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update kolmogorov-crespi examples

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This commit is contained in:
Axel Kohlmeyer
2018-03-22 19:42:07 -04:00
parent 8de7c449fc
commit c398eb6b57
11 changed files with 131 additions and 570 deletions
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266
examples/USER/misc/kolmogorov_crespi/data.bilayer-graphene
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@ -1,266 +0,0 @@
info: xyz2data 18:31, Mon 27-02-2017
256 atoms
2 atom types
0.00000000 17.04000000 xlo xhi
0.00000000 19.67609717 ylo yhi
-20.00000000 40.00000000 zlo zhi
Atoms
1 1 0.00000000 0.00000000 0.00000000
2 1 1.42000000 0.00000000 0.00000000
3 2 1.42000000 0.00000000 3.30000000
4 2 2.84000000 0.00000000 3.30000000
5 1 2.13000000 1.22975607 0.00000000
6 1 3.55000000 1.22975607 0.00000000
7 2 3.55000000 1.22975607 3.30000000
8 2 4.97000000 1.22975607 3.30000000
9 1 0.00000000 2.45951215 0.00000000
10 1 1.42000000 2.45951215 0.00000000
11 2 1.42000000 2.45951215 3.30000000
12 2 2.84000000 2.45951215 3.30000000
13 1 2.13000000 3.68926822 0.00000000
14 1 3.55000000 3.68926822 0.00000000
15 2 3.55000000 3.68926822 3.30000000
16 2 4.97000000 3.68926822 3.30000000
17 1 0.00000000 4.91902429 0.00000000
18 1 1.42000000 4.91902429 0.00000000
19 2 1.42000000 4.91902429 3.30000000
20 2 2.84000000 4.91902429 3.30000000
21 1 2.13000000 6.14878037 0.00000000
22 1 3.55000000 6.14878037 0.00000000
23 2 3.55000000 6.14878037 3.30000000
24 2 4.97000000 6.14878037 3.30000000
25 1 0.00000000 7.37853644 0.00000000
26 1 1.42000000 7.37853644 0.00000000
27 2 1.42000000 7.37853644 3.30000000
28 2 2.84000000 7.37853644 3.30000000
29 1 2.13000000 8.60829251 0.00000000
30 1 3.55000000 8.60829251 0.00000000
31 2 3.55000000 8.60829251 3.30000000
32 2 4.97000000 8.60829251 3.30000000
33 1 0.00000000 9.83804859 0.00000000
34 1 1.42000000 9.83804859 0.00000000
35 2 1.42000000 9.83804859 3.30000000
36 2 2.84000000 9.83804859 3.30000000
37 1 2.13000000 11.06780466 0.00000000
38 1 3.55000000 11.06780466 0.00000000
39 2 3.55000000 11.06780466 3.30000000
40 2 4.97000000 11.06780466 3.30000000
41 1 0.00000000 12.29756073 0.00000000
42 1 1.42000000 12.29756073 0.00000000
43 2 1.42000000 12.29756073 3.30000000
44 2 2.84000000 12.29756073 3.30000000
45 1 2.13000000 13.52731681 0.00000000
46 1 3.55000000 13.52731681 0.00000000
47 2 3.55000000 13.52731681 3.30000000
48 2 4.97000000 13.52731681 3.30000000
49 1 0.00000000 14.75707288 0.00000000
50 1 1.42000000 14.75707288 0.00000000
51 2 1.42000000 14.75707288 3.30000000
52 2 2.84000000 14.75707288 3.30000000
53 1 2.13000000 15.98682895 0.00000000
54 1 3.55000000 15.98682895 0.00000000
55 2 3.55000000 15.98682895 3.30000000
56 2 4.97000000 15.98682895 3.30000000
57 1 0.00000000 17.21658503 0.00000000
58 1 1.42000000 17.21658503 0.00000000
59 2 1.42000000 17.21658503 3.30000000
60 2 2.84000000 17.21658503 3.30000000
61 1 2.13000000 18.44634110 0.00000000
62 1 3.55000000 18.44634110 0.00000000
63 2 3.55000000 18.44634110 3.30000000
64 2 4.97000000 18.44634110 3.30000000
65 1 4.26000000 0.00000000 0.00000000
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67 2 5.68000000 0.00000000 3.30000000
68 2 7.10000000 0.00000000 3.30000000
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73 1 4.26000000 2.45951215 0.00000000
74 1 5.68000000 2.45951215 0.00000000
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81 1 4.26000000 4.91902429 0.00000000
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83 2 5.68000000 4.91902429 3.30000000
84 2 7.10000000 4.91902429 3.30000000
85 1 6.39000000 6.14878037 0.00000000
86 1 7.81000000 6.14878037 0.00000000
87 2 7.81000000 6.14878037 3.30000000
88 2 9.23000000 6.14878037 3.30000000
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90 1 5.68000000 7.37853644 0.00000000
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102 1 7.81000000 11.06780466 0.00000000
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104 2 9.23000000 11.06780466 3.30000000
105 1 4.26000000 12.29756073 0.00000000
106 1 5.68000000 12.29756073 0.00000000
107 2 5.68000000 12.29756073 3.30000000
108 2 7.10000000 12.29756073 3.30000000
109 1 6.39000000 13.52731681 0.00000000
110 1 7.81000000 13.52731681 0.00000000
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112 2 9.23000000 13.52731681 3.30000000
113 1 4.26000000 14.75707288 0.00000000
114 1 5.68000000 14.75707288 0.00000000
115 2 5.68000000 14.75707288 3.30000000
116 2 7.10000000 14.75707288 3.30000000
117 1 6.39000000 15.98682895 0.00000000
118 1 7.81000000 15.98682895 0.00000000
119 2 7.81000000 15.98682895 3.30000000
120 2 9.23000000 15.98682895 3.30000000
121 1 4.26000000 17.21658503 0.00000000
122 1 5.68000000 17.21658503 0.00000000
123 2 5.68000000 17.21658503 3.30000000
124 2 7.10000000 17.21658503 3.30000000
125 1 6.39000000 18.44634110 0.00000000
126 1 7.81000000 18.44634110 0.00000000
127 2 7.81000000 18.44634110 3.30000000
128 2 9.23000000 18.44634110 3.30000000
129 1 8.52000000 0.00000000 0.00000000
130 1 9.94000000 0.00000000 0.00000000
131 2 9.94000000 0.00000000 3.30000000
132 2 11.36000000 0.00000000 3.30000000
133 1 10.65000000 1.22975607 0.00000000
134 1 12.07000000 1.22975607 0.00000000
135 2 12.07000000 1.22975607 3.30000000
136 2 13.49000000 1.22975607 3.30000000
137 1 8.52000000 2.45951215 0.00000000
138 1 9.94000000 2.45951215 0.00000000
139 2 9.94000000 2.45951215 3.30000000
140 2 11.36000000 2.45951215 3.30000000
141 1 10.65000000 3.68926822 0.00000000
142 1 12.07000000 3.68926822 0.00000000
143 2 12.07000000 3.68926822 3.30000000
144 2 13.49000000 3.68926822 3.30000000
145 1 8.52000000 4.91902429 0.00000000
146 1 9.94000000 4.91902429 0.00000000
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148 2 11.36000000 4.91902429 3.30000000
149 1 10.65000000 6.14878037 0.00000000
150 1 12.07000000 6.14878037 0.00000000
151 2 12.07000000 6.14878037 3.30000000
152 2 13.49000000 6.14878037 3.30000000
153 1 8.52000000 7.37853644 0.00000000
154 1 9.94000000 7.37853644 0.00000000
155 2 9.94000000 7.37853644 3.30000000
156 2 11.36000000 7.37853644 3.30000000
157 1 10.65000000 8.60829251 0.00000000
158 1 12.07000000 8.60829251 0.00000000
159 2 12.07000000 8.60829251 3.30000000
160 2 13.49000000 8.60829251 3.30000000
161 1 8.52000000 9.83804859 0.00000000
162 1 9.94000000 9.83804859 0.00000000
163 2 9.94000000 9.83804859 3.30000000
164 2 11.36000000 9.83804859 3.30000000
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166 1 12.07000000 11.06780466 0.00000000
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168 2 13.49000000 11.06780466 3.30000000
169 1 8.52000000 12.29756073 0.00000000
170 1 9.94000000 12.29756073 0.00000000
171 2 9.94000000 12.29756073 3.30000000
172 2 11.36000000 12.29756073 3.30000000
173 1 10.65000000 13.52731681 0.00000000
174 1 12.07000000 13.52731681 0.00000000
175 2 12.07000000 13.52731681 3.30000000
176 2 13.49000000 13.52731681 3.30000000
177 1 8.52000000 14.75707288 0.00000000
178 1 9.94000000 14.75707288 0.00000000
179 2 9.94000000 14.75707288 3.30000000
180 2 11.36000000 14.75707288 3.30000000
181 1 10.65000000 15.98682895 0.00000000
182 1 12.07000000 15.98682895 0.00000000
183 2 12.07000000 15.98682895 3.30000000
184 2 13.49000000 15.98682895 3.30000000
185 1 8.52000000 17.21658503 0.00000000
186 1 9.94000000 17.21658503 0.00000000
187 2 9.94000000 17.21658503 3.30000000
188 2 11.36000000 17.21658503 3.30000000
189 1 10.65000000 18.44634110 0.00000000
190 1 12.07000000 18.44634110 0.00000000
191 2 12.07000000 18.44634110 3.30000000
192 2 13.49000000 18.44634110 3.30000000
193 1 12.78000000 0.00000000 0.00000000
194 1 14.20000000 0.00000000 0.00000000
195 2 14.20000000 0.00000000 3.30000000
196 2 15.62000000 0.00000000 3.30000000
197 1 14.91000000 1.22975607 0.00000000
198 1 16.33000000 1.22975607 0.00000000
199 2 16.33000000 1.22975607 3.30000000
200 2 17.75000000 1.22975607 3.30000000
201 1 12.78000000 2.45951215 0.00000000
202 1 14.20000000 2.45951215 0.00000000
203 2 14.20000000 2.45951215 3.30000000
204 2 15.62000000 2.45951215 3.30000000
205 1 14.91000000 3.68926822 0.00000000
206 1 16.33000000 3.68926822 0.00000000
207 2 16.33000000 3.68926822 3.30000000
208 2 17.75000000 3.68926822 3.30000000
209 1 12.78000000 4.91902429 0.00000000
210 1 14.20000000 4.91902429 0.00000000
211 2 14.20000000 4.91902429 3.30000000
212 2 15.62000000 4.91902429 3.30000000
213 1 14.91000000 6.14878037 0.00000000
214 1 16.33000000 6.14878037 0.00000000
215 2 16.33000000 6.14878037 3.30000000
216 2 17.75000000 6.14878037 3.30000000
217 1 12.78000000 7.37853644 0.00000000
218 1 14.20000000 7.37853644 0.00000000
219 2 14.20000000 7.37853644 3.30000000
220 2 15.62000000 7.37853644 3.30000000
221 1 14.91000000 8.60829251 0.00000000
222 1 16.33000000 8.60829251 0.00000000
223 2 16.33000000 8.60829251 3.30000000
224 2 17.75000000 8.60829251 3.30000000
225 1 12.78000000 9.83804859 0.00000000
226 1 14.20000000 9.83804859 0.00000000
227 2 14.20000000 9.83804859 3.30000000
228 2 15.62000000 9.83804859 3.30000000
229 1 14.91000000 11.06780466 0.00000000
230 1 16.33000000 11.06780466 0.00000000
231 2 16.33000000 11.06780466 3.30000000
232 2 17.75000000 11.06780466 3.30000000
233 1 12.78000000 12.29756073 0.00000000
234 1 14.20000000 12.29756073 0.00000000
235 2 14.20000000 12.29756073 3.30000000
236 2 15.62000000 12.29756073 3.30000000
237 1 14.91000000 13.52731681 0.00000000
238 1 16.33000000 13.52731681 0.00000000
239 2 16.33000000 13.52731681 3.30000000
240 2 17.75000000 13.52731681 3.30000000
241 1 12.78000000 14.75707288 0.00000000
242 1 14.20000000 14.75707288 0.00000000
243 2 14.20000000 14.75707288 3.30000000
244 2 15.62000000 14.75707288 3.30000000
245 1 14.91000000 15.98682895 0.00000000
246 1 16.33000000 15.98682895 0.00000000
247 2 16.33000000 15.98682895 3.30000000
248 2 17.75000000 15.98682895 3.30000000
249 1 12.78000000 17.21658503 0.00000000
250 1 14.20000000 17.21658503 0.00000000
251 2 14.20000000 17.21658503 3.30000000
252 2 15.62000000 17.21658503 3.30000000
253 1 14.91000000 18.44634110 0.00000000
254 1 16.33000000 18.44634110 0.00000000
255 2 16.33000000 18.44634110 3.30000000
256 2 17.75000000 18.44634110 3.30000000

139
examples/USER/misc/kolmogorov_crespi/data.graphene-adsorbant
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@ -1,139 +0,0 @@
info: xyz2data 11:52, Tue 28-02-2017
129 atoms
2 atom types
0.00000000 17.04000000 xlo xhi
0.00000000 19.67609717 ylo yhi
-10.00000000 40.00000000 zlo zhi
Atoms
1 1 0.00000000 0.00000000 0.00000000
2 1 1.42000000 0.00000000 0.00000000
3 1 2.13000000 1.22975607 0.00000000
4 1 3.55000000 1.22975607 0.00000000
5 1 0.00000000 2.45951215 0.00000000
6 1 1.42000000 2.45951215 0.00000000
7 1 2.13000000 3.68926822 0.00000000
8 1 3.55000000 3.68926822 0.00000000
9 1 0.00000000 4.91902429 0.00000000
10 1 1.42000000 4.91902429 0.00000000
11 1 2.13000000 6.14878037 0.00000000
12 1 3.55000000 6.14878037 0.00000000
13 1 0.00000000 7.37853644 0.00000000
14 1 1.42000000 7.37853644 0.00000000
15 1 2.13000000 8.60829251 0.00000000
16 1 3.55000000 8.60829251 0.00000000
17 1 0.00000000 9.83804859 0.00000000
18 1 1.42000000 9.83804859 0.00000000
19 1 2.13000000 11.06780466 0.00000000
20 1 3.55000000 11.06780466 0.00000000
21 1 0.00000000 12.29756073 0.00000000
22 1 1.42000000 12.29756073 0.00000000
23 1 2.13000000 13.52731681 0.00000000
24 1 3.55000000 13.52731681 0.00000000
25 1 0.00000000 14.75707288 0.00000000
26 1 1.42000000 14.75707288 0.00000000
27 1 2.13000000 15.98682895 0.00000000
28 1 3.55000000 15.98682895 0.00000000
29 1 0.00000000 17.21658503 0.00000000
30 1 1.42000000 17.21658503 0.00000000
31 1 2.13000000 18.44634110 0.00000000
32 1 3.55000000 18.44634110 0.00000000
33 1 4.26000000 0.00000000 0.00000000
34 1 5.68000000 0.00000000 0.00000000
35 1 6.39000000 1.22975607 0.00000000
36 1 7.81000000 1.22975607 0.00000000
37 1 4.26000000 2.45951215 0.00000000
38 1 5.68000000 2.45951215 0.00000000
39 1 6.39000000 3.68926822 0.00000000
40 1 7.81000000 3.68926822 0.00000000
41 1 4.26000000 4.91902429 0.00000000
42 1 5.68000000 4.91902429 0.00000000
43 1 6.39000000 6.14878037 0.00000000
44 1 7.81000000 6.14878037 0.00000000
45 1 4.26000000 7.37853644 0.00000000
46 1 5.68000000 7.37853644 0.00000000
47 1 6.39000000 8.60829251 0.00000000
48 1 7.81000000 8.60829251 0.00000000
49 1 4.26000000 9.83804859 0.00000000
50 1 5.68000000 9.83804859 0.00000000
51 1 6.39000000 11.06780466 0.00000000
52 1 7.81000000 11.06780466 0.00000000
53 1 4.26000000 12.29756073 0.00000000
54 1 5.68000000 12.29756073 0.00000000
55 1 6.39000000 13.52731681 0.00000000
56 1 7.81000000 13.52731681 0.00000000
57 1 4.26000000 14.75707288 0.00000000
58 1 5.68000000 14.75707288 0.00000000
59 1 6.39000000 15.98682895 0.00000000
60 1 7.81000000 15.98682895 0.00000000
61 1 4.26000000 17.21658503 0.00000000
62 1 5.68000000 17.21658503 0.00000000
63 1 6.39000000 18.44634110 0.00000000
64 1 7.81000000 18.44634110 0.00000000
65 1 8.52000000 0.00000000 0.00000000
66 1 9.94000000 0.00000000 0.00000000
67 1 10.65000000 1.22975607 0.00000000
68 1 12.07000000 1.22975607 0.00000000
69 1 8.52000000 2.45951215 0.00000000
70 1 9.94000000 2.45951215 0.00000000
71 1 10.65000000 3.68926822 0.00000000
72 1 12.07000000 3.68926822 0.00000000
73 1 8.52000000 4.91902429 0.00000000
74 1 9.94000000 4.91902429 0.00000000
75 1 10.65000000 6.14878037 0.00000000
76 1 12.07000000 6.14878037 0.00000000
77 1 8.52000000 7.37853644 0.00000000
78 1 9.94000000 7.37853644 0.00000000
79 1 10.65000000 8.60829251 0.00000000
80 1 12.07000000 8.60829251 0.00000000
81 1 8.52000000 9.83804859 0.00000000
82 1 9.94000000 9.83804859 0.00000000
83 1 10.65000000 11.06780466 0.00000000
84 1 12.07000000 11.06780466 0.00000000
85 1 8.52000000 12.29756073 0.00000000
86 1 9.94000000 12.29756073 0.00000000
87 1 10.65000000 13.52731681 0.00000000
88 1 12.07000000 13.52731681 0.00000000
89 1 8.52000000 14.75707288 0.00000000
90 1 9.94000000 14.75707288 0.00000000
91 1 10.65000000 15.98682895 0.00000000
92 1 12.07000000 15.98682895 0.00000000
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94 1 9.94000000 17.21658503 0.00000000
95 1 10.65000000 18.44634110 0.00000000
96 1 12.07000000 18.44634110 0.00000000
97 1 12.78000000 0.00000000 0.00000000
98 1 14.20000000 0.00000000 0.00000000
99 1 14.91000000 1.22975607 0.00000000
100 1 16.33000000 1.22975607 0.00000000
101 1 12.78000000 2.45951215 0.00000000
102 1 14.20000000 2.45951215 0.00000000
103 1 14.91000000 3.68926822 0.00000000
104 1 16.33000000 3.68926822 0.00000000
105 1 12.78000000 4.91902429 0.00000000
106 1 14.20000000 4.91902429 0.00000000
107 1 14.91000000 6.14878037 0.00000000
108 1 16.33000000 6.14878037 0.00000000
109 1 12.78000000 7.37853644 0.00000000
110 1 14.20000000 7.37853644 0.00000000
111 1 14.91000000 8.60829251 0.00000000
112 1 16.33000000 8.60829251 0.00000000
113 1 12.78000000 9.83804859 0.00000000
114 1 14.20000000 9.83804859 0.00000000
115 1 14.91000000 11.06780466 0.00000000
116 1 16.33000000 11.06780466 0.00000000
117 1 12.78000000 12.29756073 0.00000000
118 1 14.20000000 12.29756073 0.00000000
119 1 14.91000000 13.52731681 0.00000000
120 1 16.33000000 13.52731681 0.00000000
121 1 12.78000000 14.75707288 0.00000000
122 1 14.20000000 14.75707288 0.00000000
123 1 14.91000000 15.98682895 0.00000000
124 1 16.33000000 15.98682895 0.00000000
125 1 12.78000000 17.21658503 0.00000000
126 1 14.20000000 17.21658503 0.00000000
127 1 14.91000000 18.44634110 0.00000000
128 1 16.33000000 18.44634110 0.00000000
129 2 10.00000000 10.00000000 3.30000000

45
examples/USER/misc/kolmogorov_crespi/in.atom-diffusion
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@ -1,45 +0,0 @@
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.graphene-adsorbant # read lammps data file
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
group adsorbant type 2
######################## Potential defition ########################
pair_style hybrid/overlay kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * none
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
fix thermostat adsorbant nve
fix rigid_membrane membrane setforce 0 0 0
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 100
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 10000

45
examples/USER/misc/kolmogorov_crespi/in.bilayer-graphene
View File

@ -1,45 +0,0 @@
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.bilayer-graphene # read lammps data file
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
group adsorbant type 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * rebo CH.airebo C C # chemical
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
velocity all create 300.0 12345
fix thermostat all nve
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 10
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 1000

12
examples/USER/misc/kolmogorov_crespi_full/in.bilayer-graphene
View File

@ -18,7 +18,7 @@ group adsorbate type 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
####################################################################
pair_coeff * * rebo CH.airebo NULL C # chemical
pair_coeff * * rebo CH.airebo NULL C # chemical
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
####################################################################
# Neighbor update settings
@ -49,12 +49,12 @@ variable KC equal c_1
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.16f
thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore
dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 10000
run 1000

1
examples/USER/misc/kolmogorov_crespi_z/CC.KC Symbolic link
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@ -0,0 +1 @@
../../../../potentials/CC.KC

1
examples/USER/misc/kolmogorov_crespi_z/CH.airebo Symbolic link
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../../../../potentials/CH.airebo

37
examples/USER/misc/kolmogorov_crespi/log.atom-diffusion → examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.1
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@ -1,4 +1,5 @@
LAMMPS (17 Nov 2016)
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
@ -51,13 +52,23 @@ thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8 -> bins = 3 3 7
Memory usage per processor = 2.48399 Mbytes
binsize = 8, bins = 3 3 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair kolmogorov/crespi/z, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.206 | 3.206 | 3.206 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
@ -160,20 +171,20 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
Loop time of 0.381846 on 1 procs for 10000 steps with 129 atoms
Loop time of 0.34689 on 1 procs for 10000 steps with 129 atoms
Performance: 226.269 ns/day, 0.106 hours/ns, 26188.568 timesteps/s
131.8% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 249.070 ns/day, 0.096 hours/ns, 28827.585 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.30936 | 0.30936 | 0.30936 | 0.0 | 81.02
Neigh | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.04
Comm | 0.051287 | 0.051287 | 0.051287 | 0.0 | 13.43
Output | 0.00181 | 0.00181 | 0.00181 | 0.0 | 0.47
Modify | 0.005645 | 0.005645 | 0.005645 | 0.0 | 1.48
Other | | 0.01361 | | | 3.56
Pair | 0.2028 | 0.2028 | 0.2028 | 0.0 | 58.46
Neigh | 0.00021529 | 0.00021529 | 0.00021529 | 0.0 | 0.06
Comm | 0.10656 | 0.10656 | 0.10656 | 0.0 | 30.72
Output | 0.0015109 | 0.0015109 | 0.0015109 | 0.0 | 0.44
Modify | 0.011605 | 0.011605 | 0.011605 | 0.0 | 3.35
Other | | 0.0242 | | | 6.98
Nlocal: 129 ave 129 max 129 min
Histogram: 1 0 0 0 0 0 0 0 0 0

51
examples/USER/misc/kolmogorov_crespi_z/log.atom-diffusion → examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.4
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@ -1,4 +1,5 @@
LAMMPS (17 Nov 2016)
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
@ -10,7 +11,7 @@ processors * * 1 # domain decomposition over x and y
# interactions can be specified separately
read_data data.graphene-adsorbant # read lammps data file
orthogonal box = (0 0 -10) to (17.04 19.6761 40)
1 by 1 by 1 MPI processor grid
2 by 2 by 1 MPI processor grid
reading atoms ...
129 atoms
mass 1 12.0107 # carbon mass (g/mole) | membrane
@ -51,13 +52,23 @@ thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8 -> bins = 3 3 7
Memory usage per processor = 2.48399 Mbytes
binsize = 8, bins = 3 3 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair kolmogorov/crespi/z, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.167 | 3.167 | 3.168 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
@ -160,27 +171,27 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
Loop time of 0.381846 on 1 procs for 10000 steps with 129 atoms
Loop time of 0.524797 on 4 procs for 10000 steps with 129 atoms
Performance: 226.269 ns/day, 0.106 hours/ns, 26188.568 timesteps/s
131.8% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 164.635 ns/day, 0.146 hours/ns, 19054.971 timesteps/s
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.30936 | 0.30936 | 0.30936 | 0.0 | 81.02
Neigh | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.04
Comm | 0.051287 | 0.051287 | 0.051287 | 0.0 | 13.43
Output | 0.00181 | 0.00181 | 0.00181 | 0.0 | 0.47
Modify | 0.005645 | 0.005645 | 0.005645 | 0.0 | 1.48
Other | | 0.01361 | | | 3.56
Pair | 0.043099 | 0.060851 | 0.10153 | 9.7 | 11.60
Neigh | 6.2704e-05 | 6.628e-05 | 6.8188e-05 | 0.0 | 0.01
Comm | 0.35059 | 0.39384 | 0.41232 | 4.0 | 75.05
Output | 0.0028515 | 0.0031345 | 0.0037408 | 0.6 | 0.60
Modify | 0.0063083 | 0.0065277 | 0.0066838 | 0.2 | 1.24
Other | | 0.06038 | | | 11.50
Nlocal: 129 ave 129 max 129 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1867 ave 1867 max 1867 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 290 ave 290 max 290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nlocal: 32.25 ave 33 max 32 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 1305.75 ave 1306 max 1305 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 72.5 ave 144 max 43 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 290
Ave neighs/atom = 2.24806

60
examples/USER/misc/kolmogorov_crespi/log.bilayer-graphene → examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1
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@ -1,4 +1,5 @@
LAMMPS (17 Nov 2016)
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
@ -10,7 +11,7 @@ processors * * 1 # domain decomposition over x and y
# interactions can be specified separately
read_data data.bilayer-graphene # read lammps data file
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
2 by 2 by 1 MPI processor grid
1 by 1 by 1 MPI processor grid
reading atoms ...
256 atoms
mass 1 12.0107 # carbon mass (g/mole) | membrane
@ -52,13 +53,28 @@ thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
3 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8 -> bins = 3 3 8
Memory usage per processor = 3.22197 Mbytes
binsize = 8, bins = 3 3 8
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
@ -161,32 +177,32 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
Loop time of 2.21183 on 4 procs for 1000 steps with 256 atoms
Loop time of 3.90147 on 1 procs for 1000 steps with 256 atoms
Performance: 3.906 ns/day, 6.144 hours/ns, 452.115 timesteps/s
120.2% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 2.215 ns/day, 10.837 hours/ns, 256.314 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9363 | 1.9928 | 2.0303 | 2.5 | 90.10
Pair | 3.8786 | 3.8786 | 3.8786 | 0.0 | 99.41
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.16714 | 0.20465 | 0.26123 | 7.8 | 9.25
Output | 0.002469 | 0.0028505 | 0.003949 | 1.2 | 0.13
Modify | 0.002423 | 0.0026275 | 0.002853 | 0.4 | 0.12
Other | | 0.008904 | | | 0.40
Comm | 0.010816 | 0.010816 | 0.010816 | 0.0 | 0.28
Output | 0.002461 | 0.002461 | 0.002461 | 0.0 | 0.06
Modify | 0.0051703 | 0.0051703 | 0.0051703 | 0.0 | 0.13
Other | | 0.004447 | | | 0.11
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1265 ave 1265 max 1265 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 11824 ave 11824 max 11824 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 23648 ave 23648 max 23648 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1721 ave 1721 max 1721 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 37312 ave 37312 max 37312 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 94592 ave 94592 max 94592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 94592
Ave neighs/atom = 369.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:03

44
examples/USER/misc/kolmogorov_crespi_z/log.bilayer-graphene → examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (17 Nov 2016)
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
@ -52,13 +53,28 @@ thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
3 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8 -> bins = 3 3 8
Memory usage per processor = 3.22197 Mbytes
binsize = 8, bins = 3 3 8
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
@ -161,26 +177,26 @@ Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
Loop time of 2.21183 on 4 procs for 1000 steps with 256 atoms
Loop time of 1.32192 on 4 procs for 1000 steps with 256 atoms
Performance: 3.906 ns/day, 6.144 hours/ns, 452.115 timesteps/s
120.2% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 6.536 ns/day, 3.672 hours/ns, 756.476 timesteps/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9363 | 1.9928 | 2.0303 | 2.5 | 90.10
Pair | 1.1157 | 1.172 | 1.2369 | 4.0 | 88.66
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.16714 | 0.20465 | 0.26123 | 7.8 | 9.25
Output | 0.002469 | 0.0028505 | 0.003949 | 1.2 | 0.13
Modify | 0.002423 | 0.0026275 | 0.002853 | 0.4 | 0.12
Other | | 0.008904 | | | 0.40
Comm | 0.071678 | 0.13667 | 0.19304 | 11.8 | 10.34
Output | 0.0029244 | 0.0031272 | 0.0035112 | 0.4 | 0.24
Modify | 0.0016961 | 0.0017477 | 0.0017846 | 0.1 | 0.13
Other | | 0.008334 | | | 0.63
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1265 ave 1265 max 1265 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 11824 ave 11824 max 11824 min
Neighs: 9328 ave 9328 max 9328 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 23648 ave 23648 max 23648 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -189,4 +205,4 @@ Total # of neighbors = 94592
Ave neighs/atom = 369.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:01