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lammps/examples/ASPHERE/line/log.line.srd.1Feb14
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LAMMPS (1 Feb 2014)
# 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
reading atoms ...
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:439)
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:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
# 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 = 7.79007 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 1.1071958 0.00058011072 0 0 0 0.32625408
2000 0 1.0254475 1.0231236 0.00072347646 -2.3144253e-06 -0.00011736451 -0.00011736451 0.44526308
3000 0 1.0089214 0.99966408 0.00061511441 -0.00023298189 -0.011814512 -0.011814512 0.87208025
4000 0 1.0066185 0.99391102 0.00079065587 -0.0021630644 -0.10968899 -0.10968899 1.3901494
5000 0 1.0109003 1.0009124 0.00071588733 -0.0040023493 -0.20295913 -0.20295913 1.2736445
6000 0 1.0119642 1.0105049 0.00080741361 -0.0067908165 -0.34436231 -0.34436231 2.5492857
7000 0 1.0048989 0.98912274 0.00098851463 -0.010933999 -0.55446309 -0.55446309 3.5707613
8000 0 1.0021597 0.99377939 0.0008405671 -0.015690841 -0.79568252 -0.79568252 6.685381
9000 0 1.0197546 1.00114 0.0012645557 -0.021124602 -1.0712286 -1.0712286 18.907993
10000 0 1.0401079 1.0184189 0.0036111452 0.0099395852 0.50403637 0.50403637 96.909257
Loop time of 3.93391 on 8 procs for 10000 steps with 20284 atoms
Pair time (%) = 0.110261 (2.80284)
Neigh time (%) = 0.32853 (8.35124)
Comm time (%) = 0.199613 (5.07416)
Outpt time (%) = 0.00108692 (0.0276295)
Other time (%) = 3.29442 (83.7441)
Nlocal: 2535.5 ave 2850 max 2226 min
Histogram: 1 0 1 1 1 1 1 0 1 1
Nghost: 109.25 ave 117 max 102 min
Histogram: 1 0 2 0 1 1 1 1 0 1
Neighs: 526 ave 665 max 407 min
Histogram: 1 2 0 1 0 1 1 1 0 1
Total # of neighbors = 4208
Ave neighs/atom = 0.207454
Neighbor list builds = 522
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:2853)
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875)
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2877)
# of rescaled SRD velocities = 1
ave/max small velocity = 12.724 40
ave/max big velocity = 1.54523 5.36901
Memory usage per processor = 4.23847 Mbytes
Step Temp tsmall 2[9] 1 TotEng pebig ebig Press
10000 0 1.0277413 0 0.0036111452 0.010135973 0.51399517 0.51399517 60.794865
11000 0 1.0024742 1 0.00040482851 -0.031643325 -1.604633 -1.604633 55.531632
12000 0 1.0036177 1 0.00036416993 -0.030844063 -1.5641024 -1.5641024 56.694788
13000 0 1.0043067 1 0.00068862721 -0.030673787 -1.5554677 -1.5554677 56.852537
14000 0 1.0042533 1 0.00050997053 -0.035967153 -1.8238943 -1.8238943 51.254109
15000 0 1.003956 1 0.00048458218 -0.038060147 -1.9300301 -1.9300301 50.346943
16000 0 1.0059929 1 0.0004740426 -0.037433402 -1.8982478 -1.8982478 49.82532
17000 0 1.0042401 1 0.00039855238 -0.034314446 -1.7400855 -1.7400855 48.430648
18000 0 1.0025952 1 0.00046207703 -0.034166102 -1.732563 -1.732563 53.883613
19000 0 1.0025881 1 0.00034818943 -0.037341367 -1.8935807 -1.8935807 48.90662
20000 0 1.0009932 1 0.00031244041 -0.035274728 -1.7887814 -1.7887814 47.665935
21000 0 1.0025603 1 0.0005514826 -0.034350221 -1.7418997 -1.7418997 63.290704
22000 0 1.0038575 1 0.00034453716 -0.03576596 -1.8136918 -1.8136918 49.805726
23000 0 1.0030321 1 0.00049535709 -0.035873083 -1.819124 -1.819124 48.973244
24000 0 1.0048593 1 0.00034225992 -0.03322158 -1.6846663 -1.6846663 52.557383
25000 0 1.0024423 1 0.00059157362 -0.030152319 -1.5290241 -1.5290241 56.733821
26000 0 1.0022703 1 0.00047512976 -0.029563064 -1.499143 -1.499143 56.271943
27000 0 1.0024537 1 0.00054158319 -0.02957039 -1.4995145 -1.4995145 55.246787
28000 0 1.0023325 1 0.00051129428 -0.035115211 -1.7806924 -1.7806924 49.718172
29000 0 1.002865 1 0.00056728135 -0.035484703 -1.7994293 -1.7994293 48.387401
30000 0 1.0022693 1 0.00040284402 -0.033844303 -1.7162446 -1.7162446 50.486676
31000 0 1.0037106 1 0.00056291948 -0.036529699 -1.852421 -1.852421 52.011803
32000 0 1.0022542 1 0.00041877447 -0.036903458 -1.8713743 -1.8713743 52.712289
33000 0 1.0021364 1 0.00040871451 -0.033616728 -1.7047043 -1.7047043 55.199593
34000 0 1.003779 1 0.00040667148 -0.031745412 -1.6098098 -1.6098098 51.055261
35000 0 1.0015547 1 0.00042509365 -0.033603064 -1.7040114 -1.7040114 53.887389
36000 0 1.0024849 1 0.00040589851 -0.032151258 -1.6303903 -1.6303903 55.673615
37000 0 1.0038204 1 0.00040542177 -0.033643242 -1.7060488 -1.7060488 51.834694
38000 0 1.0031777 1 0.00040237126 -0.034711811 -1.7602359 -1.7602359 56.275778
39000 0 1.002777 1 0.00051021239 -0.034375104 -1.7431615 -1.7431615 48.461145
40000 0 1.0053762 1 0.00041566465 -0.036016384 -1.8263908 -1.8263908 48.937456
41000 0 1.0039078 1 0.00049726673 -0.036481888 -1.8499966 -1.8499966 49.290465
42000 0 1.0033408 1 0.00045236191 -0.034254524 -1.7370469 -1.7370469 52.146603
43000 0 1.0039893 1 0.00048362351 -0.032519474 -1.6490625 -1.6490625 53.320599
44000 0 1.0036667 1 0.00046834006 -0.031099875 -1.5770747 -1.5770747 55.907531
45000 0 1.0035765 1 0.0005195031 -0.029559708 -1.4989728 -1.4989728 56.191165
46000 0 1.004514 1 0.00050134348 -0.028852909 -1.463131 -1.463131 57.547696
47000 0 1.003864 1 0.00038963389 -0.031339229 -1.5892123 -1.5892123 55.775764
48000 0 1.003145 1 0.00035436452 -0.032390682 -1.6425315 -1.6425315 55.233354
49000 0 1.0042615 1 0.00053161075 -0.029960468 -1.5192953 -1.5192953 54.611685
50000 0 1.0037096 1 0.00031191389 -0.02942011 -1.4918938 -1.4918938 58.653762
Loop time of 27.1275 on 8 procs for 40000 steps with 20284 atoms
Pair time (%) = 1.54277 (5.68709)
Neigh time (%) = 1.26864 (4.67658)
Comm time (%) = 1.19871 (4.4188)
Outpt time (%) = 0.00421953 (0.0155544)
Other time (%) = 23.1132 (85.202)
Nlocal: 2535.5 ave 2670 max 2406 min
Histogram: 1 1 1 0 0 2 1 1 0 1
Nghost: 114.5 ave 124 max 103 min
Histogram: 1 0 1 0 2 1 0 1 0 2
Neighs: 521.5 ave 692 max 442 min
Histogram: 3 1 1 1 0 0 0 1 0 1
Total # of neighbors = 4172
Ave neighs/atom = 0.205679
Neighbor list builds = 2002
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
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