git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10748 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
412
examples/ASPHERE/dimer/data.dimer
Normal file
412
examples/ASPHERE/dimer/data.dimer
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@ -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
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||||
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
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||||
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
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||||
125 1 1 1 1.38027 -6.51875 0 0 0 0
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||||
126 1 1 1 2.11513 -6.83494 0 0 0 0
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||||
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
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||||
148 1 1 1 8.10445 6.14443 0 0 0 0
|
||||
149 1 1 1 0.639774 -8.90856 0 0 0 0
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||||
150 1 1 1 0.110051 -8.30906 0 0 0 0
|
||||
151 1 1 1 2.68553 -3.09643 0 0 0 0
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||||
152 1 1 1 3.19558 -3.71275 0 0 0 0
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||||
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
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||||
162 1 1 1 9.33046 2.45406 0 -1 0 0
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||||
163 1 1 1 -1.13608 0.273721 0 0 0 0
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||||
164 1 1 1 -1.75716 0.777961 0 0 0 0
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||||
165 1 1 1 -8.80553 -4.13121 0 0 0 0
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||||
166 1 1 1 -8.64169 -4.91425 0 0 0 0
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||||
167 1 1 1 1.65687 8.8975 0 0 0 0
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||||
168 1 1 1 1.65839 -8.9858 0 0 1 0
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||||
169 1 1 1 8.36746 2.59565 0 0 0 0
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||||
170 1 1 1 9.06956 2.21219 0 0 0 0
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||||
171 1 1 1 -5.98437 -7.01768 0 0 0 0
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||||
172 1 1 1 -5.34019 -6.5433 0 0 0 0
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||||
173 1 1 1 -4.08999 -4.58535 0 0 0 0
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||||
174 1 1 1 -3.50681 -5.13298 0 0 0 0
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||||
175 1 1 1 4.12068 -2.66213 0 0 0 0
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||||
176 1 1 1 4.47739 -3.3782 0 0 0 0
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||||
177 1 1 1 -8.21813 3.61652 0 0 0 0
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||||
178 1 1 1 -7.83713 4.31997 0 0 0 0
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||||
179 1 1 1 5.3708 8.01903 0 0 0 0
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||||
180 1 1 1 4.66332 8.39249 0 0 0 0
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||||
181 1 1 1 -7.99312 -7.49248 0 0 0 0
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182 1 1 1 -7.40112 -8.03055 0 0 0 0
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183 1 1 1 6.52577 7.66337 0 0 0 0
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184 1 1 1 5.74291 7.49865 0 0 0 0
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185 1 1 1 -1.68136 9.16388 0 0 0 0
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186 1 1 1 -1.62497 8.36587 0 0 0 0
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187 1 1 1 -9.06593 -8.69211 0 0 0 0
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188 1 1 1 9.24439 -7.98438 0 -1 0 0
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189 1 1 1 -1.84034 8.97585 0 0 0 0
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190 1 1 1 -1.22441 8.46534 0 0 0 0
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191 1 1 1 -2.52855 7.20926 0 0 0 0
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192 1 1 1 -3.32354 7.11991 0 0 0 0
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193 1 1 1 2.00449 3.54871 0 0 0 0
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194 1 1 1 1.4845 4.15666 0 0 0 0
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195 1 1 1 5.6526 -1.31637 0 0 0 0
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196 1 1 1 4.86095 -1.43166 0 0 0 0
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197 1 1 1 -6.41619 3.12674 0 0 0 0
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198 1 1 1 -6.93879 3.73245 0 0 0 0
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199 1 1 1 -4.38345 -4.37207 0 0 0 0
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200 1 1 1 -3.84213 -4.96112 0 0 0 0
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Molecules
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1 1
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2 1
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3 2
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4 2
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5 3
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6 3
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7 4
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8 4
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9 5
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10 5
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11 6
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12 6
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13 7
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14 7
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15 8
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16 8
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17 9
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18 9
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19 10
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20 10
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21 11
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22 11
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23 12
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24 12
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25 13
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26 13
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27 14
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28 14
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29 15
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30 15
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31 16
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32 16
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33 17
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34 17
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35 18
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36 18
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37 19
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38 19
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39 20
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40 20
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41 21
|
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42 21
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43 22
|
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44 22
|
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45 23
|
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46 23
|
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47 24
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48 24
|
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49 25
|
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50 25
|
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51 26
|
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52 26
|
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53 27
|
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54 27
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55 28
|
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56 28
|
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57 29
|
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58 29
|
||||
59 30
|
||||
60 30
|
||||
61 31
|
||||
62 31
|
||||
63 32
|
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64 32
|
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65 33
|
||||
66 33
|
||||
67 34
|
||||
68 34
|
||||
69 35
|
||||
70 35
|
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71 36
|
||||
72 36
|
||||
73 37
|
||||
74 37
|
||||
75 38
|
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76 38
|
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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
|
||||
10
examples/ASPHERE/dimer/dimer.py
Normal file
10
examples/ASPHERE/dimer/dimer.py
Normal file
@ -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")
|
||||
104
examples/ASPHERE/dimer/in.dimer
Normal file
104
examples/ASPHERE/dimer/in.dimer
Normal file
@ -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
|
||||
105
examples/ASPHERE/dimer/in.dimer.mp
Normal file
105
examples/ASPHERE/dimer/in.dimer.mp
Normal file
@ -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
|
||||
285
examples/ASPHERE/dimer/log.dimer.10Sep13
Normal file
285
examples/ASPHERE/dimer/log.dimer.10Sep13
Normal file
@ -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
|
||||
|
||||
236
examples/ASPHERE/dimer/log.dimer.mp.10Sep13
Normal file
236
examples/ASPHERE/dimer/log.dimer.mp.10Sep13
Normal file
@ -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
|
||||
|
||||
Reference in New Issue
Block a user