jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10989 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-11-07 20:05:59 +00:00
parent cf04ab3943
commit 5c97843367
26 changed files with 235737 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

108
examples/USER/lb/confined_colloid/in.confined_colloids Executable file
View File

@ -0,0 +1,108 @@
#===========================================================================#
# System of colloidal particles under shear. #
# #
# Run consists of 10x12x4 particles, each composed of 3613 particle nodes #
# (3612 particles forming a spherical shell, and 1 central particle). #
# 280 x 280 x 101 lattice-Boltzmann grid sites. #
# #
# This simulation is used to illustrate the simulation time of a realistic #
# implementation of the lb_fluid fix. #
# The data file "confinedcolloids.dat" is quite large and so is not #
# included here. It can be obtained from: #
# http://www.apmaths.uwo.ca/~cdennist/confinedcolloids.dat.gz #
# #
# Sample output from this run can be found in the file: #
# results64.out #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style molecular
read_data confinedcolloids.dat
mass * 0.00010287
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 0.03 bin
neigh_modify delay 0 every 1
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each colloidal object which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
#----------------------------------------------------------------------------
group ForceAtoms type 1
#----------------------------------------------------------------------------
# FluidAtoms are the particles representing the surface of the colloidal
# object which do interact with the fluid.
#----------------------------------------------------------------------------
group FluidAtoms type 2
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each colloidal object (use a truncated and shifted Lennard-Jones
# potential).
#----------------------------------------------------------------------------
pair_style lj/cut 1.572
pair_coeff * * 0.0 0.0 1.572
pair_coeff 1 1 10.0 1.400492785 1.572
pair_modify shift yes
timestep 0.0006
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the viscous_lb fix).
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=0.06, and mass unit, dm=0.00003.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation makes use of the surface area
# of the composite object represented by each particle node. Since this is
# not equal to dx*dx, it is input through the setArea keyword (i.e.
# particles of type 2 correspond to a surface area of 0.0018337299).
# Implement walls moving at speeds of 20.0 in opposite directions.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 1 1.0 1.0 dx 0.06 dm 0.00003 setArea 2 0.0018337299 zwall_velocity -20.0 20.0
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the FluidAtoms particles (again,
# these atoms represent the surface of the colloidal object, which should
# interact with the fluid).
#----------------------------------------------------------------------------
fix 2 FluidAtoms lb/viscous
#----------------------------------------------------------------------------
# Each colloidal object (spherical shell of particles and central particle)
# is specified as a separate molecule in the confinedcolloids.dat data
# file. Integrate the motion of each of these sets of particles as rigid
# objects which move and rotate together.
#----------------------------------------------------------------------------
fix 3 all rigid molecule
#----------------------------------------------------------------------------
# Implement a repulsive interaction between the ForceAtoms particles, and the
# upper and lower z-walls. (A truncated and shifted Lennard-Jones potential
# is used).
#----------------------------------------------------------------------------
fix wallhi ForceAtoms wall/lj126 zhi 5.88 20.0 0.8071542386 0.906 units box
fix walllo ForceAtoms wall/lj126 zlo 0.0 20.0 0.8071542386 0.906 units box
#dump ParticleTracking ForceAtoms custom 50 test.track id mol x y z vx vy vz
run 400

41
examples/USER/lb/confined_colloid/results64.out Executable file
View File

@ -0,0 +1,41 @@
LAMMPS (22 Feb 2013)
Scanning data file ...
Reading data file ...
orthogonal box = (0 0 0) to (16.8 16.8 6)
4 by 8 by 2 MPI processor grid
1734240 atoms
Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
480 atoms in group ForceAtoms
1733760 atoms in group FluidAtoms
Using a lattice-Boltzmann grid of 280 by 280 by 101 total grid points. (fix_lb_fluid.cpp:341)
480 rigid bodies with 1734240 atoms
Setting up run ...
Memory usage per processor = 79.5765 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0
400 65143387 608.21941 0 1902.0097 4.5858406
Loop time of 503.932 on 64 procs for 400 steps with 1734240 atoms
Pair time (%) = 0.151149 (0.0299939)
Bond time (%) = 0.000111468 (2.21197e-05)
Neigh time (%) = 308.546 (61.2278)
Comm time (%) = 88.6413 (17.5899)
Outpt time (%) = 0.00124746 (0.000247546)
Other time (%) = 106.592 (21.152)
Nlocal: 27097.5 ave 27415 max 26825 min
Histogram: 8 0 12 12 8 0 8 4 8 4
Nghost: 159582 ave 161567 max 158145 min
Histogram: 32 0 0 0 0 4 12 0 0 16
Neighs: 3.75 ave 6 max 2 min
Histogram: 16 0 16 0 0 16 0 0 0 16
Total # of neighbors = 240
Ave neighs/atom = 0.000138389
Ave special neighs/atom = 0
Neighbor list builds = 68
Dangerous builds = 0

330
examples/USER/lb/dragforce/data.one_radius16d2 Executable file
View File

@ -0,0 +1,330 @@
Position data for rigid sphere
320 atoms
1 atom types
-160.0 160.0 xlo xhi
-160.0 160.0 ylo yhi
-160.0 160.0 zlo zhi
Atoms
1 1 0.0256796 -15.8876046 3.1659732
2 1 -0.0065539 -9.7285354 12.9535934
3 1 15.1406371 -4.8466739 3.1162295
4 1 9.3951884 -12.8727816 -2.9089440
5 1 14.4184503 -7.2812703 -1.2375049
6 1 12.9636755 -9.3139592 -2.7628439
7 1 14.3780078 -7.2818634 1.6393238
8 1 12.8903958 -9.3502145 2.9750983
9 1 12.2367531 -8.9637467 5.6879825
10 1 10.3382023 -10.5487465 6.6547385
11 1 11.4527893 -11.3685971 -1.4243042
12 1 11.4327788 -11.3846531 1.4564573
13 1 9.4216981 -12.8838973 2.7707077
14 1 9.0417300 -12.3516471 5.3032025
15 1 4.9205584 -15.1900605 -2.7368211
16 1 2.5481336 -15.9533355 -1.1992196
17 1 7.3427635 -14.3712624 -1.4109098
18 1 7.3764066 -14.3481077 1.4698484
19 1 2.5722631 -15.9062191 1.6779995
20 1 5.0013810 -15.1135985 3.0008920
21 1 4.8441349 -14.3648217 5.7119418
22 1 6.9359013 -13.0346534 6.6656665
23 1 -2.4554485 -14.2783985 7.2483193
24 1 -2.4559375 -12.7204259 9.7262100
25 1 0.0193595 -15.0501989 5.9942607
26 1 2.4878886 -14.2677016 7.2583143
27 1 0.0067480 -11.9153251 10.9756552
28 1 2.4800580 -12.7078927 9.7364676
29 1 4.8222915 -11.3485960 10.5068976
30 1 6.9005138 -11.6360921 8.9120310
31 1 2.4839865 -5.8135494 14.9155114
32 1 4.8472826 -4.0868468 14.9077684
33 1 2.5299584 -8.3862632 13.6275429
34 1 4.9695889 -9.2262534 12.3539249
35 1 12.9092381 -1.4901082 9.6732194
36 1 14.3807969 -1.9808593 7.1908902
37 1 14.3572494 -4.5759518 5.9472750
38 1 12.8674198 -6.6841240 7.2244043
39 1 11.3990899 -3.5900514 10.9367410
40 1 11.3956647 -6.1931435 9.7068958
41 1 9.3917619 -8.0099376 10.4916983
42 1 9.0260982 -10.0834728 8.9046702
43 1 9.3270143 -2.9086132 12.9223372
44 1 7.2796368 -4.9160264 13.6117448
45 1 7.3330855 -7.4994968 12.3459883
46 1 14.6303758 -4.7441678 -5.0877304
47 1 13.3165082 -6.5796622 -6.4667363
48 1 12.4142121 -8.8458738 -5.4843304
49 1 15.2266664 -4.9164661 -2.5331831
50 1 15.9543648 -2.5065880 -1.2709382
51 1 2.1937994 -14.7058789 -6.4315158
52 1 0.0524420 -15.3953996 -5.0417205
53 1 0.0450846 -16.0082576 -2.4846893
54 1 4.6305782 -14.5324426 -5.4594764
55 1 6.4781630 -13.0859896 -7.0164310
56 1 13.2500173 3.0334672 8.8133502
57 1 14.5793859 2.5897758 6.5707377
58 1 15.1906868 0.2145539 5.6246801
59 1 12.3450280 1.1640407 10.4252251
60 1 10.3843754 1.9758295 12.2760283
61 1 2.0980481 -0.5590157 16.0538382
62 1 -0.0373101 -2.1192280 16.0607442
63 1 -0.0289491 -4.6890599 15.5065117
64 1 4.5417074 -1.3494889 15.4916687
65 1 -2.5322491 -5.8277372 14.9018529
66 1 -6.8897824 -11.6914960 8.8475897
67 1 -6.8851099 -13.0720100 6.6451365
68 1 -4.8240131 -14.3759856 5.7008737
69 1 -4.8165626 -11.3787988 10.4768167
70 1 -4.9530402 -15.1344151 2.9760537
71 1 15.9340934 -2.4420318 1.6066033
72 1 15.9359147 0.1231686 2.9105799
73 1 8.9220667 -12.2374060 -5.7517515
74 1 10.4680949 -10.1710530 -7.0291318
75 1 -2.5113228 -15.9172575 1.6655921
76 1 -2.4662206 -15.9651661 -1.2129514
77 1 -2.5565800 -8.4010108 13.6134838
78 1 -4.9864191 -9.2555630 12.3251857
79 1 8.8386497 -0.0747899 13.5761814
80 1 6.3845019 0.6873366 14.8729865
81 1 -1.3705233 1.9464428 16.0241396
82 1 1.2735447 1.9534712 16.0312838
83 1 -2.1807894 -0.5703931 16.0424074
84 1 -4.6173570 -1.3747746 15.4670629
85 1 13.2456249 6.6552694 6.5345876
86 1 14.5764323 4.8284046 5.1627663
87 1 12.4259824 5.5462264 8.7905835
88 1 10.5808239 6.5422869 10.3771226
89 1 13.3121909 -2.9570640 -8.7453628
90 1 12.5021095 -5.4745377 -8.7273547
91 1 14.6273981 -2.5058936 -6.4961332
92 1 12.4050668 -1.0916597 -10.3615936
93 1 12.9502111 1.5658112 -9.6062633
94 1 11.4349307 3.6572751 -10.8768894
95 1 15.2202954 -0.1258618 -5.5467822
96 1 14.4059058 2.0649981 -7.1165783
97 1 14.3606031 4.6603554 -5.8731755
98 1 -1.2654400 -13.6068217 -8.7001776
99 1 -2.0842667 -14.7163406 -6.4440031
100 1 2.8872975 -12.1669710 -10.2989492
101 1 -9.0251564 -10.1295854 8.8531393
102 1 -8.9848815 -12.4100243 5.2633854
103 1 -9.3686839 -12.9395919 2.6897486
104 1 -4.8299303 -15.2139532 -2.7653979
105 1 -4.5272638 -14.5552738 -5.4852450
106 1 -7.3132721 -14.3856378 1.4175692
107 1 -7.2614320 -14.4079192 -1.4572212
108 1 -7.3593442 -7.5415086 12.3047034
109 1 -4.9050218 -4.1139714 14.8813986
110 1 -7.3262020 -4.9567440 13.5719372
111 1 5.4723072 3.4683529 14.8480439
112 1 2.7777659 4.0285019 15.4432902
113 1 9.4721551 4.7569512 12.2511109
114 1 7.0053161 5.5146622 13.5260516
115 1 15.9326824 2.6002331 1.3521995
116 1 15.1845840 5.0052968 2.6106390
117 1 14.3690529 7.3657085 1.3102219
118 1 14.3416984 7.3687182 -1.5677063
119 1 12.8475944 9.4286670 -2.9119719
120 1 12.2166052 9.0298117 -5.6264628
121 1 12.8662212 6.7582131 -7.1572992
122 1 11.4106348 6.2591511 -9.6467852
123 1 15.9510353 -0.0298232 -2.8290650
124 1 15.9274194 2.5359043 -1.5252949
125 1 15.1271998 4.9368044 -3.0390482
126 1 9.5665347 -8.9478830 -9.5318848
127 1 10.6707563 -6.4808635 -10.3234390
128 1 9.5616726 -4.7006007 -12.2032288
129 1 10.4585858 -1.9140157 -12.2227064
130 1 5.5765804 -11.8627400 -9.5193054
131 1 7.1099309 -9.7788265 -10.7825535
132 1 5.8339497 -8.0410365 -12.7963584
133 1 7.1052177 -5.4715075 -13.4914236
134 1 -9.3248466 2.9175747 -12.9218813
135 1 -15.1375334 4.8548550 -3.1185719
136 1 -9.3111581 -12.9212442 -2.9637489
137 1 -5.7308605 -8.0696208 -12.8249165
138 1 -6.3729508 -13.1187845 -7.0514548
139 1 -5.4671100 -11.8901908 -9.5485128
140 1 -8.8249345 -12.2853141 -5.7992770
141 1 -10.3737388 -10.2306287 -7.0823588
142 1 -12.3371918 -8.9093984 -5.5548485
143 1 -13.2439194 -6.6281697 -6.5655153
144 1 -7.0057000 -9.8141168 -10.8186554
145 1 -9.4733291 -8.9973181 -9.5783260
146 1 -10.6075344 -6.5246087 -10.3609710
147 1 -12.4393344 -5.5324416 -8.7803801
148 1 -5.4746734 -3.4608016 -14.8489336
149 1 -6.3842501 -0.6784543 -14.8735024
150 1 -7.0096341 -5.5070415 -13.5269194
151 1 -9.4770980 -4.7464300 -12.2513690
152 1 -8.8358275 0.0859988 -13.5779520
153 1 -10.3809678 -1.9634656 -12.2808931
154 1 -12.3437928 -1.1616621 -10.4269528
155 1 -13.2468480 -3.0623204 -8.8081346
156 1 -11.3935570 6.1977648 -9.7064204
157 1 -12.8648559 6.6884726 -7.2249458
158 1 -11.3969506 3.5970792 -10.9366615
159 1 -12.9078717 1.4962508 -9.6740946
160 1 -14.3545533 4.5826942 -5.9485912
161 1 -14.3793203 1.9869663 -7.1921582
162 1 -15.1904010 -0.2078580 -5.6257032
163 1 -14.5788501 -2.5898860 -6.5718830
164 1 -15.9534284 2.5139065 1.2682355
165 1 -15.9514379 0.0365712 2.8267147
166 1 -15.9326162 2.4504105 -1.6084949
167 1 -15.9358686 -0.1147825 -2.9111751
168 1 -12.8509837 -9.4247231 2.9097831
169 1 -11.3781439 -11.4474081 1.3909399
170 1 -11.3841695 -11.4292144 -1.4878738
171 1 -12.8986987 -9.3829696 -2.8325742
172 1 -14.3446670 -7.3635117 1.5650080
173 1 -14.3714597 -7.3603859 -1.3137314
174 1 -15.1863513 -4.9986180 -2.6131547
175 1 -14.5768311 -4.8181967 -5.1711702
176 1 -15.1296886 -4.9307145 3.0365444
177 1 -15.9286405 -2.5292665 1.5235636
178 1 -15.9338457 -2.5926968 -1.3529638
179 1 -2.7736130 -12.1803879 -10.3143224
180 1 -1.2765063 -1.9475831 -16.0317646
181 1 -2.0996208 0.5655931 -16.0534022
182 1 -4.5418707 1.3574926 -15.4909215
183 1 -2.7810842 -4.0221128 -15.4443583
184 1 -1.4108069 -6.3995413 -14.8153812
185 1 -10.3338593 -10.5784290 6.6142436
186 1 -12.2203706 -9.0253530 5.6254397
187 1 -12.8708443 -6.7512124 7.1555937
188 1 -14.6281030 2.5109030 6.4926107
189 1 -14.6299424 4.7489211 5.0845412
190 1 -15.2251018 4.9229332 2.5300253
191 1 -15.2212809 0.1321644 5.5439305
192 1 -14.4156623 7.2873839 1.2339941
193 1 -10.3578787 10.5235658 -6.6640031
194 1 -9.0286826 10.0800429 -8.9059335
195 1 -9.3904589 8.0141101 -10.4896781
196 1 -12.2358615 8.9632563 -5.6906725
197 1 -7.3324931 7.5061801 -12.3422781
198 1 -2.8877183 -8.4872967 -13.4932169
199 1 -1.4070287 -10.5816192 -12.1856321
200 1 -7.2786047 4.9240102 -13.6094108
201 1 -4.8472629 4.0945126 -14.9056712
202 1 -14.3731744 7.2904653 -1.6434714
203 1 -12.8834674 9.3583030 -2.9796740
204 1 -14.3637655 -4.6537884 5.8706489
205 1 -14.4081061 -2.0585302 7.1139972
206 1 -12.5024169 5.4787800 8.7242516
207 1 -13.3131523 2.9623024 8.7421259
208 1 -13.3162933 6.5828309 6.4639535
209 1 -12.4134403 8.8484433 5.4819319
210 1 -10.4678133 10.1729297 7.0268351
211 1 -9.4058811 -8.0601670 10.4404565
212 1 1.3788766 -13.6008644 -8.6922501
213 1 2.1784590 0.5763924 -16.0425096
214 1 0.0356722 2.1248726 -16.0600021
215 1 1.3676695 -1.9404489 -16.0251104
216 1 4.6146153 1.3805889 -15.4673632
217 1 4.9021788 4.1194791 -14.8808118
218 1 2.5300699 5.8332098 -14.9000817
219 1 2.5549034 8.4059833 -13.6107288
220 1 2.8791664 -4.0073693 -15.4302112
221 1 5.5677866 -3.4329508 -14.8207498
222 1 6.4650412 -0.6466977 -14.8399814
223 1 8.9081036 0.1286054 -13.5303058
224 1 9.3775051 2.9650833 -12.8728669
225 1 7.3230290 4.9619061 -13.5717633
226 1 -6.9034520 13.0472852 -6.6746328
227 1 -9.0441039 12.3576032 -5.2852486
228 1 -6.8939231 11.6399012 -8.9121574
229 1 -4.8418898 14.3649315 -5.7135691
230 1 -4.8212371 11.3521902 -10.5034983
231 1 -2.4787797 12.7103108 -9.7336363
232 1 -0.0043348 11.9195801 -10.9710353
233 1 -2.4847655 5.8199251 -14.9128950
234 1 0.0273092 4.6952202 -15.5046505
235 1 -4.9701145 9.2321521 -12.3493059
236 1 -2.5306081 8.3921393 -13.6238044
237 1 0.0066805 9.7337503 -12.9496751
238 1 -11.4296234 11.3881974 -1.4535103
239 1 -9.4243209 12.8887459 -2.7390565
240 1 -7.3801183 14.3465995 -1.4659336
241 1 -12.9618573 9.3171866 2.7604919
242 1 -11.4512873 11.3701451 1.4240243
243 1 -9.3949910 12.8726639 2.9101019
244 1 -12.9527425 -1.5593712 9.6038975
245 1 -12.4068811 1.0975416 10.3587996
246 1 -11.4150161 -6.2521081 9.6461690
247 1 -11.4384045 -3.6504527 10.8755286
248 1 -9.3806396 -2.9591486 12.8719488
249 1 -8.9109096 -0.1228238 13.5285117
250 1 1.5203716 -10.5746676 -12.1780499
251 1 1.5164098 -6.3920899 -14.8081637
252 1 2.9965383 -8.4728098 -13.4785859
253 1 -5.5708234 3.4384815 14.8183264
254 1 -6.4679889 0.6524436 14.8384454
255 1 -2.8827398 4.0131868 15.4280319
256 1 -1.5206182 6.3976551 14.8053286
257 1 -9.5632934 4.7054433 12.2000922
258 1 -10.6714449 6.4846077 10.3203756
259 1 -10.4606216 1.9195418 12.2200974
260 1 -7.1076846 5.4763591 13.4881554
261 1 -9.5670810 8.9506660 9.5287231
262 1 2.8816845 8.4931563 13.4908197
263 1 1.4060490 6.4055988 14.8132156
264 1 5.7239064 8.0763838 12.8237648
265 1 9.4670152 9.0025344 9.5796671
266 1 7.0002636 9.8199794 10.8168544
267 1 12.3356112 8.9161112 5.5475836
268 1 10.3744789 10.2298514 7.0823974
269 1 12.8959122 9.3878926 2.8289478
270 1 11.3810794 11.4327262 1.4845290
271 1 11.3746065 11.4506339 -1.3933180
272 1 9.3679618 12.9401567 -2.6895465
273 1 9.0036993 12.4072960 -5.2375978
274 1 6.8662717 13.0853102 -6.6384482
275 1 2.7690276 12.1843008 10.3109323
276 1 1.4017330 10.5861363 12.1823186
277 1 5.4627952 11.8945097 9.5456027
278 1 8.8242152 12.2865257 5.7978045
279 1 9.3085882 12.9240350 2.9596501
280 1 6.3704754 13.1216117 7.0484306
281 1 -1.5248387 10.5781499 12.1744666
282 1 -3.0004476 8.4771926 13.4749599
283 1 -5.8366133 8.0449897 12.7926584
284 1 -7.1116479 9.7814482 10.7790427
285 1 2.0820361 14.7183307 6.4401779
286 1 1.2620330 13.6096482 8.6962505
287 1 4.5242115 14.5576431 5.4814745
288 1 4.8259422 15.2160227 2.7609708
289 1 7.2578789 14.4104537 1.4498421
290 1 7.3087468 14.3869684 -1.4273703
291 1 -2.1964383 14.7067030 6.4287301
292 1 -1.3821860 13.6026891 8.6888685
293 1 -0.0556372 15.3962319 5.0391440
294 1 -4.6331090 14.5324801 5.4572289
295 1 -4.9242542 15.1891716 2.7351071
296 1 -7.3445790 14.3702987 1.4112754
297 1 -2.8905852 12.1690516 10.2955682
298 1 -5.5788354 11.8642286 9.5161284
299 1 -6.4796338 13.0864149 7.0142794
300 1 -8.9221495 12.2378961 5.7505801
301 1 -0.0504861 16.0086074 2.4823305
302 1 2.4603866 15.9662714 1.2102480
303 1 2.5033861 15.9183772 -1.6668385
304 1 4.9429821 15.1373357 -2.9779224
305 1 4.7926158 14.3914809 -5.6882456
306 1 2.4488603 14.2817550 -7.2439342
307 1 2.4595386 12.7238564 -9.7208113
308 1 -0.0353290 15.8876578 -3.1656132
309 1 -0.0257921 15.0507446 -5.9928663
310 1 -2.4895607 14.2682398 -7.2566827
311 1 -2.5822044 15.9043746 -1.6802125
312 1 -5.0105239 15.1099456 -3.0040336
313 1 -2.5546580 15.9524586 1.1970007
314 1 9.0197693 10.1296833 -8.8585158
315 1 6.8765145 11.6774520 -8.8764118
316 1 10.3350078 10.5802893 -6.6094718
317 1 9.4016683 8.0649147 -10.4405847
318 1 7.3559706 7.5456009 -12.3042118
319 1 4.9835159 9.2589832 -12.3237909
320 1 4.8135124 11.3784814 -10.4785631

10035
examples/USER/lb/dragforce/defaultgamma_drag.out Executable file
View File

File diff suppressed because it is too large Load Diff

80
examples/USER/lb/dragforce/in.defaultgamma_drag Executable file
View File

@ -0,0 +1,80 @@
#===========================================================================#
# Drag force on a single sphere. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. The resulting equilibrium drag force #
# should correspond to the Stokes drag force on a sphere with a slightly #
# larger "hydrodynamic" radius, than that given by the placement of the #
# particle nodes. #
# #
# Sample output from this run can be found in the file: #
# 'defaultgamma_drag.out' #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1
read_data data.one_radius16d2
#----------------------------------------------------------------------------
# None of the particles comprising the spherical colloidal object should
# interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
#----------------------------------------------------------------------------
# Need to use a large particle mass in order to approximate an infintely
# massive particle, moving at constant velocity through the fluid.
#----------------------------------------------------------------------------
mass * 10000.0
timestep 3.0
velocity all set 0.0 0.0001 0.0 units box
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 1
# correspond to a surface area of 10.3059947).
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh (results in a smaller hydrodynamic
# radius than if the Peskin stencil is used).
# Print the force and torque acting on the particle to the screen at each
# timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 1 1.0 1.0 setArea 1 10.3059947 dx 4.0 dm 10.0 trilinear calcforce 10 all
#---------------------------------------------------------------------------
# For this simulation the colloidal particle moves at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto the object. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motion using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 100000

68
examples/USER/lb/dragforce/in.setgamma_drag Executable file
View File

@ -0,0 +1,68 @@
#===========================================================================#
# Drag force on a single sphere. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 13.0 for this simulation.) This #
# type of simulation is used to calibrate the value for gamma which will #
# give the desired Stokes drag force. #
# #
# Sample output from this run can be found in the file: #
# 'setgamma13d0_drag.out' #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1
read_data data.one_radius16d2
#----------------------------------------------------------------------------
# None of the particles comprising the spherical colloidal object should
# interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
mass * 1.0
timestep 4.0
velocity all set 0.0 0.0001 0.0 units box
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid density = 1.0, fluid viscosity = 1.0, value
# for gamma=13.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Print the force and torque acting on the particle to the screen at each
# timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce 10 all
#---------------------------------------------------------------------------
# For this simulation the colloidal particle moves at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto the object. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motion using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 100000

10035
examples/USER/lb/dragforce/setgamma13d0_drag.out Executable file
View File

File diff suppressed because it is too large Load Diff

1290
examples/USER/lb/fourspheres/data.four Executable file
View File

File diff suppressed because it is too large Load Diff

15039
examples/USER/lb/fourspheres/fourspheres_velocity0d0001_defaultgamma.out Executable file
View File

File diff suppressed because it is too large Load Diff

15039
examples/USER/lb/fourspheres/fourspheres_velocity0d0001_setgamma.out Executable file
View File

File diff suppressed because it is too large Load Diff

84
examples/USER/lb/fourspheres/in.fourspheres_default_gamma Executable file
View File

@ -0,0 +1,84 @@
#===========================================================================#
# Sytem of 2 pairs of rigid particles moving towards one another. #
# At each timestep, the hydrodynamic force acting on one of these four #
# rigid particles is printed to the screen. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. Thus, the colloidal objects will have #
# slightly larger "hydrodynamic" radii than given by the placement of the #
# particle nodes. #
# #
# Sample output from this run can be found in the file: #
# 'fourspheres_velocity0d0001_defaultgamma.out' #
#===========================================================================#
units micro
dimension 3
boundary p p p
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1 exclude type 1 1
read_data data.four
#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
#----------------------------------------------------------------------------
# Need to use a large particle mass in order to approximate an infintely
# massive particle, moving at constant velocity through the fluid.
#----------------------------------------------------------------------------
mass * 10000.0
timestep 3.0
group sphere1 id <> 1 320
group sphere2 id <> 321 640
group sphere3 id <> 641 960
group sphere4 id <> 961 1280
velocity sphere1 set 0.0 0.0001 0.0 units box
velocity sphere2 set 0.0 -0.0001 0.0 units box
velocity sphere3 set 0.0 0.0001 0.0 units box
velocity sphere4 set 0.0 -0.0001 0.0 units box
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 1
# correspond to a surface area of 2.640508625).
# Print the force and torque acting on one of the spherical colloidal objects
# to the screen at each timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 1 1.0 1.0 setArea 1 2.640508625 dx 4.0 dm 10.0 calcforce 20 sphere1
#---------------------------------------------------------------------------
# For this simulation the colloidal particles move at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto these objects. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motions using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 300000

76
examples/USER/lb/fourspheres/in.fourspheres_set_gamma Executable file
View File

@ -0,0 +1,76 @@
#===========================================================================#
# Sytem of 2 pairs of rigid particles moving towards one another. #
# At each timestep, the hydrodynamic force acting on one of these four #
# rigid particles is printed to the screen. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 3.303 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# #
# Sample output from this run can be found in the file: #
# 'fourspheres_velocity0d0001_setgamma.out' #
#===========================================================================#
units micro
dimension 3
boundary p p p
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1 exclude type 1 1
read_data data.four
#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
mass * 1.0
timestep 4.0
group sphere1 id <> 1 320
group sphere2 id <> 321 640
group sphere3 id <> 641 960
group sphere4 id <> 961 1280
velocity sphere1 set 0.0 0.0001 0.0 units box
velocity sphere2 set 0.0 -0.0001 0.0 units box
velocity sphere3 set 0.0 0.0001 0.0 units box
velocity sphere4 set 0.0 -0.0001 0.0 units box
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid density = 1.0, fluid viscosity = 1.0, value
# for gamma=3.303, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Print the force and torque acting on one of the spherical colloidal objects
# to the screen at each timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 3.303 dx 4.0 dm 10.0 calcforce 20 sphere1
#---------------------------------------------------------------------------
# For this simulation the colloidal particles move at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto these objects. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motions using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 300000

492
examples/USER/lb/microrheology/data.two Executable file
View File

@ -0,0 +1,492 @@
Position data for 2 rigid spheres
482 atoms
2 atom types
-48.0 48.0 xlo xhi
-48.0 48.0 ylo yhi
-48.0 48.0 zlo zhi
Atoms
1 1 1 -6.0000000 -6.0000000 -6.0000000
2 1 2 -6.7952777 -4.4006421 -4.3970064
3 1 2 -6.7405150 -4.0805060 -4.7642084
4 1 2 -7.0635930 -4.0269889 -5.1420970
5 1 2 -6.9102948 -3.8206505 -5.5736202
6 1 2 -7.1629508 -3.9005861 -6.0026248
7 1 2 -7.5284249 -4.6245350 -4.7622544
8 1 2 -7.4734408 -4.3145503 -5.1349960
9 1 2 -7.7329999 -4.3958626 -5.5716836
10 1 2 -7.5816972 -4.1949471 -5.9957368
11 1 2 -7.1999802 -4.6834872 -4.3916338
12 1 2 -5.9456722 -4.3526196 -4.2555268
13 1 2 -5.9407925 -4.0508260 -4.6009948
14 1 2 -6.3094846 -3.9229486 -4.8380717
15 1 2 -6.3818784 -4.5418136 -4.1324182
16 1 2 -6.8068328 -5.2499343 -3.8677658
17 1 2 -6.3950594 -4.9626408 -3.8721338
18 1 2 -7.2130891 -5.1099464 -4.1301818
19 1 2 -7.8265771 -4.9757623 -4.8275864
20 1 2 -7.5436538 -5.4562570 -4.2445864
21 1 2 -7.8338039 -5.3576996 -4.5912367
22 1 2 -5.1048807 -4.4441784 -4.4068330
23 1 2 -5.1488961 -4.1183327 -4.7773183
24 1 2 -4.8412821 -4.0771239 -5.1515185
25 1 2 -4.9979972 -3.8583817 -5.5883425
26 1 2 -4.7642840 -3.9426042 -6.0113608
27 1 2 -5.5776821 -3.9411450 -4.8412230
28 1 2 -5.5077240 -4.5644710 -4.1407202
29 1 2 -7.7586089 -6.2770096 -4.3904780
30 1 2 -8.0515736 -6.1253893 -4.7609182
31 1 2 -8.2001515 -6.4124252 -5.1344139
32 1 2 -8.3524599 -6.2006142 -5.5690863
33 1 2 -8.3545801 -6.4646677 -5.9939368
34 1 2 -8.0675455 -5.6661016 -4.8279215
35 1 2 -7.5022688 -5.9341094 -4.1294794
36 1 2 -7.0976014 -6.0743581 -3.8669875
37 1 2 -5.9730238 -5.6190570 -3.6305791
38 1 2 -6.3420491 -5.8742451 -3.6278304
39 1 2 -6.7706933 -5.7271236 -3.7435491
40 1 2 -5.9561398 -5.1716011 -3.7479272
41 1 2 -5.5194627 -4.9865858 -3.8781904
42 1 2 -4.7078155 -4.7446884 -4.4142976
43 1 2 -4.3927148 -4.6985244 -4.7822989
44 1 2 -4.4405528 -4.3803402 -5.1604604
45 1 2 -4.2023727 -4.4635348 -5.5903524
46 1 2 -4.3557693 -4.2518140 -6.0187526
47 1 2 -6.4903408 -6.6698329 -3.7481363
48 1 2 -6.2197822 -6.3089775 -3.6301415
49 1 2 -6.9592862 -6.5596456 -3.8724269
50 1 2 -7.2110751 -6.8938219 -4.1306739
51 1 2 -7.6185403 -6.7518635 -4.3953103
52 1 2 -7.7726194 -7.0401864 -4.7607126
53 1 2 -8.0542798 -6.8909074 -5.1361602
54 1 2 -8.0561386 -7.1598369 -5.5674809
55 1 2 -8.2031793 -6.9518203 -5.9937208
56 1 2 -4.7168104 -5.1735782 -4.1478520
57 1 2 -5.1134539 -5.2927063 -3.8848707
58 1 2 -5.1768909 -5.7657673 -3.7577630
59 1 2 -5.6097202 -5.8909412 -3.6344581
60 1 2 -5.7596531 -6.3242774 -3.6341856
61 1 2 -4.1112684 -5.0595209 -4.8562376
62 1 2 -4.2310922 -6.3572201 -4.4177991
63 1 2 -3.9397694 -6.2161833 -4.7880945
64 1 2 -3.8076047 -6.4979682 -5.1601006
65 1 2 -3.6515251 -6.2841926 -5.5951538
66 1 2 -3.6604108 -6.5348884 -6.0147447
67 1 2 -3.9040494 -5.7574153 -4.8562587
68 1 2 -4.1182963 -5.4451476 -4.6174913
69 1 2 -4.4010966 -5.5325758 -4.2722781
70 1 2 -6.9506251 -7.8722988 -4.8377568
71 1 2 -6.5075117 -7.9975430 -4.7702624
72 1 2 -6.2842778 -8.2255866 -5.1479725
73 1 2 -6.5314876 -8.3018016 -5.5766437
74 1 2 -6.2854114 -8.3829657 -6.0039208
75 1 2 -6.2755344 -7.7717019 -4.4046462
76 1 2 -6.5170365 -7.4213959 -4.1365872
77 1 2 -6.9891478 -7.3173191 -4.2546469
78 1 2 -7.1695994 -7.5566991 -4.5968872
79 1 2 -7.5324845 -7.4317062 -4.8330771
80 1 2 -4.8022344 -6.9490265 -4.1494037
81 1 2 -4.3943534 -6.8245357 -4.4182160
82 1 2 -4.4687465 -6.0082061 -4.1519752
83 1 2 -4.8688054 -6.1281702 -3.8871887
84 1 2 -5.0373232 -6.6047950 -3.8863593
85 1 2 -5.5066441 -6.6938624 -3.7560848
86 1 2 -5.7777256 -7.7813598 -4.4070933
87 1 2 -5.5197225 -7.4445112 -4.1445428
88 1 2 -5.7551534 -7.0993829 -3.8807058
89 1 2 -6.2642119 -7.0880312 -3.8771763
90 1 2 -5.0461565 -7.3605319 -4.2681987
91 1 2 -4.8782334 -7.6050254 -4.6123639
92 1 2 -5.5555749 -8.0165003 -4.7768020
93 1 2 -5.7826688 -8.2331182 -5.1479725
94 1 2 -5.5320239 -8.3166130 -5.5825036
95 1 2 -5.7736181 -8.3892973 -6.0031528
96 1 2 -5.1091648 -7.9075427 -4.8477439
97 1 2 -4.2552281 -7.1132012 -4.7848644
98 1 2 -3.9709494 -6.9707084 -5.1629341
99 1 2 -3.9781973 -7.2264634 -5.5899977
100 1 2 -3.8267282 -7.0181313 -6.0172887
101 1 2 -4.5113931 -7.4928371 -4.8530529
102 1 2 -6.1745939 -3.7324082 -5.2334853
103 1 2 -5.7179557 -3.7418356 -5.2376713
104 1 2 -6.4416778 -3.6723558 -5.6166025
105 1 2 -6.2127659 -3.6098471 -6.0435904
106 1 2 -5.4660045 -3.6916829 -5.6172185
107 1 2 -5.7081405 -3.6183340 -6.0498532
108 1 2 -8.2096805 -5.4766646 -5.2231906
109 1 2 -8.0611666 -5.0459535 -5.2245078
110 1 2 -8.3495662 -5.7107234 -5.6052112
111 1 2 -8.3407755 -5.4711407 -6.0328398
112 1 2 -8.0331260 -4.7879827 -5.6032465
113 1 2 -8.1794608 -4.9956415 -6.0348556
114 1 2 -7.1746606 -7.9460853 -5.2299838
115 1 2 -7.5384533 -7.6725739 -5.2282110
116 1 2 -6.9976804 -8.1481558 -5.6126228
117 1 2 -7.2230459 -8.0646497 -6.0371593
118 1 2 -7.7761766 -7.5650782 -5.6053770
119 1 2 -7.6255152 -7.7653471 -6.0353595
120 1 2 -4.5127778 -7.7256620 -5.2448436
121 1 2 -4.8848190 -7.9859965 -5.2435679
122 1 2 -4.2684184 -7.6195122 -5.6274336
123 1 2 -4.4184165 -7.8045057 -6.0485095
124 1 2 -5.0603330 -8.1752054 -5.6185454
125 1 2 -4.8270739 -8.0932929 -6.0486775
126 1 2 -3.8923944 -5.1305549 -5.2502904
127 1 2 -3.7611086 -5.5659007 -5.2523882
128 1 2 -3.9187275 -4.8626714 -5.6328640
129 1 2 -3.7920107 -5.0610275 -6.0558038
130 1 2 -3.6382097 -5.7905610 -5.6284057
131 1 2 -3.6449814 -5.5413416 -6.0593308
132 1 2 -7.1230241 -4.0343774 -6.7969599
133 1 2 -7.4917041 -4.2959302 -6.7943334
134 1 2 -7.7338622 -4.3969950 -6.4290657
135 1 2 -6.9361472 -3.8320336 -6.4284282
136 1 2 -6.9022071 -4.1117633 -7.1749830
137 1 2 -7.5007264 -4.5407034 -7.1739993
138 1 2 -7.1345113 -4.4282729 -7.4151179
139 1 2 -8.2202906 -6.4623921 -6.7851774
140 1 2 -8.0838645 -6.8946907 -6.7855175
141 1 2 -8.0589712 -7.1596712 -6.4192862
142 1 2 -8.3521533 -6.2250375 -6.4203968
143 1 2 -8.0798082 -6.2792578 -7.1646517
144 1 2 -7.8513989 -6.9814171 -7.1701038
145 1 2 -7.8500182 -6.5987835 -7.4067308
146 1 2 -7.5135150 -7.6422286 -6.8788390
147 1 2 -7.1209463 -7.9318652 -6.8782806
148 1 2 -6.9773364 -8.1434442 -6.4587602
149 1 2 -7.7669427 -7.5589203 -6.4557209
150 1 2 -7.5587960 -7.3361552 -7.2429178
151 1 2 -6.8044111 -7.8894085 -7.2421992
152 1 2 -6.8431747 -7.5756119 -7.6020312
153 1 2 -8.0292813 -5.0696171 -6.8811388
154 1 2 -8.1844076 -5.5324168 -6.8773425
155 1 2 -8.3414517 -5.7330681 -6.4542598
156 1 2 -8.0275531 -4.7996714 -6.4563335
157 1 2 -7.7503410 -4.9318773 -7.2471650
158 1 2 -8.0456485 -5.8229537 -7.2425688
159 1 2 -7.7569463 -5.6900948 -7.6053345
160 1 2 -6.2451373 -8.2520538 -6.7925666
161 1 2 -5.7944957 -8.2556334 -6.7936539
162 1 2 -5.5383532 -8.3148447 -6.4340236
163 1 2 -6.5110221 -8.3058625 -6.4264444
164 1 2 -6.3800393 -8.0627770 -7.1664140
165 1 2 -5.6470426 -8.0656396 -7.1698523
166 1 2 -6.0086015 -7.9444180 -7.4068280
167 1 2 -4.9117543 -7.9468655 -6.8862487
168 1 2 -4.5158847 -7.6656338 -6.8849103
169 1 2 -4.2705890 -7.5964195 -6.4696623
170 1 2 -5.0655461 -8.1612970 -6.4643184
171 1 2 -5.2174595 -7.8964183 -7.2454832
172 1 2 -4.4614009 -7.3539758 -7.2487845
173 1 2 -4.7724191 -7.2946057 -7.6053166
174 1 2 -3.9414374 -6.9367351 -6.8030241
175 1 2 -3.7972992 -6.5102837 -6.8048105
176 1 2 -3.6594813 -6.2870468 -6.4467399
177 1 2 -3.9713955 -7.2058720 -6.4366198
178 1 2 -4.1645984 -7.0057108 -7.1746690
179 1 2 -3.9338575 -6.3111680 -7.1807752
180 1 2 -4.1628098 -6.6170472 -7.4156218
181 1 2 -3.8154809 -5.5743119 -6.8981462
182 1 2 -3.9593523 -5.1079932 -6.8944727
183 1 2 -3.9464260 -4.8534471 -6.4777559
184 1 2 -3.6570583 -5.7885109 -6.4752860
185 1 2 -3.9608279 -5.8499439 -7.2566864
186 1 2 -4.2414948 -4.9585858 -7.2582195
187 1 2 -4.3965914 -5.2378194 -7.6149805
188 1 2 -4.4739317 -4.3325223 -6.8066191
189 1 2 -4.8350047 -4.0621067 -6.8045844
190 1 2 -5.0026703 -3.8626372 -6.4438628
191 1 2 -4.2247888 -4.4460632 -6.4403480
192 1 2 -4.4799961 -4.5665028 -7.1809633
193 1 2 -5.0693927 -4.1300456 -7.1820496
194 1 2 -4.8504474 -4.4439617 -7.4203078
195 1 2 -5.7325882 -3.7887189 -6.8937155
196 1 2 -6.2221540 -3.7814851 -6.8881665
197 1 2 -6.4613934 -3.6915699 -6.4671908
198 1 2 -5.4768490 -3.7052483 -6.4694975
199 1 2 -5.5165937 -4.0127236 -7.2558070
200 1 2 -6.4543644 -4.0046476 -7.2538430
201 1 2 -6.2368896 -4.2397517 -7.6141281
202 1 2 -5.4990325 -4.5859278 -7.8733478
203 1 2 -5.7462228 -4.2440000 -7.6161874
204 1 2 -5.0328870 -4.6873014 -7.7611120
205 1 2 -4.7983310 -5.1007559 -7.8727926
206 1 2 -4.4957731 -6.0464201 -7.8695313
207 1 2 -4.2498222 -5.7047583 -7.6154598
208 1 2 -4.4481398 -6.5204207 -7.7552472
209 1 2 -4.7658651 -6.8718496 -7.8646152
210 1 2 -5.5668285 -7.4520812 -7.8611349
211 1 2 -5.1681199 -7.5787775 -7.6048170
212 1 2 -6.0029659 -7.6443452 -7.7481763
213 1 2 -6.4359404 -7.4519906 -7.8605590
214 1 2 -7.2404643 -6.8683558 -7.8620438
215 1 2 -7.2386250 -7.2873173 -7.6026923
216 1 2 -7.5608237 -6.5123820 -7.7496555
217 1 2 -7.5109703 -6.0405531 -7.8642223
218 1 2 -7.2015713 -5.0939277 -7.8695614
219 1 2 -7.6030838 -5.2238764 -7.6086501
220 1 2 -6.9604988 -4.6788626 -7.7584193
221 1 2 -6.4934515 -4.5824546 -7.8727175
222 1 2 -5.5085670 -5.3353900 -8.2531728
223 1 2 -5.7462781 -4.9203051 -8.1283526
224 1 2 -5.0407525 -5.4355019 -8.1263082
225 1 2 -5.7737388 -5.7012777 -8.3705635
226 1 2 -5.2052286 -6.2702555 -8.2483996
227 1 2 -4.8867707 -5.9153629 -8.1245135
228 1 2 -5.1559840 -6.7455380 -8.1193892
229 1 2 -5.6334957 -6.1315014 -8.3682024
230 1 2 -5.9978064 -6.8481561 -8.2451340
231 1 2 -5.5624203 -7.0406368 -8.1179234
232 1 2 -6.4355734 -7.0418454 -8.1177428
233 1 2 -5.9985768 -6.3979494 -8.3667773
234 1 2 -6.7950195 -6.2721742 -8.2480804
235 1 2 -6.8443240 -6.7464696 -8.1189386
236 1 2 -7.1169660 -5.9149325 -8.1225341
237 1 2 -6.3654414 -6.1329795 -8.3682841
238 1 2 -6.4919254 -5.3357825 -8.2531811
239 1 2 -6.9606836 -5.4343377 -8.1253502
240 1 2 -6.2510842 -4.9190988 -8.1280530
241 1 2 -6.2263758 -5.7019597 -8.3706384
242 2 1 6.0000000 6.0000000 6.0000000
243 2 2 5.2047223 7.5993579 7.6029936
244 2 2 5.2594850 7.9194940 7.2357916
245 2 2 4.9364070 7.9730111 6.8579030
246 2 2 5.0897052 8.1793495 6.4263798
247 2 2 4.8370492 8.0994139 5.9973752
248 2 2 4.4715751 7.3754650 7.2377456
249 2 2 4.5265592 7.6854497 6.8650040
250 2 2 4.2670001 7.6041374 6.4283164
251 2 2 4.4183028 7.8050529 6.0042632
252 2 2 4.8000198 7.3165128 7.6083662
253 2 2 6.0543278 7.6473804 7.7444732
254 2 2 6.0592075 7.9491740 7.3990052
255 2 2 5.6905154 8.0770514 7.1619283
256 2 2 5.6181216 7.4581864 7.8675818
257 2 2 5.1931672 6.7500657 8.1322342
258 2 2 5.6049406 7.0373592 8.1278662
259 2 2 4.7869109 6.8900536 7.8698182
260 2 2 4.1734229 7.0242377 7.1724136
261 2 2 4.4563462 6.5437430 7.7554136
262 2 2 4.1661961 6.6423004 7.4087633
263 2 2 6.8951193 7.5558216 7.5931670
264 2 2 6.8511039 7.8816673 7.2226817
265 2 2 7.1587179 7.9228761 6.8484815
266 2 2 7.0020028 8.1416183 6.4116575
267 2 2 7.2357160 8.0573958 5.9886392
268 2 2 6.4223179 8.0588550 7.1587770
269 2 2 6.4922760 7.4355290 7.8592798
270 2 2 4.2413911 5.7229904 7.6095220
271 2 2 3.9484264 5.8746107 7.2390818
272 2 2 3.7998485 5.5875748 6.8655861
273 2 2 3.6475401 5.7993858 6.4309137
274 2 2 3.6454199 5.5353323 6.0060632
275 2 2 3.9324545 6.3338984 7.1720785
276 2 2 4.4977312 6.0658906 7.8705206
277 2 2 4.9023986 5.9256419 8.1330125
278 2 2 6.0269762 6.3809430 8.3694209
279 2 2 5.6579509 6.1257549 8.3721696
280 2 2 5.2293067 6.2728764 8.2564509
281 2 2 6.0438602 6.8283989 8.2520728
282 2 2 6.4805373 7.0134142 8.1218096
283 2 2 7.2921845 7.2553116 7.5857024
284 2 2 7.6072852 7.3014756 7.2177011
285 2 2 7.5594472 7.6196598 6.8395396
286 2 2 7.7976273 7.5364652 6.4096476
287 2 2 7.6442307 7.7481860 5.9812474
288 2 2 5.5096592 5.3301671 8.2518637
289 2 2 5.7802178 5.6910225 8.3698585
290 2 2 5.0407138 5.4403544 8.1275731
291 2 2 4.7889249 5.1061781 7.8693261
292 2 2 4.3814597 5.2481365 7.6046897
293 2 2 4.2273806 4.9598136 7.2392874
294 2 2 3.9457202 5.1090926 6.8638398
295 2 2 3.9438614 4.8401631 6.4325191
296 2 2 3.7968207 5.0481797 6.0062792
297 2 2 7.2831896 6.8264218 7.8521480
298 2 2 6.8865461 6.7072937 8.1151293
299 2 2 6.8231091 6.2342327 8.2422370
300 2 2 6.3902798 6.1090588 8.3655419
301 2 2 6.2403469 5.6757226 8.3658144
302 2 2 7.8887316 6.9404791 7.1437624
303 2 2 7.7689078 5.6427799 7.5822009
304 2 2 8.0602306 5.7838167 7.2119055
305 2 2 8.1923953 5.5020318 6.8398994
306 2 2 8.3484749 5.7158074 6.4048462
307 2 2 8.3395892 5.4651116 5.9852553
308 2 2 8.0959506 6.2425847 7.1437413
309 2 2 7.8817037 6.5548524 7.3825087
310 2 2 7.5989034 6.4674242 7.7277219
311 2 2 5.0493749 4.1277012 7.1622432
312 2 2 5.4924883 4.0024570 7.2297376
313 2 2 5.7157222 3.7744134 6.8520275
314 2 2 5.4685124 3.6981984 6.4233563
315 2 2 5.7145886 3.6170343 5.9960792
316 2 2 5.7244656 4.2282981 7.5953538
317 2 2 5.4829635 4.5786041 7.8634128
318 2 2 5.0108522 4.6826809 7.7453531
319 2 2 4.8304006 4.4433009 7.4031128
320 2 2 4.4675155 4.5682938 7.1669229
321 2 2 7.1977656 5.0509735 7.8505963
322 2 2 7.6056466 5.1754643 7.5817840
323 2 2 7.5312535 5.9917939 7.8480248
324 2 2 7.1311946 5.8718298 8.1128113
325 2 2 6.9626768 5.3952050 8.1136407
326 2 2 6.4933559 5.3061376 8.2439152
327 2 2 6.2222744 4.2186402 7.5929067
328 2 2 6.4802775 4.5554888 7.8554572
329 2 2 6.2448466 4.9006171 8.1192942
330 2 2 5.7357881 4.9119688 8.1228237
331 2 2 6.9538435 4.6394681 7.7318013
332 2 2 7.1217666 4.3949746 7.3876361
333 2 2 6.4444251 3.9834997 7.2231980
334 2 2 6.2173312 3.7668818 6.8520275
335 2 2 6.4679761 3.6833870 6.4174964
336 2 2 6.2263819 3.6107027 5.9968472
337 2 2 6.8908352 4.0924573 7.1522561
338 2 2 7.7447719 4.8867988 7.2151356
339 2 2 8.0290506 5.0292916 6.8370659
340 2 2 8.0218027 4.7735366 6.4100023
341 2 2 8.1732718 4.9818687 5.9827113
342 2 2 7.4886069 4.5071629 7.1469471
343 2 2 5.8254061 8.2675918 6.7665147
344 2 2 6.2820443 8.2581644 6.7623287
345 2 2 5.5583222 8.3276442 6.3833975
346 2 2 5.7872341 8.3901529 5.9564096
347 2 2 6.5339955 8.3083171 6.3827815
348 2 2 6.2918595 8.3816660 5.9501468
349 2 2 3.7903195 6.5233354 6.7768094
350 2 2 3.9388334 6.9540465 6.7754922
351 2 2 3.6504338 6.2892766 6.3947888
352 2 2 3.6592245 6.5288593 5.9671602
353 2 2 3.9668740 7.2120173 6.3967535
354 2 2 3.8205392 7.0043585 5.9651444
355 2 2 4.8253394 4.0539147 6.7700162
356 2 2 4.4615467 4.3274261 6.7717890
357 2 2 5.0023196 3.8518442 6.3873772
358 2 2 4.7769541 3.9353503 5.9628407
359 2 2 4.2238234 4.4349218 6.3946230
360 2 2 4.3744848 4.2346529 5.9646405
361 2 2 7.4872222 4.2743380 6.7551564
362 2 2 7.1151810 4.0140035 6.7564321
363 2 2 7.7315816 4.3804878 6.3725664
364 2 2 7.5815835 4.1954943 5.9514905
365 2 2 6.9396670 3.8247946 6.3814546
366 2 2 7.1729261 3.9067071 5.9513225
367 2 2 8.1076056 6.8694451 6.7497096
368 2 2 8.2388914 6.4340993 6.7476118
369 2 2 8.0812725 7.1373286 6.3671360
370 2 2 8.2079893 6.9389725 5.9441962
371 2 2 8.3617903 6.2094390 6.3715943
372 2 2 8.3550186 6.4586584 5.9406692
373 2 2 4.8769759 7.9656226 5.2030401
374 2 2 4.5082959 7.7040698 5.2056666
375 2 2 4.2661378 7.6030050 5.5709343
376 2 2 5.0638528 8.1679664 5.5715718
377 2 2 5.0977929 7.8882367 4.8250170
378 2 2 4.4992736 7.4592966 4.8260007
379 2 2 4.8654887 7.5717271 4.5848821
380 2 2 3.7797094 5.5376079 5.2148226
381 2 2 3.9161355 5.1053093 5.2144825
382 2 2 3.9410288 4.8403288 5.5807138
383 2 2 3.6478467 5.7749625 5.5796032
384 2 2 3.9201918 5.7207422 4.8353483
385 2 2 4.1486011 5.0185829 4.8298962
386 2 2 4.1499818 5.4012165 4.5932692
387 2 2 4.4864850 4.3577714 5.1211610
388 2 2 4.8790537 4.0681348 5.1217194
389 2 2 5.0226636 3.8565558 5.5412398
390 2 2 4.2330573 4.4410797 5.5442791
391 2 2 4.4412040 4.6638448 4.7570822
392 2 2 5.1955889 4.1105915 4.7578008
393 2 2 5.1568253 4.4243881 4.3979688
394 2 2 3.9707187 6.9303829 5.1188612
395 2 2 3.8155924 6.4675832 5.1226575
396 2 2 3.6585483 6.2669319 5.5457402
397 2 2 3.9724469 7.2003286 5.5436665
398 2 2 4.2496590 7.0681227 4.7528350
399 2 2 3.9543515 6.1770463 4.7574312
400 2 2 4.2430537 6.3099052 4.3946655
401 2 2 5.7548627 3.7479462 5.2074334
402 2 2 6.2055043 3.7443666 5.2063461
403 2 2 6.4616468 3.6851553 5.5659764
404 2 2 5.4889779 3.6941375 5.5735556
405 2 2 5.6199607 3.9372230 4.8335860
406 2 2 6.3529574 3.9343604 4.8301477
407 2 2 5.9913985 4.0555820 4.5931720
408 2 2 7.0882457 4.0531345 5.1137513
409 2 2 7.4841153 4.3343662 5.1150897
410 2 2 7.7294110 4.4035805 5.5303377
411 2 2 6.9344539 3.8387030 5.5356816
412 2 2 6.7825405 4.1035817 4.7545168
413 2 2 7.5385991 4.6460242 4.7512155
414 2 2 7.2275809 4.7053943 4.3946834
415 2 2 8.0585626 5.0632649 5.1969759
416 2 2 8.2027008 5.4897163 5.1951895
417 2 2 8.3405187 5.7129532 5.5532601
418 2 2 8.0286045 4.7941280 5.5633802
419 2 2 7.8354016 4.9942892 4.8253310
420 2 2 8.0661425 5.6888320 4.8192248
421 2 2 7.8371902 5.3829528 4.5843782
422 2 2 8.1845191 6.4256881 5.1018538
423 2 2 8.0406477 6.8920068 5.1055273
424 2 2 8.0535740 7.1465529 5.5222441
425 2 2 8.3429417 6.2114891 5.5247140
426 2 2 8.0391721 6.1500561 4.7433136
427 2 2 7.7585052 7.0414142 4.7417805
428 2 2 7.6034086 6.7621806 4.3850195
429 2 2 7.5260683 7.6674777 5.1933809
430 2 2 7.1649953 7.9378933 5.1954156
431 2 2 6.9973297 8.1373628 5.5561372
432 2 2 7.7752112 7.5539368 5.5596520
433 2 2 7.5200039 7.4334972 4.8190367
434 2 2 6.9306073 7.8699544 4.8179504
435 2 2 7.1495526 7.5560383 4.5796922
436 2 2 6.2674118 8.2112811 5.1062845
437 2 2 5.7778460 8.2185149 5.1118335
438 2 2 5.5386066 8.3084301 5.5328092
439 2 2 6.5231510 8.2947517 5.5305025
440 2 2 6.4834063 7.9872764 4.7441930
441 2 2 5.5456356 7.9953524 4.7461570
442 2 2 5.7631104 7.7602483 4.3858719
443 2 2 6.5009675 7.4140722 4.1266522
444 2 2 6.2537772 7.7560000 4.3838126
445 2 2 6.9671130 7.3126986 4.2388880
446 2 2 7.2016690 6.8992441 4.1272074
447 2 2 7.5042269 5.9535799 4.1304687
448 2 2 7.7501778 6.2952417 4.3845402
449 2 2 7.5518602 5.4795793 4.2447528
450 2 2 7.2341349 5.1281504 4.1353848
451 2 2 6.4331715 4.5479188 4.1388651
452 2 2 6.8318801 4.4212225 4.3951830
453 2 2 5.9970341 4.3556548 4.2518237
454 2 2 5.5640596 4.5480094 4.1394410
455 2 2 4.7595357 5.1316442 4.1379562
456 2 2 4.7613750 4.7126827 4.3973077
457 2 2 4.4391763 5.4876180 4.2503445
458 2 2 4.4890297 5.9594469 4.1357777
459 2 2 4.7984287 6.9060723 4.1304386
460 2 2 4.3969162 6.7761236 4.3913499
461 2 2 5.0395012 7.3211374 4.2415807
462 2 2 5.5065485 7.4175454 4.1272825
463 2 2 6.4914330 6.6646100 3.7468272
464 2 2 6.2537219 7.0796949 3.8716474
465 2 2 6.9592475 6.5644981 3.8736918
466 2 2 6.2262612 6.2987223 3.6294365
467 2 2 6.7947714 5.7297445 3.7516004
468 2 2 7.1132293 6.0846371 3.8754865
469 2 2 6.8440160 5.2544620 3.8806108
470 2 2 6.3665043 5.8684986 3.6317976
471 2 2 6.0021936 5.1518439 3.7548660
472 2 2 6.4375797 4.9593632 3.8820766
473 2 2 5.5644266 4.9581546 3.8822572
474 2 2 6.0014232 5.6020506 3.6332227
475 2 2 5.2049805 5.7278258 3.7519196
476 2 2 5.1556760 5.2535304 3.8810614
477 2 2 4.8830340 6.0850675 3.8774659
478 2 2 5.6345586 5.8670205 3.6317159
479 2 2 5.5080746 6.6642175 3.7468189
480 2 2 5.0393164 6.5656623 3.8746498
481 2 2 5.7489158 7.0809012 3.8719470
482 2 2 5.7736242 6.2980403 3.6293616

119
examples/USER/lb/microrheology/in.microrheology_default_gamma Executable file
View File

@ -0,0 +1,119 @@
#===========================================================================#
# 2 particle microrheology test #
# #
# Run consists of 2 colloidal particles undergoing Brownian motion in a #
# thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. Thus, the colloidal objects will have #
# a slightly larger "hydrodynamic" radii than given by the placement of #
# the particle nodes. #
# #
# Sample output from this run can be found in the file: #
# 'microrheology_setgamma.out' #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style molecular
read_data data.two
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 0.3 bin
neigh_modify delay 0 every 1
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each colloidal object (use a truncated and shifted Lennard-Jones
# potential).
#----------------------------------------------------------------------------
pair_style lj/cut 5.88
pair_coeff * * 0.0 0.0 5.88
pair_coeff 1 1 100.0 5.238484463 5.88
pair_modify shift yes
mass * 0.0002398
timestep 0.00025
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each colloidal object which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the colloidal
# object which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the viscous_lb fix).
# Use the standard LB integration scheme, a fluid viscosity = 1.0, fluid
# density= 0.0009982071, lattice spacing dx=1.2, and mass unit, dm=0.003.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 2
# correspond to a surface area of 0.3015928947).
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=2762). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 1 1.0 0.0009982071 setArea 2 0.3015928947 dx 1.2 dm 0.003 trilinear noise 300.0 2762
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the FluidAtoms particles (again,
# these atoms represent the surface of the colloidal object, which should
# interact with the fluid).
#----------------------------------------------------------------------------
fix 2 FluidAtoms lb/viscous
#----------------------------------------------------------------------------
# Each colloidal object (spherical shell of particles and central particle)
# is specified as a separate molecule in the confinedcolloids.dat data
# file. Integrate the motion of these sets of particles as rigid objects
# which each move and rotate together.
#----------------------------------------------------------------------------
fix 3 all rigid molecule
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 4 all lb/momentum 10000 linear 1 1 1
#----------------------------------------------------------------------------
# Create variables containing the positions of the central atoms (these
# values should correspond to the center of mass of each composite
# colloidal particle), and output these quantities to the screen.
#----------------------------------------------------------------------------
variable x1 equal x[1]
variable y1 equal y[1]
variable z1 equal z[1]
variable x2 equal x[242]
variable y2 equal y[242]
variable z2 equal z[242]
thermo_style custom v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
thermo 1
run 2000000000

113
examples/USER/lb/microrheology/in.microrheology_set_gamma Executable file
View File

@ -0,0 +1,113 @@
#===========================================================================#
# 2 particle microrheology test #
# #
# Run consists of 2 colloidal particles undergoing Brownian motion in a #
# thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 1.4692 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# #
# Sample output from this run can be found in the file: #
# 'microrheology_setgamma.out' #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style molecular
read_data data.two
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 0.3 bin
neigh_modify delay 0 every 1
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each colloidal object (use a truncated and shifted Lennard-Jones
# potential).
#----------------------------------------------------------------------------
pair_style lj/cut 5.88
pair_coeff * * 0.0 0.0 5.88
pair_coeff 1 1 100.0 5.238484463 5.88
pair_modify shift yes
mass * 0.0002398
timestep 0.00045
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each colloidal object which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the colloidal
# object which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid viscosity = 1.0, fluid density= 0.0009982071,
# value for gamma=1.4692, lattice spacing dx=1.2, and mass unit, dm=0.003.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=2762). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 2 1.0 0.0009982071 setGamma 1.4692 dx 1.2 dm 0.003 noise 300.0 2762
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all of
# the atoms in the system. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the fluid force
# calculation through the use of the 'innerNodes' keyword.
# NOTE: This fix should only be used when the user specifies a value for
# gamma (through the setGamma keyword) in the lb_fluid fix.
#----------------------------------------------------------------------------
fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 3 all lb/momentum 10000 linear 1 1 1
#----------------------------------------------------------------------------
# Create variables containing the positions of the central atoms (these
# values should correspond to the center of mass of each composite
# colloidal particle), and output these quantities to the screen.
#----------------------------------------------------------------------------
variable x1 equal x[1]
variable y1 equal y[1]
variable z1 equal z[1]
variable x2 equal x[242]
variable y2 equal y[242]
variable z2 equal z[242]
thermo_style custom v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
thermo 1
run 2000000000

50000
examples/USER/lb/microrheology/microrheology_defaultgamma.out Executable file
View File

File diff suppressed because it is too large Load Diff

50000
examples/USER/lb/microrheology/microrheology_setgamma.out Executable file
View File

File diff suppressed because it is too large Load Diff

330
examples/USER/lb/planewall/data.one_radius16d2 Executable file
View File

@ -0,0 +1,330 @@
Position data for rigid sphere
320 atoms
1 atom types
-160.0 160.0 xlo xhi
-160.0 160.0 ylo yhi
-40.0 280.0 zlo zhi
Atoms
1 1 0.0256796 -15.8876046 3.1659732
2 1 -0.0065539 -9.7285354 12.9535934
3 1 15.1406371 -4.8466739 3.1162295
4 1 9.3951884 -12.8727816 -2.9089440
5 1 14.4184503 -7.2812703 -1.2375049
6 1 12.9636755 -9.3139592 -2.7628439
7 1 14.3780078 -7.2818634 1.6393238
8 1 12.8903958 -9.3502145 2.9750983
9 1 12.2367531 -8.9637467 5.6879825
10 1 10.3382023 -10.5487465 6.6547385
11 1 11.4527893 -11.3685971 -1.4243042
12 1 11.4327788 -11.3846531 1.4564573
13 1 9.4216981 -12.8838973 2.7707077
14 1 9.0417300 -12.3516471 5.3032025
15 1 4.9205584 -15.1900605 -2.7368211
16 1 2.5481336 -15.9533355 -1.1992196
17 1 7.3427635 -14.3712624 -1.4109098
18 1 7.3764066 -14.3481077 1.4698484
19 1 2.5722631 -15.9062191 1.6779995
20 1 5.0013810 -15.1135985 3.0008920
21 1 4.8441349 -14.3648217 5.7119418
22 1 6.9359013 -13.0346534 6.6656665
23 1 -2.4554485 -14.2783985 7.2483193
24 1 -2.4559375 -12.7204259 9.7262100
25 1 0.0193595 -15.0501989 5.9942607
26 1 2.4878886 -14.2677016 7.2583143
27 1 0.0067480 -11.9153251 10.9756552
28 1 2.4800580 -12.7078927 9.7364676
29 1 4.8222915 -11.3485960 10.5068976
30 1 6.9005138 -11.6360921 8.9120310
31 1 2.4839865 -5.8135494 14.9155114
32 1 4.8472826 -4.0868468 14.9077684
33 1 2.5299584 -8.3862632 13.6275429
34 1 4.9695889 -9.2262534 12.3539249
35 1 12.9092381 -1.4901082 9.6732194
36 1 14.3807969 -1.9808593 7.1908902
37 1 14.3572494 -4.5759518 5.9472750
38 1 12.8674198 -6.6841240 7.2244043
39 1 11.3990899 -3.5900514 10.9367410
40 1 11.3956647 -6.1931435 9.7068958
41 1 9.3917619 -8.0099376 10.4916983
42 1 9.0260982 -10.0834728 8.9046702
43 1 9.3270143 -2.9086132 12.9223372
44 1 7.2796368 -4.9160264 13.6117448
45 1 7.3330855 -7.4994968 12.3459883
46 1 14.6303758 -4.7441678 -5.0877304
47 1 13.3165082 -6.5796622 -6.4667363
48 1 12.4142121 -8.8458738 -5.4843304
49 1 15.2266664 -4.9164661 -2.5331831
50 1 15.9543648 -2.5065880 -1.2709382
51 1 2.1937994 -14.7058789 -6.4315158
52 1 0.0524420 -15.3953996 -5.0417205
53 1 0.0450846 -16.0082576 -2.4846893
54 1 4.6305782 -14.5324426 -5.4594764
55 1 6.4781630 -13.0859896 -7.0164310
56 1 13.2500173 3.0334672 8.8133502
57 1 14.5793859 2.5897758 6.5707377
58 1 15.1906868 0.2145539 5.6246801
59 1 12.3450280 1.1640407 10.4252251
60 1 10.3843754 1.9758295 12.2760283
61 1 2.0980481 -0.5590157 16.0538382
62 1 -0.0373101 -2.1192280 16.0607442
63 1 -0.0289491 -4.6890599 15.5065117
64 1 4.5417074 -1.3494889 15.4916687
65 1 -2.5322491 -5.8277372 14.9018529
66 1 -6.8897824 -11.6914960 8.8475897
67 1 -6.8851099 -13.0720100 6.6451365
68 1 -4.8240131 -14.3759856 5.7008737
69 1 -4.8165626 -11.3787988 10.4768167
70 1 -4.9530402 -15.1344151 2.9760537
71 1 15.9340934 -2.4420318 1.6066033
72 1 15.9359147 0.1231686 2.9105799
73 1 8.9220667 -12.2374060 -5.7517515
74 1 10.4680949 -10.1710530 -7.0291318
75 1 -2.5113228 -15.9172575 1.6655921
76 1 -2.4662206 -15.9651661 -1.2129514
77 1 -2.5565800 -8.4010108 13.6134838
78 1 -4.9864191 -9.2555630 12.3251857
79 1 8.8386497 -0.0747899 13.5761814
80 1 6.3845019 0.6873366 14.8729865
81 1 -1.3705233 1.9464428 16.0241396
82 1 1.2735447 1.9534712 16.0312838
83 1 -2.1807894 -0.5703931 16.0424074
84 1 -4.6173570 -1.3747746 15.4670629
85 1 13.2456249 6.6552694 6.5345876
86 1 14.5764323 4.8284046 5.1627663
87 1 12.4259824 5.5462264 8.7905835
88 1 10.5808239 6.5422869 10.3771226
89 1 13.3121909 -2.9570640 -8.7453628
90 1 12.5021095 -5.4745377 -8.7273547
91 1 14.6273981 -2.5058936 -6.4961332
92 1 12.4050668 -1.0916597 -10.3615936
93 1 12.9502111 1.5658112 -9.6062633
94 1 11.4349307 3.6572751 -10.8768894
95 1 15.2202954 -0.1258618 -5.5467822
96 1 14.4059058 2.0649981 -7.1165783
97 1 14.3606031 4.6603554 -5.8731755
98 1 -1.2654400 -13.6068217 -8.7001776
99 1 -2.0842667 -14.7163406 -6.4440031
100 1 2.8872975 -12.1669710 -10.2989492
101 1 -9.0251564 -10.1295854 8.8531393
102 1 -8.9848815 -12.4100243 5.2633854
103 1 -9.3686839 -12.9395919 2.6897486
104 1 -4.8299303 -15.2139532 -2.7653979
105 1 -4.5272638 -14.5552738 -5.4852450
106 1 -7.3132721 -14.3856378 1.4175692
107 1 -7.2614320 -14.4079192 -1.4572212
108 1 -7.3593442 -7.5415086 12.3047034
109 1 -4.9050218 -4.1139714 14.8813986
110 1 -7.3262020 -4.9567440 13.5719372
111 1 5.4723072 3.4683529 14.8480439
112 1 2.7777659 4.0285019 15.4432902
113 1 9.4721551 4.7569512 12.2511109
114 1 7.0053161 5.5146622 13.5260516
115 1 15.9326824 2.6002331 1.3521995
116 1 15.1845840 5.0052968 2.6106390
117 1 14.3690529 7.3657085 1.3102219
118 1 14.3416984 7.3687182 -1.5677063
119 1 12.8475944 9.4286670 -2.9119719
120 1 12.2166052 9.0298117 -5.6264628
121 1 12.8662212 6.7582131 -7.1572992
122 1 11.4106348 6.2591511 -9.6467852
123 1 15.9510353 -0.0298232 -2.8290650
124 1 15.9274194 2.5359043 -1.5252949
125 1 15.1271998 4.9368044 -3.0390482
126 1 9.5665347 -8.9478830 -9.5318848
127 1 10.6707563 -6.4808635 -10.3234390
128 1 9.5616726 -4.7006007 -12.2032288
129 1 10.4585858 -1.9140157 -12.2227064
130 1 5.5765804 -11.8627400 -9.5193054
131 1 7.1099309 -9.7788265 -10.7825535
132 1 5.8339497 -8.0410365 -12.7963584
133 1 7.1052177 -5.4715075 -13.4914236
134 1 -9.3248466 2.9175747 -12.9218813
135 1 -15.1375334 4.8548550 -3.1185719
136 1 -9.3111581 -12.9212442 -2.9637489
137 1 -5.7308605 -8.0696208 -12.8249165
138 1 -6.3729508 -13.1187845 -7.0514548
139 1 -5.4671100 -11.8901908 -9.5485128
140 1 -8.8249345 -12.2853141 -5.7992770
141 1 -10.3737388 -10.2306287 -7.0823588
142 1 -12.3371918 -8.9093984 -5.5548485
143 1 -13.2439194 -6.6281697 -6.5655153
144 1 -7.0057000 -9.8141168 -10.8186554
145 1 -9.4733291 -8.9973181 -9.5783260
146 1 -10.6075344 -6.5246087 -10.3609710
147 1 -12.4393344 -5.5324416 -8.7803801
148 1 -5.4746734 -3.4608016 -14.8489336
149 1 -6.3842501 -0.6784543 -14.8735024
150 1 -7.0096341 -5.5070415 -13.5269194
151 1 -9.4770980 -4.7464300 -12.2513690
152 1 -8.8358275 0.0859988 -13.5779520
153 1 -10.3809678 -1.9634656 -12.2808931
154 1 -12.3437928 -1.1616621 -10.4269528
155 1 -13.2468480 -3.0623204 -8.8081346
156 1 -11.3935570 6.1977648 -9.7064204
157 1 -12.8648559 6.6884726 -7.2249458
158 1 -11.3969506 3.5970792 -10.9366615
159 1 -12.9078717 1.4962508 -9.6740946
160 1 -14.3545533 4.5826942 -5.9485912
161 1 -14.3793203 1.9869663 -7.1921582
162 1 -15.1904010 -0.2078580 -5.6257032
163 1 -14.5788501 -2.5898860 -6.5718830
164 1 -15.9534284 2.5139065 1.2682355
165 1 -15.9514379 0.0365712 2.8267147
166 1 -15.9326162 2.4504105 -1.6084949
167 1 -15.9358686 -0.1147825 -2.9111751
168 1 -12.8509837 -9.4247231 2.9097831
169 1 -11.3781439 -11.4474081 1.3909399
170 1 -11.3841695 -11.4292144 -1.4878738
171 1 -12.8986987 -9.3829696 -2.8325742
172 1 -14.3446670 -7.3635117 1.5650080
173 1 -14.3714597 -7.3603859 -1.3137314
174 1 -15.1863513 -4.9986180 -2.6131547
175 1 -14.5768311 -4.8181967 -5.1711702
176 1 -15.1296886 -4.9307145 3.0365444
177 1 -15.9286405 -2.5292665 1.5235636
178 1 -15.9338457 -2.5926968 -1.3529638
179 1 -2.7736130 -12.1803879 -10.3143224
180 1 -1.2765063 -1.9475831 -16.0317646
181 1 -2.0996208 0.5655931 -16.0534022
182 1 -4.5418707 1.3574926 -15.4909215
183 1 -2.7810842 -4.0221128 -15.4443583
184 1 -1.4108069 -6.3995413 -14.8153812
185 1 -10.3338593 -10.5784290 6.6142436
186 1 -12.2203706 -9.0253530 5.6254397
187 1 -12.8708443 -6.7512124 7.1555937
188 1 -14.6281030 2.5109030 6.4926107
189 1 -14.6299424 4.7489211 5.0845412
190 1 -15.2251018 4.9229332 2.5300253
191 1 -15.2212809 0.1321644 5.5439305
192 1 -14.4156623 7.2873839 1.2339941
193 1 -10.3578787 10.5235658 -6.6640031
194 1 -9.0286826 10.0800429 -8.9059335
195 1 -9.3904589 8.0141101 -10.4896781
196 1 -12.2358615 8.9632563 -5.6906725
197 1 -7.3324931 7.5061801 -12.3422781
198 1 -2.8877183 -8.4872967 -13.4932169
199 1 -1.4070287 -10.5816192 -12.1856321
200 1 -7.2786047 4.9240102 -13.6094108
201 1 -4.8472629 4.0945126 -14.9056712
202 1 -14.3731744 7.2904653 -1.6434714
203 1 -12.8834674 9.3583030 -2.9796740
204 1 -14.3637655 -4.6537884 5.8706489
205 1 -14.4081061 -2.0585302 7.1139972
206 1 -12.5024169 5.4787800 8.7242516
207 1 -13.3131523 2.9623024 8.7421259
208 1 -13.3162933 6.5828309 6.4639535
209 1 -12.4134403 8.8484433 5.4819319
210 1 -10.4678133 10.1729297 7.0268351
211 1 -9.4058811 -8.0601670 10.4404565
212 1 1.3788766 -13.6008644 -8.6922501
213 1 2.1784590 0.5763924 -16.0425096
214 1 0.0356722 2.1248726 -16.0600021
215 1 1.3676695 -1.9404489 -16.0251104
216 1 4.6146153 1.3805889 -15.4673632
217 1 4.9021788 4.1194791 -14.8808118
218 1 2.5300699 5.8332098 -14.9000817
219 1 2.5549034 8.4059833 -13.6107288
220 1 2.8791664 -4.0073693 -15.4302112
221 1 5.5677866 -3.4329508 -14.8207498
222 1 6.4650412 -0.6466977 -14.8399814
223 1 8.9081036 0.1286054 -13.5303058
224 1 9.3775051 2.9650833 -12.8728669
225 1 7.3230290 4.9619061 -13.5717633
226 1 -6.9034520 13.0472852 -6.6746328
227 1 -9.0441039 12.3576032 -5.2852486
228 1 -6.8939231 11.6399012 -8.9121574
229 1 -4.8418898 14.3649315 -5.7135691
230 1 -4.8212371 11.3521902 -10.5034983
231 1 -2.4787797 12.7103108 -9.7336363
232 1 -0.0043348 11.9195801 -10.9710353
233 1 -2.4847655 5.8199251 -14.9128950
234 1 0.0273092 4.6952202 -15.5046505
235 1 -4.9701145 9.2321521 -12.3493059
236 1 -2.5306081 8.3921393 -13.6238044
237 1 0.0066805 9.7337503 -12.9496751
238 1 -11.4296234 11.3881974 -1.4535103
239 1 -9.4243209 12.8887459 -2.7390565
240 1 -7.3801183 14.3465995 -1.4659336
241 1 -12.9618573 9.3171866 2.7604919
242 1 -11.4512873 11.3701451 1.4240243
243 1 -9.3949910 12.8726639 2.9101019
244 1 -12.9527425 -1.5593712 9.6038975
245 1 -12.4068811 1.0975416 10.3587996
246 1 -11.4150161 -6.2521081 9.6461690
247 1 -11.4384045 -3.6504527 10.8755286
248 1 -9.3806396 -2.9591486 12.8719488
249 1 -8.9109096 -0.1228238 13.5285117
250 1 1.5203716 -10.5746676 -12.1780499
251 1 1.5164098 -6.3920899 -14.8081637
252 1 2.9965383 -8.4728098 -13.4785859
253 1 -5.5708234 3.4384815 14.8183264
254 1 -6.4679889 0.6524436 14.8384454
255 1 -2.8827398 4.0131868 15.4280319
256 1 -1.5206182 6.3976551 14.8053286
257 1 -9.5632934 4.7054433 12.2000922
258 1 -10.6714449 6.4846077 10.3203756
259 1 -10.4606216 1.9195418 12.2200974
260 1 -7.1076846 5.4763591 13.4881554
261 1 -9.5670810 8.9506660 9.5287231
262 1 2.8816845 8.4931563 13.4908197
263 1 1.4060490 6.4055988 14.8132156
264 1 5.7239064 8.0763838 12.8237648
265 1 9.4670152 9.0025344 9.5796671
266 1 7.0002636 9.8199794 10.8168544
267 1 12.3356112 8.9161112 5.5475836
268 1 10.3744789 10.2298514 7.0823974
269 1 12.8959122 9.3878926 2.8289478
270 1 11.3810794 11.4327262 1.4845290
271 1 11.3746065 11.4506339 -1.3933180
272 1 9.3679618 12.9401567 -2.6895465
273 1 9.0036993 12.4072960 -5.2375978
274 1 6.8662717 13.0853102 -6.6384482
275 1 2.7690276 12.1843008 10.3109323
276 1 1.4017330 10.5861363 12.1823186
277 1 5.4627952 11.8945097 9.5456027
278 1 8.8242152 12.2865257 5.7978045
279 1 9.3085882 12.9240350 2.9596501
280 1 6.3704754 13.1216117 7.0484306
281 1 -1.5248387 10.5781499 12.1744666
282 1 -3.0004476 8.4771926 13.4749599
283 1 -5.8366133 8.0449897 12.7926584
284 1 -7.1116479 9.7814482 10.7790427
285 1 2.0820361 14.7183307 6.4401779
286 1 1.2620330 13.6096482 8.6962505
287 1 4.5242115 14.5576431 5.4814745
288 1 4.8259422 15.2160227 2.7609708
289 1 7.2578789 14.4104537 1.4498421
290 1 7.3087468 14.3869684 -1.4273703
291 1 -2.1964383 14.7067030 6.4287301
292 1 -1.3821860 13.6026891 8.6888685
293 1 -0.0556372 15.3962319 5.0391440
294 1 -4.6331090 14.5324801 5.4572289
295 1 -4.9242542 15.1891716 2.7351071
296 1 -7.3445790 14.3702987 1.4112754
297 1 -2.8905852 12.1690516 10.2955682
298 1 -5.5788354 11.8642286 9.5161284
299 1 -6.4796338 13.0864149 7.0142794
300 1 -8.9221495 12.2378961 5.7505801
301 1 -0.0504861 16.0086074 2.4823305
302 1 2.4603866 15.9662714 1.2102480
303 1 2.5033861 15.9183772 -1.6668385
304 1 4.9429821 15.1373357 -2.9779224
305 1 4.7926158 14.3914809 -5.6882456
306 1 2.4488603 14.2817550 -7.2439342
307 1 2.4595386 12.7238564 -9.7208113
308 1 -0.0353290 15.8876578 -3.1656132
309 1 -0.0257921 15.0507446 -5.9928663
310 1 -2.4895607 14.2682398 -7.2566827
311 1 -2.5822044 15.9043746 -1.6802125
312 1 -5.0105239 15.1099456 -3.0040336
313 1 -2.5546580 15.9524586 1.1970007
314 1 9.0197693 10.1296833 -8.8585158
315 1 6.8765145 11.6774520 -8.8764118
316 1 10.3350078 10.5802893 -6.6094718
317 1 9.4016683 8.0649147 -10.4405847
318 1 7.3559706 7.5456009 -12.3042118
319 1 4.9835159 9.2589832 -12.3237909
320 1 4.8135124 11.3784814 -10.4785631

99
examples/USER/lb/planewall/in.planewall_default_gamma Executable file
View File

@ -0,0 +1,99 @@
#===========================================================================#
# Rigid sphere freely moving near a stationary plane wall in a system #
# undergoing shear flow. #
# Every 10 time steps the center of mass velocity and angular velocity of #
# the sphere are printed to the screen. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. Thus, the colloidal objects will have #
# a slightly larger "hydrodynamic" radii than given by the placement of #
# the particle nodes. #
# #
# Sample output from this run can be found in the file: #
# 'wall_defaultgamma.out' #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1
read_data data.one_radius16d2
#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
mass * 100.0
timestep 3.0
group sphere1 id <> 1 320
#----------------------------------------------------------------------------
# Colloidal particle is initially stationary.
#----------------------------------------------------------------------------
velocity all set 0.0 0.0 0.0 units box
#----------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the viscous_lb fix.
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 1
# correspond to a surface area of 10.3059947).
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh.
# Create shear in the system, by giving the upper z-wall a velocity of 0.0001
# along the y-direction, while keeping the lower z-wall stationary.
#-----------------------------------------------------------------------------
fix 1 all lb/fluid 1 1 1.0 1.0 setArea 1 10.3059947 dx 4.0 dm 10.0 trilinear zwall_velocity 0.0 0.0001
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the particles.
#----------------------------------------------------------------------------
fix 2 all lb/viscous
#----------------------------------------------------------------------------
# Integrate the motion of the particles, constraining them to move and
# rotate together as a single rigid spherical object.
#----------------------------------------------------------------------------
fix 3 all rigid group 1 sphere1
#----------------------------------------------------------------------------
# Create variables for the center-of-mass and angular velocities, and output
# these quantities to the screen.
#----------------------------------------------------------------------------
variable vx equal vcm(all,x)
variable vy equal vcm(all,y)
variable vz equal vcm(all,z)
variable omegax equal omega(all,x)
variable omegay equal omega(all,y)
variable omegaz equal omega(all,z)
thermo_style custom v_vx v_vy v_vz v_omegax v_omegay v_omegaz
thermo 10
run 200000

92
examples/USER/lb/planewall/in.planewall_set_gamma Executable file
View File

@ -0,0 +1,92 @@
#===========================================================================#
# Rigid sphere freely moving near a stationary plane wall in a system #
# undergoing shear flow. #
# Every 10 time steps the center of mass velocity and angular velocity of #
# the sphere are printed to the screen. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 13.655 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# #
# Sample output from this run can be found in the file: #
# 'wall_setgamma.out' #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1
read_data data.one_radius16d2
#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
mass * 100.0
timestep 4.0
group sphere1 id <> 1 320
#----------------------------------------------------------------------------
# Colloidal particle is initially stationary.
#----------------------------------------------------------------------------
velocity all set 0.0 0.0 0.0 units box
#----------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid density = 1.0, fluid viscosity = 1.0, value
# for gamma=13.655, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Create shear in the system, by giving the upper z-wall a velocity of 0.0001
# along the y-direction, while keeping the lower z-wall stationary.
#-----------------------------------------------------------------------------
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.655 dx 4.0 dm 10.0 zwall_velocity 0.0 0.0001
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
# NOTE: This fix should only be used when the user specifies a value for
# gamma (through the setGamma keyword) in the lb_fluid fix.
#----------------------------------------------------------------------------
fix 2 all lb/rigid/pc/sphere group 1 sphere1
#----------------------------------------------------------------------------
# Create variables for the center-of-mass and angular velocities, and output
# these quantities to the screen.
#----------------------------------------------------------------------------
variable vx equal vcm(all,x)
variable vy equal vcm(all,y)
variable vz equal vcm(all,z)
variable omegax equal omega(all,x)
variable omegay equal omega(all,y)
variable omegaz equal omega(all,z)
thermo_style custom v_vx v_vy v_vz v_omegax v_omegay v_omegaz
thermo 10
run 200000

20031
examples/USER/lb/planewall/wall_defaultgamma.out Executable file
View File

File diff suppressed because it is too large Load Diff

20031
examples/USER/lb/planewall/wall_setgamma.out Executable file
View File

File diff suppressed because it is too large Load Diff

1040
examples/USER/lb/polymer/data.polymer Executable file
View File

File diff suppressed because it is too large Load Diff

41041
examples/USER/lb/polymer/dump.polymer.lammpstrj Executable file
View File

File diff suppressed because it is too large Load Diff

105
examples/USER/lb/polymer/in.polymer Executable file
View File

@ -0,0 +1,105 @@
#===========================================================================#
# polymer test #
# #
# Run consists of a lone 32-bead coarse-grained polymer #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the monomer-fluid interaction #
# force) is set by the user (gamma = 0.03 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# Sample output from this run can be found in the file: #
# 'dump.polymer.lammpstrj' #
# and viewed using, e.g., the VMD software. #
# #
# Santtu Ollila #
# santtu.ollila@aalto.fi #
# Aalto University #
# August 14, 2013 #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style hybrid molecular
special_bonds fene
read_data data.polymer
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
#----------------------------------------------------------------------------
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each monomer (use a truncated and shifted Lennard-Jones potential).
#----------------------------------------------------------------------------
bond_style fene
bond_coeff 1 60.0 2.25 4.14195 1.5
pair_style lj/cut 1.68369
pair_coeff 1 1 4.14195 1.5 1.68369
pair_coeff 1 2 4.14195 1.5 1.68369
pair_coeff 2 2 0 1.0
mass * 0.000000771064
timestep 0.00003
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
# particles. This is accomplished through the use of the rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid viscosity = 0.023333333,
# fluid density= 0.0000166368,
# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=15003). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all of
# the atoms in the system. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the force
# calculation through the use of the 'innerNodes' keyword.
# NOTE: This fix should only be used when the user specifies a value for
# gamma (through the setGamma keyword) in the lb_fluid fix.
#----------------------------------------------------------------------------
fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 3 all lb/momentum 10000 linear 1 1 1
#----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------
dump 1 ForceAtoms custom 2000 dump.polymer.lammpstrj id x y z vx vy vz
run 2000001

19
examples/USER/lb/polymer/out.polymer Executable file
View File

@ -0,0 +1,19 @@
LAMMPS (22 Feb 2013)
Scanning data file ...
1 = max bonds/atom
Reading data file ...
orthogonal box = (0 0 0) to (40 40 40)
2 by 2 by 2 MPI processor grid
992 atoms
31 bonds
Finding 1-2 1-3 1-4 neighbors ...
2 = max # of 1-2 neighbors
2 = max # of special neighbors
32 atoms in group ForceAtoms
960 atoms in group FluidAtoms
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (fix_lb_fluid.cpp:354)
32 rigid bodies with 992 atoms
Setting up run ...
Memory usage per processor = 0.539707 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8.2758489 2790.7741 2782.4982 1.8503717e-20