0 18 0
30000 5.2012183 8727 0.23342066 37.182671 38.030276 7.0247835 13553 56 56 0 27017 57680 11236 8727 0.92161183 0 18 0
31000 4.5592454 8768 0.23267999 37.166615 37.909603 5.0184914 13886 58 58 0 28054 57680 11236 8768 0.92601626 0 18 0
32000 4.2038581 8767 0.23226731 37.157293 37.842366 7.7446627 13776 66 66 0 29191 57680 11236 8767 0.92081307 0 18 0
33000 3.4146018 8766 0.23184673 37.217389 37.773843 6.061227 13762 60 60 0 30282 57680 11236 8766 0.91467148 0 18 0
34000 4.9666166 8768 0.23362817 37.254711 38.064085 4.54391 13794 57 57 0 31277 57680 11236 8768 0.91500925 0 18 0
35000 5.4336125 8772 0.23410227 37.255851 38.141329 7.1441975 13991 54 54 0 32372 57680 11236 8772 0.91787825 0 18 0
36000 5.3731031 8775 0.23399853 37.24881 38.124427 10.645457 14200 61 61 0 33353 57680 11236 8775 0.9068932 0 18 0
37000 4.6930013 8756 0.23342164 37.265652 38.030437 1.6378965 13904 58 58 0 34474 57680 11236 8756 0.91857412 0 18 0
38000 4.6072618 8770 0.23383244 37.346553 38.097366 3.4294948 13897 52 52 0 35614 57680 11236 8770 0.93119652 0 18 0
39000 6.3083841 8755 0.23513182 37.281037 38.30907 9.545092 13877 71 72 0 36775 57680 11236 8755 0.90357387 0 18 0
40000 4.7439426 8760 0.23359501 37.285596 38.058683 5.2222395 13722 59 59 0 37862 57680 11236 8760 0.92609151 0 18 0
41000 5.631049 8746 0.23426434 37.250081 38.167734 7.8831121 13871 58 58 0 38995 57680 11236 8746 0.92364048 0 18 0
42000 4.4937786 8763 0.23315762 37.255102 37.987422 6.0814276 14059 56 56 0 40128 57680 11236 8763 0.90560182 0 18 0
43000 4.6349594 8738 0.23340275 37.272032 38.027359 6.4946772 13789 60 60 0 41304 57680 11236 8738 0.92056988 0 18 0
44000 4.9216105 8770 0.23378718 37.287952 38.089993 12.069456 14010 60 60 0 42438 57680 11236 8770 0.90919838 0 18 0
45000 6.1003723 8742 0.23518324 37.323312 38.317447 8.8564785 14012 51 51 0 43588 57680 11236 8742 0.91297931 0 18 0
46000 5.9976719 8739 0.23513128 37.331584 38.308982 10.332623 13865 61 61 0 44701 57680 11236 8739 0.91184414 0 18 0
47000 5.7529929 8750 0.2346755 37.297198 38.234722 9.1421763 13767 53 53 0 45947 57680 11236 8750 0.91644332 0 18 0
48000 6.0414916 8782 0.23481097 37.272255 38.256795 4.11784 14101 67 67 0 47098 57680 11236 8782 0.91322689 0 18 0
49000 5.9069569 8751 0.234598 37.259482 38.222097 6.2678445 13866 52 52 0 48288 57680 11236 8751 0.9146273 0 18 0
50000 5.3699426 8774 0.23420718 37.28332 38.158422 4.9995799 14096 57 57 0 49368 57680 11236 8774 0.91397612 0 18 0
51000 5.3951124 8767 0.23440907 37.312111 38.191314 7.0908474 13687 58 58 0 50615 57680 11236 8767 0.91626012 0 18 0
52000 5.0477469 8746 0.23402296 37.305812 38.128407 5.8280874 13914 56 56 1 51790 57680 11236 8746 0.91904159 0 18 0
53000 5.0027801 8755 0.23400414 37.310073 38.125341 10.739261 14129 57 57 0 52949 57680 11236 8755 0.92315612 0 18 0
54000 5.4679296 8761 0.23459667 37.330809 38.221879 6.8113028 13993 46 46 0 54120 57680 11236 8761 0.92267151 0 18 0
55000 5.8410648 8761 0.23461213 37.272522 38.224399 3.5247967 13976 71 71 0 55365 57680 11236 8761 0.91123977 0 18 0
56000 5.3206693 8766 0.23418385 37.287548 38.15462 5.6396887 14038 55 55 0 56521 57680 11236 8766 0.93368011 0 18 0
57000 4.9281952 8780 0.23366116 37.266348 38.069461 3.1285423 13969 56 56 0 57638 57680 11236 8780 0.92255818 0 18 0
58000 5.1613227 8756 0.23347937 37.198737 38.039842 7.6464505 13934 63 63 0 58773 57680 11236 8756 0.92220195 0 18 0
59000 5.1076252 8756 0.23352166 37.214379 38.046732 7.5306693 13817 62 62 0 59943 57680 11236 8756 0.92510594 0 18 0
60000 5.6556257 8746 0.23422971 37.240434 38.162092 2.9325607 13922 53 53 0 61090 57680 11236 8746 0.91834472 0 18 0
61000 5.5661669 8773 0.23411882 37.236947 38.144026 7.2514093 13945 49 49 0 62183 57680 11236 8773 0.90739365 0 18 0
62000 5.8495975 8753 0.23460373 37.269763 38.223031 7.0060167 13970 46 46 0 63299 57680 11236 8753 0.91634009 0 18 0
63000 6.6712653 8759 0.23570628 37.315495 38.402664 8.3394411 13579 50 50 0 64393 57680 11236 8759 0.91836652 0 18 0
64000 6.0479009 8746 0.23472337 37.256939 38.242522 4.8644232 13733 53 53 0 65627 57680 11236 8746 0.92355966 0 18 0
65000 6.3822214 8746 0.23478129 37.211894 38.25196 7.7582836 13738 49 49 1 66686 57680 11236 8746 0.92230762 0 18 0
66000 5.8364524 8749 0.23463571 37.277114 38.22824 9.5192708 13699 60 60 0 67818 57680 11236 8749 0.91792656 0 18 0
67000 5.9827412 8758 0.23439358 37.213826 38.188792 10.337844 13706 40 40 0 68985 57680 11236 8758 0.9224571 0 18 0
68000 5.7052083 8778 0.23427038 37.238981 38.168719 9.538817 14045 50 50 0 70137 57680 11236 8778 0.92678095 0 18 0
69000 6.1907575 8732 0.23509559 37.294303 38.303167 7.8570847 13753 63 63 0 71368 57680 11236 8732 0.92864702 0 18 0
70000 6.7558311 8741 0.23548884 37.266287 38.367237 8.165295 13734 48 48 0 72588 57680 11236 8741 0.92931286 0 18 0
71000 6.3006829 8768 0.23498477 37.258334 38.285112 6.6049258 13846 56 56 0 73691 57680 11236 8768 0.92696341 0 18 0
72000 7.2727152 8763 0.23598161 37.262339 38.447522 10.51197 13841 84 84 0 74864 57680 11236 8763 0.91909538 0 18 0
73000 6.2312628 8782 0.23498109 37.269046 38.284511 7.4903877 13965 75 75 0 76071 57680 11236 8782 0.91794598 0 18 0
74000 6.1722061 8727 0.23506951 37.293076 38.298917 4.3305249 13792 46 46 0 77240 57680 11236 8727 0.91814755 0 18 0
75000 7.378049 8773 0.23590581 37.232824 38.435173 6.3355081 13923 52 52 0 78535 57680 11236 8773 0.91995009 0 18 0
76000 7.812152 8740 0.23641193 37.244542 38.517633 8.9619859 13779 53 53 0 79829 57680 11236 8740 0.92788947 0 18 0
77000 7.2456022 8750 0.23586328 37.247479 38.428244 8.4006134 13766 58 58 0 81069 57680 11236 8750 0.92890367 0 18 0
78000 7.4885209 8762 0.2360823 37.243575 38.463927 4.8584808 13818 63 63 0 82265 57680 11236 8762 0.91978471 0 18 0
79000 6.768778 8758 0.23523283 37.222466 38.325526 9.2798759 13853 46 46 1 83493 57680 11236 8758 0.92133736 0 18 0
80000 6.2390912 8778 0.23501251 37.27289 38.28963 8.066911 13895 54 54 1 84665 57680 11236 8778 0.92327324 0 36 0
81000 7.2711702 8787 0.23608324 37.279149 38.46408 9.2144197 13806 65 66 0 85828 57680 11236 8787 0.92188232 0 36 0
82000 6.0206472 8744 0.2350438 37.313587 38.294729 9.3897281 13820 56 56 1 87015 57680 11236 8744 0.92698133 0 36 0
83000 5.8815517 8770 0.23423001 37.203666 38.162142 4.3928971 13962 52 52 0 88169 57680 11236 8770 0.9234476 0 36 0
84000 5.3127425 8753 0.23338022 37.157909 38.023689 6.2750977 13890 63 63 1 89381 57680 11236 8753 0.91831133 0 113 0
85000 6.4943314 8779 0.2346802 37.177153 38.235488 10.568493 14079 72 72 1 90614 57680 11236 8779 0.92206389 0 113 0
86000 6.7895778 8751 0.2350697 37.192498 38.298948 5.9925063 13835 77 77 0 91790 57680 11236 8751 0.91712004 0 113 0
87000 7.5845758 8746 0.23586106 37.191877 38.427882 5.7337473 13766 56 56 0 93001 57680 11236 8746 0.92432006 0 113 0
88000 6.9933387 8797 0.23528814 37.194883 38.334538 6.5123227 14127 64 64 1 94309 57680 11236 8797 0.92081946 0 113 0
89000 7.2164543 8789 0.23569422 37.224684 38.400699 7.3516314 13831 57 57 0 95527 57680 11236 8789 0.91778416 0 113 0
90000 6.3777786 8760 0.23511292 37.266649 38.305991 5.0520629 13961 55 55 0 96763 57680 11236 8760 0.9262025 0 113 0
91000 5.9805319 8742 0.23465699 37.257103 38.231708 8.0050839 13761 53 53 0 97921 57680 11236 8742 0.9261716 0 113 0
92000 6.4485837 8784 0.23547302 37.313779 38.36466 6.6770663 13723 39 39 0 99103 57680 11236 8784 0.9291658 0 113 0
93000 6.4434559 8749 0.23487177 37.216656 38.2667 5.7028222 13637 50 50 0 100312 57680 11236 8749 0.92621809 0 113 0
94000 6.1854322 8759 0.23477076 37.242246 38.250243 10.130767 14009 68 69 0 101529 57680 11236 8759 0.92239553 0 113 0
95000 5.242726 8764 0.23388878 37.252175 38.106545 10.741635 14033 58 58 0 102596 57680 11236 8764 0.91894338 0 113 0
96000 5.4946819 8770 0.23425506 37.270793 38.166223 2.1154106 13710 56 56 0 103697 57680 11236 8770 0.93225466 0 113 0
97000 6.253365 8759 0.23501257 37.270573 38.28964 9.0479264 13591 66 66 0 104831 57680 11236 8759 0.93238386 0 113 0
98000 6.1587546 8755 0.2348896 37.265956 38.269605 10.461501 13914 41 41 1 105983 57680 11236 8755 0.92076121 0 113 0
99000 5.5267342 8780 0.23419291 37.255444 38.156097 4.2845395 14016 58 58 0 107118 57680 11236 8780 0.9233616 0 113 0
100000 5.355333 8734 0.23420455 37.285273 38.157994 8.6683443 14028 58 58 1 108173 57680 11236 8734 0.92043276 0 113 0
Loop time of 41.1602 on 8 procs for 100000 steps with 43990 atoms
Pair time (%) = 0.416294 (1.0114)
Neigh time (%) = 2.09636 (5.09318)
Comm time (%) = 2.34013 (5.68543)
Outpt time (%) = 0.00730702 (0.0177526)
Other time (%) = 36.3001 (88.1922)
Nlocal: 5498.75 ave 6126 max 4805 min
Histogram: 1 0 2 0 0 1 1 1 1 1
Nghost: 54.375 ave 61 max 45 min
Histogram: 1 1 0 1 0 0 2 0 1 2
Neighs: 185.25 ave 270 max 112 min
Histogram: 1 0 2 1 1 1 0 0 1 1
Total # of neighbors = 1482
Ave neighs/atom = 0.0336895
Neighbor list builds = 5000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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