Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/ASPHERE/line/log.line.srd.10Sep13
d9b19cf6ba16efficient_neuronet

Last Change
Raw File

log.line.srd.10Sep13
View Options

LAMMPS (9 Sep 2013)
# Aspherical shear demo - 2d line boxes, solvated by SRD particles
units lj
atom_style line
atom_modify first big
dimension 2
read_data data.line.srd
orthogonal box = (-28.7968 -28.7968 -0.5) to (28.7968 28.7968 0.5)
4 by 2 by 1 MPI processor grid
400 atoms
400 lines
# 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 INF INF INF INF -0.001 0.001
lattice sq 10.0
Lattice spacing in x,y,z = 0.316228 0.316228 0.316228
create_atoms 2 region plane
Created 33489 atoms
group big type 1
400 atoms in group big
group small type 2
33489 atoms in group small
set group small mass 0.01
33489 settings made for mass
# delete overlaps
# must set 1-2 cutoff to non-zero value
pair_style lj/cut 1.5
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
delete_atoms overlap 1.5 small big
Deleted 13605 atoms, new total = 20284
# SRD run
reset_timestep 0
velocity small create 1.44 87287 loop geom
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude molecule big include big
communicate multi group big vel yes
neigh_modify include big
# no pairwise interactions with small particles
pair_style line/lj 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
100 rigid bodies with 400 atoms
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
fix 3 all deform 1 x scale 0.35 y scale 0.35
fix 4 all enforce2d
# diagnostics
compute tsmall small temp/deform
compute tbig big temp
variable pebig equal pe*atoms/count(big)
variable ebig equal etotal*atoms/count(big)
compute 1 big erotate/asphere
compute 2 all ke
compute 3 all pe
variable toteng equal (c_1+c_2+c_3)/atoms
thermo 1000
thermo_style custom step temp c_tsmall f_2[9] c_1 etotal v_pebig v_ebig press
thermo_modify temp tbig
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
compute 10 big property/atom end1x end1y end2x end2y
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump1.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
run 10000
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385)
SRD info:
SRD/big particles = 19884 400
big particle diameter max/min = 1.99882 0.503306
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 230 230 1
SRD grid size: request, actual (xyz) = 0.25, 0.250407 0.250407 1
SRD per actual grid cell = 0.444963
SRD viscosity = 4.2356
big/SRD mass density ratio = 14.0918
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2737)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
# of rescaled SRD velocities = 0
ave/max small velocity = 15.906 29.1054
ave/max big velocity = 0 0
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76)
Memory usage per processor = 6.55683 Mbytes
Step Temp tsmall 2[9] 1 TotEng pebig ebig Press
0 0 1.4528554 0 0 0 0 0 0
1000 0 1.1122612 0.23295528 0.00058011072 0 0 0 0.32625408
2000 0 1.0254475 0.24958277 0.00072347646 -2.3144253e-06 -0.00011736451 -0.00011736451 0.44526308
3000 0 1.0089214 0.28044476 0.00061511441 -0.00023298189 -0.011814512 -0.011814512 0.87208025
4000 0 1.0066185 0.32869834 0.00079065587 -0.0021630643 -0.10968899 -0.10968899 1.3901494
5000 0 1.0109003 0.38401607 0.00071588732 -0.0040023493 -0.20295913 -0.20295913 1.2736445
6000 0 1.0195293 0.45846226 0.00086525328 -0.0068440002 -0.34705925 -0.34705925 2.6190768
7000 0 1.0093653 0.54708911 0.00088011006 -0.011012313 -0.55843441 -0.55843441 3.4171735
8000 0 1.0041894 0.65768809 0.0007998991 -0.01619324 -0.82115921 -0.82115921 6.9499615
9000 0 1.0148795 0.80396735 0.00093224535 -0.021747967 -1.1028394 -1.1028394 18.165751
10000 0 1.0377326 0.88469468 0.0039065571 0.011847093 0.60076606 0.60076606 105.95133
Loop time of 5.25724 on 8 procs for 10000 steps with 20284 atoms
Pair time (%) = 0.12938 (2.46098)
Neigh time (%) = 0.323687 (6.15698)
Comm time (%) = 0.201078 (3.82479)
Outpt time (%) = 0.00122145 (0.0232336)
Other time (%) = 4.60188 (87.534)
Nlocal: 2535.5 ave 2832 max 2244 min
Histogram: 2 0 0 1 1 2 0 0 0 2
Nghost: 113.375 ave 119 max 109 min
Histogram: 2 1 1 0 0 1 0 0 1 2
Neighs: 520.625 ave 640 max 388 min
Histogram: 2 0 1 0 0 1 0 2 1 1
Total # of neighbors = 4165
Ave neighs/atom = 0.205334
Neighbor list builds = 508
Dangerous builds = 0
#undump 1
#undump 2
unfix 3
change_box all triclinic
triclinic box = (-10.0789 -10.0789 -0.5) to (10.0789 10.0789 0.5) with tilt (0 0 0)
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
#dump 2 all custom 500 dump2.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
fix 3 all deform 1 xy erate 0.05 units box remap v
run 40000
SRD info:
SRD/big particles = 19884 400
big particle diameter max/min = 1.99882 0.503306
SRD temperature & lamda = 1 0.2
SRD max distance & max velocity = 0.8 40
SRD grid counts: 81 81 1
SRD grid size: request, actual (xyz) = 0.25, 0.248861 0.248861 1
SRD per actual grid cell = -11.3331
SRD viscosity = -1920.36
big/SRD mass density ratio = -0.546468
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2737)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2761)
# of rescaled SRD velocities = 5
ave/max small velocity = 12.7055 40
ave/max big velocity = 1.43831 4.07637
Memory usage per processor = 4.07906 Mbytes
Step Temp tsmall 2[9] 1 TotEng pebig ebig Press
10000 0 1.0285209 0 0.0039065571 0.012056063 0.61136294 0.61136294 70.259237
11000 0 1.0391738 0.9421875 0.00039699357 -0.034840076 -1.7667403 -1.7667403 51.907585
12000 0 1.038934 0.93340757 0.00033545803 -0.035181234 -1.7840404 -1.7840404 51.039479
13000 0 1.0363741 0.94084946 0.0004529039 -0.033018255 -1.6743557 -1.6743557 54.138717
14000 0 1.0373865 0.93242943 0.0004722244 -0.032766048 -1.6615663 -1.6615663 54.092833
15000 0 1.0289967 0.92957433 0.00041639952 -0.033696503 -1.7087497 -1.7087497 48.76136
16000 0 1.0315281 0.9336746 0.00044091467 -0.034047366 -1.7265419 -1.7265419 49.368354
17000 0 1.0310976 0.92846069 0.00058265838 -0.036251651 -1.8383212 -1.8383212 47.527648
18000 0 1.0387834 0.93270079 0.00064962838 -0.03849464 -1.9520632 -1.9520632 55.151324
19000 0 1.034225 0.94028857 0.00042052385 -0.037457059 -1.8994474 -1.8994474 47.746045
20000 0 1.0377609 0.93927936 0.0005218884 -0.034132243 -1.7308461 -1.7308461 87.048419
21000 0 1.0404827 0.93995585 0.00057654739 -0.0306282 -1.553156 -1.553156 57.122553
22000 0 1.0399735 0.93639576 0.00037285284 -0.026102398 -1.3236526 -1.3236526 59.315805
23000 0 1.0396421 0.93234579 0.00042714044 -0.024751467 -1.2551469 -1.2551469 78.461174
24000 0 1.0376317 0.93328901 0.00055283478 -0.0276932 -1.4043222 -1.4043222 61.533389
25000 0 1.0358692 0.93697479 0.0004225622 -0.026282283 -1.3327746 -1.3327746 62.554247
26000 0 1.0397631 0.9336746 0.00054058432 -0.024075759 -1.2208817 -1.2208817 64.975611
27000 0 1.0405916 0.94307316 0.0003904132 -0.028426222 -1.4414937 -1.4414937 55.128234
28000 0 1.037771 0.94115025 0.00038432308 -0.030313284 -1.5371866 -1.5371866 56.493375
29000 0 1.0395232 0.92801772 0.00038560341 -0.029991249 -1.5208562 -1.5208562 57.427874
30000 0 1.0354662 0.93958984 0.0004698422 -0.02938728 -1.490229 -1.490229 54.222732
31000 0 1.0384932 0.93606594 0.00041385391 -0.028759403 -1.4583893 -1.4583893 55.483372
32000 0 1.0387759 0.94189671 0.00049520206 -0.029553008 -1.498633 -1.498633 58.747733
33000 0 1.0378057 0.93424537 0.00052622477 -0.031085566 -1.576349 -1.576349 53.836967
34000 0 1.0372805 0.93826338 0.00054888869 -0.036504286 -1.8511323 -1.8511323 44.792497
35000 0 1.0382469 0.93704278 0.0004307863 -0.038148625 -1.9345168 -1.9345168 42.582442
36000 0 1.0380694 0.93714033 0.00039730159 -0.036405598 -1.8461279 -1.8461279 47.104593
37000 0 1.0402138 0.93799823 0.00051417836 -0.032909885 -1.6688603 -1.6688603 55.244687
38000 0 1.0384244 0.93708166 0.00043306898 -0.030288286 -1.535919 -1.535919 55.538198
39000 0 1.0410634 0.93284574 0.00053167091 -0.030864158 -1.5651214 -1.5651214 56.136389
40000 0 1.0434316 0.94540613 0.0004625865 -0.035063246 -1.7780572 -1.7780572 51.415561
41000 0 1.0369369 0.93512798 0.00048692231 -0.03501711 -1.7757177 -1.7757177 52.27068
42000 0 1.037407 0.9277082 0.00044677419 -0.035686429 -1.8096588 -1.8096588 47.812559
43000 0 1.0391707 0.93974302 0.00037562628 -0.034697463 -1.7595083 -1.7595083 60.19428
44000 0 1.0369685 0.93745842 0.00041027797 -0.035341149 -1.7921497 -1.7921497 52.091971
45000 0 1.036099 0.9321397 0.00042455475 -0.033947768 -1.7214913 -1.7214913 49.730151
46000 0 1.032015 0.9300885 0.00033912308 -0.032997968 -1.6733269 -1.6733269 56.703006
47000 0 1.0326688 0.9375833 0.00043809093 -0.034003679 -1.7243266 -1.7243266 53.212731
48000 0 1.0380837 0.94267232 0.00047529732 -0.033961575 -1.7221915 -1.7221915 48.821619
49000 0 1.0364529 0.93990652 0.00054656191 -0.031215986 -1.5829626 -1.5829626 55.420703
50000 0 1.0335509 0.93651862 0.00049456314 -0.03110686 -1.5774289 -1.5774289 56.656467
Loop time of 43.1064 on 8 procs for 40000 steps with 20284 atoms
Pair time (%) = 1.73269 (4.01956)
Neigh time (%) = 1.43244 (3.32304)
Comm time (%) = 1.08363 (2.51385)
Outpt time (%) = 0.00464779 (0.0107821)
Other time (%) = 38.853 (90.1328)
Nlocal: 2535.5 ave 2610 max 2448 min
Histogram: 2 0 1 0 0 1 1 1 0 2
Nghost: 114.875 ave 125 max 106 min
Histogram: 2 0 0 1 1 2 0 1 0 1
Neighs: 516.5 ave 599 max 465 min
Histogram: 3 0 0 1 1 1 1 0 0 1
Total # of neighbors = 4132
Ave neighs/atom = 0.203707
Neighbor list builds = 2002
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
c4science · Help