forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10748 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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This directory has examples of how to model aspherical particles with
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or without solvent, in 3 styles LAMMPS provides. Namely point
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ellipsoids, rigid bodies, and generalized aspherical bodies built from
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line/triangle surface facets in 2d/3d.
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Each directory has an input script, a data file (if needed), and an
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output log file. Most of the systems are 2d, but many of the runs
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take a minute or two on 8 processors, since these are complicated
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systems. Some of the directories include a Python script, which can
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be used with the Pizza.py tool to create the data file, e.g. for
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collections of rigid bodies.
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The web site for Pizza.py is http://pizza.sandia.gov
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For example, If you have Pizza.py installed you can type "pizza.py -f
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box.py", which creates the data.box data file in the box dir.
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If you uncomment the dump or dump image lines in the input scripts the
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runs will produce dump files or JPG images which you can view or
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animate. See the Movies page of the LAMMPS web site
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(http://lammps.sandia.gov/movies.html), for animations of these
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scripts. Most were done using the dump image command. A few were
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done using the gl tool in Pizza.py; the Pizza.py scripts that do the
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animation are given in the directory, e.g. as line.viz.py.
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These are the directories in ASPHERE. SRD refers to a coarse-grained
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stochastic rotation dynamics solvent, using the fix srd command.
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box = 2d rigid box particles in SRDs, self-diffusion and viscosity
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dimer = 2d rigid dimers in SRDs, self-diffusion and viscosity
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ellipsoid = 2d ellipsoids in SRDs, self-diffusion and viscosity
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line = 2d line-faceted rigid particles, NEMD shearing for viscosity,
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implicit and in SRDs
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poly = 2d poly-disperse spheroids in SRDs, self-diffusion and viscosity
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star = 2d rigid star particles in SRDs, self-diffusion and viscosity
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tri = 3d triangle-faceted rigid particles in SRDs, NEMD shearing for viscosity
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# create set of randomly oriented boxes
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p = patch(0.15)
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p.dim = 2
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p.extratype = 1
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p.style = "sphere"
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p.extra = "Molecules"
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p.seed = 596982
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p.build(30,"box2d",6,3,0.8,1)
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p.write("data.box")
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LAMMPS data file for Nanoparticles
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420 atoms
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2 atom types
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-19.1446896794 19.1446896794 xlo xhi
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-19.1446896794 19.1446896794 ylo yhi
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-0.5 0.5 zlo zhi
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Atoms
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5 1 1 1 16.1084 0.749953 0 0 0 0
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6 1 1 1 16.5645 1.40721 0 0 0 0
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7 1 1 1 12.9696 -0.966879 0 0 0 0
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8 1 1 1 13.4257 -0.309626 0 0 0 0
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9 1 1 1 13.8818 0.347628 0 0 0 0
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72 1 1 1 1.7036 0.600906 0 0 0 0
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76 1 1 1 0.407695 3.52676 0 0 0 0
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90 1 1 1 8.72854 18.7732 0 0 -1 0
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93 1 1 1 10.3656 -17.1413 0 0 0 0
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104 1 1 1 -8.54334 7.72348 0 0 0 0
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105 1 1 1 -8.65091 3.41669 0 0 0 0
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106 1 1 1 -8.92938 4.16666 0 0 0 0
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111 1 1 1 -7.90094 3.69516 0 0 0 0
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115 1 1 1 2.46688 13.9727 0 0 0 0
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|
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
228 1 1 1 -6.06238 1.74552 0 0 0 0
|
||||
229 1 1 1 -6.54472 1.10728 0 0 0 0
|
||||
230 1 1 1 -7.02706 0.469034 0 0 0 0
|
||||
231 1 1 1 -3.33889 2.69557 0 0 0 0
|
||||
232 1 1 1 -3.82123 2.05733 0 0 0 0
|
||||
233 1 1 1 -4.30357 1.41909 0 0 0 0
|
||||
234 1 1 1 -4.7859 0.780844 0 0 0 0
|
||||
235 1 1 1 -5.26824 0.142603 0 0 0 0
|
||||
236 1 1 1 -5.75057 -0.495638 0 0 0 0
|
||||
237 1 1 1 -3.97713 3.1779 0 0 0 0
|
||||
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|
||||
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|
||||
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|
||||
241 1 1 1 5.97301 4.23888 0 0 0 0
|
||||
242 1 1 1 5.34275 3.74616 0 0 0 0
|
||||
243 1 1 1 4.71249 3.25345 0 0 0 0
|
||||
244 1 1 1 4.08223 2.76073 0 0 0 0
|
||||
245 1 1 1 8.21897 3.96379 0 0 0 0
|
||||
246 1 1 1 7.58871 3.47108 0 0 0 0
|
||||
247 1 1 1 6.95845 2.97836 0 0 0 0
|
||||
248 1 1 1 6.32818 2.48564 0 0 0 0
|
||||
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|
||||
250 1 1 1 5.06766 1.50021 0 0 0 0
|
||||
251 1 1 1 7.72625 4.59406 0 0 0 0
|
||||
252 1 1 1 4.57494 2.13047 0 0 0 0
|
||||
253 1 1 1 -6.11367 16.186 0 0 0 0
|
||||
254 1 1 1 -6.91119 16.123 0 0 0 0
|
||||
255 1 1 1 -7.7087 16.06 0 0 0 0
|
||||
256 1 1 1 -8.50621 15.997 0 0 0 0
|
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257 1 1 1 -9.30373 15.9339 0 0 0 0
|
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258 1 1 1 -10.1012 15.8709 0 0 0 0
|
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259 1 1 1 -5.98763 14.591 0 0 0 0
|
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260 1 1 1 -6.78514 14.528 0 0 0 0
|
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261 1 1 1 -7.58265 14.4649 0 0 0 0
|
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262 1 1 1 -8.38017 14.4019 0 0 0 0
|
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263 1 1 1 -9.17768 14.3389 0 0 0 0
|
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264 1 1 1 -9.97519 14.2759 0 0 0 0
|
||||
265 1 1 1 -6.05065 15.3885 0 0 0 0
|
||||
266 1 1 1 -10.0382 15.0734 0 0 0 0
|
||||
267 1 1 1 -2.11365 8.3904 0 0 0 0
|
||||
268 1 1 1 -2.85146 8.69966 0 0 0 0
|
||||
269 1 1 1 -3.58926 9.00892 0 0 0 0
|
||||
270 1 1 1 -4.32707 9.31818 0 0 0 0
|
||||
271 1 1 1 -5.06488 9.62744 0 0 0 0
|
||||
272 1 1 1 -5.80268 9.9367 0 0 0 0
|
||||
273 1 1 1 -2.73217 6.91479 0 0 0 0
|
||||
274 1 1 1 -3.46998 7.22405 0 0 0 0
|
||||
275 1 1 1 -4.20779 7.53331 0 0 0 0
|
||||
276 1 1 1 -4.94559 7.84257 0 0 0 0
|
||||
277 1 1 1 -5.6834 8.15183 0 0 0 0
|
||||
278 1 1 1 -6.4212 8.46109 0 0 0 0
|
||||
279 1 1 1 -2.42291 7.65259 0 0 0 0
|
||||
280 1 1 1 -6.11194 9.19889 0 0 0 0
|
||||
281 1 1 1 -9.72915 16.046 0 0 0 0
|
||||
282 1 1 1 -10.3097 15.4955 0 0 0 0
|
||||
283 1 1 1 -10.8902 14.9451 0 0 0 0
|
||||
284 1 1 1 -11.4706 14.3946 0 0 0 0
|
||||
285 1 1 1 -12.0511 13.8441 0 0 0 0
|
||||
286 1 1 1 -12.6316 13.2936 0 0 0 0
|
||||
287 1 1 1 -8.62821 14.885 0 0 0 0
|
||||
288 1 1 1 -9.2087 14.3345 0 0 0 0
|
||||
289 1 1 1 -9.7892 13.7841 0 0 0 0
|
||||
290 1 1 1 -10.3697 13.2336 0 0 0 0
|
||||
291 1 1 1 -10.9502 12.6831 0 0 0 0
|
||||
292 1 1 1 -11.5307 12.1326 0 0 0 0
|
||||
293 1 1 1 -9.17868 15.4655 0 0 0 0
|
||||
294 1 1 1 -12.0812 12.7131 0 0 0 0
|
||||
295 1 1 1 5.72033 -3.07105 0 0 0 0
|
||||
296 1 1 1 6.51888 -3.02294 0 0 0 0
|
||||
297 1 1 1 7.31743 -2.97482 0 0 0 0
|
||||
298 1 1 1 8.11598 -2.92671 0 0 0 0
|
||||
299 1 1 1 8.91454 -2.8786 0 0 0 0
|
||||
300 1 1 1 9.71309 -2.83049 0 0 0 0
|
||||
301 1 1 1 5.62411 -1.47394 0 0 0 0
|
||||
302 1 1 1 6.42266 -1.42583 0 0 0 0
|
||||
303 1 1 1 7.22121 -1.37772 0 0 0 0
|
||||
304 1 1 1 8.01976 -1.32961 0 0 0 0
|
||||
305 1 1 1 8.81831 -1.2815 0 0 0 0
|
||||
306 1 1 1 9.61687 -1.23338 0 0 0 0
|
||||
307 1 1 1 5.67222 -2.27249 0 0 0 0
|
||||
308 1 1 1 9.66498 -2.03194 0 0 0 0
|
||||
309 1 1 1 15.2831 18.234 0 0 0 0
|
||||
310 1 1 1 14.9534 18.9629 0 0 0 0
|
||||
311 1 1 1 14.6237 -18.5976 0 0 1 0
|
||||
312 1 1 1 14.2939 -17.8687 0 0 1 0
|
||||
313 1 1 1 13.9642 -17.1398 0 0 1 0
|
||||
314 1 1 1 13.6345 -16.4109 0 0 1 0
|
||||
315 1 1 1 13.8253 17.5745 0 0 0 0
|
||||
316 1 1 1 13.4956 18.3034 0 0 0 0
|
||||
317 1 1 1 13.1659 19.0323 0 0 0 0
|
||||
318 1 1 1 12.8361 -18.5282 0 0 1 0
|
||||
319 1 1 1 12.5064 -17.7993 0 0 1 0
|
||||
320 1 1 1 12.1767 -17.0704 0 0 1 0
|
||||
321 1 1 1 14.5542 17.9043 0 0 0 0
|
||||
322 1 1 1 12.9056 -16.7407 0 0 1 0
|
||||
323 1 1 1 2.47062 17.9997 0 0 0 0
|
||||
324 1 1 1 2.25129 17.2303 0 0 0 0
|
||||
325 1 1 1 2.03196 16.461 0 0 0 0
|
||||
326 1 1 1 1.81263 15.6916 0 0 0 0
|
||||
327 1 1 1 1.59329 14.9223 0 0 0 0
|
||||
328 1 1 1 1.37396 14.1529 0 0 0 0
|
||||
329 1 1 1 4.00931 17.561 0 0 0 0
|
||||
330 1 1 1 3.78998 16.7917 0 0 0 0
|
||||
331 1 1 1 3.57065 16.0223 0 0 0 0
|
||||
332 1 1 1 3.35132 15.253 0 0 0 0
|
||||
333 1 1 1 3.13199 14.4836 0 0 0 0
|
||||
334 1 1 1 2.91266 13.7143 0 0 0 0
|
||||
335 1 1 1 3.23997 17.7803 0 0 0 0
|
||||
336 1 1 1 2.14331 13.9336 0 0 0 0
|
||||
337 1 1 1 15.0414 14.311 0 0 0 0
|
||||
338 1 1 1 14.3946 13.8403 0 0 0 0
|
||||
339 1 1 1 13.7477 13.3696 0 0 0 0
|
||||
340 1 1 1 13.1009 12.8988 0 0 0 0
|
||||
341 1 1 1 12.454 12.4281 0 0 0 0
|
||||
342 1 1 1 11.8072 11.9574 0 0 0 0
|
||||
343 1 1 1 15.9829 13.0173 0 0 0 0
|
||||
344 1 1 1 15.336 12.5466 0 0 0 0
|
||||
345 1 1 1 14.6892 12.0759 0 0 0 0
|
||||
346 1 1 1 14.0423 11.6051 0 0 0 0
|
||||
347 1 1 1 13.3955 11.1344 0 0 0 0
|
||||
348 1 1 1 12.7486 10.6637 0 0 0 0
|
||||
349 1 1 1 15.5121 13.6642 0 0 0 0
|
||||
350 1 1 1 12.2779 11.3105 0 0 0 0
|
||||
351 1 1 1 18.9199 -6.6268 0 0 0 0
|
||||
352 1 1 1 18.1207 -6.66214 0 0 0 0
|
||||
353 1 1 1 17.3215 -6.69749 0 0 0 0
|
||||
354 1 1 1 16.5222 -6.73284 0 0 0 0
|
||||
355 1 1 1 15.723 -6.76818 0 0 0 0
|
||||
356 1 1 1 14.9238 -6.80353 0 0 0 0
|
||||
357 1 1 1 18.9906 -8.22523 0 0 0 0
|
||||
358 1 1 1 18.1914 -8.26058 0 0 0 0
|
||||
359 1 1 1 17.3922 -8.29593 0 0 0 0
|
||||
360 1 1 1 16.5929 -8.33127 0 0 0 0
|
||||
361 1 1 1 15.7937 -8.36662 0 0 0 0
|
||||
362 1 1 1 14.9945 -8.40197 0 0 0 0
|
||||
363 1 1 1 18.9552 -7.42601 0 0 0 0
|
||||
364 1 1 1 14.9591 -7.60275 0 0 0 0
|
||||
365 1 1 1 9.86402 -8.4027 0 0 0 0
|
||||
366 1 1 1 9.55201 -7.66605 0 0 0 0
|
||||
367 1 1 1 9.24 -6.9294 0 0 0 0
|
||||
368 1 1 1 8.92799 -6.19276 0 0 0 0
|
||||
369 1 1 1 8.61599 -5.45611 0 0 0 0
|
||||
370 1 1 1 8.30398 -4.71946 0 0 0 0
|
||||
371 1 1 1 8.39073 -9.02672 0 0 0 0
|
||||
372 1 1 1 8.07872 -8.29007 0 0 0 0
|
||||
373 1 1 1 7.76671 -7.55342 0 0 0 0
|
||||
374 1 1 1 7.4547 -6.81677 0 0 0 0
|
||||
375 1 1 1 7.14269 -6.08013 0 0 0 0
|
||||
376 1 1 1 6.83068 -5.34348 0 0 0 0
|
||||
377 1 1 1 9.12737 -8.71471 0 0 0 0
|
||||
378 1 1 1 7.56733 -5.03147 0 0 0 0
|
||||
379 1 1 1 -16.2195 -19.1437 0 0 0 0
|
||||
380 1 1 1 -15.7317 18.5116 0 0 -1 0
|
||||
381 1 1 1 -15.244 17.8775 0 0 -1 0
|
||||
382 1 1 1 -14.7562 17.2434 0 0 -1 0
|
||||
383 1 1 1 -14.2684 16.6093 0 0 -1 0
|
||||
384 1 1 1 -13.7806 15.9752 0 0 -1 0
|
||||
385 1 1 1 -14.9513 -18.1681 0 0 0 0
|
||||
386 1 1 1 -14.4635 -18.8022 0 0 0 0
|
||||
387 1 1 1 -13.9758 18.853 0 0 -1 0
|
||||
388 1 1 1 -13.488 18.2189 0 0 -1 0
|
||||
389 1 1 1 -13.0002 17.5849 0 0 -1 0
|
||||
390 1 1 1 -12.5124 16.9508 0 0 -1 0
|
||||
391 1 1 1 -15.5854 -18.6559 0 0 0 0
|
||||
392 1 1 1 -13.1465 16.463 0 0 -1 0
|
||||
393 1 1 1 0.198913 11.9537 0 0 0 0
|
||||
394 1 1 1 -0.594369 12.0571 0 0 0 0
|
||||
395 1 1 1 -1.38765 12.1606 0 0 0 0
|
||||
396 1 1 1 -2.18093 12.264 0 0 0 0
|
||||
397 1 1 1 -2.97421 12.3675 0 0 0 0
|
||||
398 1 1 1 -3.7675 12.471 0 0 0 0
|
||||
399 1 1 1 -0.00800755 10.3671 0 0 0 0
|
||||
400 1 1 1 -0.801289 10.4706 0 0 0 0
|
||||
401 1 1 1 -1.59457 10.574 0 0 0 0
|
||||
402 1 1 1 -2.38785 10.6775 0 0 0 0
|
||||
403 1 1 1 -3.18113 10.7809 0 0 0 0
|
||||
404 1 1 1 -3.97442 10.8844 0 0 0 0
|
||||
405 1 1 1 0.0954527 11.1604 0 0 0 0
|
||||
406 1 1 1 -3.87096 11.6777 0 0 0 0
|
||||
407 1 1 1 -3.4936 18.9783 0 0 0 0
|
||||
408 1 1 1 -3.96865 -18.6674 0 0 1 0
|
||||
409 1 1 1 -4.44369 -18.0237 0 0 1 0
|
||||
410 1 1 1 -4.91874 -17.38 0 0 1 0
|
||||
411 1 1 1 -5.39379 -16.7363 0 0 1 0
|
||||
412 1 1 1 -5.86883 -16.0927 0 0 1 0
|
||||
413 1 1 1 -4.78097 18.0282 0 0 0 0
|
||||
414 1 1 1 -5.25602 18.6719 0 0 0 0
|
||||
415 1 1 1 -5.73106 -18.9738 0 0 1 0
|
||||
416 1 1 1 -6.20611 -18.3301 0 0 1 0
|
||||
417 1 1 1 -6.68116 -17.6864 0 0 1 0
|
||||
418 1 1 1 -7.1562 -17.0427 0 0 1 0
|
||||
419 1 1 1 -4.13728 18.5033 0 0 0 0
|
||||
420 1 1 1 -6.51252 -16.5677 0 0 1 0
|
||||
|
||||
Molecules
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 2
|
||||
16 2
|
||||
17 2
|
||||
18 2
|
||||
19 2
|
||||
20 2
|
||||
21 2
|
||||
22 2
|
||||
23 2
|
||||
24 2
|
||||
25 2
|
||||
26 2
|
||||
27 2
|
||||
28 2
|
||||
29 3
|
||||
30 3
|
||||
31 3
|
||||
32 3
|
||||
33 3
|
||||
34 3
|
||||
35 3
|
||||
36 3
|
||||
37 3
|
||||
38 3
|
||||
39 3
|
||||
40 3
|
||||
41 3
|
||||
42 3
|
||||
43 4
|
||||
44 4
|
||||
45 4
|
||||
46 4
|
||||
47 4
|
||||
48 4
|
||||
49 4
|
||||
50 4
|
||||
51 4
|
||||
52 4
|
||||
53 4
|
||||
54 4
|
||||
55 4
|
||||
56 4
|
||||
57 5
|
||||
58 5
|
||||
59 5
|
||||
60 5
|
||||
61 5
|
||||
62 5
|
||||
63 5
|
||||
64 5
|
||||
65 5
|
||||
66 5
|
||||
67 5
|
||||
68 5
|
||||
69 5
|
||||
70 5
|
||||
71 6
|
||||
72 6
|
||||
73 6
|
||||
74 6
|
||||
75 6
|
||||
76 6
|
||||
77 6
|
||||
78 6
|
||||
79 6
|
||||
80 6
|
||||
81 6
|
||||
82 6
|
||||
83 6
|
||||
84 6
|
||||
85 7
|
||||
86 7
|
||||
87 7
|
||||
88 7
|
||||
89 7
|
||||
90 7
|
||||
91 7
|
||||
92 7
|
||||
93 7
|
||||
94 7
|
||||
95 7
|
||||
96 7
|
||||
97 7
|
||||
98 7
|
||||
99 8
|
||||
100 8
|
||||
101 8
|
||||
102 8
|
||||
103 8
|
||||
104 8
|
||||
105 8
|
||||
106 8
|
||||
107 8
|
||||
108 8
|
||||
109 8
|
||||
110 8
|
||||
111 8
|
||||
112 8
|
||||
113 9
|
||||
114 9
|
||||
115 9
|
||||
116 9
|
||||
117 9
|
||||
118 9
|
||||
119 9
|
||||
120 9
|
||||
121 9
|
||||
122 9
|
||||
123 9
|
||||
124 9
|
||||
125 9
|
||||
126 9
|
||||
127 10
|
||||
128 10
|
||||
129 10
|
||||
130 10
|
||||
131 10
|
||||
132 10
|
||||
133 10
|
||||
134 10
|
||||
135 10
|
||||
136 10
|
||||
137 10
|
||||
138 10
|
||||
139 10
|
||||
140 10
|
||||
141 11
|
||||
142 11
|
||||
143 11
|
||||
144 11
|
||||
145 11
|
||||
146 11
|
||||
147 11
|
||||
148 11
|
||||
149 11
|
||||
150 11
|
||||
151 11
|
||||
152 11
|
||||
153 11
|
||||
154 11
|
||||
155 12
|
||||
156 12
|
||||
157 12
|
||||
158 12
|
||||
159 12
|
||||
160 12
|
||||
161 12
|
||||
162 12
|
||||
163 12
|
||||
164 12
|
||||
165 12
|
||||
166 12
|
||||
167 12
|
||||
168 12
|
||||
169 13
|
||||
170 13
|
||||
171 13
|
||||
172 13
|
||||
173 13
|
||||
174 13
|
||||
175 13
|
||||
176 13
|
||||
177 13
|
||||
178 13
|
||||
179 13
|
||||
180 13
|
||||
181 13
|
||||
182 13
|
||||
183 14
|
||||
184 14
|
||||
185 14
|
||||
186 14
|
||||
187 14
|
||||
188 14
|
||||
189 14
|
||||
190 14
|
||||
191 14
|
||||
192 14
|
||||
193 14
|
||||
194 14
|
||||
195 14
|
||||
196 14
|
||||
197 15
|
||||
198 15
|
||||
199 15
|
||||
200 15
|
||||
201 15
|
||||
202 15
|
||||
203 15
|
||||
204 15
|
||||
205 15
|
||||
206 15
|
||||
207 15
|
||||
208 15
|
||||
209 15
|
||||
210 15
|
||||
211 16
|
||||
212 16
|
||||
213 16
|
||||
214 16
|
||||
215 16
|
||||
216 16
|
||||
217 16
|
||||
218 16
|
||||
219 16
|
||||
220 16
|
||||
221 16
|
||||
222 16
|
||||
223 16
|
||||
224 16
|
||||
225 17
|
||||
226 17
|
||||
227 17
|
||||
228 17
|
||||
229 17
|
||||
230 17
|
||||
231 17
|
||||
232 17
|
||||
233 17
|
||||
234 17
|
||||
235 17
|
||||
236 17
|
||||
237 17
|
||||
238 17
|
||||
239 18
|
||||
240 18
|
||||
241 18
|
||||
242 18
|
||||
243 18
|
||||
244 18
|
||||
245 18
|
||||
246 18
|
||||
247 18
|
||||
248 18
|
||||
249 18
|
||||
250 18
|
||||
251 18
|
||||
252 18
|
||||
253 19
|
||||
254 19
|
||||
255 19
|
||||
256 19
|
||||
257 19
|
||||
258 19
|
||||
259 19
|
||||
260 19
|
||||
261 19
|
||||
262 19
|
||||
263 19
|
||||
264 19
|
||||
265 19
|
||||
266 19
|
||||
267 20
|
||||
268 20
|
||||
269 20
|
||||
270 20
|
||||
271 20
|
||||
272 20
|
||||
273 20
|
||||
274 20
|
||||
275 20
|
||||
276 20
|
||||
277 20
|
||||
278 20
|
||||
279 20
|
||||
280 20
|
||||
281 21
|
||||
282 21
|
||||
283 21
|
||||
284 21
|
||||
285 21
|
||||
286 21
|
||||
287 21
|
||||
288 21
|
||||
289 21
|
||||
290 21
|
||||
291 21
|
||||
292 21
|
||||
293 21
|
||||
294 21
|
||||
295 22
|
||||
296 22
|
||||
297 22
|
||||
298 22
|
||||
299 22
|
||||
300 22
|
||||
301 22
|
||||
302 22
|
||||
303 22
|
||||
304 22
|
||||
305 22
|
||||
306 22
|
||||
307 22
|
||||
308 22
|
||||
309 23
|
||||
310 23
|
||||
311 23
|
||||
312 23
|
||||
313 23
|
||||
314 23
|
||||
315 23
|
||||
316 23
|
||||
317 23
|
||||
318 23
|
||||
319 23
|
||||
320 23
|
||||
321 23
|
||||
322 23
|
||||
323 24
|
||||
324 24
|
||||
325 24
|
||||
326 24
|
||||
327 24
|
||||
328 24
|
||||
329 24
|
||||
330 24
|
||||
331 24
|
||||
332 24
|
||||
333 24
|
||||
334 24
|
||||
335 24
|
||||
336 24
|
||||
337 25
|
||||
338 25
|
||||
339 25
|
||||
340 25
|
||||
341 25
|
||||
342 25
|
||||
343 25
|
||||
344 25
|
||||
345 25
|
||||
346 25
|
||||
347 25
|
||||
348 25
|
||||
349 25
|
||||
350 25
|
||||
351 26
|
||||
352 26
|
||||
353 26
|
||||
354 26
|
||||
355 26
|
||||
356 26
|
||||
357 26
|
||||
358 26
|
||||
359 26
|
||||
360 26
|
||||
361 26
|
||||
362 26
|
||||
363 26
|
||||
364 26
|
||||
365 27
|
||||
366 27
|
||||
367 27
|
||||
368 27
|
||||
369 27
|
||||
370 27
|
||||
371 27
|
||||
372 27
|
||||
373 27
|
||||
374 27
|
||||
375 27
|
||||
376 27
|
||||
377 27
|
||||
378 27
|
||||
379 28
|
||||
380 28
|
||||
381 28
|
||||
382 28
|
||||
383 28
|
||||
384 28
|
||||
385 28
|
||||
386 28
|
||||
387 28
|
||||
388 28
|
||||
389 28
|
||||
390 28
|
||||
391 28
|
||||
392 28
|
||||
393 29
|
||||
394 29
|
||||
395 29
|
||||
396 29
|
||||
397 29
|
||||
398 29
|
||||
399 29
|
||||
400 29
|
||||
401 29
|
||||
402 29
|
||||
403 29
|
||||
404 29
|
||||
405 29
|
||||
406 29
|
||||
407 30
|
||||
408 30
|
||||
409 30
|
||||
410 30
|
||||
411 30
|
||||
412 30
|
||||
413 30
|
||||
414 30
|
||||
415 30
|
||||
416 30
|
||||
417 30
|
||||
418 30
|
||||
419 30
|
||||
420 30
|
||||
|
|
@ -0,0 +1,107 @@
|
|||
# SRD diffusion demo - rigid box particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.box fix molprop NULL Molecules
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.box.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 1.0
|
||||
|
||||
delete_atoms overlap 1.0 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
|
||||
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
|
||||
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.box
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
|
|
@ -0,0 +1,108 @@
|
|||
# SRD viscosity demo - rigid box particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.box fix molprop NULL Molecules
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.box.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 1.0
|
||||
|
||||
delete_atoms overlap 1.0 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
|
||||
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
|
||||
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.box.mp
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
|
|
@ -0,0 +1,289 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# SRD diffusion demo - rigid box particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.box fix molprop NULL Molecules
|
||||
orthogonal box = (-19.1447 -19.1447 -0.5) to (19.1447 19.1447 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
420 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
420 settings made for mass
|
||||
group big type 1
|
||||
420 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 420 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.box.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 0.443016 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 -8.770036
|
||||
100 0 3.4203218 0 3.4203218 0.49351517
|
||||
200 0 5.3315601 0 5.3315601 0.26965614
|
||||
300 0 7.2094878 0 7.2094878 0.43326479
|
||||
400 0 9.2008598 0 9.2008598 0.27649318
|
||||
500 0 11.562353 0 11.562353 0.60730421
|
||||
600 0 13.731564 0 13.731564 0.27272312
|
||||
700 0 15.850142 0 15.850142 0.0032862218
|
||||
800 0 18.395444 0 18.395444 1.0272658
|
||||
900 0 20.3322 0 20.3322 -0.16729762
|
||||
1000 0 22.600716 0 22.600716 -0.13023705
|
||||
Loop time of 0.0545385 on 8 procs for 1000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.00437456 (8.02105)
|
||||
Neigh time (%) = 0.00148079 (2.71512)
|
||||
Comm time (%) = 0.0152201 (27.9071)
|
||||
Outpt time (%) = 0.000281721 (0.516555)
|
||||
Other time (%) = 0.0331814 (60.8402)
|
||||
|
||||
Nlocal: 52.5 ave 67 max 35 min
|
||||
Histogram: 1 1 1 0 1 0 0 1 1 2
|
||||
Nghost: 30.625 ave 41 max 17 min
|
||||
Histogram: 1 0 0 1 1 1 2 0 1 1
|
||||
Neighs: 70.25 ave 90 max 44 min
|
||||
Histogram: 2 0 0 1 1 0 1 0 0 3
|
||||
|
||||
Total # of neighbors = 562
|
||||
Ave neighs/atom = 1.3381
|
||||
Neighbor list builds = 158
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 2 region plane
|
||||
Created 124609 atoms
|
||||
|
||||
set type 2 mass 0.1
|
||||
124609 settings made for mass
|
||||
group small type 2
|
||||
124609 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 1.0
|
||||
|
||||
delete_atoms overlap 1.0 small big
|
||||
Deleted 51030 atoms, new total = 73999
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 420 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.box
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 73579 420
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 153 153 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250257 0.250257 1
|
||||
SRD per actual grid cell = 4.05573
|
||||
SRD viscosity = 0.229297
|
||||
big/SRD mass density ratio = 0.196614
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.19668 7.72762
|
||||
ave/max big velocity = 2.12757 5.83591
|
||||
Memory usage per processor = 13.4256 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 3.4640099 17794 0.24158286 42.201127 42.564024 10.312083 10282 38 38 0 958 90440 23409 17794 0.83363455 0 69 0
|
||||
2000 1.8731193 17757 0.24043583 42.165699 42.361931 8.6094692 10336 34 34 0 1779 90440 23409 17757 0.83414447 0 69 0
|
||||
3000 1.2193752 17775 0.24002443 42.161704 42.289448 9.6884156 10041 43 43 0 2420 90440 23409 17775 0.84700093 0 69 0
|
||||
4000 1.1297717 17824 0.23999784 42.166405 42.284762 10.426248 10121 39 39 0 3126 90440 23409 17824 0.85633304 0 69 0
|
||||
5000 1.1615474 17837 0.24000689 42.164671 42.286357 9.7517646 10150 27 27 0 3852 90440 23409 17837 0.85320758 0 69 0
|
||||
6000 0.90652092 17750 0.23996236 42.183542 42.278511 16.586628 9996 56 56 0 4564 90440 23409 17750 0.86506192 0 69 0
|
||||
7000 0.83910042 17804 0.23978466 42.159296 42.247202 10.856698 10135 40 40 0 5229 90440 23409 17804 0.85548326 0 69 0
|
||||
8000 0.99144403 17793 0.23987007 42.158385 42.262251 9.5637223 10222 32 32 0 5954 90440 23409 17793 0.86291538 0 69 0
|
||||
9000 1.1109778 17818 0.2398755 42.14682 42.263208 10.917584 10423 42 42 0 6692 90440 23409 17818 0.86552775 0 69 0
|
||||
10000 1.0782518 17840 0.23985498 42.146632 42.259591 8.85358 10308 36 36 0 7397 90440 23409 17840 0.86462939 0 69 0
|
||||
11000 1.0268236 17833 0.23980517 42.143244 42.250816 12.172006 10254 44 44 0 8080 90440 23409 17833 0.861416 0 69 0
|
||||
12000 1.060866 17842 0.23979196 42.137351 42.248489 10.419562 10353 34 34 0 8810 90440 23409 17842 0.86289215 0 69 0
|
||||
13000 1.1876599 17763 0.23989166 42.141633 42.266054 7.8240476 10268 34 34 0 9525 90440 23409 17763 0.87071361 0 69 0
|
||||
14000 0.95206604 17823 0.23970806 42.133967 42.233707 12.293388 10359 40 40 0 10306 90440 23409 17823 0.86909841 0 69 0
|
||||
15000 1.1155458 17822 0.23974949 42.124139 42.241006 12.521383 10256 36 36 0 11029 90440 23409 17822 0.87234166 0 69 0
|
||||
16000 1.1574448 17829 0.2398005 42.128737 42.249993 8.5872634 10044 38 38 0 11766 90440 23409 17829 0.87292148 0 69 0
|
||||
17000 0.87868625 17815 0.23968874 42.13825 42.230303 10.488609 10092 37 37 0 12571 90440 23409 17815 0.87070803 0 69 0
|
||||
18000 1.1008021 17797 0.23970316 42.117521 42.232843 8.91155 9964 31 31 0 13349 90440 23409 17797 0.87684173 0 69 0
|
||||
19000 0.90843127 17832 0.23953614 42.108247 42.203416 10.681924 10353 33 33 0 14070 90440 23409 17832 0.87489631 0 69 0
|
||||
20000 1.1525128 17827 0.23958362 42.091043 42.211782 10.324591 10318 42 42 0 14891 90440 23409 17827 0.87472282 0 69 0
|
||||
21000 0.97088045 17831 0.23963415 42.118973 42.220685 8.9525609 10150 23 23 0 15681 90440 23409 17831 0.8744301 0 69 0
|
||||
22000 0.86024198 17818 0.23946932 42.101523 42.191644 12.817308 9929 47 47 0 16514 90440 23409 17818 0.87940492 0 69 0
|
||||
23000 1.0365388 17841 0.23960538 42.107025 42.215615 8.3943475 10190 36 36 0 17300 90440 23409 17841 0.88076259 0 69 0
|
||||
24000 1.0134969 17828 0.23957307 42.103748 42.209924 11.013413 10329 40 40 0 18153 90440 23409 17828 0.87875237 0 69 0
|
||||
25000 0.90091994 17843 0.23954136 42.109953 42.204335 13.312428 10143 45 45 0 18852 90440 23409 17843 0.87388578 0 69 0
|
||||
26000 1.0221933 17846 0.23961351 42.10996 42.217047 9.2279785 10329 35 35 0 19615 90440 23409 17846 0.87558424 0 69 0
|
||||
27000 0.93940255 17835 0.23950604 42.099699 42.198112 13.504134 10291 39 39 0 20431 90440 23409 17835 0.87190502 0 69 0
|
||||
28000 1.0710516 17829 0.23960837 42.103937 42.216142 7.9022268 10251 35 35 0 21197 90440 23409 17829 0.87583025 0 69 0
|
||||
29000 0.83696568 17783 0.23958234 42.123874 42.211556 9.8273998 10121 47 47 0 22044 90440 23409 17783 0.8820577 0 69 0
|
||||
30000 1.0180681 17800 0.2396419 42.115395 42.22205 11.18041 10160 39 39 0 22803 90440 23409 17800 0.87992368 0 69 0
|
||||
31000 1.233447 17832 0.23970136 42.103307 42.232526 11.388978 10169 45 45 0 23608 90440 23409 17832 0.87847887 0 69 0
|
||||
32000 0.96295204 17849 0.23957991 42.110247 42.211128 12.911795 10118 41 41 0 24364 90440 23409 17849 0.87317056 0 69 0
|
||||
33000 1.0254742 17836 0.23958855 42.10522 42.21265 11.197726 10202 43 43 0 25162 90440 23409 17836 0.87655301 0 69 0
|
||||
34000 1.0255122 17812 0.23948733 42.087383 42.194817 10.238978 10253 42 42 0 25996 90440 23409 17812 0.87150515 0 69 0
|
||||
35000 1.0719997 17824 0.23953256 42.090481 42.202785 9.1594527 10190 37 37 0 26786 90440 23409 17824 0.86960071 0 69 0
|
||||
36000 0.86929827 17801 0.2394198 42.091849 42.182919 12.021567 10145 36 36 0 27586 90440 23409 17801 0.87124989 0 69 0
|
||||
37000 0.9195314 17801 0.23946164 42.093958 42.19029 11.122704 10083 42 43 0 28321 90440 23409 17801 0.87692574 0 69 0
|
||||
38000 0.88209926 17821 0.23936949 42.081644 42.174055 9.3732038 10239 37 37 0 29094 90440 23409 17821 0.87364127 0 69 0
|
||||
39000 1.0463087 17819 0.23943558 42.076086 42.185699 11.373309 10300 44 44 0 29804 90440 23409 17819 0.87650979 0 69 0
|
||||
40000 0.97425688 17807 0.2394417 42.084711 42.186776 13.415635 10171 50 50 0 30544 90440 23409 17807 0.87219589 0 69 0
|
||||
41000 1.0314516 17853 0.23945459 42.080991 42.189047 9.7139261 10050 38 38 0 31307 90440 23409 17853 0.87283313 0 69 0
|
||||
42000 1.0804164 17808 0.23949436 42.082868 42.196055 12.340256 10377 35 35 0 32052 90440 23409 17808 0.87185243 0 69 0
|
||||
43000 1.0687043 17835 0.2394289 42.072563 42.184523 12.276278 10187 41 42 0 32870 90440 23409 17835 0.87231717 0 69 0
|
||||
44000 1.0355523 17787 0.23942635 42.075587 42.184073 13.512133 10013 38 38 0 33661 90440 23409 17787 0.87400868 0 69 0
|
||||
45000 1.194095 17794 0.23944632 42.062495 42.187591 10.205101 10159 30 30 0 34402 90440 23409 17794 0.8739309 0 69 0
|
||||
46000 0.84466181 17796 0.23920256 42.056156 42.144644 10.087591 9986 38 38 1 35149 90440 23409 17796 0.87869701 0 69 0
|
||||
47000 0.93714931 17806 0.239206 42.047072 42.14525 13.876772 10228 47 47 0 35938 90440 23409 17806 0.87830705 0 69 0
|
||||
48000 0.72949249 17796 0.23910309 42.050694 42.127117 9.8468313 10017 47 47 0 36668 90440 23409 17796 0.87327264 0 69 0
|
||||
49000 1.0645999 17790 0.23930769 42.051637 42.163166 7.4358626 10277 32 32 0 37413 90440 23409 17790 0.8752094 0 69 0
|
||||
50000 0.83794425 17817 0.23913221 42.044463 42.132248 8.9803438 10132 31 33 0 38183 90440 23409 17817 0.87857184 0 69 0
|
||||
51000 1.062864 17789 0.23932593 42.055033 42.166381 17.329071 9926 42 42 1 38978 90440 23409 17789 0.8802125 0 69 0
|
||||
52000 1.1722666 17829 0.23941856 42.059892 42.1827 10.825667 10158 44 44 0 39819 90440 23409 17829 0.87723184 0 69 0
|
||||
53000 1.0628181 17744 0.23938195 42.064907 42.17625 11.797173 10008 34 34 0 40601 90440 23409 17744 0.87283218 0 69 0
|
||||
54000 0.99372853 17841 0.23927037 42.052486 42.156591 12.17125 10068 45 45 0 41361 90440 23409 17841 0.86254752 0 69 0
|
||||
55000 0.98975398 17807 0.23931559 42.06087 42.164558 9.4176785 10050 40 40 0 42113 90440 23409 17807 0.86704764 0 69 0
|
||||
56000 1.2416282 17834 0.23940795 42.050755 42.180831 10.979518 10103 32 32 0 42836 90440 23409 17834 0.87721916 0 69 0
|
||||
57000 1.1624419 17798 0.23935794 42.050239 42.172019 12.160453 10291 47 47 0 43564 90440 23409 17798 0.86494273 0 69 0
|
||||
58000 0.76060878 17840 0.23906489 42.040706 42.120388 10.124046 10057 41 41 0 44303 90440 23409 17840 0.87205383 0 69 0
|
||||
59000 0.8928696 17800 0.23908927 42.031144 42.124683 9.5453786 10054 40 40 0 45052 90440 23409 17800 0.87434651 0 69 0
|
||||
60000 0.94592548 17794 0.23911586 42.03027 42.129367 9.2638612 10243 36 36 0 45825 90440 23409 17794 0.87526045 0 69 0
|
||||
61000 1.1130865 17809 0.23930525 42.046126 42.162735 10.750849 10002 35 35 0 46608 90440 23409 17809 0.8747269 0 69 0
|
||||
62000 1.211348 17822 0.2392555 42.027069 42.153972 7.371417 10008 24 24 0 47366 90440 23409 17822 0.87452709 0 69 0
|
||||
63000 0.80855346 17834 0.23891571 42.009398 42.094104 9.812354 10122 34 34 0 48089 90440 23409 17834 0.86767806 0 69 0
|
||||
64000 1.0823604 17785 0.23907804 42.009314 42.122704 12.694543 9780 40 40 0 48834 90440 23409 17785 0.87010421 0 69 0
|
||||
65000 1.1681262 17819 0.23899593 41.985863 42.108239 13.521338 9939 50 50 0 49566 90440 23409 17819 0.87537564 0 69 0
|
||||
66000 1.0903421 17856 0.23903071 42.00014 42.114366 12.301665 9888 40 40 0 50342 90440 23409 17856 0.87239173 0 69 0
|
||||
67000 1.118394 17844 0.23901798 41.994958 42.112123 8.8459568 9818 25 25 0 51083 90440 23409 17844 0.86584906 0 69 0
|
||||
68000 0.93948628 17859 0.23892088 41.996592 42.095014 14.068409 9749 43 44 0 51827 90440 23409 17859 0.87202088 0 69 0
|
||||
69000 0.990697 17820 0.2389651 41.999019 42.102807 10.194771 9842 40 40 0 52556 90440 23409 17820 0.87288445 0 69 0
|
||||
70000 1.1688722 17813 0.2391014 42.004367 42.12682 8.7519297 9844 29 29 0 53315 90440 23409 17813 0.86525878 0 69 0
|
||||
71000 1.1452575 17818 0.23899789 41.988604 42.108583 8.7612004 9845 40 40 0 54037 90440 23409 17818 0.86500198 0 69 0
|
||||
72000 0.72969657 17836 0.23879062 41.99562 42.072064 11.153851 9829 38 38 0 54737 90440 23409 17836 0.86237278 0 69 0
|
||||
73000 1.3107884 17813 0.23912958 41.994464 42.131785 10.862806 9844 40 40 0 55443 90440 23409 17813 0.86460503 0 69 0
|
||||
74000 1.1126473 17809 0.23897768 41.98846 42.105023 9.663087 10106 35 35 0 56166 90440 23409 17809 0.87193847 0 69 0
|
||||
75000 1.0693301 17794 0.23895603 41.989183 42.101208 8.9374157 10022 32 32 0 56941 90440 23409 17794 0.86326628 0 69 0
|
||||
76000 0.74083943 17831 0.23870905 41.98008 42.057692 7.4143173 10015 37 37 0 57653 90440 23409 17831 0.86354244 0 69 0
|
||||
77000 0.98084748 17842 0.23886095 41.9817 42.084455 9.4554943 9716 31 31 0 58336 90440 23409 17842 0.8620535 0 69 0
|
||||
78000 0.91225901 17815 0.23882673 41.982857 42.078427 13.333677 9926 43 43 1 59053 90440 23409 17815 0.8676841 0 69 0
|
||||
79000 1.1488535 17820 0.2389454 41.978979 42.099335 10.298772 9750 29 29 0 59744 90440 23409 17820 0.86385906 0 69 0
|
||||
80000 0.84064371 17821 0.23872693 41.972776 42.060843 9.8779227 9978 30 30 0 60450 90440 23409 17821 0.8629371 0 69 0
|
||||
81000 1.0935129 17803 0.23886127 41.969953 42.084512 7.1940139 9938 35 35 0 61155 90440 23409 17803 0.86416591 0 69 0
|
||||
82000 1.0216631 17879 0.23884983 41.975465 42.082497 8.6808843 9987 36 36 0 61901 90440 23409 17879 0.87201261 0 69 0
|
||||
83000 1.1155302 17808 0.23890657 41.975628 42.092493 11.387186 10066 49 49 0 62668 90440 23409 17808 0.8655501 0 69 0
|
||||
84000 1.2958273 17773 0.23908145 41.987553 42.123306 11.222215 9969 44 44 0 63341 90440 23409 17773 0.86573453 0 69 0
|
||||
85000 0.74628215 17829 0.23869483 41.977005 42.055187 11.073853 9949 43 43 0 64140 90440 23409 17829 0.86391947 0 69 0
|
||||
86000 0.80359232 17803 0.23872195 41.97578 42.059966 9.6085498 9716 31 31 0 64837 90440 23409 17803 0.865418 0 69 0
|
||||
87000 1.1098155 17802 0.23884012 41.96452 42.080786 13.693733 9576 45 45 0 65543 90440 23409 17802 0.86275585 0 69 0
|
||||
88000 1.1138796 17818 0.23881314 41.95934 42.076033 11.517335 9714 36 36 0 66248 90440 23409 17818 0.85491105 0 69 0
|
||||
89000 0.93926562 17840 0.2387707 41.970156 42.068555 9.6487297 9615 46 46 0 66962 90440 23409 17840 0.85885199 0 69 0
|
||||
90000 1.0870662 17806 0.2388668 41.971603 42.085486 7.4390878 9564 31 31 0 67698 90440 23409 17806 0.86503288 0 69 0
|
||||
91000 1.0454873 17807 0.2388344 41.970251 42.079778 12.514272 9645 46 46 1 68392 90440 23409 17807 0.86550889 0 69 0
|
||||
92000 0.9113326 17794 0.23875573 41.970444 42.065917 7.9745011 9858 31 31 0 69167 90440 23409 17794 0.86294582 0 69 0
|
||||
93000 0.78689269 17806 0.23871392 41.976114 42.05855 7.7081978 9499 35 35 0 69893 90440 23409 17806 0.87091194 0 69 0
|
||||
94000 1.0352085 17794 0.23883458 41.971359 42.079809 14.612099 9789 43 43 0 70667 90440 23409 17794 0.87298934 0 69 0
|
||||
95000 0.91726046 17789 0.2387641 41.971297 42.067391 10.210387 9513 38 38 0 71405 90440 23409 17789 0.87024642 0 69 0
|
||||
96000 0.81485499 17819 0.23874488 41.97864 42.064006 11.759393 9924 42 42 0 72083 90440 23409 17819 0.87063449 0 69 0
|
||||
97000 1.3260071 17811 0.23919656 42.004672 42.143587 9.8667031 9417 44 44 0 72818 90440 23409 17811 0.8655796 0 69 0
|
||||
98000 1.0837996 17805 0.2389241 41.982041 42.095581 7.1836799 9975 23 23 0 73551 90440 23409 17805 0.86800841 0 69 0
|
||||
99000 1.1892528 17831 0.23911593 42.004792 42.12938 9.6721123 9972 36 36 0 74319 90440 23409 17831 0.87381766 0 69 0
|
||||
100000 0.85151797 17820 0.23885094 41.993485 42.082692 12.111833 9709 33 33 0 75042 90440 23409 17820 0.86631253 0 69 0
|
||||
Loop time of 61.6618 on 8 procs for 100000 steps with 73999 atoms
|
||||
|
||||
Pair time (%) = 0.679072 (1.10128)
|
||||
Neigh time (%) = 3.89789 (6.3214)
|
||||
Comm time (%) = 3.42736 (5.55832)
|
||||
Outpt time (%) = 0.0100309 (0.0162676)
|
||||
Other time (%) = 53.6475 (87.0027)
|
||||
|
||||
Nlocal: 9249.88 ave 10571 max 6409 min
|
||||
Histogram: 1 0 0 0 1 0 2 1 0 3
|
||||
Nghost: 66.625 ave 92 max 38 min
|
||||
Histogram: 1 0 2 0 0 2 0 1 0 2
|
||||
Neighs: 345.875 ave 740 max 150 min
|
||||
Histogram: 3 1 0 0 2 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2767
|
||||
Ave neighs/atom = 0.0373924
|
||||
Neighbor list builds = 5000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,290 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# SRD viscosity demo - rigid box particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.box fix molprop NULL Molecules
|
||||
orthogonal box = (-19.1447 -19.1447 -0.5) to (19.1447 19.1447 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
420 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
420 settings made for mass
|
||||
group big type 1
|
||||
420 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 420 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.box.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 0.443016 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 -8.770036
|
||||
100 0 3.4203218 0 3.4203218 0.49351517
|
||||
200 0 5.3315601 0 5.3315601 0.26965614
|
||||
300 0 7.2094878 0 7.2094878 0.43326479
|
||||
400 0 9.2008598 0 9.2008598 0.27649318
|
||||
500 0 11.562353 0 11.562353 0.60730421
|
||||
600 0 13.731564 0 13.731564 0.27272312
|
||||
700 0 15.850142 0 15.850142 0.0032862218
|
||||
800 0 18.395444 0 18.395444 1.0272658
|
||||
900 0 20.3322 0 20.3322 -0.16729762
|
||||
1000 0 22.600716 0 22.600716 -0.13023705
|
||||
Loop time of 0.0532217 on 8 procs for 1000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.00440922 (8.28463)
|
||||
Neigh time (%) = 0.00149104 (2.80156)
|
||||
Comm time (%) = 0.0167182 (31.4124)
|
||||
Outpt time (%) = 0.000243604 (0.457716)
|
||||
Other time (%) = 0.0303596 (57.0437)
|
||||
|
||||
Nlocal: 52.5 ave 67 max 35 min
|
||||
Histogram: 1 1 1 0 1 0 0 1 1 2
|
||||
Nghost: 30.625 ave 41 max 17 min
|
||||
Histogram: 1 0 0 1 1 1 2 0 1 1
|
||||
Neighs: 70.25 ave 90 max 44 min
|
||||
Histogram: 2 0 0 1 1 0 1 0 0 3
|
||||
|
||||
Total # of neighbors = 562
|
||||
Ave neighs/atom = 1.3381
|
||||
Neighbor list builds = 158
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 2 region plane
|
||||
Created 124609 atoms
|
||||
|
||||
set type 2 mass 0.1
|
||||
124609 settings made for mass
|
||||
group small type 2
|
||||
124609 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 1.0
|
||||
|
||||
delete_atoms overlap 1.0 small big
|
||||
Deleted 51030 atoms, new total = 73999
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 420 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.box.mp
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 73579 420
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 153 153 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250257 0.250257 1
|
||||
SRD per actual grid cell = 4.05573
|
||||
SRD viscosity = 0.229297
|
||||
big/SRD mass density ratio = 0.196614
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.19668 7.72762
|
||||
ave/max big velocity = 2.12757 5.83591
|
||||
Memory usage per processor = 13.4256 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 27.381112 0 0.25599398 42.234595 45.103092 0.74047865 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 3.0049838 17777 0.24126663 42.1935 42.508307 10.275827 10158 39 39 0 969 90440 23409 17777 0.82992658 0 5 0
|
||||
2000 2.0594027 17777 0.24067675 42.188632 42.404379 11.627774 10292 36 36 0 1771 90440 23409 17777 0.83080952 0 5 0
|
||||
3000 2.4040501 17797 0.24079277 42.172967 42.42482 10.156226 10095 36 36 0 2459 90440 23409 17797 0.83998735 0 5 0
|
||||
4000 2.2632838 17786 0.24072895 42.17647 42.413576 8.3000432 10226 39 39 0 3110 90440 23409 17786 0.84926739 0 11 0
|
||||
5000 2.1615321 17771 0.2406319 42.17003 42.396476 12.614305 10146 42 42 0 3839 90440 23409 17771 0.84253705 0 12 0
|
||||
6000 2.3404925 17788 0.24071728 42.166325 42.41152 8.4651458 10135 26 26 1 4611 90440 23409 17788 0.85083081 0 12 0
|
||||
7000 2.7255145 17818 0.24092294 42.162224 42.447755 11.46372 10080 38 38 0 5374 90440 23409 17818 0.85293665 0 12 0
|
||||
8000 3.365919 17803 0.24133267 42.167324 42.519944 9.3928156 9855 37 37 0 6193 90440 23409 17803 0.86064998 0 12 0
|
||||
9000 3.9996052 17822 0.24169619 42.164986 42.583992 11.684546 10254 45 45 0 7098 90440 23409 17822 0.85610583 0 12 0
|
||||
10000 3.7140801 17805 0.24148598 42.157861 42.546956 9.1699669 10100 26 26 0 7937 90440 23409 17805 0.85065679 0 12 0
|
||||
11000 4.3731562 17827 0.24205487 42.189047 42.647187 9.2341771 10070 41 41 0 8764 90440 23409 17827 0.85807862 0 12 0
|
||||
12000 4.1186516 17820 0.24193208 42.194074 42.625552 11.406041 10255 39 39 0 9655 90440 23409 17820 0.85643788 0 12 0
|
||||
13000 4.762793 17824 0.24236854 42.203492 42.702451 12.157288 10474 47 47 1 10593 90440 23409 17824 0.85306532 0 12 0
|
||||
14000 4.5224167 17792 0.24219742 42.198524 42.672301 7.1302951 10288 23 23 0 11429 90440 23409 17792 0.86236239 0 12 0
|
||||
15000 5.1569684 17782 0.24264166 42.210318 42.750572 10.214491 10093 33 33 0 12370 90440 23409 17782 0.86348982 0 12 0
|
||||
16000 6.5556642 17850 0.24347578 42.210751 42.897534 11.002602 10037 40 40 0 13271 90440 23409 17850 0.85200011 0 12 0
|
||||
17000 5.5387674 17824 0.24266758 42.174887 42.755139 10.385285 10397 36 36 0 14175 90440 23409 17824 0.85533339 0 12 0
|
||||
18000 5.6130858 17801 0.24266531 42.166701 42.754738 9.2072479 10173 31 31 0 15091 90440 23409 17801 0.85880719 0 12 0
|
||||
19000 6.3690838 17731 0.24305026 42.155324 42.822562 11.000565 9904 35 35 0 16055 90440 23409 17731 0.8568314 0 12 0
|
||||
20000 6.5345137 17804 0.24301313 42.131453 42.816021 8.6244348 10271 39 39 0 17065 90440 23409 17804 0.86184074 0 12 0
|
||||
21000 7.8000849 17796 0.24367166 42.114894 42.932046 10.5203 10324 34 34 0 18083 90440 23409 17796 0.85189595 0 12 0
|
||||
22000 7.2889302 17808 0.24348814 42.13611 42.899712 12.592106 10316 40 40 0 19144 90440 23409 17808 0.8551435 0 12 0
|
||||
23000 8.0622172 17796 0.24398439 42.142531 42.987144 10.997293 10207 44 44 0 20246 90440 23409 17796 0.85458036 0 12 0
|
||||
24000 9.1284316 17847 0.24461098 42.141231 43.097543 14.324353 10266 39 39 0 21367 90440 23409 17847 0.84705694 0 12 0
|
||||
25000 9.0312955 17813 0.24455129 42.140891 43.087027 9.8503895 10026 38 38 0 22521 90440 23409 17813 0.84644311 0 12 0
|
||||
26000 9.4732213 17795 0.24480929 42.140049 43.132482 7.2348444 10154 30 30 1 23615 90440 23409 17795 0.85372054 0 12 0
|
||||
27000 9.8524378 17798 0.24513826 42.158283 43.190443 8.8910315 9894 27 27 0 24683 90440 23409 17798 0.84368629 0 12 0
|
||||
28000 9.839534 17794 0.24506721 42.147117 43.177925 8.6536124 9936 36 36 0 25855 90440 23409 17794 0.85902123 0 20 0
|
||||
29000 9.8880033 17788 0.24525763 42.175588 43.211474 12.57859 10393 54 54 0 26999 90440 23409 17788 0.8525183 0 20 0
|
||||
30000 9.9944497 17784 0.24531874 42.175204 43.222242 7.6191563 10160 30 30 0 28150 90440 23409 17784 0.8525876 0 20 0
|
||||
31000 9.4091213 17817 0.24497685 42.176287 43.162004 9.447269 10174 37 37 0 29298 90440 23409 17817 0.85820536 0 20 0
|
||||
32000 9.8338203 17830 0.24533925 42.195645 43.225855 10.392617 10157 41 41 0 30497 90440 23409 17830 0.84673558 0 20 0
|
||||
33000 10.170531 17841 0.24537715 42.167048 43.232533 9.4789613 10317 30 30 0 31653 90440 23409 17841 0.84189893 0 20 0
|
||||
34000 9.3223103 17813 0.24482667 42.158922 43.135545 11.041395 10308 42 42 0 32824 90440 23409 17813 0.84966151 0 20 0
|
||||
35000 10.3926 17793 0.24553346 42.171325 43.260073 9.9878588 10055 46 46 0 34035 90440 23409 17793 0.84654238 0 20 0
|
||||
36000 9.0321397 17754 0.24478751 42.182421 43.128645 9.8056393 10047 34 34 0 35216 90440 23409 17754 0.84780342 0 20 0
|
||||
37000 10.558279 17810 0.2457091 42.184913 43.291018 10.775504 10226 32 32 0 36453 90440 23409 17810 0.84924776 0 20 0
|
||||
38000 10.020575 17810 0.2455366 42.210852 43.260627 9.1515261 10348 37 37 0 37802 90440 23409 17810 0.84427762 0 20 0
|
||||
39000 9.9512554 17827 0.24554005 42.218721 43.261233 9.2917714 10326 33 33 0 39048 90440 23409 17827 0.84214883 0 20 0
|
||||
40000 9.8735348 17774 0.24552032 42.223387 43.257758 11.642544 10168 29 29 0 40364 90440 23409 17774 0.84500349 0 20 0
|
||||
41000 10.365156 17804 0.24566955 42.198177 43.284051 11.008578 10300 42 42 0 41686 90440 23409 17804 0.84403351 0 20 0
|
||||
42000 10.226635 17818 0.24555953 42.193305 43.264667 9.4647805 10114 31 31 0 42984 90440 23409 17818 0.84572892 0 20 0
|
||||
43000 9.8210408 17796 0.24514315 42.162435 43.191305 11.789151 10485 49 49 0 44223 90440 23409 17796 0.84076768 0 20 0
|
||||
44000 7.9254401 17772 0.24398374 42.156747 42.987031 10.041925 10224 32 33 0 45547 90440 23409 17772 0.8483164 0 20 0
|
||||
45000 8.5724312 17801 0.24441451 42.164862 43.062926 10.851835 10248 45 45 0 46831 90440 23409 17801 0.84635099 0 20 0
|
||||
46000 9.5815129 17740 0.24508371 42.177055 43.180832 8.5573763 9951 29 29 1 48174 90440 23409 17740 0.84142197 0 20 0
|
||||
47000 9.2724336 17815 0.24490579 42.178087 43.149485 10.749442 10324 41 41 0 49494 90440 23409 17815 0.84305403 0 20 0
|
||||
48000 9.8698295 17829 0.2453373 42.19153 43.225512 10.992529 10010 44 44 0 50894 90440 23409 17829 0.84635867 0 20 0
|
||||
49000 9.8650214 17775 0.24527147 42.180435 43.213913 9.9258034 10084 40 40 0 52221 90440 23409 17775 0.83690751 0 20 0
|
||||
50000 11.52467 17800 0.24636922 42.199977 43.407323 9.5477158 10105 32 32 0 53667 90440 23409 17800 0.84402538 0 20 0
|
||||
51000 9.5447655 17779 0.24527025 42.213771 43.213698 9.7717222 9994 39 39 1 54997 90440 23409 17779 0.83802916 0 20 0
|
||||
52000 9.9738008 17814 0.24545383 42.201169 43.246043 9.9256895 10405 27 27 0 56351 90440 23409 17814 0.84021845 0 20 0
|
||||
53000 10.294974 17805 0.24553341 42.181543 43.260064 10.07833 10251 43 43 0 57678 90440 23409 17805 0.83588955 0 20 0
|
||||
54000 11.00851 17818 0.24588587 42.16889 43.322163 10.905345 10010 38 38 0 59118 90440 23409 17818 0.83044357 0 20 0
|
||||
55000 12.200856 17797 0.24645934 42.145016 43.423201 10.929419 10103 45 45 0 60512 90440 23409 17797 0.83533437 0 20 0
|
||||
56000 10.240644 17782 0.24544908 42.172377 43.245207 12.311462 9968 39 39 0 61888 90440 23409 17782 0.8334708 0 20 0
|
||||
57000 11.858526 17799 0.24642127 42.174172 43.416493 11.602562 9675 44 44 0 63241 90440 23409 17799 0.83579075 0 20 0
|
||||
58000 9.9579114 17781 0.24522905 42.16323 43.206439 9.8939621 9920 47 47 0 64565 90440 23409 17781 0.83252812 0 20 0
|
||||
59000 9.4966125 17793 0.24495112 42.162588 43.157471 10.243383 9951 39 39 1 65879 90440 23409 17793 0.82795782 0 20 0
|
||||
60000 9.3889539 17763 0.24483753 42.153854 43.137459 6.7498755 9893 26 26 0 67171 90440 23409 17763 0.83255788 0 98 0
|
||||
61000 9.8219129 17760 0.24497944 42.133499 43.162462 10.026948 10063 39 39 0 68464 90440 23409 17760 0.83382901 0 98 0
|
||||
62000 8.9772784 17744 0.24430051 42.102364 43.042841 6.7992672 9830 31 31 0 69793 90440 23409 17744 0.83040933 0 98 0
|
||||
63000 9.4555226 17778 0.2446845 42.119917 43.110495 9.3613489 9507 33 33 0 71025 90440 23409 17778 0.81990914 0 98 0
|
||||
64000 10.822236 17791 0.24553255 42.126154 43.259912 10.978102 9950 44 44 0 72302 90440 23409 17791 0.8205428 0 98 0
|
||||
65000 10.643375 17749 0.24553889 42.146009 43.261029 9.8170035 9751 33 33 0 73657 90440 23409 17749 0.81737668 0 98 0
|
||||
66000 10.65446 17802 0.24577045 42.185645 43.301827 10.068015 9838 38 38 0 74926 90440 23409 17802 0.82017685 0 98 0
|
||||
67000 11.320004 17810 0.24637556 42.222536 43.408441 13.28653 9779 39 39 0 76258 90440 23409 17810 0.82794931 0 98 0
|
||||
68000 11.235171 17769 0.2461615 42.193708 43.370726 11.789643 9847 37 37 0 77534 90440 23409 17769 0.81709561 0 98 0
|
||||
69000 10.833468 17779 0.2459244 42.194017 43.328952 9.0530182 9896 39 39 0 78894 90440 23409 17779 0.82041697 0 98 0
|
||||
70000 11.565202 17794 0.24641358 42.203546 43.415139 6.0770107 9643 29 29 0 80167 90440 23409 17794 0.82167076 0 98 0
|
||||
71000 11.125212 17790 0.24620537 42.212956 43.378454 14.351282 9877 38 38 1 81552 90440 23409 17790 0.82508123 0 98 0
|
||||
72000 12.644174 17763 0.24699557 42.193051 43.517679 10.531064 9953 42 42 0 82972 90440 23409 17763 0.82933853 0 98 0
|
||||
73000 12.165673 17828 0.24657837 42.169674 43.444173 11.982241 10132 39 39 0 84372 90440 23409 17828 0.82853038 0 98 0
|
||||
74000 13.565669 17790 0.24748187 42.182194 43.60336 11.810898 9964 32 32 0 85794 90440 23409 17790 0.83238035 0 98 0
|
||||
75000 13.850885 17779 0.24764619 42.181266 43.632311 11.595796 9829 40 40 0 87294 90440 23409 17779 0.82452835 0 98 0
|
||||
76000 13.730794 17774 0.24760357 42.186337 43.624801 10.314049 9977 39 39 0 88621 90440 23409 17774 0.82554866 0 98 0
|
||||
77000 14.2192 17789 0.24787267 42.182584 43.672214 9.9780185 9834 32 32 0 90146 90440 23409 17789 0.82713865 0 98 0
|
||||
78000 14.316206 17801 0.24800412 42.19558 43.695373 8.3314161 10132 38 39 0 91616 90440 23409 17801 0.82824877 0 98 0
|
||||
79000 13.703006 17815 0.24778437 42.221104 43.656656 8.1390498 10001 35 35 0 93114 90440 23409 17815 0.82396879 0 98 0
|
||||
80000 14.21882 17804 0.24812482 42.227048 43.716639 9.0164253 9950 41 41 0 94643 90440 23409 17804 0.83049102 0 98 0
|
||||
81000 13.61083 17812 0.24765862 42.208604 43.634501 8.7498353 10205 30 30 0 96165 90440 23409 17812 0.83215993 0 98 0
|
||||
82000 14.24814 17780 0.24806178 42.212871 43.705533 8.9596483 9898 33 33 0 97690 90440 23409 17780 0.82682824 0 98 0
|
||||
83000 13.18484 17803 0.24743025 42.212995 43.594264 12.116538 9833 39 39 0 99222 90440 23409 17803 0.82225356 0 98 0
|
||||
84000 12.665093 17787 0.24718115 42.223556 43.550375 7.0430872 9857 33 33 0 100749 90440 23409 17787 0.8216466 0 98 0
|
||||
85000 12.22937 17748 0.24700172 42.23759 43.518762 14.858066 9924 35 35 0 102174 90440 23409 17748 0.82012834 0 98 0
|
||||
86000 11.637126 17741 0.24648333 42.208301 43.427429 8.8309049 10034 38 38 0 103545 90440 23409 17741 0.82310449 0 98 0
|
||||
87000 13.172172 17780 0.24761541 42.246946 43.626888 11.997785 9793 34 34 0 105003 90440 23409 17780 0.8231062 0 98 0
|
||||
88000 13.867288 17774 0.2478372 42.213201 43.665964 13.008322 9930 45 45 0 106424 90440 23409 17774 0.81835323 0 98 0
|
||||
89000 14.409874 17792 0.24817672 42.216177 43.725783 8.9017208 9873 33 33 0 107941 90440 23409 17792 0.812681 0 98 0
|
||||
90000 14.175277 17745 0.24802753 42.21447 43.699499 7.8889612 9838 37 37 0 109384 90440 23409 17745 0.82045281 0 98 0
|
||||
91000 13.80886 17809 0.24773522 42.201354 43.647996 10.153291 10077 34 34 0 110836 90440 23409 17809 0.8142495 0 98 0
|
||||
92000 14.391083 17743 0.24814425 42.212425 43.720062 12.167713 9928 28 28 0 112372 90440 23409 17743 0.82301567 0 98 0
|
||||
93000 13.425843 17771 0.24744975 42.191184 43.597701 10.962936 9854 29 29 0 113801 90440 23409 17771 0.81953388 0 98 0
|
||||
94000 12.969876 17828 0.24733041 42.217925 43.576674 10.432208 10160 32 32 1 115320 90440 23409 17828 0.81861088 0 98 0
|
||||
95000 13.550396 17812 0.24762509 42.209027 43.628593 9.1923817 10139 27 27 0 116845 90440 23409 17812 0.82254819 0 98 0
|
||||
96000 14.303773 17807 0.24819751 42.230956 43.729446 8.2304906 9666 33 33 0 118316 90440 23409 17807 0.82304543 0 98 0
|
||||
97000 14.027408 17825 0.24788054 42.204061 43.673599 11.160576 10211 43 43 0 119812 90440 23409 17825 0.82817945 0 98 0
|
||||
98000 14.515459 17805 0.24814196 42.198993 43.71966 13.355885 10078 43 43 0 121293 90440 23409 17805 0.82291353 0 98 0
|
||||
99000 13.502344 17774 0.24757651 42.205502 43.620034 9.1790624 9865 31 31 0 122780 90440 23409 17774 0.8281067 0 98 0
|
||||
100000 14.173632 17761 0.24801238 42.211971 43.696828 10.204956 9866 35 35 0 124297 90440 23409 17761 0.83321256 0 98 0
|
||||
Loop time of 62.3427 on 8 procs for 100000 steps with 73999 atoms
|
||||
|
||||
Pair time (%) = 0.637287 (1.02223)
|
||||
Neigh time (%) = 3.81362 (6.11719)
|
||||
Comm time (%) = 3.39013 (5.4379)
|
||||
Outpt time (%) = 0.010035 (0.0160965)
|
||||
Other time (%) = 54.4916 (87.4066)
|
||||
|
||||
Nlocal: 9249.88 ave 11502 max 7978 min
|
||||
Histogram: 1 2 2 0 1 0 0 1 0 1
|
||||
Nghost: 53 ave 68 max 41 min
|
||||
Histogram: 3 0 0 0 0 3 0 0 1 1
|
||||
Neighs: 288.625 ave 518 max 152 min
|
||||
Histogram: 2 1 1 1 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 2309
|
||||
Ave neighs/atom = 0.0312031
|
||||
Neighbor list builds = 5000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,412 @@
|
|||
LAMMPS data file for Nanoparticles
|
||||
200 atoms
|
||||
2 atom types
|
||||
-9.34165202733 9.34165202733 xlo xhi
|
||||
-9.34165202733 9.34165202733 ylo yhi
|
||||
-0.5 0.5 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 1 -3.10486 -0.950915 0 0 0 0
|
||||
2 1 1 1 -3.63859 -1.54685 0 0 0 0
|
||||
3 1 1 1 6.88603 9.18501 0 0 0 0
|
||||
4 1 1 1 6.31995 8.61972 0 0 0 0
|
||||
5 1 1 1 -5.96916 5.60904 0 0 0 0
|
||||
6 1 1 1 -5.27086 5.21869 0 0 0 0
|
||||
7 1 1 1 0.706846 -2.62101 0 0 0 0
|
||||
8 1 1 1 0.713613 -3.42098 0 0 0 0
|
||||
9 1 1 1 1.1571 -1.88132 0 0 0 0
|
||||
10 1 1 1 1.79537 -2.36362 0 0 0 0
|
||||
11 1 1 1 7.06424 -3.66256 0 0 0 0
|
||||
12 1 1 1 6.40541 -4.11636 0 0 0 0
|
||||
13 1 1 1 1.6281 -7.5987 0 0 0 0
|
||||
14 1 1 1 2.1523 -8.20302 0 0 0 0
|
||||
15 1 1 1 -4.93656 3.76623 0 0 0 0
|
||||
16 1 1 1 -5.34377 3.07763 0 0 0 0
|
||||
17 1 1 1 -6.32136 8.81986 0 0 0 0
|
||||
18 1 1 1 -6.51362 8.04331 0 0 0 0
|
||||
19 1 1 1 -8.36182 -1.34514 0 0 0 0
|
||||
20 1 1 1 -7.57433 -1.20422 0 0 0 0
|
||||
21 1 1 1 0.761896 7.11678 0 0 0 0
|
||||
22 1 1 1 1.56189 7.11405 0 0 0 0
|
||||
23 1 1 1 3.04971 8.20581 0 0 0 0
|
||||
24 1 1 1 3.73117 8.62487 0 0 0 0
|
||||
25 1 1 1 -9.24655 0.919604 0 0 0 0
|
||||
26 1 1 1 -8.61999 0.422185 0 0 0 0
|
||||
27 1 1 1 3.47654 7.52517 0 0 0 0
|
||||
28 1 1 1 3.88419 8.21352 0 0 0 0
|
||||
29 1 1 1 -8.12416 -5.23584 0 0 0 0
|
||||
30 1 1 1 -8.91222 -5.37357 0 0 0 0
|
||||
31 1 1 1 1.20614 0.287681 0 0 0 0
|
||||
32 1 1 1 1.05887 -0.498647 0 0 0 0
|
||||
33 1 1 1 6.74904 4.83018 0 0 0 0
|
||||
34 1 1 1 7.04361 5.57397 0 0 0 0
|
||||
35 1 1 1 -6.89076 4.75479 0 0 0 0
|
||||
36 1 1 1 -6.09243 4.80642 0 0 0 0
|
||||
37 1 1 1 5.71967 4.96927 0 0 0 0
|
||||
38 1 1 1 6.43406 4.60919 0 0 0 0
|
||||
39 1 1 1 -4.7844 1.52053 0 0 0 0
|
||||
40 1 1 1 -4.10449 1.9421 0 0 0 0
|
||||
41 1 1 1 -0.278393 -8.12051 0 0 0 0
|
||||
42 1 1 1 -0.676094 -7.42637 0 0 0 0
|
||||
43 1 1 1 9.12239 4.80748 0 0 0 0
|
||||
44 1 1 1 9.02285 4.01369 0 0 0 0
|
||||
45 1 1 1 1.25863 4.31012 0 0 0 0
|
||||
46 1 1 1 1.02322 3.54554 0 0 0 0
|
||||
47 1 1 1 6.06446 7.96693 0 0 0 0
|
||||
48 1 1 1 6.79746 7.64644 0 0 0 0
|
||||
49 1 1 1 -7.12827 -7.54209 0 0 0 0
|
||||
50 1 1 1 -6.60788 -6.93448 0 0 0 0
|
||||
51 1 1 1 -9.09101 -0.563476 0 0 0 0
|
||||
52 1 1 1 -8.30401 -0.419872 0 0 0 0
|
||||
53 1 1 1 -1.14788 7.48057 0 0 0 0
|
||||
54 1 1 1 -1.65618 8.09833 0 0 0 0
|
||||
55 1 1 1 -9.04712 8.38759 0 0 0 0
|
||||
56 1 1 1 -8.63766 9.07486 0 0 0 0
|
||||
57 1 1 1 -6.16596 5.02939 0 0 0 0
|
||||
58 1 1 1 -6.05435 4.23722 0 0 0 0
|
||||
59 1 1 1 0.142814 8.81325 0 0 0 0
|
||||
60 1 1 1 0.740918 8.28196 0 0 0 0
|
||||
61 1 1 1 -9.08007 -3.52882 0 0 0 0
|
||||
62 1 1 1 -8.80786 -4.28109 0 0 0 0
|
||||
63 1 1 1 -8.17071 -2.76935 0 0 0 0
|
||||
64 1 1 1 -8.14354 -1.96981 0 0 0 0
|
||||
65 1 1 1 -7.18538 4.21884 0 0 0 0
|
||||
66 1 1 1 -7.48843 3.47847 0 0 0 0
|
||||
67 1 1 1 1.97647 -0.445177 0 0 0 0
|
||||
68 1 1 1 2.65924 -0.0282648 0 0 0 0
|
||||
69 1 1 1 -3.89062 1.94653 0 0 0 0
|
||||
70 1 1 1 -4.39305 2.56907 0 0 0 0
|
||||
71 1 1 1 -2.82376 -3.36281 0 0 0 0
|
||||
72 1 1 1 -3.05339 -4.12915 0 0 0 0
|
||||
73 1 1 1 -5.25325 5.95125 0 0 0 0
|
||||
74 1 1 1 -5.92836 6.38046 0 0 0 0
|
||||
75 1 1 1 -0.417047 -3.06895 0 0 0 0
|
||||
76 1 1 1 -1.17149 -3.33507 0 0 0 0
|
||||
77 1 1 1 7.81153 0.749356 0 0 0 0
|
||||
78 1 1 1 8.27664 1.40025 0 0 0 0
|
||||
79 1 1 1 5.8217 0.868095 0 0 0 0
|
||||
80 1 1 1 6.39405 1.42704 0 0 0 0
|
||||
81 1 1 1 -4.55751 3.48043 0 0 0 0
|
||||
82 1 1 1 -5.29677 3.17466 0 0 0 0
|
||||
83 1 1 1 4.88466 2.03045 0 0 0 0
|
||||
84 1 1 1 4.28066 2.55503 0 0 0 0
|
||||
85 1 1 1 9.10305 -2.66451 0 0 0 0
|
||||
86 1 1 1 -9.32846 -3.42385 0 1 0 0
|
||||
87 1 1 1 7.63902 -2.65395 0 0 0 0
|
||||
88 1 1 1 8.14543 -3.27326 0 0 0 0
|
||||
89 1 1 1 7.06766 -2.21634 0 0 0 0
|
||||
90 1 1 1 7.83814 -2.00103 0 0 0 0
|
||||
91 1 1 1 4.23888 3.49195 0 0 0 0
|
||||
92 1 1 1 3.43912 3.5115 0 0 0 0
|
||||
93 1 1 1 -4.86556 1.30066 0 0 0 0
|
||||
94 1 1 1 -4.42725 1.9699 0 0 0 0
|
||||
95 1 1 1 3.29484 -0.985779 0 0 0 0
|
||||
96 1 1 1 3.71109 -1.66896 0 0 0 0
|
||||
97 1 1 1 -8.73443 -4.87107 0 0 0 0
|
||||
98 1 1 1 -8.87639 -5.65837 0 0 0 0
|
||||
99 1 1 1 -6.36058 3.67969 0 0 0 0
|
||||
100 1 1 1 -7.15698 3.75548 0 0 0 0
|
||||
101 1 1 1 5.26697 0.405769 0 0 0 0
|
||||
102 1 1 1 5.6903 -0.273046 0 0 0 0
|
||||
103 1 1 1 -6.20073 -0.149187 0 0 0 0
|
||||
104 1 1 1 -5.69507 0.470738 0 0 0 0
|
||||
105 1 1 1 -5.22944 -4.905 0 0 0 0
|
||||
106 1 1 1 -5.01264 -4.13493 0 0 0 0
|
||||
107 1 1 1 -7.365 -6.74284 0 0 0 0
|
||||
108 1 1 1 -8.13713 -6.53351 0 0 0 0
|
||||
109 1 1 1 -8.50673 -7.96756 0 0 0 0
|
||||
110 1 1 1 -8.2159 -7.2223 0 0 0 0
|
||||
111 1 1 1 -7.36396 -7.93443 0 0 0 0
|
||||
112 1 1 1 -6.73415 -8.42773 0 0 0 0
|
||||
113 1 1 1 -5.64348 5.1665 0 0 0 0
|
||||
114 1 1 1 -6.43991 5.09105 0 0 0 0
|
||||
115 1 1 1 9.22358 5.40182 0 0 0 0
|
||||
116 1 1 1 -8.90846 5.98157 0 1 0 0
|
||||
117 1 1 1 -1.75563 -6.00712 0 0 0 0
|
||||
118 1 1 1 -2.29051 -5.41222 0 0 0 0
|
||||
119 1 1 1 3.45169 0.843932 0 0 0 0
|
||||
120 1 1 1 3.78117 1.57293 0 0 0 0
|
||||
121 1 1 1 3.0644 -6.45436 0 0 0 0
|
||||
122 1 1 1 3.62762 -7.0225 0 0 0 0
|
||||
123 1 1 1 -6.71456 -4.50165 0 0 0 0
|
||||
124 1 1 1 -5.98388 -4.82738 0 0 0 0
|
||||
125 1 1 1 1.38027 -6.51875 0 0 0 0
|
||||
126 1 1 1 2.11513 -6.83494 0 0 0 0
|
||||
127 1 1 1 4.87497 7.33007 0 0 0 0
|
||||
128 1 1 1 5.47159 7.86303 0 0 0 0
|
||||
129 1 1 1 -2.0439 6.70325 0 0 0 0
|
||||
130 1 1 1 -2.45433 6.01655 0 0 0 0
|
||||
131 1 1 1 -3.29924 1.80238 0 0 0 0
|
||||
132 1 1 1 -2.98662 1.06599 0 0 0 0
|
||||
133 1 1 1 -5.60541 -8.88809 0 0 0 0
|
||||
134 1 1 1 -6.18332 9.24203 0 0 -1 0
|
||||
135 1 1 1 -2.88234 2.32173 0 0 0 0
|
||||
136 1 1 1 -3.20525 1.58979 0 0 0 0
|
||||
137 1 1 1 -5.04271 -5.39036 0 0 0 0
|
||||
138 1 1 1 -5.74302 -5.77709 0 0 0 0
|
||||
139 1 1 1 5.69287 2.81762 0 0 0 0
|
||||
140 1 1 1 6.10348 2.13104 0 0 0 0
|
||||
141 1 1 1 8.00042 -0.612514 0 0 0 0
|
||||
142 1 1 1 8.71994 -0.262798 0 0 0 0
|
||||
143 1 1 1 -3.97629 0.742529 0 0 0 0
|
||||
144 1 1 1 -3.36658 1.26047 0 0 0 0
|
||||
145 1 1 1 -4.90708 -5.18588 0 0 0 0
|
||||
146 1 1 1 -4.15949 -4.90107 0 0 0 0
|
||||
147 1 1 1 8.69119 6.68826 0 0 0 0
|
||||
148 1 1 1 8.10445 6.14443 0 0 0 0
|
||||
149 1 1 1 0.639774 -8.90856 0 0 0 0
|
||||
150 1 1 1 0.110051 -8.30906 0 0 0 0
|
||||
151 1 1 1 2.68553 -3.09643 0 0 0 0
|
||||
152 1 1 1 3.19558 -3.71275 0 0 0 0
|
||||
153 1 1 1 1.08943 0.377274 0 0 0 0
|
||||
154 1 1 1 1.43495 1.09881 0 0 0 0
|
||||
155 1 1 1 -2.27965 5.316 0 0 0 0
|
||||
156 1 1 1 -2.93006 5.7818 0 0 0 0
|
||||
157 1 1 1 1.40484 -4.62045 0 0 0 0
|
||||
158 1 1 1 1.94018 -4.02598 0 0 0 0
|
||||
159 1 1 1 -2.30481 -6.48448 0 0 0 0
|
||||
160 1 1 1 -1.53751 -6.71087 0 0 0 0
|
||||
161 1 1 1 -9.21316 1.66635 0 0 0 0
|
||||
162 1 1 1 9.33046 2.45406 0 -1 0 0
|
||||
163 1 1 1 -1.13608 0.273721 0 0 0 0
|
||||
164 1 1 1 -1.75716 0.777961 0 0 0 0
|
||||
165 1 1 1 -8.80553 -4.13121 0 0 0 0
|
||||
166 1 1 1 -8.64169 -4.91425 0 0 0 0
|
||||
167 1 1 1 1.65687 8.8975 0 0 0 0
|
||||
168 1 1 1 1.65839 -8.9858 0 0 1 0
|
||||
169 1 1 1 8.36746 2.59565 0 0 0 0
|
||||
170 1 1 1 9.06956 2.21219 0 0 0 0
|
||||
171 1 1 1 -5.98437 -7.01768 0 0 0 0
|
||||
172 1 1 1 -5.34019 -6.5433 0 0 0 0
|
||||
173 1 1 1 -4.08999 -4.58535 0 0 0 0
|
||||
174 1 1 1 -3.50681 -5.13298 0 0 0 0
|
||||
175 1 1 1 4.12068 -2.66213 0 0 0 0
|
||||
176 1 1 1 4.47739 -3.3782 0 0 0 0
|
||||
177 1 1 1 -8.21813 3.61652 0 0 0 0
|
||||
178 1 1 1 -7.83713 4.31997 0 0 0 0
|
||||
179 1 1 1 5.3708 8.01903 0 0 0 0
|
||||
180 1 1 1 4.66332 8.39249 0 0 0 0
|
||||
181 1 1 1 -7.99312 -7.49248 0 0 0 0
|
||||
182 1 1 1 -7.40112 -8.03055 0 0 0 0
|
||||
183 1 1 1 6.52577 7.66337 0 0 0 0
|
||||
184 1 1 1 5.74291 7.49865 0 0 0 0
|
||||
185 1 1 1 -1.68136 9.16388 0 0 0 0
|
||||
186 1 1 1 -1.62497 8.36587 0 0 0 0
|
||||
187 1 1 1 -9.06593 -8.69211 0 0 0 0
|
||||
188 1 1 1 9.24439 -7.98438 0 -1 0 0
|
||||
189 1 1 1 -1.84034 8.97585 0 0 0 0
|
||||
190 1 1 1 -1.22441 8.46534 0 0 0 0
|
||||
191 1 1 1 -2.52855 7.20926 0 0 0 0
|
||||
192 1 1 1 -3.32354 7.11991 0 0 0 0
|
||||
193 1 1 1 2.00449 3.54871 0 0 0 0
|
||||
194 1 1 1 1.4845 4.15666 0 0 0 0
|
||||
195 1 1 1 5.6526 -1.31637 0 0 0 0
|
||||
196 1 1 1 4.86095 -1.43166 0 0 0 0
|
||||
197 1 1 1 -6.41619 3.12674 0 0 0 0
|
||||
198 1 1 1 -6.93879 3.73245 0 0 0 0
|
||||
199 1 1 1 -4.38345 -4.37207 0 0 0 0
|
||||
200 1 1 1 -3.84213 -4.96112 0 0 0 0
|
||||
|
||||
Molecules
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 2
|
||||
4 2
|
||||
5 3
|
||||
6 3
|
||||
7 4
|
||||
8 4
|
||||
9 5
|
||||
10 5
|
||||
11 6
|
||||
12 6
|
||||
13 7
|
||||
14 7
|
||||
15 8
|
||||
16 8
|
||||
17 9
|
||||
18 9
|
||||
19 10
|
||||
20 10
|
||||
21 11
|
||||
22 11
|
||||
23 12
|
||||
24 12
|
||||
25 13
|
||||
26 13
|
||||
27 14
|
||||
28 14
|
||||
29 15
|
||||
30 15
|
||||
31 16
|
||||
32 16
|
||||
33 17
|
||||
34 17
|
||||
35 18
|
||||
36 18
|
||||
37 19
|
||||
38 19
|
||||
39 20
|
||||
40 20
|
||||
41 21
|
||||
42 21
|
||||
43 22
|
||||
44 22
|
||||
45 23
|
||||
46 23
|
||||
47 24
|
||||
48 24
|
||||
49 25
|
||||
50 25
|
||||
51 26
|
||||
52 26
|
||||
53 27
|
||||
54 27
|
||||
55 28
|
||||
56 28
|
||||
57 29
|
||||
58 29
|
||||
59 30
|
||||
60 30
|
||||
61 31
|
||||
62 31
|
||||
63 32
|
||||
64 32
|
||||
65 33
|
||||
66 33
|
||||
67 34
|
||||
68 34
|
||||
69 35
|
||||
70 35
|
||||
71 36
|
||||
72 36
|
||||
73 37
|
||||
74 37
|
||||
75 38
|
||||
76 38
|
||||
77 39
|
||||
78 39
|
||||
79 40
|
||||
80 40
|
||||
81 41
|
||||
82 41
|
||||
83 42
|
||||
84 42
|
||||
85 43
|
||||
86 43
|
||||
87 44
|
||||
88 44
|
||||
89 45
|
||||
90 45
|
||||
91 46
|
||||
92 46
|
||||
93 47
|
||||
94 47
|
||||
95 48
|
||||
96 48
|
||||
97 49
|
||||
98 49
|
||||
99 50
|
||||
100 50
|
||||
101 51
|
||||
102 51
|
||||
103 52
|
||||
104 52
|
||||
105 53
|
||||
106 53
|
||||
107 54
|
||||
108 54
|
||||
109 55
|
||||
110 55
|
||||
111 56
|
||||
112 56
|
||||
113 57
|
||||
114 57
|
||||
115 58
|
||||
116 58
|
||||
117 59
|
||||
118 59
|
||||
119 60
|
||||
120 60
|
||||
121 61
|
||||
122 61
|
||||
123 62
|
||||
124 62
|
||||
125 63
|
||||
126 63
|
||||
127 64
|
||||
128 64
|
||||
129 65
|
||||
130 65
|
||||
131 66
|
||||
132 66
|
||||
133 67
|
||||
134 67
|
||||
135 68
|
||||
136 68
|
||||
137 69
|
||||
138 69
|
||||
139 70
|
||||
140 70
|
||||
141 71
|
||||
142 71
|
||||
143 72
|
||||
144 72
|
||||
145 73
|
||||
146 73
|
||||
147 74
|
||||
148 74
|
||||
149 75
|
||||
150 75
|
||||
151 76
|
||||
152 76
|
||||
153 77
|
||||
154 77
|
||||
155 78
|
||||
156 78
|
||||
157 79
|
||||
158 79
|
||||
159 80
|
||||
160 80
|
||||
161 81
|
||||
162 81
|
||||
163 82
|
||||
164 82
|
||||
165 83
|
||||
166 83
|
||||
167 84
|
||||
168 84
|
||||
169 85
|
||||
170 85
|
||||
171 86
|
||||
172 86
|
||||
173 87
|
||||
174 87
|
||||
175 88
|
||||
176 88
|
||||
177 89
|
||||
178 89
|
||||
179 90
|
||||
180 90
|
||||
181 91
|
||||
182 91
|
||||
183 92
|
||||
184 92
|
||||
185 93
|
||||
186 93
|
||||
187 94
|
||||
188 94
|
||||
189 95
|
||||
190 95
|
||||
191 96
|
||||
192 96
|
||||
193 97
|
||||
194 97
|
||||
195 98
|
||||
196 98
|
||||
197 99
|
||||
198 99
|
||||
199 100
|
||||
200 100
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
# create set of randomly oriented dimers
|
||||
|
||||
p = patch(0.3)
|
||||
p.dim = 2
|
||||
p.extratype = 1
|
||||
p.style = "sphere"
|
||||
p.extra = "Molecules"
|
||||
p.seed = 54321
|
||||
p.build(100,"dimer",0.8,1)
|
||||
p.write("data.dimer")
|
||||
|
|
@ -0,0 +1,104 @@
|
|||
# SRD diffusion demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
|
||||
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
|
||||
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.dimer
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
|
|
@ -0,0 +1,105 @@
|
|||
# SRD viscosity demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
|
||||
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
|
||||
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 500 dump.dimer.mp
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 50000
|
||||
|
|
@ -0,0 +1,285 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# SRD diffusion demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
orthogonal box = (-9.34165 -9.34165 -0.5) to (9.34165 9.34165 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
200 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
200 settings made for mass
|
||||
group big type 1
|
||||
200 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 3.10291 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.4028231 0 0 0.83369167 -0.55065517
|
||||
100 9.5167872 2.392105 0 4.7237178 2.8319556
|
||||
200 13.564465 3.0352634 0 6.3585572 3.6388732
|
||||
300 13.133051 4.3835112 0 7.6011086 4.060051
|
||||
400 14.584346 5.5141254 0 9.0872901 4.4231056
|
||||
500 15.331515 6.6554832 0 10.411704 4.847642
|
||||
600 16.953755 7.4794317 0 11.633102 5.2020696
|
||||
700 16.503256 8.8572339 0 12.900532 5.6694613
|
||||
800 17.006131 9.877343 0 14.043845 5.5483363
|
||||
900 17.305927 11.081594 0 15.321546 6.2908201
|
||||
1000 18.122491 12.126462 0 16.566472 5.7536055
|
||||
Loop time of 0.0641297 on 8 procs for 1000 steps with 200 atoms
|
||||
|
||||
Pair time (%) = 0.00222233 (3.46537)
|
||||
Neigh time (%) = 0.000630736 (0.983532)
|
||||
Comm time (%) = 0.0137274 (21.4057)
|
||||
Outpt time (%) = 0.00027743 (0.432607)
|
||||
Other time (%) = 0.0472718 (73.7128)
|
||||
|
||||
Nlocal: 25 ave 30 max 20 min
|
||||
Histogram: 1 0 1 1 0 0 3 1 0 1
|
||||
Nghost: 28.375 ave 36 max 22 min
|
||||
Histogram: 1 0 1 2 1 0 2 0 0 1
|
||||
Neighs: 33.125 ave 45 max 22 min
|
||||
Histogram: 1 0 2 1 0 1 1 0 1 1
|
||||
|
||||
Total # of neighbors = 265
|
||||
Ave neighs/atom = 1.325
|
||||
Neighbor list builds = 99
|
||||
Dangerous builds = 96
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 2 region plane
|
||||
Created 29929 atoms
|
||||
|
||||
set type 2 mass 0.1
|
||||
29929 settings made for mass
|
||||
group small type 2
|
||||
29929 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
Deleted 12759 atoms, new total = 17370
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.dimer
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 17170 200
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 75 75 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.249111 0.249111 1
|
||||
SRD per actual grid cell = 5.5499
|
||||
SRD viscosity = 0.235551
|
||||
big/SRD mass density ratio = 0.142367
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.20347 7.72323
|
||||
ave/max big velocity = 2.64047 6.60911
|
||||
Memory usage per processor = 6.81079 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 6.9744766 0 0.30175295 21.011259 26.207244 2.7219332 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.2354587 3809 0.24719873 20.548793 21.46921 7.1295283 13581 50 50 0 709 40320 5625 3809 1.0057655 0 39 0
|
||||
2000 1.1883147 3812 0.24605507 20.484588 21.369883 4.6579756 13419 49 50 0 1601 40320 5625 3812 1.0536999 0 39 0
|
||||
3000 1.1945015 3800 0.24698055 20.560357 21.45026 8.0187045 13398 67 67 0 2485 40320 5625 3800 1.0389278 0 39 0
|
||||
4000 1.2814726 3810 0.24731813 20.524883 21.47958 7.2525742 13351 54 54 1 3331 40320 5625 3810 1.0416803 0 39 0
|
||||
5000 1.2655406 3805 0.24653329 20.468588 21.411416 5.2725197 13561 54 54 2 4170 40320 5625 3805 1.0314896 0 57 0
|
||||
6000 1.1591194 3774 0.24602165 20.503437 21.366981 7.6336076 13521 53 53 1 5013 40320 5625 3774 1.0519436 0 57 0
|
||||
7000 1.1138313 3785 0.24577139 20.515441 21.345245 9.1512158 13365 57 57 2 5946 40320 5625 3785 1.0468342 0 57 0
|
||||
8000 1.2472647 3776 0.24679288 20.504749 21.433961 9.8240373 13283 58 58 5 6956 40320 5625 3776 1.0533896 0 93 0
|
||||
9000 1.3539734 3799 0.24706895 20.449228 21.457939 8.6415706 13486 52 52 0 7868 40320 5625 3799 1.0369339 0 93 0
|
||||
10000 1.1240413 3790 0.2462023 20.545259 21.38267 7.9137395 13238 52 52 0 8779 40320 5625 3790 1.0438247 0 93 0
|
||||
11000 1.0115706 3801 0.24396454 20.4347 21.188321 5.6596258 13397 66 66 1 9697 40320 5625 3801 1.0464352 0 93 0
|
||||
12000 1.0539712 3798 0.24450261 20.449843 21.235052 8.3325065 13436 53 53 0 10590 40320 5625 3798 1.0427153 0 93 0
|
||||
13000 1.2685827 3782 0.24613472 20.431707 21.376801 9.9345777 13278 67 67 1 11460 40320 5625 3782 1.0445824 0 93 0
|
||||
14000 1.1149298 3804 0.24483169 20.433009 21.263632 7.4598905 13383 78 78 1 12335 40320 5625 3804 1.0459521 0 93 0
|
||||
15000 1.1892144 3794 0.24570719 20.453705 21.339669 9.1494223 13335 55 55 1 13146 40320 5625 3794 1.0307813 0 93 0
|
||||
16000 1.3054 3788 0.24602945 20.395135 21.367658 6.3702986 13424 47 47 0 14044 40320 5625 3788 1.0465902 0 93 0
|
||||
17000 1.1646813 3805 0.24486031 20.39843 21.266118 7.7108151 13392 51 51 0 14929 40320 5625 3805 1.0213327 0 93 0
|
||||
18000 1.1891201 3791 0.24554422 20.439621 21.325516 8.0653754 13192 60 60 2 15755 40320 5625 3791 1.0340398 0 93 0
|
||||
19000 1.0324301 3790 0.24381204 20.405915 21.175076 6.1858385 13050 45 45 0 16724 40320 5625 3790 1.0472302 0 93 0
|
||||
20000 1.3224614 3804 0.24621703 20.398715 21.383949 6.1300529 13594 54 54 1 17517 40320 5625 3804 1.030461 0 93 0
|
||||
21000 1.1530445 3784 0.24518298 20.435124 21.294142 5.4852317 13275 53 54 1 18412 40320 5625 3784 1.0535382 0 93 0
|
||||
22000 1.1977912 3784 0.24500736 20.386535 21.278889 6.1881822 13475 47 47 0 19198 40320 5625 3784 1.0210748 0 93 0
|
||||
23000 1.2514017 3797 0.24621058 20.451095 21.383389 8.7550065 13129 46 46 2 20287 40320 5625 3797 1.0368593 0 93 0
|
||||
24000 1.2176426 3810 0.2457793 20.438788 21.345932 6.9987747 13704 60 60 2 21229 40320 5625 3810 1.0454377 0 93 0
|
||||
25000 1.0891735 3798 0.24446154 20.420051 21.231485 6.1085159 13065 56 56 0 22323 40320 5625 3798 1.0505581 0 120 0
|
||||
26000 1.1352468 3815 0.24428891 20.370733 21.216492 6.7514766 13071 63 63 0 23082 40320 5625 3815 1.0574391 0 120 0
|
||||
27000 1.2096898 3767 0.24578464 20.445177 21.346396 9.2222472 13000 62 62 0 23915 40320 5625 3767 1.0322659 0 120 0
|
||||
28000 1.1822845 3810 0.24602328 20.48632 21.367122 7.6215417 13091 63 64 0 25021 40320 5625 3810 1.0109647 0 120 0
|
||||
29000 1.1681651 3774 0.24483973 20.394047 21.26433 4.8780536 13234 45 45 0 25969 40320 5625 3774 1.0139235 0 120 0
|
||||
30000 1.2469272 3753 0.24652211 20.481484 21.410445 7.3553052 12959 42 42 0 27355 40320 5625 3753 1.0372102 0 158 0
|
||||
31000 1.6007361 3784 0.25029348 20.54544 21.737988 6.4277487 13296 65 65 4 29010 40320 5625 3784 1.0232378 0 289 0
|
||||
32000 1.3008178 3782 0.24630803 20.422743 21.391852 5.1176993 13300 84 85 1 30087 40320 5625 3782 1.0396919 0 289 0
|
||||
33000 1.098991 3806 0.24419427 20.389524 21.208272 7.7403219 13385 56 57 1 31020 40320 5625 3806 1.041743 0 289 0
|
||||
34000 1.0690232 3788 0.24446214 20.435114 21.231537 7.5766596 13169 52 52 1 31883 40320 5625 3788 1.0361564 0 289 0
|
||||
35000 1.2481706 3805 0.24604847 20.439422 21.36931 8.4852719 13287 50 50 2 32742 40320 5625 3805 1.0362327 0 289 0
|
||||
36000 1.2779611 3809 0.24583215 20.398441 21.350522 4.4273482 13245 53 53 0 33581 40320 5625 3809 1.0384859 0 289 0
|
||||
37000 1.1516078 3797 0.2455632 20.469216 21.327164 6.8418541 13220 56 56 0 34676 40320 5625 3797 1.0356559 0 289 0
|
||||
38000 3.1966808 3804 0.26289728 20.451101 22.832629 8.6766153 13285 78 78 5 35584 40320 5625 3804 1.0212937 0 289 0
|
||||
39000 1.3514672 3774 0.24773001 20.508508 21.515351 6.8562512 13267 53 54 0 37060 40320 5625 3774 1.0506286 0 289 0
|
||||
40000 1.2690376 3800 0.24696212 20.503227 21.44866 7.306469 13136 48 48 1 38009 40320 5625 3800 1.0435393 0 289 0
|
||||
41000 1.1629196 3815 0.24451909 20.370108 21.236483 10.994819 13294 65 65 0 38856 40320 5625 3815 1.0231193 0 289 0
|
||||
42000 1.3071093 3794 0.24711438 20.488087 21.461884 11.635668 13377 63 63 0 39748 40320 5625 3794 1.0310415 0 289 0
|
||||
43000 1.1790643 3814 0.24525862 20.422309 21.300712 7.4899148 13167 55 55 0 40763 40320 5625 3814 1.0643207 0 289 0
|
||||
44000 1.0546224 3816 0.24416646 20.420163 21.205857 8.5184241 13383 57 57 0 41635 40320 5625 3816 1.0300963 0 289 0
|
||||
45000 1.5126923 3816 0.24957769 20.548867 21.675822 7.8342626 13593 51 51 5 43135 40320 5625 3816 1.0470194 0 289 0
|
||||
46000 1.1974681 3811 0.24522511 20.405687 21.297801 8.5828458 13253 58 58 0 44063 40320 5625 3811 1.0211266 0 289 0
|
||||
47000 1.153913 3796 0.24546332 20.458824 21.31849 12.306291 13070 46 46 1 44904 40320 5625 3796 1.0134546 0 289 0
|
||||
48000 1.0836112 3783 0.24414791 20.396955 21.204246 8.2850758 12885 57 57 1 45783 40320 5625 3783 1.0518997 0 289 0
|
||||
49000 1.0541913 3804 0.24345782 20.358939 21.144312 7.5572928 13094 67 67 1 46591 40320 5625 3804 1.022045 0 289 0
|
||||
50000 1.2626609 3801 0.24672175 20.487102 21.427784 9.6363068 12963 67 67 3 47434 40320 5625 3801 1.0417063 0 289 0
|
||||
51000 1.1865663 3788 0.24455665 20.355754 21.239745 10.07391 13119 62 63 2 48466 40320 5625 3788 1.0503342 0 289 0
|
||||
52000 1.2437795 3802 0.24570213 20.412614 21.33923 9.3613571 13065 57 57 1 49406 40320 5625 3802 1.0407195 0 289 0
|
||||
53000 1.2866363 3798 0.2458415 20.39279 21.351334 9.8245291 13109 53 53 1 50265 40320 5625 3798 1.0226426 0 289 0
|
||||
54000 1.2414003 3799 0.24595803 20.436612 21.361455 11.751574 13190 58 59 3 51613 40320 5625 3799 1.0357656 0 289 0
|
||||
55000 1.2028463 3785 0.24595746 20.465285 21.361405 6.4299111 13186 60 61 1 52735 40320 5625 3785 1.0316105 0 289 0
|
||||
56000 1.0385165 3808 0.24390301 20.409282 21.182976 6.7801109 13022 54 54 0 53622 40320 5625 3808 1.0434153 0 289 0
|
||||
57000 1.0436103 3799 0.24377932 20.394745 21.172234 7.1162927 13049 50 50 0 54495 40320 5625 3799 1.0178911 0 289 0
|
||||
58000 0.97106921 3795 0.24364318 20.436964 21.16041 9.022592 13286 50 50 0 55327 40320 5625 3795 1.0353873 0 289 0
|
||||
59000 1.1495392 3790 0.24458585 20.385874 21.242281 9.7884887 13157 63 63 1 56179 40320 5625 3790 1.0281317 0 289 0
|
||||
60000 1.188382 3781 0.24514124 20.405172 21.290516 7.3581039 12943 56 56 1 57024 40320 5625 3781 1.0596215 0 289 0
|
||||
61000 1.3366984 3768 0.24662234 20.42331 21.41915 6.109315 13068 52 52 1 57921 40320 5625 3768 1.0706378 0 289 0
|
||||
62000 1.1261613 3788 0.24432384 20.380535 21.219525 5.7818811 13296 54 54 0 58841 40320 5625 3788 1.0432485 0 289 0
|
||||
63000 1.1620503 3831 0.24430718 20.352351 21.218079 6.6114481 13321 51 51 0 59698 40320 5625 3831 1.0438264 0 289 0
|
||||
64000 1.0816323 3803 0.24367372 20.357247 21.163063 10.33086 13210 64 64 0 60543 40320 5625 3803 1.055563 0 289 0
|
||||
65000 1.2024467 3790 0.24573222 20.446021 21.341844 7.3760583 12855 54 54 0 61397 40320 5625 3790 1.0581964 0 289 0
|
||||
66000 1.2134054 3782 0.2459965 20.460809 21.364796 6.5901858 13015 59 61 0 62205 40320 5625 3782 1.0320373 0 289 0
|
||||
67000 1.2975719 3808 0.24614477 20.410982 21.377674 9.568788 13012 56 56 1 63680 40320 5625 3808 1.0555615 0 289 0
|
||||
68000 1.3311071 3811 0.24615733 20.387089 21.378764 2.2119551 13138 56 56 0 64586 40320 5625 3811 1.0417112 0 289 0
|
||||
69000 1.1764971 3803 0.24501561 20.403115 21.279606 2.3580263 12903 61 61 0 65504 40320 5625 3803 1.0345172 0 289 0
|
||||
70000 1.1603463 3806 0.24424231 20.347987 21.212445 5.2723227 13068 64 64 2 66386 40320 5625 3806 1.0504265 0 289 0
|
||||
71000 1.151703 3802 0.24460158 20.385628 21.243647 5.9863258 12868 51 51 2 67280 40320 5625 3802 1.0323304 0 289 0
|
||||
72000 1.2360087 3789 0.24540655 20.392733 21.313559 8.0678594 12835 37 37 2 68153 40320 5625 3789 1.0157807 0 289 0
|
||||
73000 1.1778901 3792 0.24516585 20.415126 21.292654 8.3383517 12980 59 59 0 68917 40320 5625 3792 1.0211893 0 289 0
|
||||
74000 1.1320033 3801 0.24465911 20.405302 21.248644 6.7423404 13244 63 63 0 69802 40320 5625 3801 1.0379895 0 289 0
|
||||
75000 1.303095 3792 0.24597801 20.392384 21.36319 7.1605507 13290 64 64 1 70966 40320 5625 3792 1.0479027 0 289 0
|
||||
76000 1.3122789 3791 0.24686821 20.462856 21.440504 5.6011815 12921 53 53 0 71853 40320 5625 3791 1.0429825 0 289 0
|
||||
77000 1.1110266 3777 0.24531121 20.477563 21.305278 7.6992351 13227 59 59 1 72625 40320 5625 3777 1.0346512 0 289 0
|
||||
78000 1.1423584 3788 0.24614751 20.526855 21.377912 9.1592588 12981 54 54 0 73534 40320 5625 3788 1.0394046 0 289 0
|
||||
79000 1.178933 3795 0.24546662 20.440471 21.318776 5.1190336 13027 61 61 0 74357 40320 5625 3795 1.0373795 0 289 0
|
||||
80000 1.2228825 3793 0.24546742 20.407798 21.318845 8.5997861 13116 61 61 2 75248 40320 5625 3793 1.0487918 0 289 0
|
||||
81000 1.2539867 3795 0.24680743 20.501006 21.435226 7.7737133 13136 65 65 0 76143 40320 5625 3795 1.057414 0 289 0
|
||||
82000 1.2163565 3809 0.24603827 20.462238 21.368423 8.4588097 13227 77 77 0 77052 40320 5625 3809 1.0281569 0 289 0
|
||||
83000 1.1372789 3800 0.24477746 20.411649 21.258922 8.6655002 13318 53 53 1 77950 40320 5625 3800 1.052126 0 289 0
|
||||
84000 1.0963118 3798 0.24395552 20.370785 21.187537 7.5285125 13298 71 72 0 78812 40320 5625 3798 1.0739334 0 289 0
|
||||
85000 1.2866517 3806 0.24577005 20.386573 21.345129 9.2812098 13301 73 73 0 79713 40320 5625 3806 1.0318108 0 289 0
|
||||
86000 1.191902 3776 0.24527268 20.413966 21.301932 9.1903108 13178 60 60 0 80629 40320 5625 3776 1.0473977 0 289 0
|
||||
87000 1.0828531 3787 0.24432069 20.412526 21.219252 4.6934397 13047 60 60 1 81448 40320 5625 3787 1.0168512 0 289 0
|
||||
88000 2.0634092 3798 0.25362055 20.489705 22.026944 8.3601433 13229 49 49 27 82676 40320 5625 3798 1.0310791 0 289 0
|
||||
89000 1.1633678 3788 0.24488709 20.401735 21.268444 7.9040117 13287 49 50 1 83644 40320 5625 3788 1.0443183 0 289 0
|
||||
90000 1.1834356 3790 0.24566829 20.454632 21.336291 6.8101979 13377 50 50 0 84466 40320 5625 3790 1.0426033 0 289 0
|
||||
91000 1.3000933 3810 0.24590334 20.388136 21.356705 6.481335 13468 62 62 4 85683 40320 5625 3810 1.0536904 0 289 0
|
||||
92000 1.282522 3775 0.24709409 20.504643 21.460122 6.0594454 13383 47 47 0 86552 40320 5625 3775 1.0455446 0 289 0
|
||||
93000 1.3337412 3787 0.24688092 20.447971 21.441608 8.2151451 13298 64 64 2 87424 40320 5625 3787 1.0304143 0 289 0
|
||||
94000 1.2200394 3816 0.24594726 20.45159 21.360519 5.75844 13608 48 48 2 88404 40320 5625 3816 1.0319527 0 289 0
|
||||
95000 1.1162136 3804 0.24520798 20.464734 21.296313 7.9641712 13316 51 51 0 89205 40320 5625 3804 1.034941 0 289 0
|
||||
96000 1.1719084 3802 0.24578082 20.472993 21.346064 5.998945 13593 59 59 0 90005 40320 5625 3802 1.0280493 0 289 0
|
||||
97000 1.3506167 3794 0.24764606 20.501851 21.508061 8.7470453 13202 56 56 1 90840 40320 5625 3794 1.0235267 0 289 0
|
||||
98000 1.2314111 3800 0.24699537 20.534146 21.451548 13.14846 13183 67 67 0 91659 40320 5625 3800 1.017929 0 289 0
|
||||
99000 1.1466628 3796 0.24472055 20.399716 21.25398 5.5941204 13335 62 62 1 92497 40320 5625 3796 1.0247856 0 289 0
|
||||
100000 1.1502546 3831 0.24457346 20.384266 21.241205 9.3619779 13566 65 65 0 93378 40320 5625 3831 1.023894 0 289 0
|
||||
Loop time of 23.1526 on 8 procs for 100000 steps with 17370 atoms
|
||||
|
||||
Pair time (%) = 0.357818 (1.54548)
|
||||
Neigh time (%) = 1.28113 (5.53343)
|
||||
Comm time (%) = 1.77444 (7.66411)
|
||||
Outpt time (%) = 0.00594333 (0.0256703)
|
||||
Other time (%) = 19.7333 (85.2313)
|
||||
|
||||
Nlocal: 2171.25 ave 2686 max 1889 min
|
||||
Histogram: 2 2 0 1 0 1 1 0 0 1
|
||||
Nghost: 65.25 ave 68 max 60 min
|
||||
Histogram: 1 0 0 1 0 1 1 0 2 2
|
||||
Neighs: 171.375 ave 213 max 87 min
|
||||
Histogram: 1 0 0 0 1 1 1 0 1 3
|
||||
|
||||
Total # of neighbors = 1371
|
||||
Ave neighs/atom = 0.0789292
|
||||
Neighbor list builds = 5094
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,236 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# SRD viscosity demo - dimer particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.dimer fix molprop NULL Molecules
|
||||
orthogonal box = (-9.34165 -9.34165 -0.5) to (9.34165 9.34165 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
200 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
200 settings made for mass
|
||||
group big type 1
|
||||
200 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.dimer.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 3.10291 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3.4028231 0 0 0.83369167 -0.55065517
|
||||
100 9.5167872 2.392105 0 4.7237178 2.8319556
|
||||
200 13.564465 3.0352634 0 6.3585572 3.6388732
|
||||
300 13.133051 4.3835112 0 7.6011086 4.060051
|
||||
400 14.584346 5.5141254 0 9.0872901 4.4231056
|
||||
500 15.331515 6.6554832 0 10.411704 4.847642
|
||||
600 16.953755 7.4794317 0 11.633102 5.2020696
|
||||
700 16.503256 8.8572339 0 12.900532 5.6694613
|
||||
800 17.006131 9.877343 0 14.043845 5.5483363
|
||||
900 17.305927 11.081594 0 15.321546 6.2908201
|
||||
1000 18.122491 12.126462 0 16.566472 5.7536055
|
||||
Loop time of 0.0627978 on 8 procs for 1000 steps with 200 atoms
|
||||
|
||||
Pair time (%) = 0.00222558 (3.54404)
|
||||
Neigh time (%) = 0.000630498 (1.00401)
|
||||
Comm time (%) = 0.0138363 (22.0331)
|
||||
Outpt time (%) = 0.000252694 (0.402393)
|
||||
Other time (%) = 0.0458528 (73.0165)
|
||||
|
||||
Nlocal: 25 ave 30 max 20 min
|
||||
Histogram: 1 0 1 1 0 0 3 1 0 1
|
||||
Nghost: 28.375 ave 36 max 22 min
|
||||
Histogram: 1 0 1 2 1 0 2 0 0 1
|
||||
Neighs: 33.125 ave 45 max 22 min
|
||||
Histogram: 1 0 2 1 0 1 1 0 1 1
|
||||
|
||||
Total # of neighbors = 265
|
||||
Ave neighs/atom = 1.325
|
||||
Neighbor list builds = 99
|
||||
Dangerous builds = 96
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 2 region plane
|
||||
Created 29929 atoms
|
||||
|
||||
set type 2 mass 0.1
|
||||
29929 settings made for mass
|
||||
group small type 2
|
||||
29929 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
Deleted 12759 atoms, new total = 17370
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 200 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 500 dump.dimer.mp
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 50000
|
||||
SRD info:
|
||||
SRD/big particles = 17170 200
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 75 75 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.249111 0.249111 1
|
||||
SRD per actual grid cell = 5.5499
|
||||
SRD viscosity = 0.235551
|
||||
big/SRD mass density ratio = 0.142367
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.20347 7.72323
|
||||
ave/max big velocity = 2.64047 6.60911
|
||||
Memory usage per processor = 6.81079 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 6.9744766 0 0.30175295 21.011259 26.207244 2.7219332 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.2992959 3806 0.24766681 20.541887 21.509863 8.3137867 13254 64 64 1 616 40320 5625 3806 1.0164848 0 4 0
|
||||
2000 1.358528 3797 0.2484409 20.564988 21.577092 11.810557 13539 50 50 1 1526 40320 5625 3797 1.0411843 0 45 0
|
||||
3000 1.4548846 3805 0.24912964 20.553021 21.63691 9.5926803 13468 60 60 4 2398 40320 5625 3805 1.0497533 0 45 0
|
||||
4000 1.8791843 3815 0.2520188 20.48784 21.887833 8.2746056 13404 60 60 0 3383 40320 5625 3815 1.0373399 0 45 0
|
||||
5000 1.6477948 3808 0.25003987 20.488356 21.715963 4.4265304 13161 48 48 1 4419 40320 5625 3808 1.0272144 0 45 0
|
||||
6000 1.6158929 3793 0.24939304 20.455945 21.659785 8.3817061 13207 59 59 0 5558 40320 5625 3793 1.0368342 0 45 0
|
||||
7000 2.0865667 3806 0.25391685 20.498186 22.052678 8.0322269 13079 60 60 0 6843 40320 5625 3806 1.0325798 0 107 0
|
||||
8000 2.2197829 3778 0.25451747 20.451104 22.104842 11.453866 13081 49 49 0 8004 40320 5625 3778 1.0191928 0 107 0
|
||||
9000 2.1397074 3798 0.25441886 20.502196 22.096278 7.8765329 13080 52 52 0 9214 40320 5625 3798 1.0344843 0 107 0
|
||||
10000 2.3083585 3791 0.25615794 20.52759 22.247317 7.8816479 12974 48 48 3 10555 40320 5625 3791 1.0281033 0 107 0
|
||||
11000 2.5639164 3803 0.25817577 20.512448 22.422565 6.768962 13177 50 50 1 11917 40320 5625 3803 1.0394491 0 107 0
|
||||
12000 2.737192 3757 0.26051986 20.586941 22.626149 7.6808761 13072 48 48 6 13993 40320 5625 3757 1.0643581 0 269 0
|
||||
13000 8.1232914 3761 0.30582339 20.508909 26.560761 10.80899 13074 48 48 20 15818 40320 5625 3761 1.029561 0 269 0
|
||||
14000 2.961704 3786 0.26050848 20.418692 22.625162 9.7685216 13369 59 59 3 17423 40320 5625 3786 1.0121975 0 269 0
|
||||
15000 2.5821822 3789 0.25834133 20.513218 22.436944 6.9498412 13183 46 46 3 18931 40320 5625 3789 1.0375525 0 269 0
|
||||
16000 2.6225045 3756 0.25795343 20.449489 22.403255 10.405912 12646 66 66 1 20473 40320 5625 3756 1.032942 0 269 0
|
||||
17000 4.1283061 3701 0.27197048 20.545048 23.620636 8.4471446 13224 65 66 15 24398 40320 5625 3701 1.0687815 0 604 0
|
||||
18000 2.8741237 3777 0.26027375 20.463553 22.604775 7.6566907 13020 61 61 1 26636 40320 5625 3777 1.0098706 0 604 0
|
||||
19000 2.713854 3784 0.25853001 20.43151 22.453331 9.1078878 12941 58 58 2 28367 40320 5625 3784 0.98796076 0 604 0
|
||||
20000 3.0035093 3791 0.2624204 20.553597 22.791212 5.8950854 12710 50 50 0 30004 40320 5625 3791 1.0127104 0 604 0
|
||||
21000 2.8304858 3794 0.25987392 20.461338 22.57005 7.4867736 13025 58 58 3 31801 40320 5625 3794 1.0303174 0 604 0
|
||||
22000 2.8055694 3785 0.26137505 20.610274 22.700423 10.823968 13074 64 64 17 33863 40320 5625 3785 1.0205053 0 604 0
|
||||
23000 2.9712363 3794 0.26117889 20.469816 22.683387 8.6172464 13263 55 55 1 35391 40320 5625 3794 1.0051398 0 604 0
|
||||
24000 2.8762937 3771 0.26137187 20.557308 22.700146 9.8024879 13172 57 57 0 36915 40320 5625 3771 1.0144035 0 604 0
|
||||
25000 2.9852963 3782 0.26142335 20.480572 22.704618 9.0597755 13168 67 67 0 38577 40320 5625 3782 1.0230792 0 604 0
|
||||
26000 2.918217 3797 0.26186781 20.569148 22.743219 5.6274781 13407 47 47 1 40096 40320 5625 3797 1.0271045 0 604 0
|
||||
27000 2.9863542 3781 0.26202524 20.532058 22.756892 6.2490454 13008 45 45 1 41815 40320 5625 3781 1.0516123 0 604 0
|
||||
28000 2.9994869 3815 0.26226247 20.542878 22.777496 7.127401 13211 59 59 0 43562 40320 5625 3815 1.0282567 0 604 0
|
||||
29000 2.8020211 3769 0.26039919 20.528164 22.61567 4.8931362 13302 46 46 1 45189 40320 5625 3769 1.0011147 0 604 0
|
||||
30000 2.9966437 3749 0.26157845 20.485589 22.718088 10.22032 12525 50 51 0 46781 40320 5625 3749 1.0337902 0 604 0
|
||||
31000 3.0907131 3807 0.26212089 20.462618 22.765199 9.2934356 12725 67 67 1 48839 40320 5625 3807 1.0232166 0 604 0
|
||||
32000 2.8402863 3804 0.25963296 20.433109 22.549122 7.7909674 12830 58 58 0 50434 40320 5625 3804 1.0068925 0 604 0
|
||||
33000 2.8936979 3788 0.26075387 20.490668 22.646473 10.184685 12687 60 60 1 51939 40320 5625 3788 1.0201495 0 604 0
|
||||
34000 2.9459329 3801 0.26184842 20.546816 22.741536 8.5616047 12962 64 64 1 53500 40320 5625 3801 0.99938958 0 604 0
|
||||
35000 2.6106008 3775 0.2586892 20.52226 22.467157 5.6792512 12967 45 45 1 55087 40320 5625 3775 1.0183544 0 604 0
|
||||
36000 5.8747699 3809 0.28651929 20.507497 24.8842 9.1933878 12750 53 53 5 56604 40320 5625 3809 1.0079212 0 604 0
|
||||
37000 3.1946428 3802 0.26494145 20.630156 23.010165 6.6564892 13029 53 53 5 58460 40320 5625 3802 1.0088282 0 604 0
|
||||
38000 2.8700233 3818 0.26040611 20.478103 22.61627 9.2908419 13033 52 52 0 60287 40320 5625 3818 1.0127385 0 604 0
|
||||
39000 2.7656892 3812 0.25998902 20.519608 22.580046 10.920034 12894 52 52 1 61786 40320 5625 3812 1.0034298 0 604 0
|
||||
40000 2.7523262 3773 0.26006389 20.536066 22.586549 11.157355 12846 68 68 1 63576 40320 5625 3773 1.0398336 0 604 0
|
||||
41000 2.9840686 3785 0.26079459 20.426879 22.65001 6.4161076 12739 51 51 1 65115 40320 5625 3785 1.0116164 0 604 0
|
||||
42000 2.7562499 3778 0.25907668 20.447404 22.50081 9.4791152 12698 53 53 2 66584 40320 5625 3778 1.0021024 0 604 0
|
||||
43000 2.5912808 3787 0.25812876 20.487979 22.418483 7.9217055 12886 50 50 1 68191 40320 5625 3787 1.0093332 0 604 0
|
||||
44000 3.0967473 3775 0.26370565 20.595759 22.902836 5.328598 12716 56 56 0 69792 40320 5625 3775 1.0050084 0 604 0
|
||||
45000 2.6575446 3777 0.25781099 20.411014 22.390885 10.088161 12878 62 62 0 71801 40320 5625 3777 1.0237185 0 604 0
|
||||
46000 2.9186207 3793 0.25950844 20.363936 22.538308 7.0759867 13243 54 54 1 73365 40320 5625 3793 0.99552398 0 604 0
|
||||
47000 2.5812503 3793 0.25694255 20.392429 22.315461 9.5971531 12615 64 64 0 74935 40320 5625 3793 1.0014236 0 604 0
|
||||
48000 3.192993 3759 0.26332768 20.491229 22.870009 10.811248 12801 68 68 2 76480 40320 5625 3759 1.0208642 0 604 0
|
||||
49000 2.5266504 3780 0.25653188 20.397439 22.279794 6.1860477 12935 67 67 1 77986 40320 5625 3780 1.0105053 0 604 0
|
||||
50000 2.8382589 3798 0.25970071 20.440504 22.555006 4.0746424 12612 62 62 1 79447 40320 5625 3798 1.0071327 0 604 0
|
||||
Loop time of 11.6101 on 8 procs for 50000 steps with 17370 atoms
|
||||
|
||||
Pair time (%) = 0.175835 (1.5145)
|
||||
Neigh time (%) = 0.643515 (5.54273)
|
||||
Comm time (%) = 0.862317 (7.42731)
|
||||
Outpt time (%) = 0.00260469 (0.0224348)
|
||||
Other time (%) = 9.92581 (85.493)
|
||||
|
||||
Nlocal: 2171.25 ave 2372 max 1614 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 4 2
|
||||
Nghost: 60.5 ave 69 max 54 min
|
||||
Histogram: 2 0 2 0 1 0 0 1 0 2
|
||||
Neighs: 167.375 ave 282 max 128 min
|
||||
Histogram: 3 2 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1339
|
||||
Ave neighs/atom = 0.0770869
|
||||
Neighbor list builds = 2593
|
||||
Dangerous builds = 2
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,116 @@
|
|||
# SRD diffusion demo - ellipsoids
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big ellipsoidal particles
|
||||
|
||||
lattice sq 0.14
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 2 box
|
||||
create_atoms 1 region box
|
||||
|
||||
set type 1 mass 1.0
|
||||
set type 1 shape 3.0 1.0 1.0
|
||||
group big type 1
|
||||
set group big quat/random 29898
|
||||
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute rot big temp/asphere
|
||||
|
||||
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z &
|
||||
# quatw quati quatj quatk
|
||||
|
||||
thermo_style custom step temp c_rot epair etotal press
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 120.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.01
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 2.0
|
||||
|
||||
neigh_modify one 10000
|
||||
|
||||
delete_atoms overlap 1.6 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
collision noslip search 0.2 inside ignore exact no bounce 50
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/asphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
|
||||
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
|
||||
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all custom 1000 dump.ellipsoid id type x y z &
|
||||
# quatw quati quatj quatk
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
|
|
@ -0,0 +1,117 @@
|
|||
# SRD viscosity demo - ellipsoids
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big ellipsoidal particles
|
||||
|
||||
lattice sq 0.14
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 2 box
|
||||
create_atoms 1 region box
|
||||
|
||||
set type 1 mass 1.0
|
||||
set type 1 shape 3.0 1.0 1.0
|
||||
group big type 1
|
||||
set group big quat/random 29898
|
||||
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute rot big temp/asphere
|
||||
|
||||
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z &
|
||||
# quatw quati quatj quatk
|
||||
|
||||
thermo_style custom step temp c_rot epair etotal press
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 120.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.01
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 2.0
|
||||
|
||||
neigh_modify one 10000
|
||||
|
||||
delete_atoms overlap 1.6 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
collision noslip search 0.2 inside ignore exact no bounce 50
|
||||
fix 3 small viscosity 20 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/asphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press &
|
||||
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
|
||||
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all custom 500 dump.ellipsoid.mp id type x y z &
|
||||
# quatw quati quatj quatk
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 50000
|
||||
|
|
@ -0,0 +1,296 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# SRD diffusion demo - ellipsoids
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big ellipsoidal particles
|
||||
|
||||
lattice sq 0.14
|
||||
Lattice spacing in x,y,z = 2.67261 2.67261 2.67261
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -1.33631) to (26.7261 26.7261 1.33631)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
100 settings made for mass
|
||||
set type 1 shape 3.0 1.0 1.0
|
||||
100 settings made for shape
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big quat/random 29898
|
||||
100 settings made for quat/random
|
||||
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute rot big temp/asphere
|
||||
|
||||
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z # quatw quati quatj quatk
|
||||
|
||||
thermo_style custom step temp c_rot epair etotal press
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 3.31955 Mbytes
|
||||
Step Temp rot E_pair TotEng Press
|
||||
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
|
||||
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
|
||||
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
|
||||
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
|
||||
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
|
||||
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
|
||||
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
|
||||
700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
|
||||
800 2.7632972 2.9060854 -0.52075353 2.2149107 0.77106777
|
||||
900 2.9905599 2.8869667 -0.49099384 2.4696604 0.6961683
|
||||
1000 2.8470141 2.9005014 -0.51282121 2.3057228 0.68817475
|
||||
Loop time of 0.0669988 on 8 procs for 1000 steps with 100 atoms
|
||||
|
||||
Pair time (%) = 0.0335407 (50.0616)
|
||||
Neigh time (%) = 0.000552475 (0.824605)
|
||||
Comm time (%) = 0.0238523 (35.601)
|
||||
Outpt time (%) = 0.000291765 (0.435477)
|
||||
Other time (%) = 0.00876167 (13.0774)
|
||||
|
||||
Nlocal: 12.5 ave 16 max 8 min
|
||||
Histogram: 1 1 0 0 0 3 0 0 1 2
|
||||
Nghost: 34.125 ave 42 max 28 min
|
||||
Histogram: 1 0 2 2 0 1 0 1 0 1
|
||||
Neighs: 46.125 ave 65 max 20 min
|
||||
Histogram: 1 0 1 0 1 2 0 0 1 2
|
||||
|
||||
Total # of neighbors = 369
|
||||
Ave neighs/atom = 3.69
|
||||
Neighbor list builds = 174
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 120.0
|
||||
Lattice spacing in x,y,z = 0.0912871 0.0912871 0.0912871
|
||||
create_atoms 2 region plane
|
||||
Created 85849 atoms
|
||||
|
||||
set type 2 mass 0.01
|
||||
85849 settings made for mass
|
||||
group small type 2
|
||||
85849 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 2.0
|
||||
|
||||
neigh_modify one 10000
|
||||
|
||||
delete_atoms overlap 1.6 small big
|
||||
Deleted 71060 atoms, new total = 14889
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/asphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all custom 1000 dump.ellipsoid id type x y z # quatw quati quatj quatk
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 14789 100
|
||||
big particle diameter max/min = 3 1
|
||||
SRD temperature & lamda = 1 0.1
|
||||
SRD max distance & max velocity = 0.4 40
|
||||
SRD grid counts: 107 107 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.249777 0.249777 2.67261
|
||||
SRD per actual grid cell = 1.92757
|
||||
SRD viscosity = 0.688101
|
||||
big/SRD mass density ratio = 1.37367
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 13.3093 24.3359
|
||||
ave/max big velocity = 2.08028 5.05672
|
||||
Memory usage per processor = 10.6335 Mbytes
|
||||
Step Temp rot 2[9] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 2.9005014 2.9005014 0 0.025582147 -0.51282121 3.8089259 0.89862319 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 7.2956023 7.2956023 0.70834055 0.069462778 -0.52813454 10.342313 2.4874745 15029 48 347 0 273688 98040 11449 6477 0.70834055 1617 50 0
|
||||
2000 2.6238614 2.6238614 0.77744331 0.023078302 -0.47342524 3.4361283 1.6052231 16178 48 140 0 570264 98040 11449 6606 0.77744331 3196 50 0
|
||||
3000 2.5809048 2.5809048 0.79907961 0.021977265 -0.57335309 3.272195 1.4275294 17045 57 504 0 875574 98040 11449 6754 0.79907961 4880 50 0
|
||||
4000 2.4645688 2.4645688 0.82651268 0.02117525 -0.51942455 3.1527829 1.1962239 16911 40 359 0 1175091 98040 11449 6770 0.82651268 6476 50 0
|
||||
5000 2.1821901 2.1821901 0.87375488 0.017835105 -0.59599444 2.6554687 0.94017756 17423 58 457 0 1473017 98040 11449 6741 0.87375488 7940 50 0
|
||||
6000 2.7347088 2.7347088 0.88378922 0.023245561 -0.61368445 3.4610316 1.0797017 18277 49 406 0 1855806 98040 11449 6785 0.88378922 9982 50 0
|
||||
7000 2.1624381 2.1624381 0.84226 0.017452531 -0.62352539 2.5985074 0.9064477 18418 55 501 0 2250403 98040 11449 6796 0.84226 12248 50 0
|
||||
8000 2.163802 2.163802 0.84086821 0.01743543 -0.62810387 2.5959612 0.898377 18731 58 195 0 2609864 98040 11449 6794 0.84086821 14239 50 0
|
||||
9000 2.4291028 2.4291028 0.881112 0.020152652 -0.61883485 3.0005284 0.87126187 17990 68 337 0 2980316 98040 11449 6785 0.881112 16375 50 0
|
||||
10000 2.2008575 2.2008575 0.86610163 0.017451237 -0.68096305 2.5983146 0.68079667 18267 55 431 0 3322267 98040 11449 6763 0.86610163 18267 50 0
|
||||
11000 3.1766901 3.1766901 0.87045337 0.027784703 -0.59640382 4.1368645 0.93469755 19172 73 636 0 3750755 98040 11449 6741 0.87045337 20726 50 0
|
||||
12000 2.1793161 2.1793161 0.86215133 0.017596582 -0.62722581 2.6199551 0.67697989 19057 69 342 0 4157139 98040 11449 6802 0.86215133 22806 50 0
|
||||
13000 4.0153206 4.0153206 0.90625671 0.038303439 -0.27982855 5.7029991 1.687034 19515 67 552 0 4624013 98040 11449 6717 0.90625671 25436 50 0
|
||||
14000 3.170604 3.170604 0.87343798 0.028601343 -0.46574612 4.2584539 1.2191953 19102 56 503 0 5018844 98040 11449 6704 0.87343798 27565 50 0
|
||||
15000 2.1598654 2.1598654 0.88571342 0.018928735 -0.39990012 2.8182993 1.2133794 19040 60 656 0 5403568 98040 11449 6800 0.88571342 29588 50 0
|
||||
16000 3.2148501 3.2148501 0.92374454 0.02852773 -0.54263291 4.2474937 0.95828981 18827 69 620 0 5805269 98040 11449 6851 0.92374454 31671 50 0
|
||||
17000 1.689719 1.689719 0.91145995 0.013016738 -0.57961912 1.9380621 0.80015733 18555 61 627 0 6238805 98040 11449 6762 0.91145995 34131 50 0
|
||||
18000 2.2363963 2.2363963 0.93262821 0.018332423 -0.60271598 2.7295145 0.98475808 18594 55 522 0 6718450 98040 11449 6784 0.93262821 36725 50 0
|
||||
19000 7.6028995 7.6028995 0.93864136 0.074005938 -0.30957605 11.018744 2.9474333 19675 93 1082 0 7229509 98040 11449 6515 0.93864136 39724 50 0
|
||||
20000 7.2192143 7.2192143 0.88957525 0.069357409 -0.43000462 10.326625 2.4966484 19158 65 394 0 7789183 98040 11449 6651 0.88957525 42820 50 0
|
||||
21000 4.5330204 4.5330204 0.86613007 0.042675657 -0.40022184 6.3539786 1.4658773 18943 52 155 0 8252829 98040 11449 6764 0.86613007 45182 50 0
|
||||
22000 2.8518378 2.8518378 0.84167594 0.025693384 -0.4237503 3.825488 1.0516739 19085 57 407 0 8608296 98040 11449 6825 0.84167594 47111 50 0
|
||||
23000 2.7181316 2.7181316 0.88923978 0.023577992 -0.53948886 3.5105272 0.82845541 18824 58 421 0 8995890 98040 11449 6748 0.88923978 49148 50 0
|
||||
24000 2.0835932 2.0835932 0.84026764 0.017047902 -0.56629177 2.5382621 0.74654075 18971 60 277 0 9341011 98040 11449 6757 0.84026764 50947 50 0
|
||||
25000 2.2109657 2.2109657 0.83305834 0.018511323 -0.53818793 2.756151 0.93069051 18531 44 277 0 9628824 98040 11449 6760 0.83305834 52412 50 0
|
||||
26000 2.5537486 2.5537486 0.84881291 0.023243574 -0.34434968 3.4607357 1.3058386 18725 55 149 0 9984117 98040 11449 6746 0.84881291 54360 50 0
|
||||
27000 2.0881562 2.0881562 0.81387145 0.017094925 -0.56608945 2.5452634 0.61664377 19345 64 157 0 10340914 98040 11449 6813 0.81387145 56350 50 0
|
||||
28000 1.9836851 1.9836851 0.84227025 0.01744767 -0.35790721 2.5977835 1.0180779 19613 57 382 0 10655060 98040 11449 6780 0.84227025 57994 50 0
|
||||
29000 1.9842246 1.9842246 0.82288658 0.017193445 -0.39656262 2.559932 1.036828 19128 57 148 0 10976578 98040 11449 6815 0.82288658 59591 50 0
|
||||
30000 4.3538432 4.3538432 0.86941094 0.043439035 -0.019588435 6.4676379 2.5038101 18862 50 406 0 11313222 98040 11449 6725 0.86941094 61467 50 0
|
||||
31000 6.6481395 6.6481395 0.86286769 0.063829591 -0.40214003 9.5035878 2.0941534 19213 67 648 0 11697823 98040 11449 6840 0.86286769 63380 50 0
|
||||
32000 2.6712732 2.6712732 0.86495327 0.025802035 -0.13853198 3.841665 1.5918499 19672 74 267 0 12044541 98040 11449 6788 0.86495327 65225 50 0
|
||||
33000 2.2525644 2.2525644 0.89687596 0.019829466 -0.40391176 2.9524092 1.1393318 19571 54 371 0 12448516 98040 11449 6763 0.89687596 67314 50 0
|
||||
34000 2.0174254 2.0174254 0.85159248 0.016836474 -0.49918117 2.5067827 0.61040005 19322 44 314 0 12826260 98040 11449 6777 0.85159248 69403 50 0
|
||||
35000 2.0636577 2.0636577 0.84737021 0.017487894 -0.47107738 2.6037726 0.9372094 19352 71 496 0 13218452 98040 11449 6847 0.84737021 71447 50 0
|
||||
36000 1.9578117 1.9578117 0.86352344 0.016804797 -0.41507332 2.5020662 0.78629324 19226 64 294 0 13618568 98040 11449 6818 0.86352344 73705 50 0
|
||||
37000 2.7216885 2.7216885 0.89497296 0.02408761 -0.46891159 3.5864043 0.84261741 19922 68 667 0 13956945 98040 11449 6751 0.89497296 75650 50 0
|
||||
38000 2.9132431 2.9132431 0.85774007 0.025736568 -0.5088146 3.8319176 0.92509444 19512 65 459 0 14315919 98040 11449 6785 0.85774007 77596 50 0
|
||||
39000 3.0646912 3.0646912 0.8862362 0.027495613 -0.47256811 4.0938218 1.1093068 19563 61 449 0 14688150 98040 11449 6782 0.8862362 79855 50 0
|
||||
40000 2.2020194 2.2020194 0.86883352 0.019197745 -0.42265669 2.8583523 0.98753706 19119 55 371 0 15084880 98040 11449 6816 0.86883352 82202 50 0
|
||||
41000 6.0976172 6.0976172 0.88377361 0.057628632 -0.5051227 8.580327 1.3963064 19079 65 306 0 15447216 98040 11449 6818 0.88377361 84366 50 0
|
||||
42000 1.9083892 1.9083892 0.88516585 0.01531336 -0.5634938 2.2800062 0.47914635 18935 61 275 0 15853289 98040 11449 6802 0.88516585 86713 50 0
|
||||
43000 1.7542467 1.7542467 0.90554851 0.015254716 -0.34255301 2.2712746 1.0497057 19154 64 304 0 16324953 98040 11449 6786 0.90554851 89455 50 0
|
||||
44000 2.2479548 2.2479548 0.91641099 0.019654899 -0.42303473 2.9264179 0.91746265 18945 74 571 0 16758611 98040 11449 6783 0.91641099 92090 50 0
|
||||
45000 2.1158512 2.1158512 0.91293716 0.018206737 -0.44181723 2.7108011 0.99334995 19184 61 485 0 17221151 98040 11449 6779 0.91293716 94841 50 0
|
||||
46000 2.0152012 2.0152012 0.89835135 0.016867945 -0.49118143 2.5114683 0.66818297 19378 58 360 0 17710361 98040 11449 6789 0.89835135 97688 50 0
|
||||
47000 2.5657032 2.5657032 0.90990935 0.021675185 -0.59567945 3.2272184 0.69894508 19451 66 427 0 18120146 98040 11449 6792 0.90990935 100021 50 0
|
||||
48000 1.8478297 1.8478297 0.91589497 0.014167966 -0.64379773 2.1094685 0.49211287 19543 68 382 0 18534853 98040 11449 6815 0.91589497 102312 50 0
|
||||
49000 2.4541697 2.4541697 0.90253297 0.022481005 -0.30951614 3.3471968 1.2611223 19472 56 286 0 18999871 98040 11449 6775 0.90253297 105133 50 0
|
||||
50000 2.3302118 2.3302118 0.89753747 0.020434678 -0.42949642 3.0425192 0.99789859 19313 67 581 0 19470693 98040 11449 6760 0.89753747 107732 50 0
|
||||
51000 1.9622255 1.9622255 0.94038395 0.016081535 -0.52933612 2.3943798 0.76520959 19556 63 598 0 19952485 98040 11449 6767 0.94038395 110585 50 0
|
||||
52000 2.0649042 2.0649042 0.90596725 0.017450187 -0.47854892 2.5981584 0.70025754 19363 47 393 0 20407302 98040 11449 6832 0.90596725 113294 50 0
|
||||
53000 1.7438902 1.7438902 0.92620113 0.014870808 -0.38428182 2.2141146 0.97045847 19199 50 320 0 20833593 98040 11449 6775 0.92620113 115753 50 0
|
||||
54000 2.4133126 2.4133126 0.91091821 0.023458785 -0.10305736 3.4927785 1.5340967 18894 60 295 0 21304132 98040 11449 6765 0.91091821 118526 50 0
|
||||
55000 2.2079351 2.2079351 0.89049352 0.019281645 -0.41897921 2.8708441 0.96570508 19047 54 377 0 21797810 98040 11449 6775 0.89049352 121460 50 0
|
||||
56000 2.1479887 2.1479887 0.89773595 0.018643072 -0.42473615 2.7757671 0.87853659 19064 54 363 0 22220051 98040 11449 6788 0.89773595 123820 50 0
|
||||
57000 2.5642675 2.5642675 0.88789613 0.023095645 -0.38204805 3.4387105 1.0057392 19304 77 395 0 22692743 98040 11449 6744 0.88789613 126497 50 0
|
||||
58000 3.7514362 3.7514362 0.85798081 0.035436484 -0.31350184 5.2761381 1.381171 19437 57 286 0 23100326 98040 11449 6788 0.85798081 128811 50 0
|
||||
59000 2.51444 2.51444 0.8979786 0.021651184 -0.52287077 3.2236448 0.77486862 19210 56 456 0 23467741 98040 11449 6766 0.8979786 131067 50 0
|
||||
60000 1.8163765 1.8163765 0.88037429 0.015000644 -0.4729551 2.2334459 0.73205061 19529 59 557 0 23864523 98040 11449 6808 0.88037429 133293 50 0
|
||||
61000 2.4385228 2.4385228 0.92121921 0.021765486 -0.39273586 3.2406631 1.0539662 19549 57 244 0 24304886 98040 11449 6789 0.92121921 135871 50 0
|
||||
62000 1.9552803 1.9552803 0.88498431 0.016067216 -0.52111994 2.3922478 0.78048821 19880 70 348 0 24725026 98040 11449 6777 0.88498431 138244 50 0
|
||||
63000 2.0485261 2.0485261 0.88137975 0.017772947 -0.40608982 2.6462141 0.81935985 19703 64 657 0 25146891 98040 11449 6795 0.88137975 140482 50 0
|
||||
64000 5.6433836 5.6433836 0.90468317 0.053600869 -0.42800818 7.9806333 1.7881383 19539 70 628 0 25566274 98040 11449 6709 0.90468317 142990 50 0
|
||||
65000 2.3294568 2.3294568 0.89455359 0.019432082 -0.57764791 2.8932427 0.82070889 19093 52 371 0 25984888 98040 11449 6763 0.89455359 145397 50 0
|
||||
66000 2.2413888 2.2413888 0.89280517 0.019499997 -0.43631477 2.9033546 1.0155381 18850 57 417 0 26391227 98040 11449 6815 0.89280517 147627 50 0
|
||||
67000 2.6544972 2.6544972 0.8630596 0.022892283 -0.5467689 3.408432 0.9203384 18921 49 226 0 26756243 98040 11449 6723 0.8630596 149679 50 0
|
||||
68000 2.176732 2.176732 0.89394188 0.01818266 -0.53611435 2.7072163 0.9195041 19030 61 652 0 27141492 98040 11449 6844 0.89394188 151897 50 0
|
||||
69000 2.0161273 2.0161273 0.88130839 0.016605036 -0.53170586 2.4723238 0.92131775 19182 66 650 0 27576227 98040 11449 6733 0.88130839 154351 50 0
|
||||
70000 3.0377466 3.0377466 0.89771966 0.027971517 -0.36156324 4.1646792 1.3934191 18997 51 234 0 28008747 98040 11449 6746 0.89771966 156777 50 0
|
||||
71000 3.1795524 3.1795524 0.8947838 0.028420307 -0.50603352 4.2314995 1.0722874 19618 55 490 0 28443736 98040 11449 6771 0.8947838 159142 50 0
|
||||
72000 3.5426182 3.5426182 0.83954036 0.033941731 -0.22491678 5.0535844 1.6042774 19563 55 275 0 28881070 98040 11449 6797 0.83954036 161794 50 0
|
||||
73000 2.2968425 2.2968425 0.86015879 0.02077218 -0.32952534 3.0927699 1.1404746 19485 70 451 0 29260883 98040 11449 6802 0.86015879 164068 50 0
|
||||
74000 2.188706 2.188706 0.9280661 0.019084686 -0.41965301 2.8415189 0.78604118 19541 50 92 0 29685043 98040 11449 6781 0.9280661 166584 50 0
|
||||
75000 1.7274084 1.7274084 0.92459156 0.01379811 -0.51943796 2.0544006 0.61217133 19550 53 316 0 30053826 98040 11449 6808 0.92459156 168827 50 0
|
||||
76000 2.4210213 2.4210213 0.89819013 0.021426261 -0.41716573 3.190156 1.1110363 19438 59 425 0 30497237 98040 11449 6804 0.89819013 171460 50 0
|
||||
77000 2.9878983 2.9878983 0.87463276 0.026030055 -0.5763537 3.8756148 0.8157204 19032 80 644 0 31000714 98040 11449 6755 0.87463276 174332 50 0
|
||||
78000 2.3345289 2.3345289 0.90593483 0.019783234 -0.53292232 2.9455257 0.85832222 18950 68 654 0 31435875 98040 11449 6791 0.90593483 176899 50 0
|
||||
79000 2.2705803 2.2705803 0.88397994 0.019430253 -0.49019424 2.8929703 0.86369694 18773 65 405 0 31880831 98040 11449 6739 0.88397994 179525 50 0
|
||||
80000 4.6907116 4.6907116 0.87251492 0.045231772 -0.2546018 6.7345585 1.9476158 19100 56 373 0 32309541 98040 11449 6783 0.87251492 181794 50 0
|
||||
81000 1.8511722 1.8511722 0.8626409 0.015075899 -0.51359597 2.2446506 0.58639182 18989 68 680 0 32724195 98040 11449 6807 0.8626409 184002 50 0
|
||||
82000 2.5791982 2.5791982 0.86974688 0.023153218 -0.3957227 3.4472827 0.987724 19449 58 770 0 33133450 98040 11449 6768 0.86974688 186208 50 0
|
||||
83000 1.7152161 1.7152161 0.87892802 0.013862381 -0.49170213 2.0639699 0.68749667 19349 58 385 0 33584010 98040 11449 6760 0.87892802 188626 50 0
|
||||
84000 2.3488628 2.3488628 0.86203202 0.020814344 -0.40075798 3.0990477 0.92218361 19294 52 374 0 33968768 98040 11449 6763 0.86203202 190822 50 0
|
||||
85000 2.116465 2.116465 0.84998598 0.018023607 -0.46999805 2.6835348 0.7339385 19382 64 561 0 34335861 98040 11449 6778 0.84998598 192856 50 0
|
||||
86000 4.4975609 4.4975609 0.89396825 0.042207794 -0.41704734 6.2843185 1.5378572 19958 56 298 0 34732431 98040 11449 6701 0.89396825 195077 50 0
|
||||
87000 2.6889768 2.6889768 0.86307648 0.02336651 -0.52753572 3.4790397 0.81754047 19936 57 641 0 35098414 98040 11449 6685 0.86307648 197104 50 0
|
||||
88000 3.9319704 3.9319704 0.85779056 0.036230526 -0.46427285 5.394363 1.2276207 19788 46 182 0 35443091 98040 11449 6771 0.85779056 198936 50 0
|
||||
89000 2.0653279 2.0653279 0.84504363 0.018343471 -0.3461792 2.7311593 1.0869811 19427 54 493 0 35777362 98040 11449 6798 0.84504363 200863 50 0
|
||||
90000 4.8706166 4.8706166 0.86365369 0.045810202 -0.4365378 6.820681 1.4919543 19259 53 211 0 36161042 98040 11449 6791 0.86365369 203020 50 0
|
||||
91000 2.2396034 2.2396034 0.8827157 0.019338006 -0.4577734 2.8792357 1.0068781 19474 69 343 0 36570010 98040 11449 6780 0.8827157 205151 50 0
|
||||
92000 2.2950736 2.2950736 0.86370947 0.019380548 -0.53408981 2.8855698 0.81686894 19200 66 385 0 36941725 98040 11449 6784 0.86370947 207169 50 0
|
||||
93000 2.8399649 2.8399649 0.86702804 0.025344222 -0.45804639 3.7735012 1.142371 18909 64 419 0 37350382 98040 11449 6827 0.86702804 209476 50 0
|
||||
94000 2.0861949 2.0861949 0.87330649 0.01715277 -0.55455457 2.5538759 0.73150124 18803 66 511 0 37691022 98040 11449 6775 0.87330649 211354 50 0
|
||||
95000 1.7673295 1.7673295 0.86863959 0.014315467 -0.50189106 2.1314299 0.73528684 18733 59 421 0 38033894 98040 11449 6761 0.86863959 213229 50 0
|
||||
96000 2.3535506 2.3535506 0.85445343 0.019960525 -0.53486773 2.9719226 0.66615354 19029 55 396 0 38382273 98040 11449 6802 0.85445343 215176 50 0
|
||||
97000 1.7008253 1.7008253 0.86268511 0.01373487 -0.48924484 2.0449848 0.78353064 19312 64 534 0 38766210 98040 11449 6794 0.86268511 217390 50 0
|
||||
98000 2.1153875 2.1153875 0.88353399 0.019971062 -0.17843601 2.9734914 1.5344523 19479 57 559 0 39171672 98040 11449 6751 0.88353399 219740 50 0
|
||||
99000 2.8415756 2.8415756 0.90324577 0.026409052 -0.30190393 3.9320437 1.5281054 19309 72 293 0 39584437 98040 11449 6746 0.90324577 222154 50 0
|
||||
100000 9.0513641 9.0513641 0.85723531 0.087635776 -0.43844176 13.048091 2.4804268 19511 68 324 0 39976323 98040 11449 6832 0.85723531 224404 50 0
|
||||
Loop time of 29.7394 on 8 procs for 100000 steps with 14889 atoms
|
||||
|
||||
Pair time (%) = 3.66754 (12.3322)
|
||||
Neigh time (%) = 2.04132 (6.864)
|
||||
Comm time (%) = 2.88159 (9.68944)
|
||||
Outpt time (%) = 0.00693083 (0.0233052)
|
||||
Other time (%) = 21.1421 (71.091)
|
||||
|
||||
Nlocal: 1861.12 ave 2131 max 1746 min
|
||||
Histogram: 4 0 1 0 1 1 0 0 0 1
|
||||
Nghost: 34.375 ave 37 max 31 min
|
||||
Histogram: 1 1 0 1 0 1 1 0 1 2
|
||||
Neighs: 45.875 ave 53 max 40 min
|
||||
Histogram: 2 0 0 2 1 1 0 0 0 2
|
||||
|
||||
Total # of neighbors = 367
|
||||
Ave neighs/atom = 0.0246491
|
||||
Neighbor list builds = 5247
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,247 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# SRD viscosity demo - ellipsoids
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big ellipsoidal particles
|
||||
|
||||
lattice sq 0.14
|
||||
Lattice spacing in x,y,z = 2.67261 2.67261 2.67261
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -1.33631) to (26.7261 26.7261 1.33631)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
100 settings made for mass
|
||||
set type 1 shape 3.0 1.0 1.0
|
||||
100 settings made for shape
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big quat/random 29898
|
||||
100 settings made for quat/random
|
||||
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute rot big temp/asphere
|
||||
|
||||
#dump 1 all custom 10 dump.ellipsoid.equil id type x y z # quatw quati quatj quatk
|
||||
|
||||
thermo_style custom step temp c_rot epair etotal press
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 3.31955 Mbytes
|
||||
Step Temp rot E_pair TotEng Press
|
||||
0 1.44 0.95677852 2.7038078 4.1294078 10.518912
|
||||
100 2.5524145 2.801098 -0.37027046 2.1566199 0.84703874
|
||||
200 2.6266386 2.7938164 -0.35322565 2.2471465 1.004886
|
||||
300 2.9987557 2.9499545 -0.58917376 2.3795944 0.73081788
|
||||
400 2.8557446 2.8208128 -0.39904801 2.4281391 0.91808964
|
||||
500 2.4399047 2.8255746 -0.40056447 2.0149412 1.0538908
|
||||
600 2.854258 2.9166789 -0.53424483 2.2914706 0.8117508
|
||||
700 2.9593679 2.8231211 -0.40051715 2.5292571 1.1630889
|
||||
800 2.7632972 2.9060854 -0.52075353 2.2149107 0.77106777
|
||||
900 2.9905599 2.8869667 -0.49099384 2.4696604 0.6961683
|
||||
1000 2.8470141 2.9005014 -0.51282121 2.3057228 0.68817475
|
||||
Loop time of 0.216003 on 8 procs for 1000 steps with 100 atoms
|
||||
|
||||
Pair time (%) = 0.033883 (15.6863)
|
||||
Neigh time (%) = 0.000561774 (0.260077)
|
||||
Comm time (%) = 0.110359 (51.0913)
|
||||
Outpt time (%) = 0.00236297 (1.09395)
|
||||
Other time (%) = 0.0688367 (31.8684)
|
||||
|
||||
Nlocal: 12.5 ave 16 max 8 min
|
||||
Histogram: 1 1 0 0 0 3 0 0 1 2
|
||||
Nghost: 34.125 ave 42 max 28 min
|
||||
Histogram: 1 0 2 2 0 1 0 1 0 1
|
||||
Neighs: 46.125 ave 65 max 20 min
|
||||
Histogram: 1 0 1 0 1 2 0 0 1 2
|
||||
|
||||
Total # of neighbors = 369
|
||||
Ave neighs/atom = 3.69
|
||||
Neighbor list builds = 174
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 120.0
|
||||
Lattice spacing in x,y,z = 0.0912871 0.0912871 0.0912871
|
||||
create_atoms 2 region plane
|
||||
Created 85849 atoms
|
||||
|
||||
set type 2 mass 0.01
|
||||
85849 settings made for mass
|
||||
group small type 2
|
||||
85849 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 2.0
|
||||
|
||||
neigh_modify one 10000
|
||||
|
||||
delete_atoms overlap 1.6 small big
|
||||
Deleted 71060 atoms, new total = 14889
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 1.0 1.0 1 1 1 1 1 1
|
||||
pair_coeff 1 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 1 1 1 1 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
fix 1 big nve/asphere
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 collision noslip search 0.2 inside ignore exact no bounce 50
|
||||
fix 3 small viscosity 20 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/asphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp c_rot f_2[9] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all custom 500 dump.ellipsoid.mp id type x y z # quatw quati quatj quatk
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 50000
|
||||
SRD info:
|
||||
SRD/big particles = 14789 100
|
||||
big particle diameter max/min = 3 1
|
||||
SRD temperature & lamda = 1 0.1
|
||||
SRD max distance & max velocity = 0.4 40
|
||||
SRD grid counts: 107 107 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.249777 0.249777 2.67261
|
||||
SRD per actual grid cell = 1.92757
|
||||
SRD viscosity = 0.688101
|
||||
big/SRD mass density ratio = 1.37367
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 13.3093 24.3359
|
||||
ave/max big velocity = 2.08028 5.05672
|
||||
Memory usage per processor = 10.6335 Mbytes
|
||||
Step Temp rot 2[9] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 2.9005014 2.9005014 0 0.025582147 -0.51282121 3.8089259 0.89862319 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 4.0772042 4.0772042 0.6709105 0.040214379 -0.08751542 5.9875189 2.7529672 14344 42 225 0 224495 98040 11449 6583 0.6709105 1320 50 0
|
||||
2000 2.7438363 2.7438363 0.76662675 0.02408678 -0.50203535 3.5862807 1.751055 15904 52 228 0 516986 98040 11449 6696 0.76662675 3017 50 0
|
||||
3000 4.3077081 4.3077081 0.80827675 0.039345067 -0.56039804 5.858087 1.7998404 16676 49 241 0 813000 98040 11449 6693 0.80827675 4732 50 0
|
||||
4000 2.6526774 2.6526774 0.78555744 0.022082331 -0.66465108 3.2878383 1.0403545 17617 43 222 0 1127008 98040 11449 6765 0.78555744 6334 50 0
|
||||
5000 2.594913 2.594913 0.82350776 0.021770968 -0.62494096 3.2414795 1.0780953 17703 57 382 0 1391570 98040 11449 6743 0.82350776 7729 50 0
|
||||
6000 3.0343473 3.0343473 0.84065515 0.026658458 -0.55199962 3.9691778 1.2301173 18015 52 363 0 1676493 98040 11449 6775 0.84065515 9263 50 0
|
||||
7000 3.0413763 3.0413763 0.79884495 0.026536497 -0.58063167 3.9510191 1.1147571 18292 55 458 0 1953690 98040 11449 6800 0.79884495 10658 50 0
|
||||
8000 2.7812045 2.7812045 0.80159783 0.024478142 -0.49944409 3.6445506 1.3707277 18408 61 475 0 2238100 98040 11449 6833 0.80159783 12186 50 0
|
||||
9000 2.7102571 2.7102571 0.82556805 0.023142083 -0.59265825 3.4456248 0.98842401 18286 61 194 0 2576779 98040 11449 6818 0.82556805 13939 50 0
|
||||
10000 3.2045912 3.2045912 0.8622825 0.027989227 -0.60752488 4.167316 1.1341927 18288 50 179 0 2962819 98040 11449 6720 0.8622825 15849 50 0
|
||||
11000 4.6098925 4.6098925 0.8551898 0.042356478 -0.56228382 6.306456 1.4720289 18764 62 280 0 3277277 98040 11449 6818 0.8551898 17581 50 0
|
||||
12000 3.5052136 3.5052136 0.85951127 0.03109149 -0.59355628 4.6292119 1.0101413 18788 51 361 0 3618996 98040 11449 6778 0.85951127 19490 50 0
|
||||
13000 3.2931183 3.2931183 0.87082756 0.030037721 -0.43442997 4.4723163 1.3509023 19082 56 519 0 3950820 98040 11449 6816 0.87082756 21387 50 0
|
||||
14000 3.3837607 3.3837607 0.84668317 0.030465137 -0.50584917 4.5359543 1.3664689 19368 59 413 0 4299096 98040 11449 6788 0.84668317 23311 50 0
|
||||
15000 3.9613429 3.9613429 0.88196505 0.038203107 -0.21434033 5.6880606 1.8415287 18619 61 472 0 4666678 98040 11449 6808 0.88196505 25272 50 0
|
||||
16000 4.2615312 4.2615312 0.82672895 0.038879833 -0.56086323 5.7888183 1.2281404 18687 49 453 0 5016630 98040 11449 6724 0.82672895 27200 50 0
|
||||
17000 3.1642486 3.1642486 0.82812979 0.028702004 -0.44128899 4.2734414 1.2224354 18918 54 385 0 5318150 98040 11449 6780 0.82812979 28796 50 0
|
||||
18000 4.326255 4.326255 0.80700754 0.039935329 -0.50014888 5.9459711 1.5337863 19242 59 417 0 5620823 98040 11449 6819 0.80700754 30496 50 0
|
||||
19000 4.7303091 4.7303091 0.82398378 0.043920179 -0.50888521 6.5392754 1.3695551 18896 56 276 0 5900972 98040 11449 6807 0.82398378 32209 50 0
|
||||
20000 3.4002668 3.4002668 0.84006847 0.031221557 -0.41781984 4.6485777 1.1290385 18861 52 142 0 6221193 98040 11449 6816 0.84006847 33883 50 0
|
||||
21000 3.8655857 3.8655857 0.85324995 0.03542669 -0.48504283 5.2746799 1.0819496 19111 53 192 0 6513564 98040 11449 6830 0.85324995 35352 50 0
|
||||
22000 3.6574509 3.6574509 0.84025473 0.033965163 -0.39252882 5.0570731 1.4286148 19280 54 269 0 6824809 98040 11449 6781 0.84025473 36941 50 0
|
||||
23000 4.4296219 4.4296219 0.86770551 0.041555285 -0.41297036 6.1871663 1.4156152 19160 37 435 0 7161579 98040 11449 6752 0.86770551 38716 50 0
|
||||
24000 4.0435169 4.0435169 0.84111419 0.036578859 -0.57861376 5.4462264 0.96478184 19059 48 379 0 7512598 98040 11449 6797 0.84111419 40660 50 0
|
||||
25000 3.8100627 3.8100627 0.84181242 0.035211679 -0.43432659 5.2426668 1.3297193 19418 54 385 0 7859647 98040 11449 6749 0.84181242 42653 50 0
|
||||
26000 4.4865488 4.4865488 0.83287786 0.041526308 -0.50210571 6.182852 1.2409485 19282 51 239 0 8238637 98040 11449 6792 0.83287786 44767 50 0
|
||||
27000 7.0852396 7.0852396 0.85841948 0.068172726 -0.40676992 10.150237 2.0194952 19317 56 283 0 8632769 98040 11449 6726 0.85841948 46983 50 0
|
||||
28000 5.1517725 5.1517725 0.87627692 0.048475654 -0.45860096 7.2175401 1.3442212 18868 59 429 0 8971998 98040 11449 6805 0.87627692 48888 50 0
|
||||
29000 3.759401 3.759401 0.85080417 0.034921423 -0.40205682 5.1994507 1.2957581 19528 51 223 0 9358797 98040 11449 6767 0.85080417 50864 50 0
|
||||
30000 4.1056897 4.1056897 0.89048135 0.038239787 -0.42395586 5.6935219 1.3427608 19322 55 320 0 9714933 98040 11449 6726 0.89048135 52987 50 0
|
||||
31000 3.9169919 3.9169919 0.83225664 0.036119283 -0.45851779 5.3778001 1.2227344 19378 56 183 0 10093157 98040 11449 6835 0.83225664 55203 50 0
|
||||
32000 4.2947449 4.2947449 0.85282769 0.040398791 -0.38419394 6.0149759 1.4475348 18971 64 192 0 10449851 98040 11449 6788 0.85282769 57103 50 0
|
||||
33000 6.3981858 6.3981858 0.8752853 0.061770539 -0.33628134 9.1970155 1.8805105 19093 65 113 0 10906186 98040 11449 6698 0.8752853 59700 50 0
|
||||
34000 4.1610677 4.1610677 0.84406404 0.038747185 -0.43092244 5.7690684 1.1157695 19427 62 413 0 11309588 98040 11449 6739 0.84406404 62078 50 0
|
||||
35000 4.8088073 4.8088073 0.87151511 0.045354512 -0.4122896 6.7528333 1.4394764 19376 66 434 0 11696476 98040 11449 6763 0.87151511 64175 50 0
|
||||
36000 4.2921897 4.2921897 0.84488024 0.039617438 -0.49672227 5.8986404 1.1291104 19529 45 264 0 12022588 98040 11449 6795 0.84488024 65897 50 0
|
||||
37000 3.7112825 3.7112825 0.8416428 0.033678706 -0.51538845 5.0144225 1.0454583 19827 69 455 0 12340474 98040 11449 6782 0.8416428 67632 50 0
|
||||
38000 3.6819111 3.6819111 0.85373497 0.034285125 -0.38133519 5.1047123 1.2393947 19380 47 149 0 12643621 98040 11449 6771 0.85373497 69404 50 0
|
||||
39000 4.271666 4.271666 0.87592802 0.040171423 -0.38365909 5.9811232 1.3509653 19208 53 437 0 12951773 98040 11449 6773 0.87592802 71144 50 0
|
||||
40000 7.8961104 7.8961104 0.83195448 0.075474381 -0.52782399 11.237381 2.0854836 19587 54 140 0 13284474 98040 11449 6739 0.83195448 73005 50 0
|
||||
41000 5.3324705 5.3324705 0.84594041 0.050595382 -0.41223462 7.5331464 1.8824 19398 60 246 0 13591740 98040 11449 6739 0.84594041 74623 50 0
|
||||
42000 5.3412052 5.3412052 0.85510315 0.050390916 -0.45569229 7.5027035 1.6185323 19004 56 411 0 13943637 98040 11449 6811 0.85510315 76708 50 0
|
||||
43000 4.538738 4.538738 0.84330484 0.04134934 -0.6062163 6.1565033 0.93340583 18747 55 166 0 14310076 98040 11449 6816 0.84330484 78713 50 0
|
||||
44000 4.7059719 4.7059719 0.87465087 0.043139856 -0.58880485 6.4230932 1.1555897 18636 55 185 0 14663012 98040 11449 6779 0.87465087 80547 50 0
|
||||
45000 4.3751196 4.3751196 0.8849121 0.039833588 -0.58810522 5.930823 1.3402888 18537 61 382 0 15031341 98040 11449 6796 0.8849121 82486 50 0
|
||||
46000 3.8815029 3.8815029 0.84817481 0.034767594 -0.60689233 5.1765471 0.94880018 18642 64 807 0 15350275 98040 11449 6877 0.84817481 84256 50 0
|
||||
47000 4.2821501 4.2821501 0.85615543 0.039739616 -0.46357218 5.9168314 1.2473512 19321 51 240 0 15717133 98040 11449 6744 0.85615543 86379 50 0
|
||||
48000 4.8566025 4.8566025 0.88283248 0.045601238 -0.44676931 6.7895684 1.3643402 19369 64 555 0 16181209 98040 11449 6711 0.88283248 89052 50 0
|
||||
49000 5.041306 5.041306 0.83860275 0.046968778 -0.51836452 6.9931814 1.2925069 19148 56 645 0 16630113 98040 11449 6767 0.83860275 91645 50 0
|
||||
50000 4.017754 4.017754 0.85846415 0.037037752 -0.47190243 5.514551 1.2505985 19331 70 388 0 17084877 98040 11449 6815 0.85846415 94299 50 0
|
||||
Loop time of 14.4429 on 8 procs for 50000 steps with 14889 atoms
|
||||
|
||||
Pair time (%) = 1.82692 (12.6493)
|
||||
Neigh time (%) = 0.991614 (6.86577)
|
||||
Comm time (%) = 1.32936 (9.20426)
|
||||
Outpt time (%) = 0.0033724 (0.02335)
|
||||
Other time (%) = 10.2916 (71.2574)
|
||||
|
||||
Nlocal: 1861.12 ave 1950 max 1735 min
|
||||
Histogram: 1 0 1 0 1 0 1 2 1 1
|
||||
Nghost: 34 ave 37 max 30 min
|
||||
Histogram: 1 0 1 0 2 1 0 0 1 2
|
||||
Neighs: 46.125 ave 64 max 32 min
|
||||
Histogram: 1 2 0 1 1 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 369
|
||||
Ave neighs/atom = 0.0247834
|
||||
Neighbor list builds = 2575
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,713 @@
|
|||
LAMMPS data file for Nanoparticles
|
||||
350 atoms
|
||||
350 lines
|
||||
1 atom types
|
||||
-22.553882286 22.553882286 xlo xhi
|
||||
-22.553882286 22.553882286 ylo yhi
|
||||
-0.5 0.5 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 1 1 -21.9309 22.372 0 0 -1 0
|
||||
2 1 1 1 1 -22.3524 -21.8641 0 0 0 0
|
||||
3 1 1 1 1 21.9309 -22.372 0 -1 0 0
|
||||
4 1 1 1 1 22.3524 21.8641 0 -1 -1 0
|
||||
5 2 1 1 1 -17.6247 22.2537 0 0 -1 0
|
||||
6 2 1 1 1 -17.8301 -22.257 0 0 0 0
|
||||
7 2 1 1 1 -18.2561 22.257 0 0 -1 0
|
||||
8 3 1 1 1 -13.0449 22.1713 0 0 -1 0
|
||||
9 3 1 1 1 -13.3179 -22.2807 0 0 0 0
|
||||
10 3 1 1 1 -13.7468 22.2807 0 0 -1 0
|
||||
11 4 1 1 1 -8.75987 22.3547 0 0 -1 0
|
||||
12 4 1 1 1 -8.66487 -22.0853 0 0 0 0
|
||||
13 4 1 1 1 -9.28324 -22.3547 0 0 0 0
|
||||
14 4 1 1 1 -9.37823 22.0853 0 0 -1 0
|
||||
15 5 1 1 1 -5.19054 22.1792 0 0 -1 0
|
||||
16 5 1 1 1 -4.30473 22.1801 0 0 -1 0
|
||||
17 5 1 1 1 -3.83102 -22.1792 0 0 0 0
|
||||
18 5 1 1 1 -4.71682 -22.1801 0 0 0 0
|
||||
19 6 1 1 1 0.436469 21.6771 0 0 -1 0
|
||||
20 6 1 1 1 0.803611 -22.1538 0 0 0 0
|
||||
21 6 1 1 1 -0.436469 -21.6771 0 0 0 0
|
||||
22 6 1 1 1 -0.803611 22.1538 0 0 -1 0
|
||||
23 7 1 1 1 4.0932 -22.1592 0 0 0 0
|
||||
24 7 1 1 1 4.32148 22.3536 0 0 -1 0
|
||||
25 7 1 1 1 4.70007 -22.3536 0 0 0 0
|
||||
26 8 1 1 1 8.90597 -22.1682 0 0 0 0
|
||||
27 8 1 1 1 8.83184 22.497 0 0 -1 0
|
||||
28 8 1 1 1 9.21127 -22.497 0 0 0 0
|
||||
29 9 1 1 1 14.0318 22.1687 0 0 -1 0
|
||||
30 9 1 1 1 13.7514 -22.2698 0 0 0 0
|
||||
31 9 1 1 1 13.3132 22.2698 0 0 -1 0
|
||||
32 10 1 1 1 18.0006 -21.8677 0 0 0 0
|
||||
33 10 1 1 1 17.7358 22.5348 0 0 -1 0
|
||||
34 10 1 1 1 18.3504 -22.5348 0 0 0 0
|
||||
35 11 1 1 1 -21.9981 -18.4031 0 0 0 0
|
||||
36 11 1 1 1 -22.358 -17.7407 0 0 0 0
|
||||
37 11 1 1 1 22.358 -18.3455 0 -1 0 0
|
||||
38 12 1 1 1 -18.6386 -17.7329 0 0 0 0
|
||||
39 12 1 1 1 -18.2077 -18.3592 0 0 0 0
|
||||
40 12 1 1 1 -17.4476 -18.3533 0 0 0 0
|
||||
41 12 1 1 1 -17.8785 -17.727 0 0 0 0
|
||||
42 13 1 1 1 -13.0344 -17.9667 0 0 0 0
|
||||
43 13 1 1 1 -13.5538 -17.9034 0 0 0 0
|
||||
44 13 1 1 1 -13.5109 -18.1828 0 0 0 0
|
||||
45 14 1 1 1 -9.32865 -17.4667 0 0 0 0
|
||||
46 14 1 1 1 -9.21311 -18.1452 0 0 0 0
|
||||
47 14 1 1 1 -8.82999 -17.941 0 0 0 0
|
||||
48 15 1 1 1 -4.21523 -17.4899 0 0 0 0
|
||||
49 15 1 1 1 -4.64996 -17.9688 0 0 0 0
|
||||
50 15 1 1 1 -4.3716 -18.1175 0 0 0 0
|
||||
51 16 1 1 1 0.355481 -17.6597 0 0 0 0
|
||||
52 16 1 1 1 -0.116783 -17.9348 0 0 0 0
|
||||
53 16 1 1 1 0.116783 -18.1514 0 0 0 0
|
||||
54 17 1 1 1 4.16941 -18.5613 0 0 0 0
|
||||
55 17 1 1 1 4.70167 -18.1689 0 0 0 0
|
||||
56 17 1 1 1 4.31988 -17.9173 0 0 0 0
|
||||
57 18 1 1 1 9.18105 -17.4322 0 0 0 0
|
||||
58 18 1 1 1 8.8305 -17.9932 0 0 0 0
|
||||
59 18 1 1 1 9.2126 -18.093 0 0 0 0
|
||||
60 19 1 1 1 13.9797 -17.4947 0 0 0 0
|
||||
61 19 1 1 1 13.0419 -17.643 0 0 0 0
|
||||
62 19 1 1 1 13.085 -18.5915 0 0 0 0
|
||||
63 19 1 1 1 14.0228 -18.4432 0 0 0 0
|
||||
64 20 1 1 1 17.6859 -17.5436 0 0 0 0
|
||||
65 20 1 1 1 17.7824 -18.2295 0 0 0 0
|
||||
66 20 1 1 1 18.3038 -17.8567 0 0 0 0
|
||||
67 21 1 1 1 -21.757 -13.1132 0 0 0 0
|
||||
68 21 1 1 1 22.1712 -12.8047 0 -1 0 0
|
||||
69 21 1 1 1 21.757 -13.9514 0 -1 0 0
|
||||
70 21 1 1 1 -22.1712 -14.26 0 0 0 0
|
||||
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20 1.24008 -23.0306 0.367142 -21.277
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310 13.5788 12.8981 14.1376 13.3372
|
||||
311 14.1376 13.3372 13.4859 14.1666
|
||||
312 18.5988 13.9501 18.097 14.2255
|
||||
313 18.097 14.2255 17.7383 12.9769
|
||||
314 17.7383 12.9769 18.5988 13.9501
|
||||
315 22.7474 18.8325 21.7537 17.9005
|
||||
316 21.7537 17.9005 22.8572 17.7197
|
||||
317 -22.2506 17.7197 -22.3604 18.8325
|
||||
318 -18.3979 17.2543 -17.1782 18.0338
|
||||
319 -17.1782 18.0338 -17.6883 18.8319
|
||||
320 -17.6883 18.8319 -18.908 18.0524
|
||||
321 -18.908 18.0524 -18.3979 17.2543
|
||||
322 -13.4292 18.7613 -14.2203 18.2735
|
||||
323 -14.2203 18.2735 -13.2399 17.5688
|
||||
324 -13.2399 17.5688 -13.4292 18.7613
|
||||
325 -8.77474 19.1982 -10.1939 17.8989
|
||||
326 -10.1939 17.8989 -9.26837 16.888
|
||||
327 -9.26837 16.888 -7.8492 18.1873
|
||||
328 -7.8492 18.1873 -8.77474 19.1982
|
||||
329 -4.41664 17.4425 -3.90954 17.9533
|
||||
330 -3.90954 17.9533 -4.85846 18.3883
|
||||
331 -4.85846 18.3883 -4.41664 17.4425
|
||||
332 0.508126 17.3719 0.263523 18.8426
|
||||
333 0.263523 18.8426 -0.508126 18.7143
|
||||
334 -0.508126 18.7143 -0.263523 17.2436
|
||||
335 -0.263523 17.2436 0.508126 17.3719
|
||||
336 4.67331 18.5578 3.98655 17.9146
|
||||
337 3.98655 17.9146 4.69162 17.85
|
||||
338 4.69162 17.85 4.67331 18.5578
|
||||
339 9.61426 17.4551 9.46127 18.7528
|
||||
340 9.46127 18.7528 8.42885 18.6311
|
||||
341 8.42885 18.6311 8.58184 17.3334
|
||||
342 8.58184 17.3334 9.61426 17.4551
|
||||
343 14.1999 17.6664 14.2426 18.3312
|
||||
344 14.2426 18.3312 12.8648 18.4198
|
||||
345 12.8648 18.4198 12.822 17.755
|
||||
346 12.822 17.755 14.1999 17.6664
|
||||
347 18.2159 18.9494 17.1522 17.8033
|
||||
348 17.1522 17.8033 17.8703 17.1368
|
||||
349 17.8703 17.1368 18.934 18.2829
|
||||
350 18.934 18.2829 18.2159 18.9494
|
||||
|
|
@ -0,0 +1,813 @@
|
|||
LAMMPS data file for Nanoparticles
|
||||
400 atoms
|
||||
400 lines
|
||||
2 atom types
|
||||
-28.7967574883 28.7967574883 xlo xhi
|
||||
-28.7967574883 28.7967574883 ylo yhi
|
||||
-0.5 0.5 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
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|
||||
2 1 1 1 1 28.2458 28.4738 0 -1 -1 0
|
||||
3 1 1 1 1 -28.5701 28.4101 0 0 -1 0
|
||||
4 1 1 1 1 -28.2458 -28.4738 0 0 0 0
|
||||
5 2 1 1 1 -22.6684 28.0669 0 0 -1 0
|
||||
6 2 1 1 1 -22.6096 -28.5805 0 0 0 0
|
||||
7 2 1 1 1 -23.4064 -28.0669 0 0 0 0
|
||||
8 2 1 1 1 -23.4652 28.5805 0 0 -1 0
|
||||
9 3 1 1 1 -16.491 28.2994 0 0 -1 0
|
||||
10 3 1 1 1 -16.8471 -28.1148 0 0 0 0
|
||||
11 3 1 1 1 -18.0651 -28.2994 0 0 0 0
|
||||
12 3 1 1 1 -17.709 28.1148 0 0 -1 0
|
||||
13 4 1 1 1 -11.4345 28.29 0 0 -1 0
|
||||
14 4 1 1 1 -11.2611 -28.754 0 0 0 0
|
||||
15 4 1 1 1 -11.6029 -28.29 0 0 0 0
|
||||
16 4 1 1 1 -11.7763 28.754 0 0 -1 0
|
||||
17 5 1 1 1 -5.47664 28.3124 0 0 -1 0
|
||||
18 5 1 1 1 -5.3706 -28.5699 0 0 0 0
|
||||
19 5 1 1 1 -6.04206 -28.3124 0 0 0 0
|
||||
20 5 1 1 1 -6.1481 28.5699 0 0 -1 0
|
||||
21 6 1 1 1 -0.226473 28.6134 0 0 -1 0
|
||||
22 6 1 1 1 0.403913 28.2978 0 0 -1 0
|
||||
23 6 1 1 1 0.226473 -28.6134 0 0 0 0
|
||||
24 6 1 1 1 -0.403913 -28.2978 0 0 0 0
|
||||
25 7 1 1 1 6.02343 -28.1725 0 0 0 0
|
||||
26 7 1 1 1 4.87903 -28.4244 0 0 0 0
|
||||
27 7 1 1 1 5.49527 28.1725 0 0 -1 0
|
||||
28 7 1 1 1 6.63967 28.4244 0 0 -1 0
|
||||
29 8 1 1 1 10.9648 -28.7746 0 0 0 0
|
||||
30 8 1 1 1 11.5059 28.4757 0 0 -1 0
|
||||
31 8 1 1 1 12.0726 28.7746 0 0 -1 0
|
||||
32 8 1 1 1 11.5316 -28.4757 0 0 0 0
|
||||
33 9 1 1 1 17.6173 28.0779 0 0 -1 0
|
||||
34 9 1 1 1 17.782 -28.5589 0 0 0 0
|
||||
35 9 1 1 1 16.9388 -28.0779 0 0 0 0
|
||||
36 9 1 1 1 16.7741 28.5589 0 0 -1 0
|
||||
37 10 1 1 1 23.8662 28.75 0 0 -1 0
|
||||
38 10 1 1 1 23.0925 -27.8211 0 0 0 0
|
||||
39 10 1 1 1 22.2086 -28.75 0 0 0 0
|
||||
40 10 1 1 1 22.9823 27.8211 0 0 -1 0
|
||||
41 11 1 1 1 -28.6738 -22.1727 0 0 0 0
|
||||
42 11 1 1 1 27.8353 -22.9007 0 -1 0 0
|
||||
43 11 1 1 1 28.6738 -23.9021 0 -1 0 0
|
||||
44 11 1 1 1 -27.8353 -23.1741 0 0 0 0
|
||||
45 12 1 1 1 -22.6787 -22.4126 0 0 0 0
|
||||
46 12 1 1 1 -23.4695 -22.7893 0 0 0 0
|
||||
47 12 1 1 1 -23.3961 -23.6622 0 0 0 0
|
||||
48 12 1 1 1 -22.6053 -23.2855 0 0 0 0
|
||||
49 13 1 1 1 -17.2139 -23.5312 0 0 0 0
|
||||
50 13 1 1 1 -16.4751 -22.9332 0 0 0 0
|
||||
51 13 1 1 1 -17.3422 -22.5436 0 0 0 0
|
||||
52 13 1 1 1 -18.081 -23.1416 0 0 0 0
|
||||
53 14 1 1 1 -10.7317 -22.4924 0 0 0 0
|
||||
54 14 1 1 1 -11.8925 -22.4977 0 0 0 0
|
||||
55 14 1 1 1 -12.3057 -23.5824 0 0 0 0
|
||||
56 14 1 1 1 -11.1449 -23.5771 0 0 0 0
|
||||
57 15 1 1 1 -5.42584 -22.4871 0 0 0 0
|
||||
58 15 1 1 1 -6.02355 -22.8773 0 0 0 0
|
||||
59 15 1 1 1 -6.09286 -23.5877 0 0 0 0
|
||||
60 15 1 1 1 -5.49515 -23.1975 0 0 0 0
|
||||
61 16 1 1 1 0.339193 -23.2446 0 0 0 0
|
||||
62 16 1 1 1 0.520941 -22.1845 0 0 0 0
|
||||
63 16 1 1 1 -0.339193 -22.8302 0 0 0 0
|
||||
64 16 1 1 1 -0.520941 -23.8903 0 0 0 0
|
||||
65 17 1 1 1 6.24268 -23.1667 0 0 0 0
|
||||
66 17 1 1 1 6.01066 -22.0977 0 0 0 0
|
||||
67 17 1 1 1 5.27603 -22.9081 0 0 0 0
|
||||
68 17 1 1 1 5.50805 -23.9771 0 0 0 0
|
||||
69 18 1 1 1 11.943 -23.149 0 0 0 0
|
||||
70 18 1 1 1 11.6256 -22.6311 0 0 0 0
|
||||
71 18 1 1 1 11.0944 -22.9258 0 0 0 0
|
||||
72 18 1 1 1 11.4118 -23.4437 0 0 0 0
|
||||
73 19 1 1 1 16.9661 -22.3518 0 0 0 0
|
||||
74 19 1 1 1 16.8992 -23.2098 0 0 0 0
|
||||
75 19 1 1 1 17.59 -23.723 0 0 0 0
|
||||
76 19 1 1 1 17.6569 -22.865 0 0 0 0
|
||||
77 20 1 1 1 22.7107 -23.0411 0 0 0 0
|
||||
78 20 1 1 1 23.0471 -23.9011 0 0 0 0
|
||||
79 20 1 1 1 23.3641 -23.0337 0 0 0 0
|
||||
80 20 1 1 1 23.0277 -22.1737 0 0 0 0
|
||||
81 21 1 1 1 -28.5944 -17.9775 0 0 0 0
|
||||
82 21 1 1 1 -28.3722 -17.1552 0 0 0 0
|
||||
83 21 1 1 1 28.5944 -16.5786 0 -1 0 0
|
||||
84 21 1 1 1 28.3722 -17.4009 0 -1 0 0
|
||||
85 22 1 1 1 -23.177 -16.5303 0 0 0 0
|
||||
86 22 1 1 1 -23.992 -17.4563 0 0 0 0
|
||||
87 22 1 1 1 -22.8978 -18.0258 0 0 0 0
|
||||
88 22 1 1 1 -22.0828 -17.0998 0 0 0 0
|
||||
89 23 1 1 1 -16.825 -17.0261 0 0 0 0
|
||||
90 23 1 1 1 -17.7076 -16.5057 0 0 0 0
|
||||
91 23 1 1 1 -17.7311 -17.53 0 0 0 0
|
||||
92 23 1 1 1 -16.8485 -18.0504 0 0 0 0
|
||||
93 24 1 1 1 -11.2382 -17.3342 0 0 0 0
|
||||
94 24 1 1 1 -11.4565 -16.9671 0 0 0 0
|
||||
95 24 1 1 1 -11.7992 -17.2219 0 0 0 0
|
||||
96 24 1 1 1 -11.5809 -17.589 0 0 0 0
|
||||
97 25 1 1 1 -5.24969 -17.5883 0 0 0 0
|
||||
98 25 1 1 1 -5.49286 -16.8403 0 0 0 0
|
||||
99 25 1 1 1 -6.26901 -16.9678 0 0 0 0
|
||||
100 25 1 1 1 -6.02584 -17.7158 0 0 0 0
|
||||
101 26 1 1 1 0.00423501 -17.633 0 0 0 0
|
||||
102 26 1 1 1 0.555598 -17.2714 0 0 0 0
|
||||
103 26 1 1 1 -0.00423501 -16.9231 0 0 0 0
|
||||
104 26 1 1 1 -0.555598 -17.2847 0 0 0 0
|
||||
105 27 1 1 1 6.34657 -17.8699 0 0 0 0
|
||||
106 27 1 1 1 6.33455 -16.7074 0 0 0 0
|
||||
107 27 1 1 1 5.17214 -16.6862 0 0 0 0
|
||||
108 27 1 1 1 5.18416 -17.8487 0 0 0 0
|
||||
109 28 1 1 1 10.6796 -17.1851 0 0 0 0
|
||||
110 28 1 1 1 11.4792 -17.6345 0 0 0 0
|
||||
111 28 1 1 1 12.3578 -17.371 0 0 0 0
|
||||
112 28 1 1 1 11.5582 -16.9216 0 0 0 0
|
||||
113 29 1 1 1 16.4602 -16.8401 0 0 0 0
|
||||
114 29 1 1 1 16.9173 -17.9518 0 0 0 0
|
||||
115 29 1 1 1 18.096 -17.716 0 0 0 0
|
||||
116 29 1 1 1 17.6388 -16.6043 0 0 0 0
|
||||
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|
||||
118 30 1 1 1 22.7001 -17.7364 0 0 0 0
|
||||
119 30 1 1 1 23.4159 -17.5566 0 0 0 0
|
||||
120 30 1 1 1 23.3747 -16.8197 0 0 0 0
|
||||
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|
||||
122 31 1 1 1 28.7694 -12.3893 0 -1 0 0
|
||||
123 31 1 1 1 -28.0134 -11.5433 0 0 0 0
|
||||
124 31 1 1 1 -28.7694 -10.6482 0 0 0 0
|
||||
125 32 1 1 1 -23.6195 -11.7701 0 0 0 0
|
||||
126 32 1 1 1 -22.7211 -12.251 0 0 0 0
|
||||
127 32 1 1 1 -22.4554 -11.2673 0 0 0 0
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
134 34 1 1 1 -11.2774 -11.7358 0 0 0 0
|
||||
135 34 1 1 1 -11.0468 -10.9942 0 0 0 0
|
||||
136 34 1 1 1 -11.76 -11.3016 0 0 0 0
|
||||
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|
||||
138 35 1 1 1 -5.50393 -11.8903 0 0 0 0
|
||||
139 35 1 1 1 -5.00558 -11.0006 0 0 0 0
|
||||
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|
||||
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|
||||
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|
||||
143 36 1 1 1 -0.709418 -11.4362 0 0 0 0
|
||||
144 36 1 1 1 -0.0522561 -11.9682 0 0 0 0
|
||||
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|
||||
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|
||||
147 37 1 1 1 5.83275 -12.1891 0 0 0 0
|
||||
148 37 1 1 1 6.34901 -11.4541 0 0 0 0
|
||||
149 38 1 1 1 11.2373 -11.121 0 0 0 0
|
||||
150 38 1 1 1 11.1645 -11.7693 0 0 0 0
|
||||
151 38 1 1 1 11.8001 -11.9164 0 0 0 0
|
||||
152 38 1 1 1 11.8729 -11.2681 0 0 0 0
|
||||
153 39 1 1 1 17.0131 -11.1875 0 0 0 0
|
||||
154 39 1 1 1 16.9991 -11.7418 0 0 0 0
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
163 41 1 1 1 28.6773 -6.47635 0 -1 0 0
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
203 51 1 1 1 -28.2322 -0.393755 0 0 0 0
|
||||
204 51 1 1 1 -28.3264 0.674341 0 0 0 0
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
211 53 1 1 1 -17.4465 -0.509402 0 0 0 0
|
||||
212 53 1 1 1 -16.6562 -0.20562 0 0 0 0
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
223 56 1 1 1 0.766331 0.636824 0 0 0 0
|
||||
224 56 1 1 1 -0.42391 0.510118 0 0 0 0
|
||||
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|
||||
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|
||||
227 57 1 1 1 5.49063 -0.69454 0 0 0 0
|
||||
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|
||||
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|
||||
230 58 1 1 1 11.3426 0.762139 0 0 0 0
|
||||
231 58 1 1 1 10.9178 -0.138821 0 0 0 0
|
||||
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|
||||
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|
||||
234 59 1 1 1 17.5637 0.518335 0 0 0 0
|
||||
235 59 1 1 1 17.0437 0.129122 0 0 0 0
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
251 63 1 1 1 -17.9564 6.23201 0 0 0 0
|
||||
252 63 1 1 1 -17.4518 5.50998 0 0 0 0
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Lines
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||||
|
||||
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|
||||
2 28.0191 28.8604 28.4724 28.0871
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||||
27 4.61495 28.5449 6.3756 27.8001
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||||
28 6.3756 27.8001 6.90375 29.0486
|
||||
29 10.9776 -28.4535 10.9519 -29.0957
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30 10.9519 28.4979 12.0598 28.4535
|
||||
31 12.0598 28.4535 12.0855 29.0957
|
||||
32 12.0855 -28.4979 10.9776 -28.4535
|
||||
33 17.1134 27.8401 18.1213 28.3158
|
||||
34 18.1213 -29.2778 17.4427 -27.8401
|
||||
35 17.4427 -27.8401 16.4349 -28.3158
|
||||
36 16.4349 29.2778 17.1134 27.8401
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37 23.8111 27.7743 23.9213 29.7257
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66 6.49398 -22.227 5.52733 -21.9685
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67 5.52733 -21.9685 5.02472 -23.8478
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68 5.02472 -23.8478 5.99137 -24.1063
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69 11.8362 -23.5553 12.0499 -22.7427
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70 12.0499 -22.7427 11.2012 -22.5195
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71 11.2012 -22.5195 10.9875 -23.3321
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72 10.9875 -23.3321 11.8362 -23.5553
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73 17.345 -22.1794 16.5873 -22.5242
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74 16.5873 -22.5242 17.2111 -23.8954
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75 17.2111 -23.8954 17.9688 -23.5507
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76 17.9688 -23.5507 17.345 -22.1794
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77 22.701 -22.1774 22.7204 -23.9048
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78 22.7204 -23.9048 23.3738 -23.8975
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79 23.3738 -23.8975 23.3544 -22.17
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80 23.3544 -22.17 22.701 -22.1774
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81 -29.0189 -18.1003 -28.1698 -17.8546
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82 -28.1698 -17.8546 -28.5746 -16.4558
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83 29.0189 -16.4558 28.1698 -16.7015
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84 28.1698 -16.7015 28.5746 -18.1003
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106 6.92176 -17.2993 5.74733 -16.1155
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107 5.74733 -16.1155 4.59694 -17.2568
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108 4.59694 -17.2568 5.77137 -18.4406
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||||
145 6.27562 -10.7838 5.0963 -10.9129
|
||||
146 5.0963 -10.9129 5.24308 -12.2536
|
||||
147 5.24308 -12.2536 6.42241 -12.1245
|
||||
148 6.42241 -12.1245 6.27562 -10.7838
|
||||
149 11.5914 -10.8704 10.8831 -11.3716
|
||||
150 10.8831 -11.3716 11.446 -12.167
|
||||
151 11.446 -12.167 12.1543 -11.6658
|
||||
152 12.1543 -11.6658 11.5914 -10.8704
|
||||
153 17.292 -10.9644 16.7342 -11.4107
|
||||
154 16.7342 -11.4107 17.2641 -12.073
|
||||
155 17.2641 -12.073 17.8219 -11.6267
|
||||
156 17.8219 -11.6267 17.292 -10.9644
|
||||
157 23.5689 -10.8101 23.0874 -10.6343
|
||||
158 23.0874 -10.6343 22.5059 -12.2273
|
||||
159 22.5059 -12.2273 22.9874 -12.4031
|
||||
160 22.9874 -12.4031 23.5689 -10.8101
|
||||
161 -27.707 -5.20405 -29.6475 -4.88066
|
||||
162 27.946 -4.88066 27.707 -6.31465
|
||||
163 27.707 -6.31465 29.6475 -6.63804
|
||||
164 -27.946 -6.63804 -27.707 -5.20405
|
||||
165 -24.2646 -5.99055 -23.0934 -7.00689
|
||||
166 -23.0934 -7.00689 -21.8102 -5.52815
|
||||
167 -21.8102 -5.52815 -22.9814 -4.51181
|
||||
168 -22.9814 -4.51181 -24.2646 -5.99055
|
||||
169 -16.6099 -5.13337 -18.1554 -5.49765
|
||||
170 -18.1554 -5.49765 -17.9462 -6.38533
|
||||
171 -17.9462 -6.38533 -16.4007 -6.02105
|
||||
172 -16.4007 -6.02105 -16.6099 -5.13337
|
||||
173 -11.7973 -4.63205 -12.6797 -5.73543
|
||||
174 -12.6797 -5.73543 -11.2401 -6.88665
|
||||
175 -11.2401 -6.88665 -10.3577 -5.78327
|
||||
176 -10.3577 -5.78327 -11.7973 -4.63205
|
||||
177 -6.75295 -5.61336 -6.4041 -6.52932
|
||||
178 -6.4041 -6.52932 -4.76576 -5.90534
|
||||
179 -4.76576 -5.90534 -5.11461 -4.98938
|
||||
180 -5.11461 -4.98938 -6.75295 -5.61336
|
||||
181 0.582467 -4.73792 -1.02405 -5.1815
|
||||
182 -1.02405 -5.1815 -0.582467 -6.78079
|
||||
183 -0.582467 -6.78079 1.02405 -6.3372
|
||||
184 1.02405 -6.3372 0.582467 -4.73792
|
||||
185 4.73121 -5.40946 5.73315 -6.84508
|
||||
186 5.73315 -6.84508 6.7875 -6.10924
|
||||
187 6.7875 -6.10924 5.78555 -4.67362
|
||||
188 5.78555 -4.67362 4.73121 -5.40946
|
||||
189 11.5023 -4.51431 10.2785 -5.87021
|
||||
190 10.2785 -5.87021 11.5351 -7.00439
|
||||
191 11.5351 -7.00439 12.7589 -5.64849
|
||||
192 12.7589 -5.64849 11.5023 -4.51431
|
||||
193 17.2052 -6.30195 17.8254 -5.76858
|
||||
194 17.8254 -5.76858 17.3509 -5.21676
|
||||
195 17.3509 -5.21676 16.7307 -5.75012
|
||||
196 16.7307 -5.75012 17.2052 -6.30195
|
||||
197 23.4914 -5.07399 22.2454 -5.97969
|
||||
198 22.2454 -5.97969 22.5834 -6.44471
|
||||
199 22.5834 -6.44471 23.8294 -5.53901
|
||||
200 23.8294 -5.53901 23.4914 -5.07399
|
||||
201 28.7025 1.0681 27.7619 -0.280586
|
||||
202 27.7619 -0.280586 28.891 -1.0681
|
||||
203 -28.7025 -1.0681 -27.7619 0.280586
|
||||
204 -27.7619 0.280586 -28.891 1.0681
|
||||
205 -23.4701 -0.877604 -22.5564 -0.8521
|
||||
206 -22.5564 -0.8521 -22.6047 0.877604
|
||||
207 -22.6047 0.877604 -23.5184 0.8521
|
||||
208 -23.5184 0.8521 -23.4701 -0.877604
|
||||
209 -16.4878 0.303781 -17.7315 0.715022
|
||||
210 -17.7315 0.715022 -18.0684 -0.303781
|
||||
211 -18.0684 -0.303781 -16.8246 -0.715022
|
||||
212 -16.8246 -0.715022 -16.4878 0.303781
|
||||
213 -11.2933 1.07169 -12.5754 -0.287524
|
||||
214 -12.5754 -0.287524 -11.7441 -1.07169
|
||||
215 -11.7441 -1.07169 -10.462 0.287524
|
||||
216 -10.462 0.287524 -11.2933 1.07169
|
||||
217 -4.68524 0.203442 -5.35656 1.0163
|
||||
218 -5.35656 1.0163 -6.83346 -0.203442
|
||||
219 -6.83346 -0.203442 -6.16215 -1.0163
|
||||
220 -6.16215 -1.0163 -4.68524 0.203442
|
||||
221 -1.19024 -0.126705 -0.342421 -1.14694
|
||||
222 -0.342421 -1.14694 1.19024 0.126705
|
||||
223 1.19024 0.126705 0.342421 1.14694
|
||||
224 0.342421 1.14694 -1.19024 -0.126705
|
||||
225 6.71344 0.429367 5.34272 0.959714
|
||||
226 5.34272 0.959714 4.80527 -0.429367
|
||||
227 4.80527 -0.429367 6.17599 -0.959714
|
||||
228 6.17599 -0.959714 6.71344 0.429367
|
||||
229 12.2957 -0.623318 11.9436 0.90096
|
||||
230 11.9436 0.90096 10.7417 0.623318
|
||||
231 10.7417 0.623318 11.0938 -0.90096
|
||||
232 11.0938 -0.90096 12.2957 -0.623318
|
||||
233 17.2267 -0.647457 17.798 0.389214
|
||||
234 17.798 0.389214 17.3294 0.647457
|
||||
235 17.3294 0.647457 16.7581 -0.389214
|
||||
236 16.7581 -0.389214 17.2267 -0.647457
|
||||
237 23.6688 0.691581 22.1073 -0.108364
|
||||
238 22.1073 -0.108364 22.406 -0.691581
|
||||
239 22.406 -0.691581 23.9675 0.108364
|
||||
240 23.9675 0.108364 23.6688 0.691581
|
||||
241 28.9557 6.2918 28.2608 5.90606
|
||||
242 28.2608 5.90606 28.6378 5.22691
|
||||
243 -28.9557 5.22691 -28.2608 5.61264
|
||||
244 -28.2608 5.61264 -28.6378 6.2918
|
||||
245 -23.89 5.89712 -22.8569 4.91473
|
||||
246 -22.8569 4.91473 -22.1848 5.62159
|
||||
247 -22.1848 5.62159 -23.2179 6.60397
|
||||
248 -23.2179 6.60397 -23.89 5.89712
|
||||
249 -16.7735 5.03733 -16.426 5.53607
|
||||
250 -16.426 5.53607 -17.7826 6.48138
|
||||
251 -17.7826 6.48138 -18.1301 5.98264
|
||||
252 -18.1301 5.98264 -16.7735 5.03733
|
||||
253 -10.9217 6.37762 -11.913 6.523
|
||||
254 -11.913 6.523 -12.1157 5.14109
|
||||
255 -12.1157 5.14109 -11.1244 4.99571
|
||||
256 -11.1244 4.99571 -10.9217 6.37762
|
||||
257 -4.98733 5.05342 -5.91516 6.7938
|
||||
258 -5.91516 6.7938 -6.53137 6.46528
|
||||
259 -6.53137 6.46528 -5.60354 4.7249
|
||||
260 -5.60354 4.7249 -4.98733 5.05342
|
||||
261 -0.26966 4.77025 0.951863 5.37856
|
||||
262 0.951863 5.37856 0.26966 6.74846
|
||||
263 0.26966 6.74846 -0.951863 6.14014
|
||||
264 -0.951863 6.14014 -0.26966 4.77025
|
||||
265 5.77436 5.10711 6.3795 5.96198
|
||||
266 6.3795 5.96198 5.74434 6.41159
|
||||
267 5.74434 6.41159 5.1392 5.55672
|
||||
268 5.1392 5.55672 5.77436 5.10711
|
||||
269 11.021 4.87869 12.5278 5.68877
|
||||
270 12.5278 5.68877 12.0164 6.64001
|
||||
271 12.0164 6.64001 10.5096 5.82993
|
||||
272 10.5096 5.82993 11.021 4.87869
|
||||
273 17.7507 6.70584 16.2315 5.60455
|
||||
274 16.2315 5.60455 16.8054 4.81286
|
||||
275 16.8054 4.81286 18.3246 5.91415
|
||||
276 18.3246 5.91415 17.7507 6.70584
|
||||
277 22.1774 5.60572 23.4977 5.01684
|
||||
278 23.4977 5.01684 23.8974 5.91298
|
||||
279 23.8974 5.91298 22.5771 6.50186
|
||||
280 22.5771 6.50186 22.1774 5.60572
|
||||
281 28.1372 11.2236 29.0247 10.833
|
||||
282 -28.5688 10.833 -28.1372 11.8138
|
||||
283 -28.1372 11.8138 -29.0247 12.2044
|
||||
284 28.5688 12.2044 28.1372 11.2236
|
||||
285 -23.6032 10.6297 -22.8136 10.489
|
||||
286 -22.8136 10.489 -22.4716 12.4077
|
||||
287 -22.4716 12.4077 -23.2612 12.5484
|
||||
288 -23.2612 12.5484 -23.6032 10.6297
|
||||
289 -17.3285 12.2602 -18.0209 11.54
|
||||
290 -18.0209 11.54 -17.2277 10.7772
|
||||
291 -17.2277 10.7772 -16.5352 11.4974
|
||||
292 -16.5352 11.4974 -17.3285 12.2602
|
||||
293 -11.1352 10.6311 -10.8786 12.2433
|
||||
294 -10.8786 12.2433 -11.9022 12.4063
|
||||
295 -11.9022 12.4063 -12.1588 10.7941
|
||||
296 -12.1588 10.7941 -11.1352 10.6311
|
||||
297 -6.65614 11.3015 -4.95121 11.0734
|
||||
298 -4.95121 11.0734 -4.86256 11.7359
|
||||
299 -4.86256 11.7359 -6.56749 11.964
|
||||
300 -6.56749 11.964 -6.65614 11.3015
|
||||
301 -0.397617 12.2445 -0.775286 11.8083
|
||||
302 -0.775286 11.8083 0.397617 10.7929
|
||||
303 0.397617 10.7929 0.775286 11.2291
|
||||
304 0.775286 11.2291 -0.397617 12.2445
|
||||
305 6.787 11.7376 5.6699 12.5656
|
||||
306 5.6699 12.5656 4.73171 11.2998
|
||||
307 4.73171 11.2998 5.8488 10.4718
|
||||
308 5.8488 10.4718 6.787 11.7376
|
||||
309 11.5952 12.6899 10.3456 11.5563
|
||||
310 10.3456 11.5563 11.4422 10.3475
|
||||
311 11.4422 10.3475 12.6918 11.4811
|
||||
312 12.6918 11.4811 11.5952 12.6899
|
||||
313 16.4971 10.5598 18.2091 10.7048
|
||||
314 18.2091 10.7048 18.059 12.4776
|
||||
315 18.059 12.4776 16.347 12.3326
|
||||
316 16.347 12.3326 16.4971 10.5598
|
||||
317 22.8131 12.5548 22.0382 11.1645
|
||||
318 22.0382 11.1645 23.2617 10.4826
|
||||
319 23.2617 10.4826 24.0366 11.8729
|
||||
320 24.0366 11.8729 22.8131 12.5548
|
||||
321 -28.3823 18.0244 -28.914 18.1236
|
||||
322 28.6795 18.1236 28.3823 16.5317
|
||||
323 28.3823 16.5317 28.914 16.4325
|
||||
324 -28.6795 16.4325 -28.3823 18.0244
|
||||
325 -23.8712 17.904 -23.8367 16.6086
|
||||
326 -23.8367 16.6086 -22.2036 16.6521
|
||||
327 -22.2036 16.6521 -22.2381 17.9475
|
||||
328 -22.2381 17.9475 -23.8712 17.904
|
||||
329 -18.3008 17.4309 -17.5668 16.2851
|
||||
330 -17.5668 16.2851 -16.2553 17.1252
|
||||
331 -16.2553 17.1252 -16.9893 18.271
|
||||
332 -16.9893 18.271 -18.3008 17.4309
|
||||
333 -10.8288 16.8808 -11.6945 18.0545
|
||||
334 -11.6945 18.0545 -12.2086 17.6753
|
||||
335 -12.2086 17.6753 -11.3429 16.5016
|
||||
336 -11.3429 16.5016 -10.8288 16.8808
|
||||
337 -6.34971 16.874 -5.63553 16.5734
|
||||
338 -5.63553 16.5734 -5.16899 17.6821
|
||||
339 -5.16899 17.6821 -5.88317 17.9827
|
||||
340 -5.88317 17.9827 -6.34971 16.874
|
||||
341 0.797709 17.2922 -0.385847 17.9764
|
||||
342 -0.385847 17.9764 -0.797709 17.2639
|
||||
343 -0.797709 17.2639 0.385847 16.5797
|
||||
344 0.385847 16.5797 0.797709 17.2922
|
||||
345 6.69703 17.35 5.64245 18.2112
|
||||
346 5.64245 18.2112 4.82167 17.2061
|
||||
347 4.82167 17.2061 5.87625 16.3449
|
||||
348 5.87625 16.3449 6.69703 17.35
|
||||
349 11.0955 16.4838 12.4136 17.1822
|
||||
350 12.4136 17.1822 11.9419 18.0723
|
||||
351 11.9419 18.0723 10.6238 17.3739
|
||||
352 10.6238 17.3739 11.0955 16.4838
|
||||
353 16.3803 17.5797 16.5627 16.6575
|
||||
354 16.5627 16.6575 18.1758 16.9764
|
||||
355 18.1758 16.9764 17.9934 17.8986
|
||||
356 17.9934 17.8986 16.3803 17.5797
|
||||
357 23.6584 17.2077 23.1963 17.8824
|
||||
358 23.1963 17.8824 22.4164 17.3484
|
||||
359 22.4164 17.3484 22.8785 16.6737
|
||||
360 22.8785 16.6737 23.6584 17.2077
|
||||
361 -29.4056 22.3564 -27.8849 23.0927
|
||||
362 -27.8849 23.0927 -28.1879 23.7184
|
||||
363 29.4056 23.7184 27.8849 22.9821
|
||||
364 27.8849 22.9821 28.1879 22.3564
|
||||
365 -23.6258 22.5959 -23.2042 22.321
|
||||
366 -23.2042 22.321 -22.449 23.4789
|
||||
367 -22.449 23.4789 -22.8706 23.7538
|
||||
368 -22.8706 23.7538 -23.6258 22.5959
|
||||
369 -18.4856 22.9301 -17.4711 21.8406
|
||||
370 -17.4711 21.8406 -16.0706 23.1447
|
||||
371 -16.0706 23.1447 -17.085 24.2342
|
||||
372 -17.085 24.2342 -18.4856 22.9301
|
||||
373 -12.2822 23.4228 -12.3545 22.8562
|
||||
374 -12.3545 22.8562 -10.7552 22.652
|
||||
375 -10.7552 22.652 -10.6829 23.2186
|
||||
376 -10.6829 23.2186 -12.2822 23.4228
|
||||
377 -4.74027 22.5332 -5.52372 24.1497
|
||||
378 -5.52372 24.1497 -6.77844 23.5416
|
||||
379 -6.77844 23.5416 -5.99499 21.9251
|
||||
380 -5.99499 21.9251 -4.74027 22.5332
|
||||
381 -0.175729 21.9424 1.1072 22.9747
|
||||
382 1.1072 22.9747 0.175729 24.1324
|
||||
383 0.175729 24.1324 -1.1072 23.1001
|
||||
384 -1.1072 23.1001 -0.175729 21.9424
|
||||
385 5.16007 23.9104 4.73267 22.7781
|
||||
386 4.73267 22.7781 6.35864 22.1644
|
||||
387 6.35864 22.1644 6.78603 23.2967
|
||||
388 6.78603 23.2967 5.16007 23.9104
|
||||
389 11.7733 23.5059 11.0423 23.2768
|
||||
390 11.0423 23.2768 11.2641 22.5689
|
||||
391 11.2641 22.5689 11.9951 22.798
|
||||
392 11.9951 22.798 11.7733 23.5059
|
||||
393 16.2588 22.373 17.9064 21.9955
|
||||
394 17.9064 21.9955 18.2973 23.7018
|
||||
395 18.2973 23.7018 16.6497 24.0793
|
||||
396 16.6497 24.0793 16.2588 22.373
|
||||
397 22.8032 21.7662 24.33 23.0263
|
||||
398 24.33 23.0263 23.2716 24.3087
|
||||
399 23.2716 24.3087 21.7448 23.0485
|
||||
400 21.7448 23.0485 22.8032 21.7662
|
||||
|
|
@ -0,0 +1,53 @@
|
|||
# Aspherical shear demo - 2d line box and triangle mixture, implicit solvent
|
||||
|
||||
units lj
|
||||
atom_style line
|
||||
dimension 2
|
||||
|
||||
read_data data.line
|
||||
|
||||
velocity all create 1.44 320984 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule all
|
||||
|
||||
pair_style line/lj 2.5
|
||||
pair_coeff * * 1.0 0.25
|
||||
|
||||
fix 2 all rigid molecule langevin 2.0 2.0 1.0 492983
|
||||
|
||||
fix 3 all deform 1 x scale 0.3 y scale 0.3
|
||||
fix 4 all enforce2d
|
||||
|
||||
compute 10 all property/atom end1x end1y end2x end2y
|
||||
|
||||
#dump 1 all custom 500 dump1.atom id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.line id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
timestep 0.004
|
||||
|
||||
compute 1 all erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp f_2 pe ke c_1 c_2 c_3 v_toteng
|
||||
|
||||
run 10000
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
|
||||
#dump 1 all custom 500 dump2.atom id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.line id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.01 units box
|
||||
|
||||
run 100000
|
||||
|
|
@ -0,0 +1,105 @@
|
|||
# Aspherical shear demo - 2d line boxes, solvated by SRD particles
|
||||
|
||||
units lj
|
||||
atom_style line
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
read_data data.line.srd
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
lattice sq 0.4
|
||||
region plane block INF INF INF INF -0.001 0.001
|
||||
lattice sq 10.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
group big type 1
|
||||
group small type 2
|
||||
set group small mass 0.01
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
|
||||
delete_atoms overlap 1.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
velocity small create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule big include big
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style line/lj 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip
|
||||
|
||||
fix 3 all deform 1 x scale 0.35 y scale 0.35
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp c_tsmall f_2[9] c_1 etotal &
|
||||
v_pebig v_ebig press
|
||||
thermo_modify temp tbig
|
||||
|
||||
compute 10 big property/atom end1x end1y end2x end2y
|
||||
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.line.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
run 10000
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip tstat yes
|
||||
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.line.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
|
||||
run 40000
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
# create set of randomly oriented line boxes and triangles
|
||||
|
||||
p = patch(0.05)
|
||||
|
||||
p.seed = 54321
|
||||
p.dim = 2
|
||||
p.lattice = [10,10,1]
|
||||
|
||||
p.build(50,"linebox",0.5,2,0.5,2,1)
|
||||
p.build(50,"linetri",0.5,1.5,0.5,1.5,1)
|
||||
|
||||
p.write("data.line")
|
||||
|
||||
print "all done ... type CTRL-D to exit Pizza.py"
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
# create set of randomly oriented line boxes
|
||||
|
||||
p = patch(0.05)
|
||||
|
||||
p.seed = 7878382
|
||||
p.dim = 2
|
||||
p.extratype = 1
|
||||
p.lattice = [10,10,1]
|
||||
|
||||
p.build(100,"linebox",0.5,2,0.5,2,1)
|
||||
|
||||
p.write("data.line.srd")
|
||||
|
||||
print "all done ... type CTRL-D to exit Pizza.py"
|
||||
|
|
@ -0,0 +1,16 @@
|
|||
# Pizza.py viz of line + SRD output
|
||||
|
||||
d = dump("dump1.atom.srd dump2.atom.srd")
|
||||
ld = ldump("dump1.line.srd dump2.line.srd")
|
||||
ld.map(1,"id",2,"type",3,"end1x",4,"end1y",5,"end2x",6,"end2y")
|
||||
d.extra(ld)
|
||||
|
||||
g = gl(d)
|
||||
g.arad(1,0.2)
|
||||
|
||||
g.arad(2,0.05)
|
||||
g.acol(2,"green")
|
||||
|
||||
g.lrad(1,5)
|
||||
g.lcol(1,"yellow")
|
||||
v = vcr(g)
|
||||
|
|
@ -0,0 +1,13 @@
|
|||
# Pizza.py viz of line output
|
||||
|
||||
d = dump("dump1.atom dump2.atom")
|
||||
ld = ldump("dump1.line dump2.line")
|
||||
ld.map(1,"id",2,"type",3,"end1x",4,"end1y",5,"end2x",6,"end2y")
|
||||
d.extra(ld)
|
||||
|
||||
g = gl(d)
|
||||
g.arad(1,0.2)
|
||||
|
||||
g.lrad(1,5)
|
||||
g.lcol(1,"yellow")
|
||||
v = vcr(g)
|
||||
|
|
@ -0,0 +1,212 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# Aspherical shear demo - 2d line box and triangle mixture, implicit solvent
|
||||
|
||||
units lj
|
||||
atom_style line
|
||||
dimension 2
|
||||
|
||||
read_data data.line
|
||||
orthogonal box = (-22.5539 -22.5539 -0.5) to (22.5539 22.5539 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
350 atoms
|
||||
350 lines
|
||||
|
||||
velocity all create 1.44 320984 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule all
|
||||
|
||||
pair_style line/lj 2.5
|
||||
pair_coeff * * 1.0 0.25
|
||||
|
||||
fix 2 all rigid molecule langevin 2.0 2.0 1.0 492983
|
||||
100 rigid bodies with 350 atoms
|
||||
|
||||
fix 3 all deform 1 x scale 0.3 y scale 0.3
|
||||
fix 4 all enforce2d
|
||||
|
||||
compute 10 all property/atom end1x end1y end2x end2y
|
||||
|
||||
#dump 1 all custom 500 dump1.atom id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.line id type # c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
timestep 0.004
|
||||
|
||||
compute 1 all erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp f_2 pe ke c_1 c_2 c_3 v_toteng
|
||||
|
||||
run 10000
|
||||
Memory usage per processor = 2.61117 Mbytes
|
||||
Step Temp 2 PotEng KinEng 1 2 3 toteng
|
||||
0 0 1.2780105 0 -0 0.037823677 0.50989511 0 0.54771879
|
||||
1000 0 1.9896906 -0.13333755 -0 0.12630626 0.72641826 -0.13333755 0.71938697
|
||||
2000 0 2.0629882 -0.27908342 -0 0.13861003 0.74552776 -0.27908342 0.60505437
|
||||
3000 0 1.8455537 -0.39250848 -0 0.095169207 0.69578236 -0.39250848 0.39844309
|
||||
4000 0 2.2658635 -0.55161143 -0 0.12832995 0.84275439 -0.55161143 0.41947292
|
||||
5000 0 1.9816994 -0.51390753 -0 0.14128637 0.70801336 -0.51390753 0.3353922
|
||||
6000 0 2.1402765 -0.68818261 -0 0.13705699 0.78020438 -0.68818261 0.22907875
|
||||
7000 0 1.8879036 -0.69389883 -0 0.11522773 0.69387383 -0.69389883 0.11520273
|
||||
8000 0 1.9256694 -1.0046071 -0 0.095344199 0.7299427 -1.0046071 -0.17932023
|
||||
9000 0 2.4839132 -1.38036 -0 0.11921387 0.94532035 -1.38036 -0.31582573
|
||||
10000 0 4.1795315 -2.4568772 -0 0.22554354 1.5656842 -2.4568772 -0.66564943
|
||||
Loop time of 2.85775 on 8 procs for 10000 steps with 350 atoms
|
||||
|
||||
Pair time (%) = 1.30584 (45.6948)
|
||||
Neigh time (%) = 0.0195708 (0.684831)
|
||||
Comm time (%) = 0.739841 (25.8889)
|
||||
Outpt time (%) = 0.000323623 (0.0113244)
|
||||
Other time (%) = 0.792173 (27.7202)
|
||||
|
||||
Nlocal: 43.75 ave 53 max 33 min
|
||||
Histogram: 1 1 0 0 1 1 1 1 0 2
|
||||
Nghost: 167.625 ave 175 max 162 min
|
||||
Histogram: 2 0 1 1 0 1 2 0 0 1
|
||||
Neighs: 965.5 ave 1275 max 592 min
|
||||
Histogram: 1 1 0 0 2 1 1 0 0 2
|
||||
|
||||
Total # of neighbors = 7724
|
||||
Ave neighs/atom = 22.0686
|
||||
Neighbor list builds = 992
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
triclinic box = (-6.76616 -6.76616 -0.5) to (6.76616 6.76616 0.5) with tilt (0 0 0)
|
||||
|
||||
#dump 1 all custom 500 dump2.atom id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.line id type # c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.01 units box
|
||||
|
||||
run 100000
|
||||
Memory usage per processor = 2.76376 Mbytes
|
||||
Step Temp 2 PotEng KinEng 1 2 3 toteng
|
||||
10000 0 4.1795315 -2.4550634 -0 0.22554354 1.5656842 -2.4550634 -0.66383559
|
||||
11000 0 2.2075241 -2.8809797 -0 0.11091434 0.83516742 -2.8809797 -1.9348979
|
||||
12000 0 1.9493319 -2.9401168 -0 0.12004101 0.71538694 -2.9401168 -2.1046889
|
||||
13000 0 2.0703379 -2.9231023 -0 0.11264143 0.77464626 -2.9231023 -2.0358146
|
||||
14000 0 2.285829 -3.0018463 -0 0.11344069 0.86620033 -3.0018463 -2.0222053
|
||||
15000 0 2.2146248 -3.0779088 -0 0.10247134 0.84665359 -3.0779088 -2.1287838
|
||||
16000 0 2.0374319 -3.096595 -0 0.12766202 0.74552307 -3.096595 -2.22341
|
||||
17000 0 2.0424578 -2.9546375 -0 0.11887099 0.75646806 -2.9546375 -2.0792985
|
||||
18000 0 2.0215091 -3.0832641 -0 0.14094822 0.7254128 -3.0832641 -2.2169031
|
||||
19000 0 1.912014 -3.0907982 -0 0.11885677 0.70057781 -3.0907982 -2.2713637
|
||||
20000 0 1.8485186 -3.1577807 -0 0.12433421 0.66788805 -3.1577807 -2.3655584
|
||||
21000 0 2.232987 -3.0999629 -0 0.13015187 0.82684257 -3.0999629 -2.1429685
|
||||
22000 0 1.9361293 -3.1342121 -0 0.1008643 0.72890539 -3.1342121 -2.3044424
|
||||
23000 0 1.9060768 -3.0615084 -0 0.12228484 0.69460521 -3.0615084 -2.2446183
|
||||
24000 0 1.9448392 -2.9606016 -0 0.14159101 0.69191153 -2.9606016 -2.1270991
|
||||
25000 0 2.1660504 -3.2140907 -0 0.14303978 0.78526755 -3.2140907 -2.2857834
|
||||
26000 0 1.8371913 -3.163434 -0 0.11009287 0.67727482 -3.163434 -2.3760663
|
||||
27000 0 1.9273228 -2.9848424 -0 0.12756607 0.69842941 -2.9848424 -2.1588469
|
||||
28000 0 2.070142 -3.0586453 -0 0.12517659 0.76202715 -3.0586453 -2.1714416
|
||||
29000 0 2.0243688 -3.1272461 -0 0.089806967 0.77777967 -3.1272461 -2.2596594
|
||||
30000 0 1.9818593 -3.0256998 -0 0.098952992 0.75041526 -3.0256998 -2.1763315
|
||||
31000 0 1.7592998 -2.8404359 -0 0.11049582 0.6434898 -2.8404359 -2.0864503
|
||||
32000 0 1.7487766 -2.9541667 -0 0.085982813 0.66349286 -2.9541667 -2.204691
|
||||
33000 0 2.0423965 -3.2877576 -0 0.10594085 0.76937192 -3.2877576 -2.4124448
|
||||
34000 0 2.0202408 -3.0287779 -0 0.13143335 0.73438411 -3.0287779 -2.1629605
|
||||
35000 0 1.7258733 -3.0829339 -0 0.12308672 0.61657327 -3.0829339 -2.3432739
|
||||
36000 0 1.946379 -3.1187644 -0 0.10475251 0.72940991 -3.1187644 -2.284602
|
||||
37000 0 1.9226333 -3.1365556 -0 0.098688654 0.72529703 -3.1365556 -2.31257
|
||||
38000 0 2.1381223 -3.2215646 -0 0.13208996 0.78424817 -3.2215646 -2.3052264
|
||||
39000 0 1.9137815 -3.1350245 -0 0.096927831 0.72326422 -3.1350245 -2.3148325
|
||||
40000 0 2.1566984 -3.1399426 -0 0.10589176 0.81840754 -3.1399426 -2.2156433
|
||||
41000 0 2.2029223 -3.0800547 -0 0.12720677 0.81690279 -3.0800547 -2.1359451
|
||||
42000 0 2.068079 -2.9537318 -0 0.13880404 0.74751552 -2.9537318 -2.0674122
|
||||
43000 0 1.8772167 -3.1130957 -0 0.1156193 0.68890213 -3.1130957 -2.3085743
|
||||
44000 0 1.8407682 -3.1109228 -0 0.097771189 0.69112948 -3.1109228 -2.3220221
|
||||
45000 0 2.0494905 -2.9840347 -0 0.095646467 0.7827066 -2.9840347 -2.1056816
|
||||
46000 0 2.2163122 -3.0658704 -0 0.12439358 0.82545449 -3.0658704 -2.1160223
|
||||
47000 0 1.8286658 -3.001659 -0 0.097764124 0.68594977 -3.001659 -2.2179451
|
||||
48000 0 1.7861007 -3.157209 -0 0.10806961 0.65740211 -3.157209 -2.3917372
|
||||
49000 0 2.3424171 -2.9952429 -0 0.12941481 0.87447821 -2.9952429 -1.9913498
|
||||
50000 0 2.0099179 -3.060017 -0 0.15393981 0.70745358 -3.060017 -2.1986236
|
||||
51000 0 1.8690805 -3.021086 -0 0.11192641 0.68910809 -3.021086 -2.2200515
|
||||
52000 0 2.0469976 -2.9563496 -0 0.13048197 0.74680271 -2.9563496 -2.0790649
|
||||
53000 0 2.2401038 -3.0559983 -0 0.10819387 0.8518506 -3.0559983 -2.0959539
|
||||
54000 0 1.8437777 -3.0802175 -0 0.13108587 0.65910459 -3.0802175 -2.290027
|
||||
55000 0 2.2485612 -2.9437394 -0 0.12178099 0.84188811 -2.9437394 -1.9800703
|
||||
56000 0 1.8222318 -3.0527441 -0 0.10915422 0.67180228 -3.0527441 -2.2717876
|
||||
57000 0 2.1561793 -3.0003336 -0 0.10358587 0.82049098 -3.0003336 -2.0762567
|
||||
58000 0 1.9379866 -3.1325759 -0 0.10665534 0.72391033 -3.1325759 -2.3020102
|
||||
59000 0 2.16112 -3.196156 -0 0.11290132 0.81329295 -3.196156 -2.2699617
|
||||
60000 0 1.8508831 -3.151339 -0 0.12640027 0.66683535 -3.151339 -2.3581033
|
||||
61000 0 1.7351238 -2.9958379 -0 0.12838235 0.61524213 -2.9958379 -2.2522134
|
||||
62000 0 1.8305334 -3.0374639 -0 0.10383968 0.68067464 -3.0374639 -2.2529496
|
||||
63000 0 2.2367673 -3.1417012 -0 0.11585772 0.84275684 -3.1417012 -2.1830867
|
||||
64000 0 2.2873947 -3.1657854 -0 0.1084843 0.87182771 -3.1657854 -2.1854734
|
||||
65000 0 1.7673149 -3.081123 -0 0.079270339 0.67815032 -3.081123 -2.3237023
|
||||
66000 0 2.1472736 -3.1099038 -0 0.12173859 0.79852151 -3.1099038 -2.1896437
|
||||
67000 0 2.1833073 -3.013818 -0 0.1400615 0.79564164 -3.013818 -2.0781148
|
||||
68000 0 1.9938003 -2.9343398 -0 0.12629592 0.72818991 -2.9343398 -2.079854
|
||||
69000 0 2.2555939 -3.0503506 -0 0.11758718 0.84909591 -3.0503506 -2.0836675
|
||||
70000 0 2.0388319 -2.9950566 -0 0.12363629 0.75014881 -2.9950566 -2.1212715
|
||||
71000 0 1.8141136 -3.0258311 -0 0.098652611 0.67882464 -3.0258311 -2.2483539
|
||||
72000 0 1.7151026 -3.0919257 -0 0.1283392 0.60670477 -3.0919257 -2.3568818
|
||||
73000 0 2.1281558 -3.0969594 -0 0.097397121 0.81466967 -3.0969594 -2.1848927
|
||||
74000 0 2.0550249 -3.0026527 -0 0.11303307 0.76769187 -3.0026527 -2.1219278
|
||||
75000 0 1.8216777 -3.0492532 -0 0.10032974 0.68038929 -3.0492532 -2.2685342
|
||||
76000 0 1.8821412 -3.1526568 -0 0.083229424 0.72340253 -3.1526568 -2.3460248
|
||||
77000 0 1.816501 -3.0123759 -0 0.084071855 0.69442857 -3.0123759 -2.2338754
|
||||
78000 0 1.7189542 -3.0214267 -0 0.11177435 0.62492029 -3.0214267 -2.2847321
|
||||
79000 0 1.8539705 -3.0793108 -0 0.10505287 0.6895059 -3.0793108 -2.2847521
|
||||
80000 0 2.2035184 -3.0527525 -0 0.12363997 0.82072506 -3.0527525 -2.1083875
|
||||
81000 0 1.945693 -3.1132684 -0 0.14600054 0.6878679 -3.1132684 -2.2794
|
||||
82000 0 1.795735 -3.0215328 -0 0.10068289 0.66891783 -3.0215328 -2.2519321
|
||||
83000 0 1.9294772 -3.0559732 -0 0.12323701 0.70368177 -3.0559732 -2.2290544
|
||||
84000 0 2.2371492 -3.1892042 -0 0.10837675 0.85040147 -3.1892042 -2.2304259
|
||||
85000 0 1.8693537 -3.0154518 -0 0.10974173 0.69140987 -3.0154518 -2.2143002
|
||||
86000 0 2.3336261 -3.0447602 -0 0.10374482 0.89638064 -3.0447602 -2.0446348
|
||||
87000 0 2.0247453 -3.0739114 -0 0.095792545 0.77195542 -3.0739114 -2.2061634
|
||||
88000 0 2.1841153 -3.0828606 -0 0.14190252 0.79414689 -3.0828606 -2.1468112
|
||||
89000 0 1.8889123 -2.9751344 -0 0.1168507 0.69268316 -2.9751344 -2.1656006
|
||||
90000 0 1.832885 -3.1223356 -0 0.086530724 0.69899142 -3.1223356 -2.3368134
|
||||
91000 0 1.8171024 -2.9626386 -0 0.10382306 0.67493513 -2.9626386 -2.1838804
|
||||
92000 0 2.1122077 -3.0302831 -0 0.12723447 0.77799742 -3.0302831 -2.1250513
|
||||
93000 0 1.9057839 -3.1117399 -0 0.10937947 0.70738507 -3.1117399 -2.2949754
|
||||
94000 0 1.9659464 -3.050968 -0 0.13636362 0.70618482 -3.050968 -2.2084195
|
||||
95000 0 1.9002035 -3.0047996 -0 0.11999382 0.69437911 -3.0047996 -2.1904267
|
||||
96000 0 1.9199317 -3.0139017 -0 0.11720599 0.70562186 -3.0139017 -2.1910738
|
||||
97000 0 2.0101513 -3.1367555 -0 0.12168713 0.73980628 -3.1367555 -2.2752621
|
||||
98000 0 1.934934 -3.1588351 -0 0.09924111 0.73001632 -3.1588351 -2.3295776
|
||||
99000 0 2.0565056 -3.1074572 -0 0.11648468 0.76487486 -3.1074572 -2.2260976
|
||||
100000 0 2.0859924 -2.9894335 -0 0.11944949 0.77454725 -2.9894335 -2.0954368
|
||||
101000 0 2.0981715 -2.9580479 -0 0.11642673 0.78278961 -2.9580479 -2.0588316
|
||||
102000 0 1.92629 -2.9768477 -0 0.1342305 0.69132234 -2.9768477 -2.1512949
|
||||
103000 0 2.1248123 -3.0934115 -0 0.13641745 0.77421638 -3.0934115 -2.1827777
|
||||
104000 0 2.069635 -3.0085236 -0 0.13547005 0.75151637 -3.0085236 -2.1215372
|
||||
105000 0 2.0300214 -3.0194685 -0 0.13103387 0.73897532 -3.0194685 -2.1494593
|
||||
106000 0 1.8606229 -3.0215675 -0 0.1058931 0.69151671 -3.0215675 -2.2241577
|
||||
107000 0 1.9293829 -3.1824818 -0 0.11199032 0.71488809 -3.1824818 -2.3556034
|
||||
108000 0 2.0917984 -3.0608178 -0 0.12926976 0.76721526 -3.0608178 -2.1643328
|
||||
109000 0 2.0073129 -3.0654045 -0 0.15651693 0.70376004 -3.0654045 -2.2051275
|
||||
110000 0 1.889167 -3.1951234 -0 0.13292304 0.67671996 -3.1951234 -2.3854804
|
||||
Loop time of 64.5556 on 8 procs for 100000 steps with 350 atoms
|
||||
|
||||
Pair time (%) = 45.1763 (69.9804)
|
||||
Neigh time (%) = 0.415894 (0.644241)
|
||||
Comm time (%) = 10.6023 (16.4235)
|
||||
Outpt time (%) = 0.00327063 (0.00506637)
|
||||
Other time (%) = 8.3579 (12.9468)
|
||||
|
||||
Nlocal: 43.75 ave 49 max 37 min
|
||||
Histogram: 1 1 1 0 0 1 0 1 1 2
|
||||
Nghost: 172.25 ave 183 max 165 min
|
||||
Histogram: 1 1 2 1 0 1 1 0 0 1
|
||||
Neighs: 957 ave 1157 max 751 min
|
||||
Histogram: 1 1 1 1 0 0 1 1 0 2
|
||||
|
||||
Total # of neighbors = 7656
|
||||
Ave neighs/atom = 21.8743
|
||||
Neighbor list builds = 7561
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,243 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# Aspherical shear demo - 2d line boxes, solvated by SRD particles
|
||||
|
||||
units lj
|
||||
atom_style line
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
read_data data.line.srd
|
||||
orthogonal box = (-28.7968 -28.7968 -0.5) to (28.7968 28.7968 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
400 atoms
|
||||
400 lines
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
lattice sq 0.4
|
||||
Lattice spacing in x,y,z = 1.58114 1.58114 1.58114
|
||||
region plane block INF INF INF INF -0.001 0.001
|
||||
lattice sq 10.0
|
||||
Lattice spacing in x,y,z = 0.316228 0.316228 0.316228
|
||||
create_atoms 2 region plane
|
||||
Created 33489 atoms
|
||||
|
||||
group big type 1
|
||||
400 atoms in group big
|
||||
group small type 2
|
||||
33489 atoms in group small
|
||||
set group small mass 0.01
|
||||
33489 settings made for mass
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
|
||||
delete_atoms overlap 1.5 small big
|
||||
Deleted 13605 atoms, new total = 20284
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
velocity small create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule big include big
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style line/lj 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
100 rigid bodies with 400 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
|
||||
|
||||
fix 3 all deform 1 x scale 0.35 y scale 0.35
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step temp c_tsmall f_2[9] c_1 etotal v_pebig v_ebig press
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
|
||||
compute 10 big property/atom end1x end1y end2x end2y
|
||||
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
run 10000
|
||||
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385)
|
||||
SRD info:
|
||||
SRD/big particles = 19884 400
|
||||
big particle diameter max/min = 1.99882 0.503306
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 230 230 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250407 0.250407 1
|
||||
SRD per actual grid cell = 0.444963
|
||||
SRD viscosity = 4.2356
|
||||
big/SRD mass density ratio = 14.0918
|
||||
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2737)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 15.906 29.1054
|
||||
ave/max big velocity = 0 0
|
||||
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76)
|
||||
Memory usage per processor = 6.55683 Mbytes
|
||||
Step Temp tsmall 2[9] 1 TotEng pebig ebig Press
|
||||
0 0 1.4528554 0 0 0 0 0 0
|
||||
1000 0 1.1122612 0.23295528 0.00058011072 0 0 0 0.32625408
|
||||
2000 0 1.0254475 0.24958277 0.00072347646 -2.3144253e-06 -0.00011736451 -0.00011736451 0.44526308
|
||||
3000 0 1.0089214 0.28044476 0.00061511441 -0.00023298189 -0.011814512 -0.011814512 0.87208025
|
||||
4000 0 1.0066185 0.32869834 0.00079065587 -0.0021630643 -0.10968899 -0.10968899 1.3901494
|
||||
5000 0 1.0109003 0.38401607 0.00071588732 -0.0040023493 -0.20295913 -0.20295913 1.2736445
|
||||
6000 0 1.0195293 0.45846226 0.00086525328 -0.0068440002 -0.34705925 -0.34705925 2.6190768
|
||||
7000 0 1.0093653 0.54708911 0.00088011006 -0.011012313 -0.55843441 -0.55843441 3.4171735
|
||||
8000 0 1.0041894 0.65768809 0.0007998991 -0.01619324 -0.82115921 -0.82115921 6.9499615
|
||||
9000 0 1.0148795 0.80396735 0.00093224535 -0.021747967 -1.1028394 -1.1028394 18.165751
|
||||
10000 0 1.0377326 0.88469468 0.0039065571 0.011847093 0.60076606 0.60076606 105.95133
|
||||
Loop time of 5.25724 on 8 procs for 10000 steps with 20284 atoms
|
||||
|
||||
Pair time (%) = 0.12938 (2.46098)
|
||||
Neigh time (%) = 0.323687 (6.15698)
|
||||
Comm time (%) = 0.201078 (3.82479)
|
||||
Outpt time (%) = 0.00122145 (0.0232336)
|
||||
Other time (%) = 4.60188 (87.534)
|
||||
|
||||
Nlocal: 2535.5 ave 2832 max 2244 min
|
||||
Histogram: 2 0 0 1 1 2 0 0 0 2
|
||||
Nghost: 113.375 ave 119 max 109 min
|
||||
Histogram: 2 1 1 0 0 1 0 0 1 2
|
||||
Neighs: 520.625 ave 640 max 388 min
|
||||
Histogram: 2 0 1 0 0 1 0 2 1 1
|
||||
|
||||
Total # of neighbors = 4165
|
||||
Ave neighs/atom = 0.205334
|
||||
Neighbor list builds = 508
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
triclinic box = (-10.0789 -10.0789 -0.5) to (10.0789 10.0789 0.5) with tilt (0 0 0)
|
||||
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes
|
||||
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.line.srd id type # c_10[1] c_10[2] c_10[3] c_10[4]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
|
||||
run 40000
|
||||
SRD info:
|
||||
SRD/big particles = 19884 400
|
||||
big particle diameter max/min = 1.99882 0.503306
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 81 81 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.248861 0.248861 1
|
||||
SRD per actual grid cell = -11.3331
|
||||
SRD viscosity = -1920.36
|
||||
big/SRD mass density ratio = -0.546468
|
||||
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2737)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2761)
|
||||
# of rescaled SRD velocities = 5
|
||||
ave/max small velocity = 12.7055 40
|
||||
ave/max big velocity = 1.43831 4.07637
|
||||
Memory usage per processor = 4.07906 Mbytes
|
||||
Step Temp tsmall 2[9] 1 TotEng pebig ebig Press
|
||||
10000 0 1.0285209 0 0.0039065571 0.012056063 0.61136294 0.61136294 70.259237
|
||||
11000 0 1.0391738 0.9421875 0.00039699357 -0.034840076 -1.7667403 -1.7667403 51.907585
|
||||
12000 0 1.038934 0.93340757 0.00033545803 -0.035181234 -1.7840404 -1.7840404 51.039479
|
||||
13000 0 1.0363741 0.94084946 0.0004529039 -0.033018255 -1.6743557 -1.6743557 54.138717
|
||||
14000 0 1.0373865 0.93242943 0.0004722244 -0.032766048 -1.6615663 -1.6615663 54.092833
|
||||
15000 0 1.0289967 0.92957433 0.00041639952 -0.033696503 -1.7087497 -1.7087497 48.76136
|
||||
16000 0 1.0315281 0.9336746 0.00044091467 -0.034047366 -1.7265419 -1.7265419 49.368354
|
||||
17000 0 1.0310976 0.92846069 0.00058265838 -0.036251651 -1.8383212 -1.8383212 47.527648
|
||||
18000 0 1.0387834 0.93270079 0.00064962838 -0.03849464 -1.9520632 -1.9520632 55.151324
|
||||
19000 0 1.034225 0.94028857 0.00042052385 -0.037457059 -1.8994474 -1.8994474 47.746045
|
||||
20000 0 1.0377609 0.93927936 0.0005218884 -0.034132243 -1.7308461 -1.7308461 87.048419
|
||||
21000 0 1.0404827 0.93995585 0.00057654739 -0.0306282 -1.553156 -1.553156 57.122553
|
||||
22000 0 1.0399735 0.93639576 0.00037285284 -0.026102398 -1.3236526 -1.3236526 59.315805
|
||||
23000 0 1.0396421 0.93234579 0.00042714044 -0.024751467 -1.2551469 -1.2551469 78.461174
|
||||
24000 0 1.0376317 0.93328901 0.00055283478 -0.0276932 -1.4043222 -1.4043222 61.533389
|
||||
25000 0 1.0358692 0.93697479 0.0004225622 -0.026282283 -1.3327746 -1.3327746 62.554247
|
||||
26000 0 1.0397631 0.9336746 0.00054058432 -0.024075759 -1.2208817 -1.2208817 64.975611
|
||||
27000 0 1.0405916 0.94307316 0.0003904132 -0.028426222 -1.4414937 -1.4414937 55.128234
|
||||
28000 0 1.037771 0.94115025 0.00038432308 -0.030313284 -1.5371866 -1.5371866 56.493375
|
||||
29000 0 1.0395232 0.92801772 0.00038560341 -0.029991249 -1.5208562 -1.5208562 57.427874
|
||||
30000 0 1.0354662 0.93958984 0.0004698422 -0.02938728 -1.490229 -1.490229 54.222732
|
||||
31000 0 1.0384932 0.93606594 0.00041385391 -0.028759403 -1.4583893 -1.4583893 55.483372
|
||||
32000 0 1.0387759 0.94189671 0.00049520206 -0.029553008 -1.498633 -1.498633 58.747733
|
||||
33000 0 1.0378057 0.93424537 0.00052622477 -0.031085566 -1.576349 -1.576349 53.836967
|
||||
34000 0 1.0372805 0.93826338 0.00054888869 -0.036504286 -1.8511323 -1.8511323 44.792497
|
||||
35000 0 1.0382469 0.93704278 0.0004307863 -0.038148625 -1.9345168 -1.9345168 42.582442
|
||||
36000 0 1.0380694 0.93714033 0.00039730159 -0.036405598 -1.8461279 -1.8461279 47.104593
|
||||
37000 0 1.0402138 0.93799823 0.00051417836 -0.032909885 -1.6688603 -1.6688603 55.244687
|
||||
38000 0 1.0384244 0.93708166 0.00043306898 -0.030288286 -1.535919 -1.535919 55.538198
|
||||
39000 0 1.0410634 0.93284574 0.00053167091 -0.030864158 -1.5651214 -1.5651214 56.136389
|
||||
40000 0 1.0434316 0.94540613 0.0004625865 -0.035063246 -1.7780572 -1.7780572 51.415561
|
||||
41000 0 1.0369369 0.93512798 0.00048692231 -0.03501711 -1.7757177 -1.7757177 52.27068
|
||||
42000 0 1.037407 0.9277082 0.00044677419 -0.035686429 -1.8096588 -1.8096588 47.812559
|
||||
43000 0 1.0391707 0.93974302 0.00037562628 -0.034697463 -1.7595083 -1.7595083 60.19428
|
||||
44000 0 1.0369685 0.93745842 0.00041027797 -0.035341149 -1.7921497 -1.7921497 52.091971
|
||||
45000 0 1.036099 0.9321397 0.00042455475 -0.033947768 -1.7214913 -1.7214913 49.730151
|
||||
46000 0 1.032015 0.9300885 0.00033912308 -0.032997968 -1.6733269 -1.6733269 56.703006
|
||||
47000 0 1.0326688 0.9375833 0.00043809093 -0.034003679 -1.7243266 -1.7243266 53.212731
|
||||
48000 0 1.0380837 0.94267232 0.00047529732 -0.033961575 -1.7221915 -1.7221915 48.821619
|
||||
49000 0 1.0364529 0.93990652 0.00054656191 -0.031215986 -1.5829626 -1.5829626 55.420703
|
||||
50000 0 1.0335509 0.93651862 0.00049456314 -0.03110686 -1.5774289 -1.5774289 56.656467
|
||||
Loop time of 43.1064 on 8 procs for 40000 steps with 20284 atoms
|
||||
|
||||
Pair time (%) = 1.73269 (4.01956)
|
||||
Neigh time (%) = 1.43244 (3.32304)
|
||||
Comm time (%) = 1.08363 (2.51385)
|
||||
Outpt time (%) = 0.00464779 (0.0107821)
|
||||
Other time (%) = 38.853 (90.1328)
|
||||
|
||||
Nlocal: 2535.5 ave 2610 max 2448 min
|
||||
Histogram: 2 0 1 0 0 1 1 1 0 2
|
||||
Nghost: 114.875 ave 125 max 106 min
|
||||
Histogram: 2 0 0 1 1 2 0 1 0 1
|
||||
Neighs: 516.5 ave 599 max 465 min
|
||||
Histogram: 3 0 0 1 1 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 4132
|
||||
Ave neighs/atom = 0.203707
|
||||
Neighbor list builds = 2002
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,113 @@
|
|||
# SRD diffusion demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
create_atoms 1 region box
|
||||
|
||||
group big type 1
|
||||
set group big type/fraction 2 0.33 394895
|
||||
set group big type/fraction 3 0.5 989894
|
||||
group big type 2 3
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
create_atoms 4 region plane
|
||||
|
||||
set type 4 mass 0.1
|
||||
group small type 4
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
pair_coeff 2 4 0.0 1.0 1.0
|
||||
pair_coeff 3 4 0.0 1.0 0.75
|
||||
|
||||
delete_atoms overlap 1.0 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 inside ignore
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
|
||||
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
|
||||
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.poly
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
|
||||
|
||||
run 100000
|
||||
|
|
@ -0,0 +1,114 @@
|
|||
# SRD viscosity demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
create_atoms 1 region box
|
||||
|
||||
group big type 1
|
||||
set group big type/fraction 2 0.33 394895
|
||||
set group big type/fraction 3 0.5 989894
|
||||
group big type 2 3
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
create_atoms 4 region plane
|
||||
|
||||
set type 4 mass 0.1
|
||||
group small type 4
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
pair_coeff 2 4 0.0 1.0 1.0
|
||||
pair_coeff 3 4 0.0 1.0 0.75
|
||||
|
||||
delete_atoms overlap 1.0 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 inside ignore
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
|
||||
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
|
||||
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 500 dump.poly.mp
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
|
||||
|
||||
run 50000
|
||||
|
|
@ -0,0 +1,288 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# SRD diffusion demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
Created orthogonal box = (0 0 -0.912871) to (18.2574 18.2574 0.912871)
|
||||
2 by 4 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big type/fraction 2 0.33 394895
|
||||
35 settings made for type/fraction
|
||||
set group big type/fraction 3 0.5 989894
|
||||
57 settings made for type/fraction
|
||||
group big type 2 3
|
||||
100 atoms in group big
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
100 settings made for mass
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 2.74744 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.16013916 0 1.2654608 1.1298975
|
||||
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
|
||||
Loop time of 0.0263424 on 8 procs for 1000 steps with 100 atoms
|
||||
|
||||
Pair time (%) = 0.000377953 (1.43477)
|
||||
Neigh time (%) = 0.000303119 (1.15069)
|
||||
Comm time (%) = 0.0153534 (58.2839)
|
||||
Outpt time (%) = 3.43621e-05 (0.130444)
|
||||
Other time (%) = 0.0102736 (39.0002)
|
||||
|
||||
Nlocal: 12.5 ave 18 max 10 min
|
||||
Histogram: 1 3 1 1 0 1 0 0 0 1
|
||||
Nghost: 27.75 ave 31 max 24 min
|
||||
Histogram: 1 0 1 0 2 2 0 0 0 2
|
||||
Neighs: 19 ave 30 max 16 min
|
||||
Histogram: 4 1 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 152
|
||||
Ave neighs/atom = 1.52
|
||||
Neighbor list builds = 115
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
Lattice spacing in x,y,z = 0.0632456 0.0632456 0.0632456
|
||||
create_atoms 4 region plane
|
||||
Created 83521 atoms
|
||||
|
||||
set type 4 mass 0.1
|
||||
83521 settings made for mass
|
||||
group small type 4
|
||||
83521 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
pair_coeff 2 4 0.0 1.0 1.0
|
||||
pair_coeff 3 4 0.0 1.0 0.75
|
||||
|
||||
delete_atoms overlap 1.0 small big
|
||||
Deleted 63410 atoms, new total = 20211
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.poly
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 20111 100
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 73 73 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250102 0.250102 1.82574
|
||||
SRD per actual grid cell = 4.93717
|
||||
SRD viscosity = 0.23322
|
||||
big/SRD mass density ratio = 0.161311
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.19344 7.74495
|
||||
ave/max big velocity = 1.43991 3.5724
|
||||
Memory usage per processor = 11.7296 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11]
|
||||
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 0.84607636 4320 0.0065245155 0.058016042 1.3186698 4.2649215 7470 26 26 0 649 36480 5329 4320 0.87250069 0 2
|
||||
2000 0.90485259 4380 0.0052749864 -0.28210286 1.0661275 2.1610016 7779 41 41 0 1285 36480 5329 4380 0.96910154 0 2
|
||||
3000 0.86997866 4359 0.0051174794 -0.26197443 1.0342938 2.0552139 7976 32 32 0 2031 36480 5329 4359 1.0066773 0 2
|
||||
4000 0.81799751 4386 0.004339179 -0.34182481 0.87699148 1.8252707 8228 36 36 0 2797 36480 5329 4386 1.0427782 0 2
|
||||
5000 0.86406909 4378 0.005062484 -0.2642843 1.0231786 2.0027892 8402 31 31 0 3662 36480 5329 4378 1.0498595 0 2
|
||||
6000 0.81122089 4390 0.0045773647 -0.28358794 0.92513119 1.6291269 8343 22 22 0 4542 36480 5329 4390 1.075211 0 2
|
||||
7000 0.86048278 4374 0.0045829051 -0.35586841 0.92625094 1.787504 8229 26 26 0 5515 36480 5329 4374 1.0816492 0 2
|
||||
8000 0.86834891 4381 0.0045794089 -0.36829555 0.92554432 1.6425705 8375 34 34 0 6432 36480 5329 4381 1.0734234 0 2
|
||||
9000 0.85897968 4394 0.0042698244 -0.4169055 0.86297422 1.4346364 8500 30 30 0 7355 36480 5329 4394 1.087639 0 2
|
||||
10000 0.70846773 4404 0.0030688471 -0.43537222 0.6202447 1.355036 8291 36 36 0 8314 36480 5329 4404 1.0788748 0 2
|
||||
11000 0.79937389 4390 0.0043439579 -0.31310977 0.87795733 1.5807555 8350 27 27 0 9281 36480 5329 4390 1.0790792 0 2
|
||||
12000 0.85824569 4411 0.0046841509 -0.33207234 0.94671374 1.591183 8327 37 37 0 10262 36480 5329 4411 1.0788503 0 2
|
||||
13000 0.81732539 4415 0.0037450448 -0.46090383 0.756911 1.1438166 8483 26 26 0 11238 36480 5329 4415 1.0917525 0 2
|
||||
14000 0.89802245 4399 0.005085064 -0.31031115 1.0277423 1.599284 8514 27 27 0 12274 36480 5329 4399 1.0749784 0 54
|
||||
15000 0.68998926 4394 0.0029236972 -0.43717555 0.59090845 1.2810011 8383 45 45 0 13277 36480 5329 4394 1.0756773 0 54
|
||||
16000 0.83208983 4407 0.004493664 -0.33159942 0.90821442 1.6639201 8320 28 28 0 14243 36480 5329 4407 1.090866 0 54
|
||||
17000 0.70920173 4404 0.003792538 -0.29020072 0.76650986 1.475147 8517 34 34 0 15183 36480 5329 4404 1.0816438 0 54
|
||||
18000 0.75974526 4395 0.003566885 -0.41111731 0.72090312 1.3301798 8506 36 36 0 16138 36480 5329 4395 1.0676888 0 54
|
||||
19000 0.8732303 4409 0.0040921591 -0.47404688 0.82706627 1.3282596 8512 38 38 0 17108 36480 5329 4409 1.0864062 0 54
|
||||
20000 0.74373268 4407 0.0037797876 -0.34422884 0.76393286 1.3084704 8505 30 30 0 18099 36480 5329 4407 1.0738575 0 54
|
||||
21000 0.73961986 4400 0.0038147704 -0.33103034 0.77100326 1.4165508 8508 32 32 0 19164 36480 5329 4400 1.0878172 0 54
|
||||
22000 0.71412304 4402 0.0033459777 -0.38778778 0.67625555 1.4732933 8571 32 32 0 20209 36480 5329 4402 1.0961455 0 54
|
||||
23000 0.6485368 4391 0.0031023431 -0.33930525 0.62701457 1.2255142 8654 32 32 0 21226 36480 5329 4391 1.0955652 0 54
|
||||
24000 0.62496852 4383 0.0031101939 -0.3026018 0.62860128 1.2574516 8456 40 40 0 22229 36480 5329 4383 1.1043661 0 54
|
||||
25000 0.71882821 4387 0.0039504377 -0.27263108 0.79842295 1.5423115 8462 38 38 0 23302 36480 5329 4387 1.0988273 0 54
|
||||
26000 0.81325766 4374 0.0046964629 -0.2625518 0.94920212 1.3027349 8469 22 22 0 24256 36480 5329 4374 1.0957156 0 54
|
||||
27000 0.75769478 4404 0.0036955181 -0.38206406 0.74690116 1.2565814 8313 36 36 0 25218 36480 5329 4404 1.096358 0 54
|
||||
28000 0.73180309 4400 0.003869417 -0.30833874 0.78204787 1.4692801 8537 33 33 0 26166 36480 5329 4400 1.0838456 0 54
|
||||
29000 0.87301447 4404 0.0049666713 -0.29697763 1.0038139 1.4686871 8561 30 30 0 27154 36480 5329 4404 1.0950654 0 54
|
||||
30000 0.90865536 4400 0.0050855318 -0.32605966 1.0278368 1.5864144 8483 20 20 0 28190 36480 5329 4400 1.0798509 0 54
|
||||
31000 0.79500293 4393 0.0038246276 -0.41155888 0.77299548 1.3568346 8454 32 32 0 29155 36480 5329 4393 1.0724713 0 54
|
||||
32000 0.87294832 4376 0.0054025526 -0.20878308 1.0919099 1.690247 8487 32 32 0 30185 36480 5329 4376 1.093595 0 54
|
||||
33000 0.7796704 4387 0.003870468 -0.37944861 0.78226028 1.3978337 8338 28 28 0 31158 36480 5329 4387 1.0950913 0 54
|
||||
34000 0.83949838 4408 0.0048589409 -0.26881205 0.98204055 1.3199495 8502 29 29 0 32212 36480 5329 4408 1.0994115 0 54
|
||||
35000 0.89882881 4386 0.0046758361 -0.3942217 0.94503323 1.1627131 8500 40 40 0 33253 36480 5329 4386 1.0952495 0 54
|
||||
36000 0.98891767 4388 0.0051298733 -0.43668865 1.0367987 1.3347621 8589 35 35 0 34383 36480 5329 4388 1.1028282 0 54
|
||||
37000 0.78021407 4404 0.0035932812 -0.4362809 0.72623807 1.0910515 8528 35 35 0 35451 36480 5329 4404 1.0910774 0 54
|
||||
38000 0.83518145 4383 0.0044236947 -0.35034742 0.89407294 1.2542227 8581 39 39 2 36623 36480 5329 4383 1.0969125 0 60
|
||||
39000 0.79413048 4410 0.0045336904 -0.26695025 0.91630417 1.628798 8573 49 49 0 37739 36480 5329 4410 1.0786676 0 60
|
||||
40000 0.69391266 4401 0.0035290325 -0.3206771 0.71325276 1.2434063 8722 24 24 0 38806 36480 5329 4401 1.0930726 0 60
|
||||
41000 0.87777539 4405 0.0046384823 -0.37040166 0.93748366 1.3485397 8591 29 29 0 39844 36480 5329 4405 1.0934857 0 60
|
||||
42000 0.88000424 4419 0.0041538556 -0.47167057 0.83953575 1.373462 8528 30 30 0 40851 36480 5329 4419 1.1058136 0 60
|
||||
43000 0.80894411 4394 0.0043471883 -0.3267165 0.87861023 1.5520932 8516 34 34 0 41927 36480 5329 4394 1.0940256 0 60
|
||||
44000 0.81278253 4413 0.0043670096 -0.32842965 0.88261632 1.7514988 8424 37 37 0 42979 36480 5329 4413 1.0890373 0 60
|
||||
45000 0.81669704 4391 0.0042902765 -0.34977079 0.86710779 1.2720081 8603 29 29 0 43991 36480 5329 4391 1.0959104 0 60
|
||||
46000 0.68105471 4415 0.0033462068 -0.33846966 0.67630186 1.3572051 8597 37 37 0 45054 36480 5329 4415 1.0831668 0 60
|
||||
47000 0.74650613 4406 0.0031567817 -0.47427698 0.63801715 1.2357289 8712 37 37 0 46111 36480 5329 4406 1.0825124 0 60
|
||||
48000 0.78925983 4419 0.0037255285 -0.42303057 0.75296657 1.2629704 8539 39 39 0 47063 36480 5329 4419 1.086451 0 60
|
||||
49000 0.76629818 4405 0.0039711762 -0.33916987 0.80261443 1.3028869 8446 38 38 0 48085 36480 5329 4405 1.0962223 0 60
|
||||
50000 0.8104353 4406 0.0041783294 -0.36306645 0.84448215 1.0644192 8664 36 36 0 49080 36480 5329 4406 1.082981 0 60
|
||||
51000 0.88113764 4402 0.0051570248 -0.27060881 1.0422863 1.4386175 8624 38 38 0 50185 36480 5329 4402 1.0798375 0 60
|
||||
52000 0.77033709 4389 0.0045371435 -0.23080019 0.91700207 1.4602717 8436 30 30 0 51245 36480 5329 4389 1.0931273 0 60
|
||||
53000 0.81214351 4410 0.0048922416 -0.22132289 0.98877095 1.7454029 8706 29 29 0 52280 36480 5329 4410 1.0939736 0 60
|
||||
54000 0.89983347 4386 0.0045215928 -0.42689275 0.91385912 1.2867976 8602 26 26 0 53359 36480 5329 4386 1.0938981 0 60
|
||||
55000 0.85535843 4388 0.0045846672 -0.34787698 0.92660708 1.4863714 8630 36 36 0 54411 36480 5329 4388 1.0865711 0 60
|
||||
56000 0.65511288 4409 0.0035485946 -0.25891173 0.71720646 1.4491969 8573 33 33 0 55419 36480 5329 4409 1.1167746 0 60
|
||||
57000 0.82787973 4393 0.004433496 -0.33748691 0.89605388 1.3780497 8608 28 28 0 56458 36480 5329 4393 1.090579 0 60
|
||||
58000 0.78199015 4411 0.0041719007 -0.32198248 0.84318285 1.5489896 8596 39 39 0 57518 36480 5329 4411 1.0950974 0 60
|
||||
59000 0.83342791 4387 0.004742265 -0.2833484 0.95845919 1.5035913 8580 23 23 0 58495 36480 5329 4387 1.1044386 0 60
|
||||
60000 0.92726046 4412 0.0054717726 -0.27571813 1.1059 1.5223588 8601 47 47 0 59516 36480 5329 4412 1.1053325 0 60
|
||||
61000 0.71162631 4397 0.0034106311 -0.37100055 0.68932266 1.4441628 8600 35 35 0 60613 36480 5329 4397 1.1205275 0 60
|
||||
62000 0.83061614 4395 0.0051751609 -0.19166627 1.0459518 1.8120796 8665 39 39 0 61539 36480 5329 4395 1.0942761 0 60
|
||||
63000 0.69264654 4404 0.003733218 -0.27752266 0.75452069 1.4946754 8671 41 41 0 62499 36480 5329 4404 1.0864782 0 60
|
||||
64000 0.81150665 4409 0.0044149583 -0.31683769 0.89230723 1.4495005 8498 45 45 0 63585 36480 5329 4409 1.0947081 0 60
|
||||
65000 0.72188875 4415 0.0034008627 -0.38826587 0.68734836 1.3906117 8707 26 26 0 64598 36480 5329 4415 1.0867011 0 60
|
||||
66000 0.66159508 4395 0.0030869268 -0.36187789 0.62389878 1.4297478 8664 32 32 0 65686 36480 5329 4395 1.0920408 0 60
|
||||
67000 0.89720139 4402 0.0047549655 -0.37580398 0.96102608 1.3498224 8561 31 31 0 66668 36480 5329 4402 1.1140343 0 60
|
||||
68000 0.77646005 4399 0.0044770291 -0.25207312 0.90485236 1.450115 8645 34 34 0 67762 36480 5329 4399 1.1031979 0 60
|
||||
69000 0.76847183 4389 0.0046195632 -0.21136311 0.93365992 1.5393165 8663 37 37 0 68816 36480 5329 4389 1.100983 0 60
|
||||
70000 0.68687373 4398 0.0036588724 -0.28394714 0.73949471 1.4069676 8686 29 29 0 69917 36480 5329 4398 1.1173713 0 60
|
||||
71000 0.85660695 4405 0.0051111547 -0.24332887 1.0330155 1.5159938 8564 32 32 0 70984 36480 5329 4405 1.088877 0 60
|
||||
72000 0.83851058 4378 0.0047881845 -0.2816408 0.96773997 1.3016234 8815 41 41 0 72066 36480 5329 4378 1.0903007 0 60
|
||||
73000 0.9574802 4405 0.0054905849 -0.31694339 1.1097021 1.3834758 8498 39 39 0 73126 36480 5329 4405 1.0835447 0 60
|
||||
74000 0.93413914 4428 0.005594213 -0.26122094 1.1306464 1.3968649 8610 36 36 0 74134 36480 5329 4428 1.0925707 0 60
|
||||
75000 0.85110304 4399 0.0050214404 -0.2532602 1.0148833 1.7151794 8533 35 35 0 75226 36480 5329 4399 1.121987 0 60
|
||||
76000 0.74293246 4402 0.004159075 -0.26637871 0.84059065 1.5301113 8744 45 45 0 76247 36480 5329 4402 1.0786119 0 60
|
||||
77000 0.69374764 4398 0.0033526037 -0.35608924 0.67759474 1.3550134 8570 38 38 0 77323 36480 5329 4398 1.1077261 0 60
|
||||
78000 0.79184739 4387 0.0041458172 -0.3419415 0.83791112 1.53132 8488 33 33 0 78545 36480 5329 4387 1.0944135 0 81
|
||||
79000 0.73855485 4399 0.0040930305 -0.27320432 0.8272424 1.4930252 8590 40 40 0 79562 36480 5329 4399 1.0921682 0 81
|
||||
80000 0.80000829 4407 0.0035856307 -0.46732053 0.72469182 1.4649608 8480 38 38 0 80554 36480 5329 4407 1.0866433 0 81
|
||||
81000 0.75614881 4386 0.0040626682 -0.30555586 0.82110586 1.5424611 8489 32 32 0 81620 36480 5329 4386 1.1065811 0 81
|
||||
82000 0.74187824 4425 0.0042618334 -0.24403944 0.86135915 1.5254143 8495 23 23 0 82648 36480 5329 4425 1.0999901 0 81
|
||||
83000 0.96795247 4379 0.0056667045 -0.29695155 1.1452976 1.434689 8542 44 44 0 83674 36480 5329 4379 1.1055145 0 81
|
||||
84000 0.71973336 4403 0.0038014078 -0.30410018 0.76830252 1.416144 8595 34 34 0 84706 36480 5329 4403 1.0730077 0 81
|
||||
85000 0.67586077 4404 0.0039613843 -0.20639716 0.80063539 1.5423424 8573 39 39 0 85773 36480 5329 4404 1.0902847 0 81
|
||||
86000 0.7824605 4400 0.0039579087 -0.36593321 0.79993293 1.2665296 8709 33 33 0 86777 36480 5329 4400 1.0796536 0 81
|
||||
87000 0.80925546 4399 0.0044421598 -0.30798573 0.89780491 1.5569681 8668 36 36 0 87785 36480 5329 4399 1.0994771 0 81
|
||||
88000 0.76586354 4417 0.0039373168 -0.34536557 0.7957711 1.3500605 8615 35 35 0 88859 36480 5329 4417 1.0895919 0 81
|
||||
89000 0.69829963 4402 0.0031383989 -0.40616466 0.63430179 1.088111 8786 45 45 0 89860 36480 5329 4402 1.0866392 0 81
|
||||
90000 0.84707532 4410 0.0049394012 -0.26383986 0.99830237 1.5746697 8414 30 30 0 90900 36480 5329 4410 1.1136544 0 81
|
||||
91000 0.81479881 4391 0.0047153823 -0.26102431 0.95302592 1.4560202 8617 30 30 0 91885 36480 5329 4391 1.0909121 0 81
|
||||
92000 0.67926947 4398 0.0033034611 -0.344449 0.66766252 1.235949 8439 37 37 0 92933 36480 5329 4398 1.0877594 0 81
|
||||
93000 0.76411115 4388 0.0035573512 -0.41954937 0.71897625 1.1042722 8524 33 33 0 94014 36480 5329 4388 1.09172 0 81
|
||||
94000 0.76881091 4402 0.0044450994 -0.24712922 0.89839904 1.4046651 8626 31 31 0 94955 36480 5329 4402 1.090443 0 81
|
||||
95000 0.8089261 4372 0.0042760848 -0.34106038 0.8642395 1.4929178 8539 43 43 0 95962 36480 5329 4372 1.0761039 0 81
|
||||
96000 0.7316235 4418 0.0039746747 -0.2867975 0.80332151 1.6570629 8580 34 34 0 96941 36480 5329 4418 1.0768381 0 81
|
||||
97000 0.7858829 4407 0.003617173 -0.4398987 0.73106683 1.312132 8467 22 22 0 97963 36480 5329 4407 1.1078034 0 81
|
||||
98000 0.72898498 4397 0.0037674527 -0.32474775 0.76143987 1.2373268 8552 33 33 0 99024 36480 5329 4397 1.1024714 0 81
|
||||
99000 0.90435165 4378 0.0049764011 -0.34170354 1.0057804 1.6945983 8417 31 31 0 100116 36480 5329 4378 1.0899259 0 81
|
||||
100000 0.69815567 4407 0.0036001551 -0.3126246 0.72762735 1.4724301 8502 42 42 0 101118 36480 5329 4407 1.0777306 0 81
|
||||
Loop time of 15.4007 on 8 procs for 100000 steps with 20211 atoms
|
||||
|
||||
Pair time (%) = 0.0612983 (0.398022)
|
||||
Neigh time (%) = 0.858353 (5.57346)
|
||||
Comm time (%) = 1.11288 (7.22617)
|
||||
Outpt time (%) = 0.00592667 (0.0384831)
|
||||
Other time (%) = 13.3623 (86.7639)
|
||||
|
||||
Nlocal: 2526.38 ave 2618 max 2409 min
|
||||
Histogram: 1 2 0 0 0 1 0 0 1 3
|
||||
Nghost: 24.5 ave 28 max 21 min
|
||||
Histogram: 1 0 2 0 1 1 0 2 0 1
|
||||
Neighs: 17.5 ave 21 max 13 min
|
||||
Histogram: 1 1 0 0 0 1 2 1 1 1
|
||||
|
||||
Total # of neighbors = 140
|
||||
Ave neighs/atom = 0.00692692
|
||||
Neighbor list builds = 5005
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,239 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# SRD viscosity demo - poydisperse spheres
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify first big
|
||||
dimension 2
|
||||
|
||||
# create big particles with 3 different types and diameters
|
||||
|
||||
lattice sq 0.3
|
||||
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 4 box
|
||||
Created orthogonal box = (0 0 -0.912871) to (18.2574 18.2574 0.912871)
|
||||
2 by 4 by 1 MPI processor grid
|
||||
create_atoms 1 region box
|
||||
Created 100 atoms
|
||||
|
||||
group big type 1
|
||||
100 atoms in group big
|
||||
set group big type/fraction 2 0.33 394895
|
||||
35 settings made for type/fraction
|
||||
set group big type/fraction 3 0.5 989894
|
||||
57 settings made for type/fraction
|
||||
group big type 2 3
|
||||
100 atoms in group big
|
||||
|
||||
set type 1*3 mass 1.0
|
||||
100 settings made for mass
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles, repulsive only to prevent aggregation
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.poly.equil
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 2.74744 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -0.16013916 0 1.2654608 1.1298975
|
||||
1000 1.3367862 -0.30816328 0 1.0152551 1.5440006
|
||||
Loop time of 0.0171109 on 8 procs for 1000 steps with 100 atoms
|
||||
|
||||
Pair time (%) = 0.000367314 (2.14666)
|
||||
Neigh time (%) = 0.000303924 (1.7762)
|
||||
Comm time (%) = 0.0108245 (63.2607)
|
||||
Outpt time (%) = 4.13954e-05 (0.241924)
|
||||
Other time (%) = 0.00557381 (32.5745)
|
||||
|
||||
Nlocal: 12.5 ave 18 max 10 min
|
||||
Histogram: 1 3 1 1 0 1 0 0 0 1
|
||||
Nghost: 27.75 ave 31 max 24 min
|
||||
Histogram: 1 0 1 0 2 2 0 0 0 2
|
||||
Neighs: 19 ave 30 max 16 min
|
||||
Histogram: 4 1 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 152
|
||||
Ave neighs/atom = 1.52
|
||||
Neighbor list builds = 115
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 250.0
|
||||
Lattice spacing in x,y,z = 0.0632456 0.0632456 0.0632456
|
||||
create_atoms 4 region plane
|
||||
Created 83521 atoms
|
||||
|
||||
set type 4 mass 0.1
|
||||
83521 settings made for mass
|
||||
group small type 4
|
||||
83521 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set *-4 cutoffs to non-zero values
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 1.0 2.0
|
||||
pair_coeff 3 3 1.0 1.5
|
||||
pair_coeff 1 4 0.0 1.0 0.5
|
||||
pair_coeff 2 4 0.0 1.0 1.0
|
||||
pair_coeff 3 4 0.0 1.0 0.75
|
||||
|
||||
delete_atoms overlap 1.0 small big
|
||||
Deleted 63410 atoms, new total = 20211
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 1.12
|
||||
pair_coeff 1 1 1.0 1.0 1.12
|
||||
pair_coeff 2 2 1.0 2.0 2.24
|
||||
pair_coeff 3 3 1.0 1.5 1.68
|
||||
pair_coeff 4 4 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big nve
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 inside ignore
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 500 dump.poly.mp
|
||||
|
||||
#dump 1 all image 500 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 2.0 adiam 3 1.5 adiam 4 0.1
|
||||
|
||||
run 50000
|
||||
SRD info:
|
||||
SRD/big particles = 20111 100
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 73 73 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250102 0.250102 1.82574
|
||||
SRD per actual grid cell = 4.93717
|
||||
SRD viscosity = 0.23322
|
||||
big/SRD mass density ratio = 0.161311
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.19344 7.74495
|
||||
ave/max big velocity = 1.43991 3.5724
|
||||
Memory usage per processor = 11.7296 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11]
|
||||
0 0.88820023 0 0.0050232797 -0.30816328 1.0152551 1.5440006 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 0.76223473 4359 0.0058318998 0.042955512 1.1786853 3.9611296 7412 29 29 0 606 36480 5329 4359 0.88595821 0 1
|
||||
2000 0.90685078 4370 0.0052567627 -0.28876335 1.0624443 2.8023345 7566 38 38 0 1219 36480 5329 4370 0.98245206 0 3
|
||||
3000 0.82349169 4363 0.0040922377 -0.39992047 0.82708216 2.4033782 7677 22 22 0 2010 36480 5329 4363 0.9951035 0 3
|
||||
4000 1.0770702 4382 0.0065800011 -0.27495058 1.329884 2.9540829 8067 43 43 0 2890 36480 5329 4382 1.0247955 0 3
|
||||
5000 1.1187379 4371 0.0070884891 -0.23426486 1.4326545 2.782956 7987 34 34 0 3819 36480 5329 4371 1.0264278 0 3
|
||||
6000 1.1529648 4390 0.00804325 -0.092296355 1.6256212 2.7035637 8260 45 45 0 4906 36480 5329 4390 1.044768 0 3
|
||||
7000 1.2166621 4394 0.0084991908 -0.095055017 1.7177715 2.7964656 8289 29 29 0 6097 36480 5329 4394 1.0681058 0 3
|
||||
8000 1.0578321 4380 0.0069270677 -0.17614024 1.4000297 2.2457489 8231 32 32 0 7318 36480 5329 4380 1.0661274 0 3
|
||||
9000 1.1745002 4384 0.0080485374 -0.12331542 1.6266899 2.6780691 8348 30 30 0 8532 36480 5329 4384 1.0674998 0 3
|
||||
10000 1.2053965 4394 0.00919032 0.061414788 1.8574556 2.9760341 8315 36 36 0 9939 36480 5329 4394 1.0698008 0 3
|
||||
11000 1.2140992 4405 0.0080187349 -0.18834127 1.6206665 2.1090843 8390 38 38 0 11379 36480 5329 4405 1.0646411 0 3
|
||||
12000 1.3314891 4370 0.0085977755 -0.24622241 1.7376964 2.1024157 8371 31 31 0 12874 36480 5329 4370 1.1085934 0 3
|
||||
13000 1.7854091 4406 0.012596422 -0.11439664 2.5458629 2.8136175 8209 31 31 0 14445 36480 5329 4406 1.0656714 0 3
|
||||
14000 1.3532948 4392 0.0096486307 -0.066324512 1.9500847 2.9946734 8436 31 31 0 15853 36480 5329 4392 1.0796035 0 3
|
||||
15000 1.3652525 4406 0.0088880459 -0.23786321 1.796363 2.3354792 8476 32 32 0 17491 36480 5329 4406 1.062359 0 3
|
||||
16000 1.7207747 4397 0.010473468 -0.44716178 2.1167926 2.0550985 8412 33 33 0 18967 36480 5329 4397 1.0727867 0 3
|
||||
17000 1.4441674 4395 0.0093810416 -0.25580709 1.8960023 2.2891681 8523 25 25 0 20633 36480 5329 4395 1.0718441 0 3
|
||||
18000 1.6353203 4369 0.011239971 -0.16491671 2.2717106 2.2715018 8350 36 36 0 22227 36480 5329 4369 1.062651 0 3
|
||||
19000 1.2336121 4400 0.0078318926 -0.25517824 1.5829038 2.1478301 8506 31 31 0 23785 36480 5329 4400 1.064015 0 6
|
||||
20000 1.348169 4385 0.0093452554 -0.12000224 1.8887696 2.7793176 8501 31 31 0 25381 36480 5329 4385 1.0749601 0 6
|
||||
21000 1.2999945 4388 0.008793608 -0.15971573 1.7772761 2.2319158 8571 31 31 0 26907 36480 5329 4388 1.057039 0 6
|
||||
22000 1.4136382 4381 0.010131428 -0.058657961 2.0476629 2.9137729 8395 33 33 0 28465 36480 5329 4381 1.0483767 0 6
|
||||
23000 1.4669336 4397 0.0094913428 -0.26743576 1.9182953 2.2607135 8414 33 33 0 30174 36480 5329 4397 1.0599821 0 54
|
||||
24000 1.2402392 4393 0.0078941135 -0.25247715 1.5954793 2.1369734 8327 27 27 0 31747 36480 5329 4393 1.0756872 0 54
|
||||
25000 1.4541683 4379 0.010209747 -0.10321883 2.063492 2.540742 8397 41 41 0 33411 36480 5329 4379 1.0672776 0 54
|
||||
26000 1.3405944 4406 0.0097712528 -0.022617748 1.9748679 2.5936783 8485 41 41 0 35118 36480 5329 4406 1.0758295 0 54
|
||||
27000 1.6558588 4405 0.012177263 -0.0060829802 2.4611467 2.8707229 8422 27 27 0 36723 36480 5329 4405 1.083128 0 54
|
||||
28000 1.4410581 4387 0.0097287673 -0.18089536 1.9662812 2.2328446 8473 33 33 0 38374 36480 5329 4387 1.0974956 0 54
|
||||
29000 1.5710587 4399 0.011438826 -0.028976305 2.3119011 3.0464022 8409 36 36 0 39977 36480 5329 4399 1.0723788 0 54
|
||||
30000 1.5822758 4390 0.010254579 -0.285038 2.072553 2.4492756 8285 43 43 0 41623 36480 5329 4390 1.0800035 0 54
|
||||
31000 1.7821546 4385 0.012457185 -0.13768863 2.5177217 2.6529479 8311 26 26 0 43266 36480 5329 4385 1.0710985 0 54
|
||||
32000 1.6106571 4376 0.01150871 -0.073853599 2.3260254 2.6925206 8227 30 30 0 44806 36480 5329 4376 1.0726823 0 54
|
||||
33000 1.631601 4397 0.011271203 -0.1530625 2.2780229 2.111596 8463 40 40 0 46536 36480 5329 4397 1.0692746 0 54
|
||||
34000 1.3427275 4390 0.0092429624 -0.13256884 1.8680951 2.3330047 8481 30 30 0 48188 36480 5329 4390 1.0598242 0 54
|
||||
35000 1.8270729 4410 0.012439006 -0.20829114 2.5140475 2.4497436 8377 43 43 0 49938 36480 5329 4410 1.0639662 0 54
|
||||
36000 1.6831749 4409 0.011556546 -0.17223706 2.3356935 2.4104909 8530 38 38 0 51575 36480 5329 4409 1.0462452 0 54
|
||||
37000 1.5041928 4387 0.010868354 -0.044644177 2.1966031 2.8240213 8314 28 28 0 53275 36480 5329 4387 1.0642241 0 54
|
||||
38000 1.63922 4400 0.011191082 -0.18060817 2.2618297 2.6036583 8460 31 31 0 54863 36480 5329 4400 1.0513104 0 54
|
||||
39000 1.7856293 4402 0.01190713 -0.25403773 2.40655 2.6037177 8373 28 28 0 56511 36480 5329 4402 1.0575221 0 54
|
||||
40000 1.5627911 4395 0.010299952 -0.24683547 2.0817233 2.097953 8604 38 38 0 58065 36480 5329 4395 1.0761208 0 54
|
||||
41000 1.6374988 4391 0.011852474 -0.044369717 2.3955035 2.8099437 8581 37 37 0 59794 36480 5329 4391 1.0691616 0 54
|
||||
42000 1.5639838 4401 0.0099361957 -0.32213138 2.0082045 2.140333 8517 26 26 0 61494 36480 5329 4401 1.0551075 0 54
|
||||
43000 1.4230074 4386 0.010145789 -0.069715647 2.0505654 2.8175539 8394 35 35 0 63053 36480 5329 4386 1.0725308 0 54
|
||||
44000 1.7426342 4421 0.012394613 -0.091449657 2.5050753 3.108882 8621 22 22 3 64860 36480 5329 4421 1.0689123 0 54
|
||||
45000 1.5920362 4402 0.010869076 -0.17538493 2.196749 2.6145992 8584 33 33 0 66553 36480 5329 4402 1.0639622 0 54
|
||||
46000 1.5470871 4381 0.010652614 -0.15215985 2.1529999 2.5774405 8385 41 41 0 68217 36480 5329 4381 1.0647713 0 54
|
||||
47000 1.5733084 4394 0.010531031 -0.21580282 2.1284266 2.5415139 8473 39 39 0 70008 36480 5329 4394 1.0737587 0 54
|
||||
48000 1.6011945 4385 0.010744982 -0.21411145 2.1716683 2.6439905 8324 32 32 0 71724 36480 5329 4385 1.0697134 0 54
|
||||
49000 1.4920792 4394 0.01155316 0.11181112 2.3350091 3.2468881 8325 35 35 0 73535 36480 5329 4394 1.0606307 0 54
|
||||
50000 1.7492562 4404 0.012682847 -0.043061576 2.5633302 2.9057702 8551 24 24 0 75221 36480 5329 4404 1.0604543 0 54
|
||||
Loop time of 7.87485 on 8 procs for 50000 steps with 20211 atoms
|
||||
|
||||
Pair time (%) = 0.030976 (0.393354)
|
||||
Neigh time (%) = 0.431914 (5.48473)
|
||||
Comm time (%) = 0.565844 (7.18546)
|
||||
Outpt time (%) = 0.00249878 (0.0317311)
|
||||
Other time (%) = 6.84361 (86.9047)
|
||||
|
||||
Nlocal: 2526.38 ave 2659 max 2437 min
|
||||
Histogram: 1 3 0 0 1 1 0 0 1 1
|
||||
Nghost: 22.75 ave 25 max 19 min
|
||||
Histogram: 1 0 0 0 0 2 2 0 2 1
|
||||
Neighs: 16.25 ave 20 max 12 min
|
||||
Histogram: 1 0 1 1 0 1 1 2 0 1
|
||||
|
||||
Total # of neighbors = 130
|
||||
Ave neighs/atom = 0.00643214
|
||||
Neighbor list builds = 2504
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,552 @@
|
|||
LAMMPS data file for Nanoparticles
|
||||
270 atoms
|
||||
2 atom types
|
||||
-13.2934038818 13.2934038818 xlo xhi
|
||||
-13.2934038818 13.2934038818 ylo yhi
|
||||
-0.5 0.5 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 1 3.07843 1.22935 0 0 0 0
|
||||
2 1 1 1 1.86321 2.27014 0 0 0 0
|
||||
3 1 1 1 2.47082 1.74975 0 0 0 0
|
||||
4 1 1 1 3.68604 0.708961 0 0 0 0
|
||||
5 1 1 1 4.29365 0.188568 0 0 0 0
|
||||
6 1 1 1 2.03764 0.0141312 0 0 0 0
|
||||
7 1 1 1 2.55804 0.621742 0 0 0 0
|
||||
8 1 1 1 3.59882 1.83696 0 0 0 0
|
||||
9 1 1 1 4.11921 2.44458 0 0 0 0
|
||||
10 1 1 1 11.9265 10.3133 0 0 0 0
|
||||
11 1 1 1 12.507 8.82229 0 0 0 0
|
||||
12 1 1 1 12.2167 9.56778 0 0 0 0
|
||||
13 1 1 1 11.6362 11.0588 0 0 0 0
|
||||
14 1 1 1 11.346 11.8042 0 0 0 0
|
||||
15 1 1 1 -13.1694 10.8938 0 1 0 0
|
||||
16 1 1 1 12.672 10.6035 0 0 0 0
|
||||
17 1 1 1 11.181 10.023 0 0 0 0
|
||||
18 1 1 1 10.4355 9.73276 0 0 0 0
|
||||
19 1 1 1 2.92771 -6.14972 0 0 0 0
|
||||
20 1 1 1 2.0477 -4.81346 0 0 0 0
|
||||
21 1 1 1 2.48771 -5.48159 0 0 0 0
|
||||
22 1 1 1 3.36771 -6.81785 0 0 0 0
|
||||
23 1 1 1 3.80772 -7.48598 0 0 0 0
|
||||
24 1 1 1 1.59145 -7.02972 0 0 0 0
|
||||
25 1 1 1 2.25958 -6.58972 0 0 0 0
|
||||
26 1 1 1 3.59584 -5.70971 0 0 0 0
|
||||
27 1 1 1 4.26397 -5.26971 0 0 0 0
|
||||
28 1 1 1 11.9757 -12.7981 0 0 0 0
|
||||
29 1 1 1 -13.1156 13.2199 0 1 -1 0
|
||||
30 1 1 1 12.7234 -13.0825 0 0 0 0
|
||||
31 1 1 1 11.228 -12.5136 0 0 0 0
|
||||
32 1 1 1 10.4803 -12.2292 0 0 0 0
|
||||
33 1 1 1 12.5446 -11.3026 0 0 0 0
|
||||
34 1 1 1 12.2602 -12.0503 0 0 0 0
|
||||
35 1 1 1 11.6913 13.041 0 0 -1 0
|
||||
36 1 1 1 11.4068 12.2933 0 0 -1 0
|
||||
37 1 1 1 11.222 0.827207 0 0 0 0
|
||||
38 1 1 1 11.4061 2.41658 0 0 0 0
|
||||
39 1 1 1 11.314 1.62189 0 0 0 0
|
||||
40 1 1 1 11.1299 0.0325207 0 0 0 0
|
||||
41 1 1 1 11.0379 -0.762166 0 0 0 0
|
||||
42 1 1 1 9.6326 1.01131 0 0 0 0
|
||||
43 1 1 1 10.4273 0.919258 0 0 0 0
|
||||
44 1 1 1 12.0167 0.735157 0 0 0 0
|
||||
45 1 1 1 12.8113 0.643107 0 0 0 0
|
||||
46 1 1 1 -0.554263 -10.1185 0 0 0 0
|
||||
47 1 1 1 -1.61026 -8.91649 0 0 0 0
|
||||
48 1 1 1 -1.08226 -9.5175 0 0 0 0
|
||||
49 1 1 1 -0.0262649 -10.7195 0 0 0 0
|
||||
50 1 1 1 0.501733 -11.3205 0 0 0 0
|
||||
51 1 1 1 -1.75629 -11.1745 0 0 0 0
|
||||
52 1 1 1 -1.15528 -10.6465 0 0 0 0
|
||||
53 1 1 1 0.0467508 -9.59052 0 0 0 0
|
||||
54 1 1 1 0.647765 -9.06252 0 0 0 0
|
||||
55 1 1 1 -5.47715 -10.9308 0 0 0 0
|
||||
56 1 1 1 -6.45589 -12.1966 0 0 0 0
|
||||
57 1 1 1 -5.96652 -11.5637 0 0 0 0
|
||||
58 1 1 1 -4.98778 -10.298 0 0 0 0
|
||||
59 1 1 1 -4.49841 -9.6651 0 0 0 0
|
||||
60 1 1 1 -4.21142 -11.9096 0 0 0 0
|
||||
61 1 1 1 -4.84429 -11.4202 0 0 0 0
|
||||
62 1 1 1 -6.11001 -10.4415 0 0 0 0
|
||||
63 1 1 1 -6.74288 -9.95209 0 0 0 0
|
||||
64 1 1 1 11.7879 -5.528 0 0 0 0
|
||||
65 1 1 1 10.627 -6.62904 0 0 0 0
|
||||
66 1 1 1 11.2075 -6.07852 0 0 0 0
|
||||
67 1 1 1 12.3684 -4.97748 0 0 0 0
|
||||
68 1 1 1 12.9488 -4.42696 0 0 0 0
|
||||
69 1 1 1 12.8889 -6.68891 0 0 0 0
|
||||
70 1 1 1 12.3384 -6.10846 0 0 0 0
|
||||
71 1 1 1 11.2374 -4.94755 0 0 0 0
|
||||
72 1 1 1 10.6869 -4.36709 0 0 0 0
|
||||
73 1 1 1 -7.98832 3.62673 0 0 0 0
|
||||
74 1 1 1 -9.58568 3.71861 0 0 0 0
|
||||
75 1 1 1 -8.787 3.67267 0 0 0 0
|
||||
76 1 1 1 -7.18964 3.58078 0 0 0 0
|
||||
77 1 1 1 -6.39096 3.53484 0 0 0 0
|
||||
78 1 1 1 -8.08021 2.02937 0 0 0 0
|
||||
79 1 1 1 -8.03427 2.82805 0 0 0 0
|
||||
80 1 1 1 -7.94238 4.42541 0 0 0 0
|
||||
81 1 1 1 -7.89644 5.22409 0 0 0 0
|
||||
82 1 1 1 5.10949 -0.142019 0 0 0 0
|
||||
83 1 1 1 4.9846 1.4531 0 0 0 0
|
||||
84 1 1 1 5.04705 0.65554 0 0 0 0
|
||||
85 1 1 1 5.17194 -0.939578 0 0 0 0
|
||||
86 1 1 1 5.23439 -1.73714 0 0 0 0
|
||||
87 1 1 1 3.51437 -0.266913 0 0 0 0
|
||||
88 1 1 1 4.31193 -0.204466 0 0 0 0
|
||||
89 1 1 1 5.90705 -0.0795721 0 0 0 0
|
||||
90 1 1 1 6.70461 -0.0171252 0 0 0 0
|
||||
91 1 1 1 -8.66384 2.7372 0 0 0 0
|
||||
92 1 1 1 -8.49225 1.14643 0 0 0 0
|
||||
93 1 1 1 -8.57805 1.94182 0 0 0 0
|
||||
94 1 1 1 -8.74964 3.53259 0 0 0 0
|
||||
95 1 1 1 -8.83543 4.32798 0 0 0 0
|
||||
96 1 1 1 -7.07307 2.90879 0 0 0 0
|
||||
97 1 1 1 -7.86846 2.823 0 0 0 0
|
||||
98 1 1 1 -9.45923 2.65141 0 0 0 0
|
||||
99 1 1 1 -10.2546 2.56561 0 0 0 0
|
||||
100 1 1 1 11.5851 -10.359 0 0 0 0
|
||||
101 1 1 1 9.99223 -10.5095 0 0 0 0
|
||||
102 1 1 1 10.7887 -10.4343 0 0 0 0
|
||||
103 1 1 1 12.3816 -10.2838 0 0 0 0
|
||||
104 1 1 1 13.178 -10.2086 0 0 0 0
|
||||
105 1 1 1 11.7356 -11.9519 0 0 0 0
|
||||
106 1 1 1 11.6604 -11.1555 0 0 0 0
|
||||
107 1 1 1 11.5099 -9.56258 0 0 0 0
|
||||
108 1 1 1 11.4347 -8.76613 0 0 0 0
|
||||
109 1 1 1 12.2327 -1.17301 0 0 0 0
|
||||
110 1 1 1 -12.9416 -0.421424 0 1 0 0
|
||||
111 1 1 1 12.9389 -0.797218 0 0 0 0
|
||||
112 1 1 1 11.5264 -1.54881 0 0 0 0
|
||||
113 1 1 1 10.8202 -1.9246 0 0 0 0
|
||||
114 1 1 1 11.4811 0.239474 0 0 0 0
|
||||
115 1 1 1 11.8569 -0.466769 0 0 0 0
|
||||
116 1 1 1 12.6085 -1.87925 0 0 0 0
|
||||
117 1 1 1 12.9843 -2.5855 0 0 0 0
|
||||
118 1 1 1 13.2863 -0.20095 0 0 0 0
|
||||
119 1 1 1 11.8698 -0.94506 0 0 0 0
|
||||
120 1 1 1 12.5781 -0.573005 0 0 0 0
|
||||
121 1 1 1 -12.5923 0.171106 0 1 0 0
|
||||
122 1 1 1 -11.8841 0.543161 0 1 0 0
|
||||
123 1 1 1 -12.5564 -1.61739 0 1 0 0
|
||||
124 1 1 1 -12.9285 -0.909169 0 1 0 0
|
||||
125 1 1 1 12.9142 0.50727 0 0 0 0
|
||||
126 1 1 1 12.5422 1.21549 0 0 0 0
|
||||
127 1 1 1 9.23705 6.72763 0 0 0 0
|
||||
128 1 1 1 10.7155 6.11582 0 0 0 0
|
||||
129 1 1 1 9.97625 6.42173 0 0 0 0
|
||||
130 1 1 1 8.49785 7.03354 0 0 0 0
|
||||
131 1 1 1 7.75864 7.33944 0 0 0 0
|
||||
132 1 1 1 9.84886 8.20604 0 0 0 0
|
||||
133 1 1 1 9.54295 7.46684 0 0 0 0
|
||||
134 1 1 1 8.93114 5.98843 0 0 0 0
|
||||
135 1 1 1 8.62524 5.24922 0 0 0 0
|
||||
136 1 1 1 11.4096 -9.51055 0 0 0 0
|
||||
137 1 1 1 11.5248 -7.9147 0 0 0 0
|
||||
138 1 1 1 11.4672 -8.71262 0 0 0 0
|
||||
139 1 1 1 11.352 -10.3085 0 0 0 0
|
||||
140 1 1 1 11.2944 -11.1064 0 0 0 0
|
||||
141 1 1 1 9.81375 -9.39538 0 0 0 0
|
||||
142 1 1 1 10.6117 -9.45297 0 0 0 0
|
||||
143 1 1 1 12.2075 -9.56813 0 0 0 0
|
||||
144 1 1 1 13.0054 -9.62572 0 0 0 0
|
||||
145 1 1 1 11.1414 2.36295 0 0 0 0
|
||||
146 1 1 1 11.582 0.824812 0 0 0 0
|
||||
147 1 1 1 11.3617 1.59388 0 0 0 0
|
||||
148 1 1 1 10.9211 3.13202 0 0 0 0
|
||||
149 1 1 1 10.7008 3.90109 0 0 0 0
|
||||
150 1 1 1 12.6795 2.80355 0 0 0 0
|
||||
151 1 1 1 11.9105 2.58325 0 0 0 0
|
||||
152 1 1 1 10.3723 2.14265 0 0 0 0
|
||||
153 1 1 1 9.60325 1.92235 0 0 0 0
|
||||
154 1 1 1 -0.718141 0.610732 0 0 0 0
|
||||
155 1 1 1 0.797274 0.0973944 0 0 0 0
|
||||
156 1 1 1 0.0395666 0.354063 0 0 0 0
|
||||
157 1 1 1 -1.47585 0.867401 0 0 0 0
|
||||
158 1 1 1 -2.23356 1.12407 0 0 0 0
|
||||
159 1 1 1 -0.204804 2.12615 0 0 0 0
|
||||
160 1 1 1 -0.461473 1.36844 0 0 0 0
|
||||
161 1 1 1 -0.97481 -0.146976 0 0 0 0
|
||||
162 1 1 1 -1.23148 -0.904684 0 0 0 0
|
||||
163 1 1 1 -8.64345 -0.12308 0 0 0 0
|
||||
164 1 1 1 -7.52017 1.01632 0 0 0 0
|
||||
165 1 1 1 -8.08181 0.446621 0 0 0 0
|
||||
166 1 1 1 -9.20509 -0.692781 0 0 0 0
|
||||
167 1 1 1 -9.76673 -1.26248 0 0 0 0
|
||||
168 1 1 1 -9.78285 1.0002 0 0 0 0
|
||||
169 1 1 1 -9.21315 0.438561 0 0 0 0
|
||||
170 1 1 1 -8.07375 -0.684721 0 0 0 0
|
||||
171 1 1 1 -7.50405 -1.24636 0 0 0 0
|
||||
172 1 1 1 -10.5175 7.98447 0 0 0 0
|
||||
173 1 1 1 -10.8363 6.41655 0 0 0 0
|
||||
174 1 1 1 -10.6769 7.20051 0 0 0 0
|
||||
175 1 1 1 -10.3581 8.76843 0 0 0 0
|
||||
176 1 1 1 -10.1987 9.55239 0 0 0 0
|
||||
177 1 1 1 -8.94958 7.66568 0 0 0 0
|
||||
178 1 1 1 -9.73354 7.82507 0 0 0 0
|
||||
179 1 1 1 -11.3015 8.14386 0 0 0 0
|
||||
180 1 1 1 -12.0854 8.30326 0 0 0 0
|
||||
181 1 1 1 7.4048 -0.393969 0 0 0 0
|
||||
182 1 1 1 6.13529 0.579859 0 0 0 0
|
||||
183 1 1 1 6.77004 0.0929451 0 0 0 0
|
||||
184 1 1 1 8.03955 -0.880882 0 0 0 0
|
||||
185 1 1 1 8.67431 -1.3678 0 0 0 0
|
||||
186 1 1 1 6.43097 -1.66348 0 0 0 0
|
||||
187 1 1 1 6.91789 -1.02872 0 0 0 0
|
||||
188 1 1 1 7.89171 0.240787 0 0 0 0
|
||||
189 1 1 1 8.37863 0.875543 0 0 0 0
|
||||
190 1 1 1 7.64402 5.65726 0 0 0 0
|
||||
191 1 1 1 6.07165 5.95329 0 0 0 0
|
||||
192 1 1 1 6.85784 5.80527 0 0 0 0
|
||||
193 1 1 1 8.43021 5.50925 0 0 0 0
|
||||
194 1 1 1 9.2164 5.36124 0 0 0 0
|
||||
195 1 1 1 7.348 4.08488 0 0 0 0
|
||||
196 1 1 1 7.49601 4.87107 0 0 0 0
|
||||
197 1 1 1 7.79204 6.44345 0 0 0 0
|
||||
198 1 1 1 7.94005 7.22964 0 0 0 0
|
||||
199 1 1 1 -4.4824 11.3315 0 0 0 0
|
||||
200 1 1 1 -4.43005 9.73232 0 0 0 0
|
||||
201 1 1 1 -4.45622 10.5319 0 0 0 0
|
||||
202 1 1 1 -4.50857 12.131 0 0 0 0
|
||||
203 1 1 1 -4.53475 12.9306 0 0 0 0
|
||||
204 1 1 1 -2.88326 11.3838 0 0 0 0
|
||||
205 1 1 1 -3.68283 11.3576 0 0 0 0
|
||||
206 1 1 1 -5.28197 11.3053 0 0 0 0
|
||||
207 1 1 1 -6.08154 11.2791 0 0 0 0
|
||||
208 1 1 1 -5.55606 -7.81186 0 0 0 0
|
||||
209 1 1 1 -3.99015 -7.48332 0 0 0 0
|
||||
210 1 1 1 -4.77311 -7.64759 0 0 0 0
|
||||
211 1 1 1 -6.33901 -7.97613 0 0 0 0
|
||||
212 1 1 1 -7.12196 -8.1404 0 0 0 0
|
||||
213 1 1 1 -5.8846 -6.24595 0 0 0 0
|
||||
214 1 1 1 -5.72033 -7.0289 0 0 0 0
|
||||
215 1 1 1 -5.39179 -8.59481 0 0 0 0
|
||||
216 1 1 1 -5.22752 -9.37776 0 0 0 0
|
||||
217 1 1 1 7.26016 -11.9863 0 0 0 0
|
||||
218 1 1 1 8.3079 -13.1956 0 0 0 0
|
||||
219 1 1 1 7.78403 -12.591 0 0 0 0
|
||||
220 1 1 1 6.73629 -11.3817 0 0 0 0
|
||||
221 1 1 1 6.21242 -10.7771 0 0 0 0
|
||||
222 1 1 1 8.46939 -10.9386 0 0 0 0
|
||||
223 1 1 1 7.86477 -11.4625 0 0 0 0
|
||||
224 1 1 1 6.65554 -12.5102 0 0 0 0
|
||||
225 1 1 1 6.05093 -13.0341 0 0 0 0
|
||||
226 1 1 1 -1.57791 -12.9126 0 0 0 0
|
||||
227 1 1 1 -0.216128 12.8343 0 0 -1 0
|
||||
228 1 1 1 -0.89702 13.2543 0 0 -1 0
|
||||
229 1 1 1 -2.2588 -12.4926 0 0 0 0
|
||||
230 1 1 1 -2.9397 -12.0726 0 0 0 0
|
||||
231 1 1 1 -0.737944 -11.5508 0 0 0 0
|
||||
232 1 1 1 -1.15793 -12.2317 0 0 0 0
|
||||
233 1 1 1 -1.9979 12.9934 0 0 -1 0
|
||||
234 1 1 1 -2.41788 12.3125 0 0 -1 0
|
||||
235 1 1 1 -11.3551 -5.31209 0 0 0 0
|
||||
236 1 1 1 -11.6961 -6.87533 0 0 0 0
|
||||
237 1 1 1 -11.5256 -6.09371 0 0 0 0
|
||||
238 1 1 1 -11.1846 -4.53047 0 0 0 0
|
||||
239 1 1 1 -11.0141 -3.74885 0 0 0 0
|
||||
240 1 1 1 -9.79187 -5.65308 0 0 0 0
|
||||
241 1 1 1 -10.5735 -5.48258 0 0 0 0
|
||||
242 1 1 1 -12.1367 -5.14159 0 0 0 0
|
||||
243 1 1 1 -12.9184 -4.9711 0 0 0 0
|
||||
244 1 1 1 -7.57077 2.60641 0 0 0 0
|
||||
245 1 1 1 -6.41133 1.50381 0 0 0 0
|
||||
246 1 1 1 -6.99105 2.05511 0 0 0 0
|
||||
247 1 1 1 -8.15048 3.1577 0 0 0 0
|
||||
248 1 1 1 -8.7302 3.709 0 0 0 0
|
||||
249 1 1 1 -6.46817 3.76584 0 0 0 0
|
||||
250 1 1 1 -7.01947 3.18612 0 0 0 0
|
||||
251 1 1 1 -8.12206 2.02669 0 0 0 0
|
||||
252 1 1 1 -8.67336 1.44697 0 0 0 0
|
||||
253 1 1 1 -3.24788 -4.3784 0 0 0 0
|
||||
254 1 1 1 -4.74604 -4.94009 0 0 0 0
|
||||
255 1 1 1 -3.99696 -4.65924 0 0 0 0
|
||||
256 1 1 1 -2.4988 -4.09755 0 0 0 0
|
||||
257 1 1 1 -1.74971 -3.8167 0 0 0 0
|
||||
258 1 1 1 -2.68619 -5.87656 0 0 0 0
|
||||
259 1 1 1 -2.96703 -5.12748 0 0 0 0
|
||||
260 1 1 1 -3.52873 -3.62931 0 0 0 0
|
||||
261 1 1 1 -3.80957 -2.88023 0 0 0 0
|
||||
262 1 1 1 -1.84958 -5.88762 0 0 0 0
|
||||
263 1 1 1 -0.343461 -5.34761 0 0 0 0
|
||||
264 1 1 1 -1.09652 -5.61762 0 0 0 0
|
||||
265 1 1 1 -2.60264 -6.15763 0 0 0 0
|
||||
266 1 1 1 -3.3557 -6.42763 0 0 0 0
|
||||
267 1 1 1 -2.38959 -4.38151 0 0 0 0
|
||||
268 1 1 1 -2.11958 -5.13456 0 0 0 0
|
||||
269 1 1 1 -1.57957 -6.64068 0 0 0 0
|
||||
270 1 1 1 -1.30957 -7.39374 0 0 0 0
|
||||
|
||||
Molecules
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 2
|
||||
11 2
|
||||
12 2
|
||||
13 2
|
||||
14 2
|
||||
15 2
|
||||
16 2
|
||||
17 2
|
||||
18 2
|
||||
19 3
|
||||
20 3
|
||||
21 3
|
||||
22 3
|
||||
23 3
|
||||
24 3
|
||||
25 3
|
||||
26 3
|
||||
27 3
|
||||
28 4
|
||||
29 4
|
||||
30 4
|
||||
31 4
|
||||
32 4
|
||||
33 4
|
||||
34 4
|
||||
35 4
|
||||
36 4
|
||||
37 5
|
||||
38 5
|
||||
39 5
|
||||
40 5
|
||||
41 5
|
||||
42 5
|
||||
43 5
|
||||
44 5
|
||||
45 5
|
||||
46 6
|
||||
47 6
|
||||
48 6
|
||||
49 6
|
||||
50 6
|
||||
51 6
|
||||
52 6
|
||||
53 6
|
||||
54 6
|
||||
55 7
|
||||
56 7
|
||||
57 7
|
||||
58 7
|
||||
59 7
|
||||
60 7
|
||||
61 7
|
||||
62 7
|
||||
63 7
|
||||
64 8
|
||||
65 8
|
||||
66 8
|
||||
67 8
|
||||
68 8
|
||||
69 8
|
||||
70 8
|
||||
71 8
|
||||
72 8
|
||||
73 9
|
||||
74 9
|
||||
75 9
|
||||
76 9
|
||||
77 9
|
||||
78 9
|
||||
79 9
|
||||
80 9
|
||||
81 9
|
||||
82 10
|
||||
83 10
|
||||
84 10
|
||||
85 10
|
||||
86 10
|
||||
87 10
|
||||
88 10
|
||||
89 10
|
||||
90 10
|
||||
91 11
|
||||
92 11
|
||||
93 11
|
||||
94 11
|
||||
95 11
|
||||
96 11
|
||||
97 11
|
||||
98 11
|
||||
99 11
|
||||
100 12
|
||||
101 12
|
||||
102 12
|
||||
103 12
|
||||
104 12
|
||||
105 12
|
||||
106 12
|
||||
107 12
|
||||
108 12
|
||||
109 13
|
||||
110 13
|
||||
111 13
|
||||
112 13
|
||||
113 13
|
||||
114 13
|
||||
115 13
|
||||
116 13
|
||||
117 13
|
||||
118 14
|
||||
119 14
|
||||
120 14
|
||||
121 14
|
||||
122 14
|
||||
123 14
|
||||
124 14
|
||||
125 14
|
||||
126 14
|
||||
127 15
|
||||
128 15
|
||||
129 15
|
||||
130 15
|
||||
131 15
|
||||
132 15
|
||||
133 15
|
||||
134 15
|
||||
135 15
|
||||
136 16
|
||||
137 16
|
||||
138 16
|
||||
139 16
|
||||
140 16
|
||||
141 16
|
||||
142 16
|
||||
143 16
|
||||
144 16
|
||||
145 17
|
||||
146 17
|
||||
147 17
|
||||
148 17
|
||||
149 17
|
||||
150 17
|
||||
151 17
|
||||
152 17
|
||||
153 17
|
||||
154 18
|
||||
155 18
|
||||
156 18
|
||||
157 18
|
||||
158 18
|
||||
159 18
|
||||
160 18
|
||||
161 18
|
||||
162 18
|
||||
163 19
|
||||
164 19
|
||||
165 19
|
||||
166 19
|
||||
167 19
|
||||
168 19
|
||||
169 19
|
||||
170 19
|
||||
171 19
|
||||
172 20
|
||||
173 20
|
||||
174 20
|
||||
175 20
|
||||
176 20
|
||||
177 20
|
||||
178 20
|
||||
179 20
|
||||
180 20
|
||||
181 21
|
||||
182 21
|
||||
183 21
|
||||
184 21
|
||||
185 21
|
||||
186 21
|
||||
187 21
|
||||
188 21
|
||||
189 21
|
||||
190 22
|
||||
191 22
|
||||
192 22
|
||||
193 22
|
||||
194 22
|
||||
195 22
|
||||
196 22
|
||||
197 22
|
||||
198 22
|
||||
199 23
|
||||
200 23
|
||||
201 23
|
||||
202 23
|
||||
203 23
|
||||
204 23
|
||||
205 23
|
||||
206 23
|
||||
207 23
|
||||
208 24
|
||||
209 24
|
||||
210 24
|
||||
211 24
|
||||
212 24
|
||||
213 24
|
||||
214 24
|
||||
215 24
|
||||
216 24
|
||||
217 25
|
||||
218 25
|
||||
219 25
|
||||
220 25
|
||||
221 25
|
||||
222 25
|
||||
223 25
|
||||
224 25
|
||||
225 25
|
||||
226 26
|
||||
227 26
|
||||
228 26
|
||||
229 26
|
||||
230 26
|
||||
231 26
|
||||
232 26
|
||||
233 26
|
||||
234 26
|
||||
235 27
|
||||
236 27
|
||||
237 27
|
||||
238 27
|
||||
239 27
|
||||
240 27
|
||||
241 27
|
||||
242 27
|
||||
243 27
|
||||
244 28
|
||||
245 28
|
||||
246 28
|
||||
247 28
|
||||
248 28
|
||||
249 28
|
||||
250 28
|
||||
251 28
|
||||
252 28
|
||||
253 29
|
||||
254 29
|
||||
255 29
|
||||
256 29
|
||||
257 29
|
||||
258 29
|
||||
259 29
|
||||
260 29
|
||||
261 29
|
||||
262 30
|
||||
263 30
|
||||
264 30
|
||||
265 30
|
||||
266 30
|
||||
267 30
|
||||
268 30
|
||||
269 30
|
||||
270 30
|
||||
|
|
@ -0,0 +1,107 @@
|
|||
# SRD diffusion demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
|
||||
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
|
||||
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
|
|
@ -0,0 +1,108 @@
|
|||
# SRD viscosity demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
|
||||
set type 1 mass 1.0
|
||||
group big type 1
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
create_atoms 2 region plane
|
||||
|
||||
set type 2 mass 0.1
|
||||
group small type 2
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 &
|
||||
search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press &
|
||||
f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] &
|
||||
f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star.mp
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
|
|
@ -0,0 +1,289 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# SRD diffusion demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
orthogonal box = (-13.2934 -13.2934 -0.5) to (13.2934 13.2934 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
270 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
270 settings made for mass
|
||||
group big type 1
|
||||
270 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 2.64859 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0.24721146
|
||||
100 0 3.291475 0 3.291475 0.69158089
|
||||
200 0 4.6176595 0 4.6176595 0.71737945
|
||||
300 0 7.0921814 0 7.0921814 1.2163497
|
||||
400 0 8.3666709 0 8.3666709 0.50645957
|
||||
500 0 10.630838 0 10.630838 0.72764487
|
||||
600 0 12.42157 0 12.42157 1.0130599
|
||||
700 0 14.349074 0 14.349074 0.74795509
|
||||
800 0 16.464746 0 16.464746 1.054549
|
||||
900 0 18.253108 0 18.253108 0.51551753
|
||||
1000 0 20.699563 0 20.699563 1.8084662
|
||||
Loop time of 0.0416153 on 8 procs for 1000 steps with 270 atoms
|
||||
|
||||
Pair time (%) = 0.0029633 (7.1207)
|
||||
Neigh time (%) = 0.0011363 (2.73049)
|
||||
Comm time (%) = 0.0124508 (29.9187)
|
||||
Outpt time (%) = 0.000216633 (0.520561)
|
||||
Other time (%) = 0.0248483 (59.7095)
|
||||
|
||||
Nlocal: 33.75 ave 42 max 22 min
|
||||
Histogram: 1 0 1 0 0 2 0 1 1 2
|
||||
Nghost: 23.375 ave 30 max 14 min
|
||||
Histogram: 1 0 1 0 0 2 1 0 1 2
|
||||
Neighs: 52.25 ave 69 max 27 min
|
||||
Histogram: 1 0 1 0 1 0 1 1 1 2
|
||||
|
||||
Total # of neighbors = 418
|
||||
Ave neighs/atom = 1.54815
|
||||
Neighbor list builds = 176
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 2 region plane
|
||||
Created 60025 atoms
|
||||
|
||||
set type 2 mass 0.1
|
||||
60025 settings made for mass
|
||||
group small type 2
|
||||
60025 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
Deleted 16305 atoms, new total = 43990
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 43720 270
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 106 106 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250819 0.250819 1
|
||||
SRD per actual grid cell = 5.55866
|
||||
SRD viscosity = 0.235582
|
||||
big/SRD mass density ratio = 0.144099
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.19085 7.72582
|
||||
ave/max big velocity = 2.20262 5.4168
|
||||
Memory usage per processor = 7.45056 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.0984098 8760 0.22959363 37.227755 37.406755 4.3729461 14167 62 62 0 669 57680 11236 8760 0.95903221 0 5 0
|
||||
2000 1.0937022 8791 0.22965168 37.237979 37.416212 7.8592382 14199 47 47 0 1473 57680 11236 8791 0.95561013 0 5 0
|
||||
3000 1.1301744 8765 0.2296652 37.234239 37.418416 5.3554554 14104 54 54 0 2227 57680 11236 8765 0.95555673 0 66 0
|
||||
4000 1.2329006 8777 0.22959864 37.206654 37.407571 5.1494579 14604 63 64 0 2969 57680 11236 8777 0.94949717 0 66 0
|
||||
5000 1.3436586 8795 0.22951427 37.174858 37.393824 4.9830237 14523 57 57 0 3769 57680 11236 8795 0.94626627 0 66 0
|
||||
6000 0.96282041 8788 0.2292679 37.196781 37.353685 9.3973109 14421 62 62 0 4513 57680 11236 8788 0.95152148 0 66 0
|
||||
7000 0.89525926 8774 0.22909802 37.180113 37.326007 8.4919264 14263 54 54 0 5313 57680 11236 8774 0.94362657 0 66 0
|
||||
8000 1.3407703 8787 0.22948792 37.171035 37.389531 6.3302799 14065 49 50 0 6028 57680 11236 8787 0.94436375 0 66 0
|
||||
9000 0.89298676 8784 0.22897425 37.160318 37.305842 13.249825 14496 65 65 0 6784 57680 11236 8784 0.94156932 0 66 0
|
||||
10000 1.5075857 8760 0.22964883 37.170068 37.415749 7.706417 14096 59 59 0 7527 57680 11236 8760 0.94760815 0 66 0
|
||||
11000 1.0507595 8786 0.22915291 37.163716 37.334951 8.0764539 14302 54 54 0 8226 57680 11236 8786 0.93676874 0 66 0
|
||||
12000 1.3608191 8795 0.22938389 37.150819 37.372582 2.2906149 14425 51 51 0 8956 57680 11236 8795 0.94320409 0 66 0
|
||||
13000 1.1201602 8776 0.22932315 37.180142 37.362687 10.481998 14229 55 55 0 9648 57680 11236 8776 0.9397721 0 66 0
|
||||
14000 1.0716401 8784 0.22905315 37.144059 37.318697 10.138958 14141 62 62 0 10352 57680 11236 8784 0.93554357 0 66 0
|
||||
15000 1.1025268 8756 0.22896359 37.124434 37.304105 7.6249828 14017 64 64 0 11073 57680 11236 8756 0.9430112 0 66 0
|
||||
16000 1.2846996 8791 0.22918958 37.131566 37.340925 11.973123 14082 61 61 0 11827 57680 11236 8791 0.93833228 0 66 0
|
||||
17000 1.1023602 8737 0.2290447 37.137676 37.31732 7.2599397 14077 70 70 0 12530 57680 11236 8737 0.94839589 0 66 0
|
||||
18000 1.1254832 8791 0.22887219 37.105801 37.289213 7.7429889 14028 67 67 0 13240 57680 11236 8791 0.93873361 0 66 0
|
||||
19000 1.0356983 8772 0.22904086 37.147914 37.316694 4.5522757 14010 66 66 0 13931 57680 11236 8772 0.93790841 0 66 0
|
||||
20000 0.71316343 8764 0.22873892 37.151281 37.2675 10.416168 14258 60 60 0 14615 57680 11236 8764 0.95207188 0 66 0
|
||||
21000 1.2373277 8776 0.22921948 37.144157 37.345796 4.5997765 14160 43 43 0 15364 57680 11236 8776 0.94242444 0 66 0
|
||||
22000 1.0036835 8717 0.22912507 37.166851 37.330414 9.6600309 14147 49 49 0 16148 57680 11236 8717 0.94673443 0 66 0
|
||||
23000 1.2216081 8747 0.22929851 37.159594 37.358671 7.9846293 13938 71 71 0 16835 57680 11236 8747 0.94804999 0 66 0
|
||||
24000 1.0032568 8793 0.22911586 37.16542 37.328913 0.60601362 14202 73 73 1 17576 57680 11236 8793 0.9414152 0 66 0
|
||||
25000 0.94965 8781 0.22909875 37.171368 37.326126 6.6584192 14261 59 59 0 18287 57680 11236 8781 0.93110924 0 66 0
|
||||
26000 1.4038862 8770 0.22955552 37.171764 37.400545 6.9399909 14168 53 53 0 18961 57680 11236 8770 0.94165291 0 66 0
|
||||
27000 1.0373393 8771 0.22927442 37.1857 37.354748 10.125555 13921 59 59 0 19684 57680 11236 8771 0.94374269 0 66 0
|
||||
28000 1.0969388 8771 0.22909362 37.146529 37.32529 6.7985501 13965 58 58 0 20453 57680 11236 8771 0.94053206 0 66 0
|
||||
29000 1.2684633 8750 0.22920667 37.136996 37.343709 9.8044908 14008 63 63 0 21157 57680 11236 8750 0.94469514 0 66 0
|
||||
30000 1.0723854 8771 0.22897873 37.131813 37.306572 7.2792401 14057 58 58 0 21801 57680 11236 8771 0.92857754 0 66 0
|
||||
31000 0.82971683 8763 0.22857114 37.104952 37.240165 7.7873396 13798 55 55 1 22447 57680 11236 8763 0.93260855 0 66 0
|
||||
32000 1.1854057 8768 0.22894391 37.107721 37.300898 4.2769411 13933 61 62 0 23177 57680 11236 8768 0.94159224 0 66 0
|
||||
33000 1.0436865 8772 0.22886047 37.117222 37.287304 6.2761906 13923 54 54 0 23961 57680 11236 8772 0.93663695 0 66 0
|
||||
34000 1.2387476 8768 0.229117 37.12723 37.3291 11.376966 14008 55 56 0 24671 57680 11236 8768 0.94134637 0 66 0
|
||||
35000 1.1827221 8777 0.22892611 37.105258 37.297998 2.5334458 14032 46 46 0 25359 57680 11236 8777 0.94278115 0 66 0
|
||||
36000 1.0401004 8786 0.22881254 37.109997 37.279495 10.60278 14096 59 59 0 26064 57680 11236 8786 0.93296672 0 66 0
|
||||
37000 1.0984228 8766 0.22869539 37.081405 37.260407 6.8054601 13808 69 69 0 26726 57680 11236 8766 0.93400815 0 66 0
|
||||
38000 1.0364646 8774 0.22857543 37.071959 37.240864 7.1036604 13800 63 63 0 27340 57680 11236 8774 0.93085761 0 66 0
|
||||
39000 0.81230064 8747 0.22852596 37.100428 37.232803 3.2521293 13917 52 52 0 28006 57680 11236 8747 0.92853969 0 66 0
|
||||
40000 1.1721059 8805 0.2288046 37.087192 37.278202 3.0925306 14118 65 65 0 28641 57680 11236 8805 0.93248575 0 66 0
|
||||
41000 1.3273673 8777 0.22903004 37.098619 37.314931 4.5511385 13847 60 60 0 29306 57680 11236 8777 0.93520024 0 66 0
|
||||
42000 1.1052507 8745 0.22888354 37.110948 37.291063 9.2630606 13743 55 55 0 29968 57680 11236 8745 0.93879074 0 66 0
|
||||
43000 0.98143573 8767 0.22866451 37.095439 37.255377 10.836032 14161 50 50 1 30636 57680 11236 8767 0.94242574 0 66 0
|
||||
44000 1.3073559 8766 0.22888363 37.078026 37.291077 7.1037959 13988 64 64 0 31356 57680 11236 8766 0.93251181 0 66 0
|
||||
45000 1.1193942 8794 0.22872075 37.082121 37.264541 10.640442 14106 64 64 0 32030 57680 11236 8794 0.92767399 0 66 0
|
||||
46000 0.97836443 8770 0.22871232 37.10373 37.263167 7.1768889 13999 46 46 0 32724 57680 11236 8770 0.92348771 0 66 0
|
||||
47000 0.87384342 8766 0.22838593 37.067584 37.209988 8.2743957 13966 59 59 1 33415 57680 11236 8766 0.94605663 0 66 0
|
||||
48000 1.1247625 8737 0.22881404 37.096444 37.279739 7.4933665 13890 58 58 0 34188 57680 11236 8737 0.94564485 0 66 0
|
||||
49000 0.97549128 8760 0.22903868 37.15737 37.316339 9.212114 13731 61 61 3 35188 57680 11236 8760 0.94181244 0 264 0
|
||||
50000 0.84795594 8792 0.22864062 37.113299 37.251484 4.554655 14066 45 45 0 35891 57680 11236 8792 0.9394553 0 264 0
|
||||
51000 1.2748335 8793 0.22896977 37.097361 37.305111 9.6671568 13935 65 65 0 36612 57680 11236 8793 0.93487065 0 264 0
|
||||
52000 1.0805373 8810 0.2285793 37.065407 37.241495 6.8776416 13980 67 67 0 37272 57680 11236 8810 0.9367572 0 264 0
|
||||
53000 1.130649 8761 0.22862734 37.065067 37.249321 2.7290713 13926 49 49 0 37929 57680 11236 8761 0.93655185 0 264 0
|
||||
54000 1.0591847 8785 0.22882065 37.108209 37.280816 6.3873447 13895 50 50 0 38580 57680 11236 8785 0.93515717 0 264 0
|
||||
55000 1.0652496 8787 0.22845918 37.048328 37.221924 8.4260372 13975 45 45 0 39233 57680 11236 8787 0.94125089 0 264 0
|
||||
56000 0.98336412 8817 0.22838409 37.049438 37.20969 5.2198817 14164 53 53 0 39880 57680 11236 8817 0.93411507 0 264 0
|
||||
57000 0.75643143 8772 0.22818592 37.054132 37.177402 6.3608331 13531 46 46 0 40586 57680 11236 8772 0.93676316 0 264 0
|
||||
58000 0.96052993 8787 0.22863449 37.093956 37.250486 5.3118075 13591 69 69 0 41316 57680 11236 8787 0.94694416 0 264 0
|
||||
59000 1.192266 8791 0.22843725 37.024055 37.21835 8.4075315 13670 69 69 0 42042 57680 11236 8791 0.93074428 0 264 0
|
||||
60000 0.86528129 8763 0.22838246 37.068415 37.209423 12.614127 13944 56 56 0 42742 57680 11236 8763 0.93980863 0 264 0
|
||||
61000 0.98392057 8781 0.22850911 37.069716 37.230059 4.1196257 13833 55 55 0 43466 57680 11236 8781 0.94055519 0 264 0
|
||||
62000 0.86377638 8769 0.22825891 37.048531 37.189294 7.5952438 13732 55 55 0 44157 57680 11236 8769 0.93273238 0 264 0
|
||||
63000 1.1345544 8753 0.2285473 37.05139 37.23628 8.4944082 13829 39 39 1 44853 57680 11236 8753 0.93637828 0 264 0
|
||||
64000 1.3052001 8761 0.22872188 37.052025 37.264725 8.1141027 13693 56 56 0 45476 57680 11236 8761 0.92802715 0 264 0
|
||||
65000 0.96041617 8760 0.22837135 37.051102 37.207614 8.9305096 13696 47 47 0 46161 57680 11236 8760 0.93690077 0 264 0
|
||||
66000 1.2667968 8773 0.22874931 37.062752 37.269193 7.0070038 13795 53 53 0 46873 57680 11236 8773 0.93548723 0 264 0
|
||||
67000 1.1041556 8805 0.22867835 37.077695 37.257632 10.315126 13719 53 53 0 47611 57680 11236 8805 0.93398934 0 264 0
|
||||
68000 1.0634591 8756 0.22833079 37.027701 37.201005 11.004387 13805 52 52 0 48261 57680 11236 8756 0.93907878 0 264 0
|
||||
69000 1.0634356 8759 0.22836391 37.033101 37.206402 7.8960556 13846 60 60 0 48930 57680 11236 8759 0.9387394 0 264 0
|
||||
70000 0.78705939 8797 0.22815713 37.044451 37.172712 5.2268623 13886 55 55 1 49637 57680 11236 8797 0.94420106 0 264 0
|
||||
71000 1.262646 8796 0.22836767 37.001249 37.207013 4.2192091 13984 55 55 0 50380 57680 11236 8796 0.93354313 0 264 0
|
||||
72000 0.89288469 8767 0.22793751 36.991423 37.13693 7.5274353 13402 48 48 0 51044 57680 11236 8767 0.93651002 0 264 0
|
||||
73000 0.99805643 8785 0.22794231 36.975066 37.137712 8.1692078 13647 61 61 0 51713 57680 11236 8785 0.92710476 0 264 0
|
||||
74000 1.1316546 8797 0.22823421 37.000852 37.18527 8.475577 13702 70 70 0 52408 57680 11236 8797 0.93300949 0 264 0
|
||||
75000 1.3589973 8782 0.22842134 36.994292 37.215758 5.4899759 13846 62 62 0 53038 57680 11236 8782 0.92968164 0 264 0
|
||||
76000 0.98311155 8765 0.22810013 37.003215 37.163426 5.8491632 13396 50 50 0 53737 57680 11236 8765 0.9332015 0 264 0
|
||||
77000 0.93588923 8768 0.22812976 37.015736 37.168252 6.1482719 13419 41 41 0 54440 57680 11236 8768 0.94649087 0 264 0
|
||||
78000 1.0726273 8763 0.22814803 36.996431 37.171229 3.7413229 13652 53 53 0 55122 57680 11236 8763 0.93732834 0 264 0
|
||||
79000 1.1142622 8747 0.22823701 37.004143 37.185727 5.3431863 13752 52 52 0 55788 57680 11236 8747 0.94102654 0 264 0
|
||||
80000 1.1877489 8777 0.22804997 36.961694 37.155253 7.5892699 13821 65 65 1 56474 57680 11236 8777 0.9388659 0 264 0
|
||||
81000 1.5174205 8789 0.22848952 36.979583 37.226866 8.2338826 13400 58 58 0 57138 57680 11236 8789 0.93859931 0 264 0
|
||||
82000 1.011418 8763 0.22816534 37.009225 37.174048 5.9285277 13389 53 53 0 57882 57680 11236 8763 0.94017606 0 264 0
|
||||
83000 1.048045 8774 0.22802349 36.980145 37.150938 1.7682458 13617 62 62 0 58587 57680 11236 8774 0.93181775 0 264 0
|
||||
84000 1.0416932 8791 0.22815029 37.00184 37.171598 1.6650384 13546 60 60 0 59277 57680 11236 8791 0.93336422 0 264 0
|
||||
85000 0.9808074 8785 0.22805209 36.995762 37.155597 5.3853011 13847 58 58 0 59941 57680 11236 8785 0.93675898 0 264 0
|
||||
86000 0.94845236 8741 0.22819508 37.024332 37.178894 9.0236195 13483 53 53 0 60569 57680 11236 8741 0.94106832 0 264 0
|
||||
87000 0.91367557 8761 0.22814468 37.021789 37.170684 2.0373865 13627 46 46 0 61240 57680 11236 8761 0.93526035 0 264 0
|
||||
88000 1.1199914 8786 0.22824582 37.004644 37.187161 12.508533 13835 61 61 0 61903 57680 11236 8786 0.93075967 0 264 0
|
||||
89000 1.1170348 8766 0.2282638 37.008056 37.190092 3.3612922 13599 53 53 0 62539 57680 11236 8766 0.93937123 0 264 0
|
||||
90000 0.80168936 8787 0.22787344 36.995845 37.126491 5.447793 14009 70 70 0 63231 57680 11236 8787 0.92972768 0 264 0
|
||||
91000 0.9278704 8748 0.22800786 36.997183 37.148392 6.9490954 13577 51 51 0 63973 57680 11236 8748 0.93217751 0 264 0
|
||||
92000 0.89936733 8761 0.22813535 37.0226 37.169164 2.7999912 13491 55 55 0 64685 57680 11236 8761 0.93392714 0 264 0
|
||||
93000 0.97509746 8750 0.22824406 37.027971 37.186875 7.5849958 13569 62 62 0 65443 57680 11236 8750 0.94168102 0 264 0
|
||||
94000 1.1704849 8741 0.22814395 36.979819 37.170565 7.3998451 13706 71 71 0 66141 57680 11236 8741 0.94474366 0 264 0
|
||||
95000 0.82884583 8779 0.22780742 36.980663 37.115734 4.1939749 13606 60 60 0 66881 57680 11236 8779 0.93030745 0 264 0
|
||||
96000 1.1004846 8783 0.22820868 37.001772 37.18111 9.7475128 13650 50 50 0 67644 57680 11236 8783 0.93134822 0 264 0
|
||||
97000 0.88396347 8767 0.22799895 37.002887 37.146941 1.417848 13564 54 54 0 68384 57680 11236 8767 0.93526241 0 264 0
|
||||
98000 1.0540322 8782 0.22821568 37.010483 37.182251 6.0103183 13539 51 51 0 69056 57680 11236 8782 0.94045268 0 264 0
|
||||
99000 0.87480326 8776 0.22814014 37.027383 37.169944 9.727466 13663 45 45 0 69714 57680 11236 8776 0.92949266 0 264 0
|
||||
100000 1.0188288 8799 0.22832221 37.033577 37.199608 5.6127459 13731 57 57 1 70429 57680 11236 8799 0.92271662 0 264 0
|
||||
Loop time of 40.6233 on 8 procs for 100000 steps with 43990 atoms
|
||||
|
||||
Pair time (%) = 0.442836 (1.0901)
|
||||
Neigh time (%) = 2.10093 (5.17173)
|
||||
Comm time (%) = 2.34834 (5.78077)
|
||||
Outpt time (%) = 0.00742877 (0.0182869)
|
||||
Other time (%) = 35.7238 (87.9391)
|
||||
|
||||
Nlocal: 5498.75 ave 6220 max 4960 min
|
||||
Histogram: 1 1 2 0 0 2 1 0 0 1
|
||||
Nghost: 57.25 ave 82 max 41 min
|
||||
Histogram: 1 1 1 1 2 1 0 0 0 1
|
||||
Neighs: 214.5 ave 270 max 148 min
|
||||
Histogram: 1 0 1 0 2 1 0 1 1 1
|
||||
|
||||
Total # of neighbors = 1716
|
||||
Ave neighs/atom = 0.0390089
|
||||
Neighbor list builds = 5001
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,290 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# SRD viscosity demo - rigid star particles
|
||||
|
||||
units lj
|
||||
atom_style sphere
|
||||
atom_modify map array first big
|
||||
dimension 2
|
||||
|
||||
# read in clusters of rigid bodies
|
||||
|
||||
fix molprop all property/atom mol
|
||||
read_data data.star fix molprop NULL Molecules
|
||||
orthogonal box = (-13.2934 -13.2934 -0.5) to (13.2934 13.2934 0.5)
|
||||
4 by 2 by 1 MPI processor grid
|
||||
270 atoms
|
||||
|
||||
set type 1 mass 1.0
|
||||
270 settings made for mass
|
||||
group big type 1
|
||||
270 atoms in group big
|
||||
velocity big create 1.44 87287 loop geom
|
||||
|
||||
# equilibrate big particles
|
||||
|
||||
pair_style soft 1.12
|
||||
pair_coeff 1 1 0.0
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 1 2 0.0 0.0
|
||||
|
||||
variable prefactor equal ramp(0,60)
|
||||
fix soft all adapt 1 pair soft a * * v_prefactor
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 10 dump.star.equil
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 2.64859 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0.24721146
|
||||
100 0 3.291475 0 3.291475 0.69158089
|
||||
200 0 4.6176595 0 4.6176595 0.71737945
|
||||
300 0 7.0921814 0 7.0921814 1.2163497
|
||||
400 0 8.3666709 0 8.3666709 0.50645957
|
||||
500 0 10.630838 0 10.630838 0.72764487
|
||||
600 0 12.42157 0 12.42157 1.0130599
|
||||
700 0 14.349074 0 14.349074 0.74795509
|
||||
800 0 16.464746 0 16.464746 1.054549
|
||||
900 0 18.253108 0 18.253108 0.51551753
|
||||
1000 0 20.699563 0 20.699563 1.8084662
|
||||
Loop time of 0.0412866 on 8 procs for 1000 steps with 270 atoms
|
||||
|
||||
Pair time (%) = 0.00292179 (7.07684)
|
||||
Neigh time (%) = 0.00114384 (2.77049)
|
||||
Comm time (%) = 0.0121986 (29.5461)
|
||||
Outpt time (%) = 0.000230491 (0.558271)
|
||||
Other time (%) = 0.0247919 (60.0483)
|
||||
|
||||
Nlocal: 33.75 ave 42 max 22 min
|
||||
Histogram: 1 0 1 0 0 2 0 1 1 2
|
||||
Nghost: 23.375 ave 30 max 14 min
|
||||
Histogram: 1 0 1 0 0 2 1 0 1 2
|
||||
Neighs: 52.25 ave 69 max 27 min
|
||||
Histogram: 1 0 1 0 1 0 1 1 1 2
|
||||
|
||||
Total # of neighbors = 418
|
||||
Ave neighs/atom = 1.54815
|
||||
Neighbor list builds = 176
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
unfix soft
|
||||
unfix 1
|
||||
unfix 2
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
region plane block INF INF INF INF -0.001 0.001 units box
|
||||
lattice sq 85.0
|
||||
Lattice spacing in x,y,z = 0.108465 0.108465 0.108465
|
||||
create_atoms 2 region plane
|
||||
Created 60025 atoms
|
||||
|
||||
set type 2 mass 0.1
|
||||
60025 settings made for mass
|
||||
group small type 2
|
||||
60025 atoms in group small
|
||||
velocity small create 1.0 593849 loop geom
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.5
|
||||
|
||||
delete_atoms overlap 0.5 small big
|
||||
Deleted 16305 atoms, new total = 43990
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule
|
||||
30 rigid bodies with 270 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 shift yes 54979 search 0.2 collision slip inside ignore overlap yes
|
||||
fix 3 small viscosity 10 x y 50
|
||||
fix 4 all enforce2d
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tbig big temp/sphere
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
thermo_style custom step temp f_2[8] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[7] f_2[8] f_2[9] f_2[10] f_2[11] f_2[12]
|
||||
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 1000 dump.star.mp
|
||||
|
||||
#dump 1 all image 1000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 1 pad 6 adiam 1 1 adiam 2 0.2
|
||||
|
||||
run 100000
|
||||
SRD info:
|
||||
SRD/big particles = 43720 270
|
||||
big particle diameter max/min = 1 1
|
||||
SRD temperature & lamda = 1 0.0632456
|
||||
SRD max distance & max velocity = 0.252982 12.6491
|
||||
SRD grid counts: 106 106 1
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.250819 0.250819 1
|
||||
SRD per actual grid cell = 5.55866
|
||||
SRD viscosity = 0.235582
|
||||
big/SRD mass density ratio = 0.144099
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 4.19085 7.72582
|
||||
ave/max big velocity = 2.20262 5.4168
|
||||
Memory usage per processor = 7.45056 Mbytes
|
||||
Step Temp 2[8] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[7] 2[8] 2[9] 2[10] 2[11] 2[12]
|
||||
0 18.299191 0 0.25067776 37.859815 40.841906 5.7680841 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1000 1.3539178 8799 0.22973169 37.20861 37.429248 8.3072473 14385 67 67 0 702 57680 11236 8799 0.95931141 0 5 0
|
||||
2000 1.2875571 8786 0.22962726 37.202411 37.412235 9.0311119 14352 63 63 0 1486 57680 11236 8786 0.95682025 0 5 0
|
||||
3000 1.4635416 8800 0.22966317 37.179581 37.418084 7.6178929 14347 59 59 0 2196 57680 11236 8800 0.94729431 0 18 0
|
||||
4000 1.8391551 8777 0.23015947 37.19923 37.498945 7.5387929 14212 56 56 0 2970 57680 11236 8777 0.94642004 0 18 0
|
||||
5000 1.3981894 8787 0.22973225 37.201487 37.42934 10.658161 14071 73 73 0 3812 57680 11236 8787 0.93244985 0 18 0
|
||||
6000 1.8148662 8786 0.2299516 37.169321 37.465077 10.11004 14154 56 56 0 4599 57680 11236 8786 0.93899702 0 18 0
|
||||
7000 1.7370183 8781 0.22991739 37.176433 37.459503 7.2981594 14125 55 55 2 5380 57680 11236 8781 0.92819844 0 18 0
|
||||
8000 1.9300809 8795 0.23020743 37.192227 37.506758 5.6733717 14193 51 51 0 6183 57680 11236 8795 0.92508922 0 18 0
|
||||
9000 2.3407111 8779 0.23065831 37.19877 37.580219 10.534106 13966 79 79 0 7043 57680 11236 8779 0.93227329 0 18 0
|
||||
10000 2.0762631 8753 0.23046098 37.209714 37.548068 6.6085525 13608 49 49 0 7866 57680 11236 8753 0.9277773 0 18 0
|
||||
11000 2.5572041 8760 0.23079582 37.185893 37.602623 5.943323 14038 51 51 0 8706 57680 11236 8760 0.92846928 0 18 0
|
||||
12000 3.2543217 8768 0.23146345 37.181063 37.711397 9.9600818 13725 58 58 0 9496 57680 11236 8768 0.92510656 0 18 0
|
||||
13000 3.7220943 8755 0.23214107 37.215236 37.821799 5.2998459 13527 58 58 1 10369 57680 11236 8755 0.92701985 0 18 0
|
||||
14000 3.1074163 8758 0.23124062 37.168698 37.675092 3.597723 13761 58 58 0 11200 57680 11236 8758 0.91892834 0 18 0
|
||||
15000 4.1027548 8760 0.23230435 37.179805 37.848402 6.0772754 13862 51 51 0 12079 57680 11236 8760 0.92753237 0 18 0
|
||||
16000 3.9133946 8792 0.23219659 37.193106 37.830844 4.7112711 13660 43 43 0 12960 57680 11236 8792 0.92647491 0 18 0
|
||||
17000 4.0903593 8765 0.2323981 37.197098 37.863675 10.318145 13986 61 61 0 13879 57680 11236 8765 0.92733119 0 18 0
|
||||
18000 3.969582 8737 0.23252501 37.237457 37.884352 6.0345677 13738 47 47 0 14857 57680 11236 8737 0.93210731 0 18 0
|
||||
19000 4.9135942 8764 0.23344004 37.232701 38.033435 9.0068701 14001 46 47 0 15797 57680 11236 8764 0.92417719 0 18 0
|
||||
20000 4.4990499 8726 0.23308081 37.241729 37.974907 3.4556204 14032 43 43 0 16823 57680 11236 8726 0.92968267 0 18 0
|
||||
21000 3.6775519 8760 0.23209383 37.214798 37.814103 8.7361012 14249 51 51 0 17880 57680 11236 8760 0.91693857 0 18 0
|
||||
22000 4.2480058 8760 0.23234702 37.163086 37.855353 9.4990008 13676 60 60 0 18840 57680 11236 8760 0.92912888 0 18 0
|
||||
23000 4.0762282 8757 0.23194558 37.125675 37.789949 6.095072 13433 60 60 0 19854 57680 11236 8757 0.93403257 0 18 0
|
||||
24000 3.7342162 8754 0.23149433 37.107889 37.716428 8.0963071 13528 45 45 0 20844 57680 11236 8754 0.92640554 0 18 0
|
||||
25000 4.4320691 8738 0.23214598 37.100336 37.822599 2.6532327 13621 47 47 0 21927 57680 11236 8738 0.91696074 0 18 0
|
||||
26000 4.739874 8795 0.2328463 37.164276 37.9367 6.0740527 13737 55 55 0 22931 57680 11236 8795 0.91601272 0 18 0
|
||||
27000 4.158987 8759 0.23253846 37.208783 37.886544 7.8062033 13770 68 68 0 23891 57680 11236 8759 0.92761375 0 18 0
|
||||
28000 4.5357507 8729 0.23252995 37.145997 37.885157 8.3229496 13735 62 62 0 24911 57680 11236 8729 0.91438776 0 18 0
|
||||
29000 5.2763283 8757 0.23343081 37.172085 38.031931 11.607728 13345 56 56 0 25962 57680 11236 8757 0.92363255 0 18 0
|
||||
30000 5.2012183 8727 0.23342066 37.182671 38.030276 7.0247835 13553 56 56 0 27017 57680 11236 8727 0.92161183 0 18 0
|
||||
31000 4.5592454 8768 0.23267999 37.166615 37.909603 5.0184914 13886 58 58 0 28054 57680 11236 8768 0.92601626 0 18 0
|
||||
32000 4.2038581 8767 0.23226731 37.157293 37.842366 7.7446627 13776 66 66 0 29191 57680 11236 8767 0.92081307 0 18 0
|
||||
33000 3.4146018 8766 0.23184673 37.217389 37.773843 6.061227 13762 60 60 0 30282 57680 11236 8766 0.91467148 0 18 0
|
||||
34000 4.9666166 8768 0.23362817 37.254711 38.064085 4.54391 13794 57 57 0 31277 57680 11236 8768 0.91500925 0 18 0
|
||||
35000 5.4336125 8772 0.23410227 37.255851 38.141329 7.1441975 13991 54 54 0 32372 57680 11236 8772 0.91787825 0 18 0
|
||||
36000 5.3731031 8775 0.23399853 37.24881 38.124427 10.645457 14200 61 61 0 33353 57680 11236 8775 0.9068932 0 18 0
|
||||
37000 4.6930013 8756 0.23342164 37.265652 38.030437 1.6378965 13904 58 58 0 34474 57680 11236 8756 0.91857412 0 18 0
|
||||
38000 4.6072618 8770 0.23383244 37.346553 38.097366 3.4294948 13897 52 52 0 35614 57680 11236 8770 0.93119652 0 18 0
|
||||
39000 6.3083841 8755 0.23513182 37.281037 38.30907 9.545092 13877 71 72 0 36775 57680 11236 8755 0.90357387 0 18 0
|
||||
40000 4.7439426 8760 0.23359501 37.285596 38.058683 5.2222395 13722 59 59 0 37862 57680 11236 8760 0.92609151 0 18 0
|
||||
41000 5.631049 8746 0.23426434 37.250081 38.167734 7.8831121 13871 58 58 0 38995 57680 11236 8746 0.92364048 0 18 0
|
||||
42000 4.4937786 8763 0.23315762 37.255102 37.987422 6.0814276 14059 56 56 0 40128 57680 11236 8763 0.90560182 0 18 0
|
||||
43000 4.6349594 8738 0.23340275 37.272032 38.027359 6.4946772 13789 60 60 0 41304 57680 11236 8738 0.92056988 0 18 0
|
||||
44000 4.9216105 8770 0.23378718 37.287952 38.089993 12.069456 14010 60 60 0 42438 57680 11236 8770 0.90919838 0 18 0
|
||||
45000 6.1003723 8742 0.23518324 37.323312 38.317447 8.8564785 14012 51 51 0 43588 57680 11236 8742 0.91297931 0 18 0
|
||||
46000 5.9976719 8739 0.23513128 37.331584 38.308982 10.332623 13865 61 61 0 44701 57680 11236 8739 0.91184414 0 18 0
|
||||
47000 5.7529929 8750 0.2346755 37.297198 38.234722 9.1421763 13767 53 53 0 45947 57680 11236 8750 0.91644332 0 18 0
|
||||
48000 6.0414916 8782 0.23481097 37.272255 38.256795 4.11784 14101 67 67 0 47098 57680 11236 8782 0.91322689 0 18 0
|
||||
49000 5.9069569 8751 0.234598 37.259482 38.222097 6.2678445 13866 52 52 0 48288 57680 11236 8751 0.9146273 0 18 0
|
||||
50000 5.3699426 8774 0.23420718 37.28332 38.158422 4.9995799 14096 57 57 0 49368 57680 11236 8774 0.91397612 0 18 0
|
||||
51000 5.3951124 8767 0.23440907 37.312111 38.191314 7.0908474 13687 58 58 0 50615 57680 11236 8767 0.91626012 0 18 0
|
||||
52000 5.0477469 8746 0.23402296 37.305812 38.128407 5.8280874 13914 56 56 1 51790 57680 11236 8746 0.91904159 0 18 0
|
||||
53000 5.0027801 8755 0.23400414 37.310073 38.125341 10.739261 14129 57 57 0 52949 57680 11236 8755 0.92315612 0 18 0
|
||||
54000 5.4679296 8761 0.23459667 37.330809 38.221879 6.8113028 13993 46 46 0 54120 57680 11236 8761 0.92267151 0 18 0
|
||||
55000 5.8410648 8761 0.23461213 37.272522 38.224399 3.5247967 13976 71 71 0 55365 57680 11236 8761 0.91123977 0 18 0
|
||||
56000 5.3206693 8766 0.23418385 37.287548 38.15462 5.6396887 14038 55 55 0 56521 57680 11236 8766 0.93368011 0 18 0
|
||||
57000 4.9281952 8780 0.23366116 37.266348 38.069461 3.1285423 13969 56 56 0 57638 57680 11236 8780 0.92255818 0 18 0
|
||||
58000 5.1613227 8756 0.23347937 37.198737 38.039842 7.6464505 13934 63 63 0 58773 57680 11236 8756 0.92220195 0 18 0
|
||||
59000 5.1076252 8756 0.23352166 37.214379 38.046732 7.5306693 13817 62 62 0 59943 57680 11236 8756 0.92510594 0 18 0
|
||||
60000 5.6556257 8746 0.23422971 37.240434 38.162092 2.9325607 13922 53 53 0 61090 57680 11236 8746 0.91834472 0 18 0
|
||||
61000 5.5661669 8773 0.23411882 37.236947 38.144026 7.2514093 13945 49 49 0 62183 57680 11236 8773 0.90739365 0 18 0
|
||||
62000 5.8495975 8753 0.23460373 37.269763 38.223031 7.0060167 13970 46 46 0 63299 57680 11236 8753 0.91634009 0 18 0
|
||||
63000 6.6712653 8759 0.23570628 37.315495 38.402664 8.3394411 13579 50 50 0 64393 57680 11236 8759 0.91836652 0 18 0
|
||||
64000 6.0479009 8746 0.23472337 37.256939 38.242522 4.8644232 13733 53 53 0 65627 57680 11236 8746 0.92355966 0 18 0
|
||||
65000 6.3822214 8746 0.23478129 37.211894 38.25196 7.7582836 13738 49 49 1 66686 57680 11236 8746 0.92230762 0 18 0
|
||||
66000 5.8364524 8749 0.23463571 37.277114 38.22824 9.5192708 13699 60 60 0 67818 57680 11236 8749 0.91792656 0 18 0
|
||||
67000 5.9827412 8758 0.23439358 37.213826 38.188792 10.337844 13706 40 40 0 68985 57680 11236 8758 0.9224571 0 18 0
|
||||
68000 5.7052083 8778 0.23427038 37.238981 38.168719 9.538817 14045 50 50 0 70137 57680 11236 8778 0.92678095 0 18 0
|
||||
69000 6.1907575 8732 0.23509559 37.294303 38.303167 7.8570847 13753 63 63 0 71368 57680 11236 8732 0.92864702 0 18 0
|
||||
70000 6.7558311 8741 0.23548884 37.266287 38.367237 8.165295 13734 48 48 0 72588 57680 11236 8741 0.92931286 0 18 0
|
||||
71000 6.3006829 8768 0.23498477 37.258334 38.285112 6.6049258 13846 56 56 0 73691 57680 11236 8768 0.92696341 0 18 0
|
||||
72000 7.2727152 8763 0.23598161 37.262339 38.447522 10.51197 13841 84 84 0 74864 57680 11236 8763 0.91909538 0 18 0
|
||||
73000 6.2312628 8782 0.23498109 37.269046 38.284511 7.4903877 13965 75 75 0 76071 57680 11236 8782 0.91794598 0 18 0
|
||||
74000 6.1722061 8727 0.23506951 37.293076 38.298917 4.3305249 13792 46 46 0 77240 57680 11236 8727 0.91814755 0 18 0
|
||||
75000 7.378049 8773 0.23590581 37.232824 38.435173 6.3355081 13923 52 52 0 78535 57680 11236 8773 0.91995009 0 18 0
|
||||
76000 7.812152 8740 0.23641193 37.244542 38.517633 8.9619859 13779 53 53 0 79829 57680 11236 8740 0.92788947 0 18 0
|
||||
77000 7.2456022 8750 0.23586328 37.247479 38.428244 8.4006134 13766 58 58 0 81069 57680 11236 8750 0.92890367 0 18 0
|
||||
78000 7.4885209 8762 0.2360823 37.243575 38.463927 4.8584808 13818 63 63 0 82265 57680 11236 8762 0.91978471 0 18 0
|
||||
79000 6.768778 8758 0.23523283 37.222466 38.325526 9.2798759 13853 46 46 1 83493 57680 11236 8758 0.92133736 0 18 0
|
||||
80000 6.2390912 8778 0.23501251 37.27289 38.28963 8.066911 13895 54 54 1 84665 57680 11236 8778 0.92327324 0 36 0
|
||||
81000 7.2711702 8787 0.23608324 37.279149 38.46408 9.2144197 13806 65 66 0 85828 57680 11236 8787 0.92188232 0 36 0
|
||||
82000 6.0206472 8744 0.2350438 37.313587 38.294729 9.3897281 13820 56 56 1 87015 57680 11236 8744 0.92698133 0 36 0
|
||||
83000 5.8815517 8770 0.23423001 37.203666 38.162142 4.3928971 13962 52 52 0 88169 57680 11236 8770 0.9234476 0 36 0
|
||||
84000 5.3127425 8753 0.23338022 37.157909 38.023689 6.2750977 13890 63 63 1 89381 57680 11236 8753 0.91831133 0 113 0
|
||||
85000 6.4943314 8779 0.2346802 37.177153 38.235488 10.568493 14079 72 72 1 90614 57680 11236 8779 0.92206389 0 113 0
|
||||
86000 6.7895778 8751 0.2350697 37.192498 38.298948 5.9925063 13835 77 77 0 91790 57680 11236 8751 0.91712004 0 113 0
|
||||
87000 7.5845758 8746 0.23586106 37.191877 38.427882 5.7337473 13766 56 56 0 93001 57680 11236 8746 0.92432006 0 113 0
|
||||
88000 6.9933387 8797 0.23528814 37.194883 38.334538 6.5123227 14127 64 64 1 94309 57680 11236 8797 0.92081946 0 113 0
|
||||
89000 7.2164543 8789 0.23569422 37.224684 38.400699 7.3516314 13831 57 57 0 95527 57680 11236 8789 0.91778416 0 113 0
|
||||
90000 6.3777786 8760 0.23511292 37.266649 38.305991 5.0520629 13961 55 55 0 96763 57680 11236 8760 0.9262025 0 113 0
|
||||
91000 5.9805319 8742 0.23465699 37.257103 38.231708 8.0050839 13761 53 53 0 97921 57680 11236 8742 0.9261716 0 113 0
|
||||
92000 6.4485837 8784 0.23547302 37.313779 38.36466 6.6770663 13723 39 39 0 99103 57680 11236 8784 0.9291658 0 113 0
|
||||
93000 6.4434559 8749 0.23487177 37.216656 38.2667 5.7028222 13637 50 50 0 100312 57680 11236 8749 0.92621809 0 113 0
|
||||
94000 6.1854322 8759 0.23477076 37.242246 38.250243 10.130767 14009 68 69 0 101529 57680 11236 8759 0.92239553 0 113 0
|
||||
95000 5.242726 8764 0.23388878 37.252175 38.106545 10.741635 14033 58 58 0 102596 57680 11236 8764 0.91894338 0 113 0
|
||||
96000 5.4946819 8770 0.23425506 37.270793 38.166223 2.1154106 13710 56 56 0 103697 57680 11236 8770 0.93225466 0 113 0
|
||||
97000 6.253365 8759 0.23501257 37.270573 38.28964 9.0479264 13591 66 66 0 104831 57680 11236 8759 0.93238386 0 113 0
|
||||
98000 6.1587546 8755 0.2348896 37.265956 38.269605 10.461501 13914 41 41 1 105983 57680 11236 8755 0.92076121 0 113 0
|
||||
99000 5.5267342 8780 0.23419291 37.255444 38.156097 4.2845395 14016 58 58 0 107118 57680 11236 8780 0.9233616 0 113 0
|
||||
100000 5.355333 8734 0.23420455 37.285273 38.157994 8.6683443 14028 58 58 1 108173 57680 11236 8734 0.92043276 0 113 0
|
||||
Loop time of 41.1602 on 8 procs for 100000 steps with 43990 atoms
|
||||
|
||||
Pair time (%) = 0.416294 (1.0114)
|
||||
Neigh time (%) = 2.09636 (5.09318)
|
||||
Comm time (%) = 2.34013 (5.68543)
|
||||
Outpt time (%) = 0.00730702 (0.0177526)
|
||||
Other time (%) = 36.3001 (88.1922)
|
||||
|
||||
Nlocal: 5498.75 ave 6126 max 4805 min
|
||||
Histogram: 1 0 2 0 0 1 1 1 1 1
|
||||
Nghost: 54.375 ave 61 max 45 min
|
||||
Histogram: 1 1 0 1 0 0 2 0 1 2
|
||||
Neighs: 185.25 ave 270 max 112 min
|
||||
Histogram: 1 0 2 1 1 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1482
|
||||
Ave neighs/atom = 0.0336895
|
||||
Neighbor list builds = 5000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,11 @@
|
|||
# create set of randomly oriented stars
|
||||
|
||||
p = patch(0.2)
|
||||
p.dim = 2
|
||||
p.extratype = 1
|
||||
p.style = "sphere"
|
||||
p.extra = "Molecules"
|
||||
p.seed = 5932894
|
||||
#p.seed = 54321
|
||||
p.build(30,"star2d",5,0.8,1)
|
||||
p.write("data.star")
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,105 @@
|
|||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style tri
|
||||
atom_modify first big
|
||||
|
||||
read_data data.tri.srd
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
lattice sc 0.4
|
||||
region box block INF INF INF INF INF INF
|
||||
lattice sc 20.0
|
||||
create_atoms 2 region box
|
||||
|
||||
group big type 1
|
||||
group small type 2
|
||||
set group small mass 0.01
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
|
||||
delete_atoms overlap 1.5 small big
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
velocity small create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule big include big
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style tri/lj 3.5
|
||||
pair_coeff 1 1 0.1 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip
|
||||
|
||||
fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step f_1 c_tsmall f_2[9] temp press
|
||||
thermo_modify temp tbig
|
||||
|
||||
compute 10 all property/atom corner1x corner1y corner1z &
|
||||
corner2x corner2y corner2z corner3x corner3y corner3z
|
||||
|
||||
#dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump1.tri.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] &
|
||||
# c_10[7] c_10[8] c_10[9]
|
||||
|
||||
run 10000
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 &
|
||||
search 0.2 cubic warn 0.0001 shift yes 49829 &
|
||||
overlap yes collision noslip tstat yes
|
||||
|
||||
#dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
#dump 2 all custom 500 dump2.tri.srd id type &
|
||||
# c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] &
|
||||
# c_10[7] c_10[8] c_10[9]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
|
||||
run 40000
|
||||
|
|
@ -0,0 +1,242 @@
|
|||
LAMMPS (9 Sep 2013)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style tri
|
||||
atom_modify first big
|
||||
|
||||
read_data data.tri.srd
|
||||
orthogonal box = (-8.43734 -8.43734 -8.43734) to (8.43734 8.43734 8.43734)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
1500 atoms
|
||||
1500 triangles
|
||||
|
||||
# add small particles as hi density lattice
|
||||
|
||||
lattice sc 0.4
|
||||
Lattice spacing in x,y,z = 1.35721 1.35721 1.35721
|
||||
region box block INF INF INF INF INF INF
|
||||
lattice sc 20.0
|
||||
Lattice spacing in x,y,z = 0.368403 0.368403 0.368403
|
||||
create_atoms 2 region box
|
||||
Created 91125 atoms
|
||||
|
||||
group big type 1
|
||||
1500 atoms in group big
|
||||
group small type 2
|
||||
91125 atoms in group small
|
||||
set group small mass 0.01
|
||||
91125 settings made for mass
|
||||
|
||||
# delete overlaps
|
||||
# must set 1-2 cutoff to non-zero value
|
||||
|
||||
pair_style lj/cut 1.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0
|
||||
|
||||
delete_atoms overlap 1.5 small big
|
||||
Deleted 76354 atoms, new total = 16271
|
||||
|
||||
# SRD run
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
velocity small create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude molecule big include big
|
||||
|
||||
communicate multi group big vel yes
|
||||
neigh_modify include big
|
||||
|
||||
# no pairwise interactions with small particles
|
||||
|
||||
pair_style tri/lj 3.5
|
||||
pair_coeff 1 1 0.1 1.0
|
||||
pair_coeff 2 2 0.0 1.0 0.0
|
||||
pair_coeff 1 2 0.0 1.0 0.0
|
||||
|
||||
# use fix SRD to push small particles out from inside big ones
|
||||
# if comment out, big particles won't see SRD particles
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 big rigid molecule #langevin 1.0 1.0 0.1 12398
|
||||
125 rigid bodies with 1500 atoms
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip
|
||||
|
||||
fix 3 all deform 1 x scale 0.6 y scale 0.6 z scale 0.6
|
||||
|
||||
# diagnostics
|
||||
|
||||
compute tsmall small temp/deform
|
||||
compute tbig big temp
|
||||
variable pebig equal pe*atoms/count(big)
|
||||
variable ebig equal etotal*atoms/count(big)
|
||||
|
||||
compute 1 big erotate/asphere
|
||||
compute 2 all ke
|
||||
compute 3 all pe
|
||||
variable toteng equal (c_1+c_2+c_3)/atoms
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step f_1 c_tsmall f_2[9] temp press
|
||||
thermo_modify temp tbig
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:438)
|
||||
|
||||
compute 10 all property/atom corner1x corner1y corner1z corner2x corner2y corner2z corner3x corner3y corner3z
|
||||
|
||||
dump 1 all custom 500 dump1.atom.srd id type x y z ix iy iz
|
||||
dump 2 all custom 500 dump1.tri.srd id type c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] c_10[7] c_10[8] c_10[9]
|
||||
|
||||
run 10000
|
||||
WARNING: Using fix srd with box deformation but no SRD thermostat (../fix_srd.cpp:385)
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 1.46014 0.436602
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 67 67 67
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.251861 0.251861 0.251861
|
||||
SRD per actual grid cell = 0.0647662
|
||||
SRD viscosity = -1.09837
|
||||
big/SRD mass density ratio = 24.668
|
||||
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2737)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2761)
|
||||
# of rescaled SRD velocities = 0
|
||||
ave/max small velocity = 19.9708 35.1504
|
||||
ave/max big velocity = 0 0
|
||||
WARNING: Using compute temp/deform with inconsistent fix deform remap option (../compute_temp_deform.cpp:76)
|
||||
Memory usage per processor = 112.926 Mbytes
|
||||
Step 1 tsmall 2[9] Temp Press
|
||||
0 0 1.4405441 0 0 -0.15917996
|
||||
1000 1.0535509 1.1241378 0.030778612 0 0.15526438
|
||||
2000 2.4635987 1.0240667 0.031199432 0 0.011069846
|
||||
3000 3.1093028 1.0070585 0.0412299 0 0.34124887
|
||||
4000 2.9091229 1.0109332 0.042413338 0 -0.43067212
|
||||
5000 3.143486 1.007502 0.047871105 0 0.44935703
|
||||
6000 3.3117859 1.0031975 0.060884331 0 -0.17753945
|
||||
7000 3.7329968 0.99472569 0.071341886 0 1.4727109
|
||||
8000 4.0314822 1.0148882 0.089434073 0 6.3915959
|
||||
9000 6.3667017 1.0144773 0.10558433 0 14.945841
|
||||
10000 14.065219 1.0159965 0.11784659 0 131.62736
|
||||
Loop time of 229.245 on 8 procs for 10000 steps with 16271 atoms
|
||||
|
||||
Pair time (%) = 142.296 (62.0717)
|
||||
Neigh time (%) = 33.5162 (14.6203)
|
||||
Comm time (%) = 44.4642 (19.396)
|
||||
Outpt time (%) = 0.822778 (0.358909)
|
||||
Other time (%) = 8.14531 (3.55311)
|
||||
|
||||
Nlocal: 2033.88 ave 2131 max 1886 min
|
||||
Histogram: 1 0 0 1 0 1 2 1 1 1
|
||||
Nghost: 2777.38 ave 2813 max 2734 min
|
||||
Histogram: 2 0 1 0 0 0 2 0 0 3
|
||||
Neighs: 30097.6 ave 35599 max 25702 min
|
||||
Histogram: 3 0 0 1 0 1 0 1 1 1
|
||||
|
||||
Total # of neighbors = 240781
|
||||
Ave neighs/atom = 14.7982
|
||||
Neighbor list builds = 500
|
||||
Dangerous builds = 0
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
unfix 3
|
||||
|
||||
change_box all triclinic
|
||||
triclinic box = (-5.0624 -5.0624 -5.0624) to (5.0624 5.0624 5.0624) with tilt (0 0 0)
|
||||
|
||||
fix 2 small srd 20 big 1.0 0.25 49894 search 0.2 cubic warn 0.0001 shift yes 49829 overlap yes collision noslip tstat yes
|
||||
|
||||
dump 1 all custom 500 dump2.atom.srd id type x y z ix iy iz
|
||||
dump 2 all custom 500 dump2.tri.srd id type c_10[1] c_10[2] c_10[3] c_10[4] c_10[5] c_10[6] c_10[7] c_10[8] c_10[9]
|
||||
|
||||
fix 3 all deform 1 xy erate 0.05 units box remap v
|
||||
|
||||
run 40000
|
||||
SRD info:
|
||||
SRD/big particles = 14771 1500
|
||||
big particle diameter max/min = 1.46014 0.436602
|
||||
SRD temperature & lamda = 1 0.2
|
||||
SRD max distance & max velocity = 0.8 40
|
||||
SRD grid counts: 40 40 40
|
||||
SRD grid size: request, actual (xyz) = 0.25, 0.25312 0.25312 0.25312
|
||||
SRD per actual grid cell = -1.93929
|
||||
SRD viscosity = -0.36972
|
||||
big/SRD mass density ratio = -0.836253
|
||||
WARNING: SRD bin size for fix srd differs from user request (../fix_srd.cpp:2737)
|
||||
WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2759)
|
||||
WARNING: Fix srd viscosity < 0.0 due to low SRD density (../fix_srd.cpp:2761)
|
||||
# of rescaled SRD velocities = 2
|
||||
ave/max small velocity = 16.086 40
|
||||
ave/max big velocity = 1.89008 7.06443
|
||||
Memory usage per processor = 67.8409 Mbytes
|
||||
Step 1 tsmall 2[9] Temp Press
|
||||
10000 14.065219 1.0159841 0 0 125.62369
|
||||
11000 15.89949 1.1021294 0.13432606 0 79.756722
|
||||
12000 13.591974 1.0986468 0.14491966 0 69.017912
|
||||
13000 10.672662 1.0974608 0.13980161 0 68.47417
|
||||
14000 10.433124 1.0970815 0.13358543 0 63.921726
|
||||
15000 11.350239 1.0919622 0.13501392 0 56.434986
|
||||
16000 9.9440024 1.0909392 0.13733839 0 60.312203
|
||||
17000 8.8069504 1.0862993 0.1331224 0 60.673373
|
||||
18000 9.7454087 1.0874377 0.14030315 0 55.359223
|
||||
19000 8.7467828 1.0955594 0.13826168 0 58.135899
|
||||
20000 9.094869 1.0853936 0.13980748 0 54.918577
|
||||
21000 8.1769632 1.0877609 0.13527913 0 59.779335
|
||||
22000 8.4802311 1.0874158 0.14097292 0 55.518841
|
||||
23000 8.5085635 1.0938995 0.13479334 0 52.444531
|
||||
24000 7.7708574 1.093106 0.13843648 0 53.619874
|
||||
25000 7.5891864 1.0892977 0.1309956 0 50.959157
|
||||
26000 7.1595504 1.0943558 0.1313863 0 50.73602
|
||||
27000 6.4924522 1.0932486 0.13264833 0 50.620315
|
||||
28000 6.8555436 1.0956448 0.1395996 0 53.675344
|
||||
29000 7.0391394 1.0867312 0.14199161 0 53.493952
|
||||
30000 7.9245188 1.0927432 0.13348801 0 50.474831
|
||||
31000 8.1045132 1.0932086 0.13605758 0 48.830305
|
||||
32000 8.3316171 1.0984609 0.13978578 0 48.671107
|
||||
33000 7.3537207 1.0866232 0.13800293 0 49.619075
|
||||
34000 7.5646404 1.0762414 0.1282765 0 48.104248
|
||||
35000 7.6598613 1.0988043 0.1399969 0 48.344193
|
||||
36000 8.2985234 1.0927025 0.13712115 0 51.995955
|
||||
37000 7.8266025 1.0986061 0.13590656 0 55.526454
|
||||
38000 8.1374325 1.0908854 0.1356955 0 51.766017
|
||||
39000 7.1742247 1.0867582 0.13871443 0 54.475644
|
||||
40000 7.1327095 1.0873612 0.13361669 0 53.584849
|
||||
41000 7.4393759 1.083626 0.13678989 0 52.190793
|
||||
42000 7.1145295 1.0867999 0.13910883 0 56.760468
|
||||
43000 7.1195706 1.1052677 0.14404153 0 58.427514
|
||||
44000 7.9713656 1.0931625 0.13568773 0 58.026623
|
||||
45000 7.9875631 1.0928839 0.13617383 0 60.495025
|
||||
46000 8.7377452 1.0927309 0.14312311 0 62.011464
|
||||
47000 8.5499453 1.0941412 0.13203028 0 64.3929
|
||||
48000 8.6633515 1.0929638 0.14189189 0 58.671573
|
||||
49000 8.6567883 1.0832134 0.1353634 0 54.667636
|
||||
50000 7.9400691 1.0942958 0.13789637 0 58.089009
|
||||
Loop time of 1633.43 on 8 procs for 40000 steps with 16271 atoms
|
||||
|
||||
Pair time (%) = 1201.96 (73.5851)
|
||||
Neigh time (%) = 184.862 (11.3174)
|
||||
Comm time (%) = 188.22 (11.523)
|
||||
Outpt time (%) = 3.30344 (0.202239)
|
||||
Other time (%) = 55.0837 (3.37226)
|
||||
|
||||
Nlocal: 2033.88 ave 2156 max 1952 min
|
||||
Histogram: 2 1 0 1 1 0 2 0 0 1
|
||||
Nghost: 2752.38 ave 2941 max 2567 min
|
||||
Histogram: 1 0 1 0 2 2 0 1 0 1
|
||||
Neighs: 30128.1 ave 38439 max 23335 min
|
||||
Histogram: 1 0 1 2 2 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 241025
|
||||
Ave neighs/atom = 14.8132
|
||||
Neighbor list builds = 2002
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
# create set of randomly oriented tri boxes
|
||||
|
||||
p = patch(0.05)
|
||||
|
||||
p.seed = 54321
|
||||
p.dim = 3
|
||||
p.extratype = 1
|
||||
p.lattice = [5,5,5]
|
||||
|
||||
p.build(125,"tribox",0.5,2,0.5,2,0.5,2,1)
|
||||
|
||||
p.write("data.tri.srd")
|
||||
|
||||
print "all done ... type CTRL-D to exit Pizza.py"
|
||||
|
|
@ -0,0 +1,18 @@
|
|||
# Pizza.py viz of triangle + SRD output
|
||||
|
||||
d = dump("dump1.atom.srd dump2.atom.srd")
|
||||
t = tdump("dump1.tri.srd dump2.tri.srd")
|
||||
t.map(1,"id",2,"type",
|
||||
3,"corner1x",4,"corner1y",5,"corner1z",
|
||||
6,"corner2x",7,"corner2y",8,"corner2z",
|
||||
9,"corner3x",10,"corner3y",11,"corner3z")
|
||||
d.extra(t)
|
||||
|
||||
g = gl(d)
|
||||
g.arad(1,0.02)
|
||||
g.acol(1,"green")
|
||||
|
||||
g.arad(2,0.05)
|
||||
g.acol(2,"green")
|
||||
|
||||
v = vcr(g)
|
||||
|
|
@ -109,6 +109,12 @@ create a GIF file suitable for viewing in a browser.
|
|||
|
||||
Upper-case directories
|
||||
|
||||
The ASPHERE directory has examples of how to model aspherical
|
||||
particles with or without solvent, in 3 styles LAMMPS provides.
|
||||
Namely point ellipsoids, rigid bodies, and generalized aspherical
|
||||
bodies built from line/triangle surface facets in 2d/3d. See the
|
||||
ASPHERE/README file to get started.
|
||||
|
||||
The COUPLE directory has examples of how to use LAMMPS as a library,
|
||||
either by itself or in tandem with another code or library. See the
|
||||
COUPLE/README file to get started.
|
||||
|
|
|
|||
Loading…
Reference in New Issue