Review akohlmey
This commit is contained in:
Ludwig Ahrens-Iwers
committed by
Shern Tee
Shern Tee
parent
7215939a89
commit
65be564cd6
2
examples/PACKAGES/electrode/check_amat/.gitignore
vendored
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2
examples/PACKAGES/electrode/check_amat/.gitignore
vendored
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*.csv
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log.lammps_*
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600
examples/PACKAGES/electrode/check_amat/charged.data
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600
examples/PACKAGES/electrode/check_amat/charged.data
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LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0
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288 atoms
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2 atom types
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0.285001 25.325067 xlo xhi
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-0.368323 24.671743 ylo yhi
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-1.043333 43.303354 zlo zhi
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Masses
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1 196.966553
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2 196.966553
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Pair Coeffs # lj/cut/coul/long
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1 0 0
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2 0 0
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Atoms # full
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2 1 1 -0.002921 2.086672 2.086672 8 0 0 0
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3 1 1 -0.04033 2.086672 0 10.086673 0 1 0
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5 1 1 -0.000757 4.173345 0 8 0 1 0
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||||
6 1 1 -0.000483 6.260016 2.086672 8 0 0 0
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||||
7 1 1 -0.02377 6.260016 0 10.086673 0 1 0
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8 1 1 -0.031311 4.173345 2.086672 10.086673 0 0 0
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9 1 1 -0.002302 8.346689 0 8 0 1 0
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||||
12 1 1 -0.03014 8.346689 2.086672 10.086673 0 0 0
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||||
26 1 1 -3e-05 2.086672 6.260016 8 0 0 0
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||||
27 1 1 -0.011104 2.086672 4.173345 10.086673 0 0 0
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||||
29 1 1 0.000807 4.173345 4.173345 8 0 0 0
|
||||
30 1 1 -0.000974 6.260016 6.260016 8 0 0 0
|
||||
31 1 1 -0.017105 6.260016 4.173345 10.086673 0 0 0
|
||||
32 1 1 -0.010937 4.173345 6.260016 10.086673 0 0 0
|
||||
33 1 1 0.001587 8.346689 4.173345 8 0 0 0
|
||||
36 1 1 0.004269 8.346689 6.260016 10.086673 0 0 0
|
||||
10 1 1 -0.000534 10.433361 2.086672 8 0 0 0
|
||||
11 1 1 -0.006246 10.433361 0 10.086673 0 1 0
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||||
13 1 1 0.000222 12.520033 0 8 0 1 0
|
||||
14 1 1 -0.000958 14.606705 2.086672 8 0 0 0
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||||
15 1 1 -0.024586 14.606705 0 10.086673 0 1 0
|
||||
16 1 1 -0.032305 12.520033 2.086672 10.086673 0 0 0
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||||
17 1 1 -0.001102 16.693378 0 8 0 1 0
|
||||
20 1 1 -0.015815 16.693378 2.086672 10.086673 0 0 0
|
||||
34 1 1 0.001733 10.433361 6.260016 8 0 0 0
|
||||
35 1 1 -0.001065 10.433361 4.173345 10.086673 0 0 0
|
||||
37 1 1 -0.000623 12.520033 4.173345 8 0 0 0
|
||||
38 1 1 -0.003876 14.606705 6.260016 8 0 0 0
|
||||
39 1 1 -0.030292 14.606705 4.173345 10.086673 0 0 0
|
||||
40 1 1 -0.024863 12.520033 6.260016 10.086673 0 0 0
|
||||
41 1 1 -0.000446 16.693378 4.173345 8 0 0 0
|
||||
44 1 1 -0.044616 16.693378 6.260016 10.086673 0 0 0
|
||||
1 1 1 -0.00023 25.040066 0 8 0 1 0
|
||||
4 1 1 -0.012754 25.040066 2.086672 10.086673 0 0 0
|
||||
18 1 1 0.00046 18.780048 2.086672 8 0 0 0
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||||
19 1 1 -0.011993 18.780048 0 10.086673 0 1 0
|
||||
21 1 1 0.001654 20.86672 0 8 0 1 0
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||||
22 1 1 0.000999 22.953394 2.086672 8 0 0 0
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||||
23 1 1 -0.010485 22.953394 0 10.086673 0 1 0
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||||
24 1 1 -0.038444 20.86672 2.086672 10.086673 0 0 0
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||||
25 1 1 3.8e-05 25.040066 4.173345 8 0 0 0
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||||
28 1 1 -0.032472 25.040066 6.260016 10.086673 0 0 0
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||||
42 1 1 -0.002036 18.780048 6.260016 8 0 0 0
|
||||
43 1 1 -0.031052 18.780048 4.173345 10.086673 0 0 0
|
||||
45 1 1 -0.001031 20.86672 4.173345 8 0 0 0
|
||||
46 1 1 -0.00021 22.953394 6.260016 8 0 0 0
|
||||
47 1 1 -0.004291 22.953394 4.173345 10.086673 0 0 0
|
||||
48 1 1 -0.020295 20.86672 6.260016 10.086673 0 0 0
|
||||
50 1 1 -0.00328 2.086672 10.433361 8 0 0 0
|
||||
51 1 1 -0.037649 2.086672 8.346689 10.086673 0 0 0
|
||||
53 1 1 -0.000151 4.173345 8.346689 8 0 0 0
|
||||
54 1 1 -0.000508 6.260016 10.433361 8 0 0 0
|
||||
55 1 1 -0.014809 6.260016 8.346689 10.086673 0 0 0
|
||||
56 1 1 -0.016074 4.173345 10.433361 10.086673 0 0 0
|
||||
57 1 1 0.00092 8.346689 8.346689 8 0 0 0
|
||||
60 1 1 -0.037118 8.346689 10.433361 10.086673 0 0 0
|
||||
74 1 1 -0.000342 2.086672 14.606705 8 0 0 0
|
||||
75 1 1 -0.027442 2.086672 12.520033 10.086673 0 0 0
|
||||
77 1 1 0.000536 4.173345 12.520033 8 0 0 0
|
||||
78 1 1 -0.000368 6.260016 14.606705 8 0 0 0
|
||||
79 1 1 -0.022015 6.260016 12.520033 10.086673 0 0 0
|
||||
80 1 1 0.003048 4.173345 14.606705 10.086673 0 0 0
|
||||
81 1 1 -0.002516 8.346689 12.520033 8 0 0 0
|
||||
84 1 1 -0.004673 8.346689 14.606705 10.086673 0 0 0
|
||||
58 1 1 -0.003585 10.433361 10.433361 8 0 0 0
|
||||
59 1 1 -0.015447 10.433361 8.346689 10.086673 0 0 0
|
||||
61 1 1 -0.000856 12.520033 8.346689 8 0 0 0
|
||||
62 1 1 0.001309 14.606705 10.433361 8 0 0 0
|
||||
63 1 1 -0.034936 14.606705 8.346689 10.086673 0 0 0
|
||||
64 1 1 -0.022444 12.520033 10.433361 10.086673 0 0 0
|
||||
65 1 1 -0.00144 16.693378 8.346689 8 0 0 0
|
||||
68 1 1 -0.008916 16.693378 10.433361 10.086673 0 0 0
|
||||
82 1 1 0.002034 10.433361 14.606705 8 0 0 0
|
||||
83 1 1 -0.012341 10.433361 12.520033 10.086673 0 0 0
|
||||
85 1 1 0.000168 12.520033 12.520033 8 0 0 0
|
||||
86 1 1 0.000653 14.606705 14.606705 8 0 0 0
|
||||
87 1 1 0.007996 14.606705 12.520033 10.086673 0 0 0
|
||||
88 1 1 0.015522 12.520033 14.606705 10.086673 0 0 0
|
||||
89 1 1 -2.2e-05 16.693378 12.520033 8 0 0 0
|
||||
92 1 1 -0.001057 16.693378 14.606705 10.086673 0 0 0
|
||||
49 1 1 -0.006345 25.040066 8.346689 8 0 0 0
|
||||
52 1 1 -0.05504 25.040066 10.433361 10.086673 0 0 0
|
||||
66 1 1 -0.004359 18.780048 10.433361 8 0 0 0
|
||||
67 1 1 -0.02956 18.780048 8.346689 10.086673 0 0 0
|
||||
69 1 1 0.0004 20.86672 8.346689 8 0 0 0
|
||||
70 1 1 0.000209 22.953394 10.433361 8 0 0 0
|
||||
71 1 1 -0.017199 22.953394 8.346689 10.086673 0 0 0
|
||||
72 1 1 -0.03354 20.86672 10.433361 10.086673 0 0 0
|
||||
73 1 1 -8e-05 25.040066 12.520033 8 0 0 0
|
||||
76 1 1 -0.025027 25.040066 14.606705 10.086673 0 0 0
|
||||
90 1 1 0.000716 18.780048 14.606705 8 0 0 0
|
||||
91 1 1 -0.013279 18.780048 12.520033 10.086673 0 0 0
|
||||
93 1 1 -0.000971 20.86672 12.520033 8 0 0 0
|
||||
94 1 1 -0.000871 22.953394 14.606705 8 0 0 0
|
||||
95 1 1 -0.014468 22.953394 12.520033 10.086673 0 0 0
|
||||
96 1 1 -0.028593 20.86672 14.606705 10.086673 0 0 0
|
||||
98 1 1 -0.001941 2.086672 18.780048 8 0 0 0
|
||||
99 1 1 -0.015815 2.086672 16.693378 10.086673 0 0 0
|
||||
101 1 1 0.000289 4.173345 16.693378 8 0 0 0
|
||||
102 1 1 7.1e-05 6.260016 18.780048 8 0 0 0
|
||||
103 1 1 -0.03149 6.260016 16.693378 10.086673 0 0 0
|
||||
104 1 1 -0.033754 4.173345 18.780048 10.086673 0 0 0
|
||||
105 1 1 -0.003025 8.346689 16.693378 8 0 0 0
|
||||
108 1 1 -0.025007 8.346689 18.780048 10.086673 0 0 0
|
||||
122 1 1 0.000623 2.086672 22.953394 8 0 0 0
|
||||
123 1 1 -0.007516 2.086672 20.86672 10.086673 0 0 0
|
||||
125 1 1 0.000878 4.173345 20.86672 8 0 0 0
|
||||
126 1 1 -0.001576 6.260016 22.953394 8 0 0 0
|
||||
127 1 1 -0.029629 6.260016 20.86672 10.086673 0 0 0
|
||||
128 1 1 0.004728 4.173345 22.953394 10.086673 0 0 0
|
||||
129 1 1 -0.003433 8.346689 20.86672 8 0 0 0
|
||||
132 1 1 -0.043264 8.346689 22.953394 10.086673 0 0 0
|
||||
106 1 1 -4.9e-05 10.433361 18.780048 8 0 0 0
|
||||
107 1 1 -0.026304 10.433361 16.693378 10.086673 0 0 0
|
||||
109 1 1 0.001185 12.520033 16.693378 8 0 0 0
|
||||
110 1 1 -0.000778 14.606705 18.780048 8 0 0 0
|
||||
111 1 1 -0.020266 14.606705 16.693378 10.086673 0 0 0
|
||||
112 1 1 -0.010312 12.520033 18.780048 10.086673 0 0 0
|
||||
113 1 1 -0.000613 16.693378 16.693378 8 0 0 0
|
||||
116 1 1 -0.029068 16.693378 18.780048 10.086673 0 0 0
|
||||
130 1 1 -0.000577 10.433361 22.953394 8 0 0 0
|
||||
131 1 1 -0.026467 10.433361 20.86672 10.086673 0 0 0
|
||||
133 1 1 -0.000921 12.520033 20.86672 8 0 0 0
|
||||
134 1 1 -0.000361 14.606705 22.953394 8 0 0 0
|
||||
135 1 1 -0.017852 14.606705 20.86672 10.086673 0 0 0
|
||||
136 1 1 -0.021653 12.520033 22.953394 10.086673 0 0 0
|
||||
137 1 1 0.000268 16.693378 20.86672 8 0 0 0
|
||||
140 1 1 -0.01542 16.693378 22.953394 10.086673 0 0 0
|
||||
97 1 1 -0.000311 25.040066 16.693378 8 0 0 0
|
||||
100 1 1 -0.012408 25.040066 18.780048 10.086673 0 0 0
|
||||
114 1 1 -0.000958 18.780048 18.780048 8 0 0 0
|
||||
115 1 1 -0.036602 18.780048 16.693378 10.086673 0 0 0
|
||||
117 1 1 -0.005554 20.86672 16.693378 8 0 0 0
|
||||
118 1 1 0.000738 22.953394 18.780048 8 0 0 0
|
||||
119 1 1 -0.027189 22.953394 16.693378 10.086673 0 0 0
|
||||
120 1 1 -0.023111 20.86672 18.780048 10.086673 0 0 0
|
||||
121 1 1 7.5e-05 25.040066 20.86672 8 0 0 0
|
||||
124 1 1 -0.014682 25.040066 22.953394 10.086673 0 0 0
|
||||
138 1 1 -0.000345 18.780048 22.953394 8 0 0 0
|
||||
139 1 1 -0.00903 18.780048 20.86672 10.086673 0 0 0
|
||||
141 1 1 0.000128 20.86672 20.86672 8 0 0 0
|
||||
142 1 1 0.000334 22.953394 22.953394 8 0 0 0
|
||||
143 1 1 -0.002285 22.953394 20.86672 10.086673 0 0 0
|
||||
144 1 1 -0.00745 20.86672 22.953394 10.086673 0 0 0
|
||||
146 2 2 0.022955 2.086672 2.086672 32.173344 0 0 0
|
||||
147 2 2 0.000876 2.086672 0 34.260021 0 1 0
|
||||
149 2 2 0.027435 4.173345 0 32.173344 0 1 0
|
||||
150 2 2 0.020862 6.260016 2.086672 32.173344 0 0 0
|
||||
151 2 2 0.001578 6.260016 0 34.260021 0 1 0
|
||||
152 2 2 0.001014 4.173345 2.086672 34.260021 0 0 0
|
||||
153 2 2 0.021009 8.346689 0 32.173344 0 1 0
|
||||
156 2 2 0.001184 8.346689 2.086672 34.260021 0 0 0
|
||||
170 2 2 0.008185 2.086672 6.260016 32.173344 0 0 0
|
||||
171 2 2 0.001602 2.086672 4.173345 34.260021 0 0 0
|
||||
173 2 2 0.022473 4.173345 4.173345 32.173344 0 0 0
|
||||
174 2 2 0.03292 6.260016 6.260016 32.173344 0 0 0
|
||||
175 2 2 0.002046 6.260016 4.173345 34.260021 0 0 0
|
||||
176 2 2 0.000803 4.173345 6.260016 34.260021 0 0 0
|
||||
177 2 2 0.032031 8.346689 4.173345 32.173344 0 0 0
|
||||
180 2 2 0.002258 8.346689 6.260016 34.260021 0 0 0
|
||||
154 2 2 0.01514 10.433361 2.086672 32.173344 0 0 0
|
||||
155 2 2 0.001872 10.433361 0 34.260021 0 1 0
|
||||
157 2 2 0.004752 12.520033 0 32.173344 0 1 0
|
||||
158 2 2 0.005408 14.606705 2.086672 32.173344 0 0 0
|
||||
159 2 2 0.000237 14.606705 0 34.260021 0 1 0
|
||||
160 2 2 0.001509 12.520033 2.086672 34.260021 0 0 0
|
||||
161 2 2 0.012702 16.693378 0 32.173344 0 1 0
|
||||
164 2 2 0.000611 16.693378 2.086672 34.260021 0 0 0
|
||||
178 2 2 0.02783 10.433361 6.260016 32.173344 0 0 0
|
||||
179 2 2 0.001241 10.433361 4.173345 34.260021 0 0 0
|
||||
181 2 2 0.019546 12.520033 4.173345 32.173344 0 0 0
|
||||
182 2 2 0.016796 14.606705 6.260016 32.173344 0 0 0
|
||||
183 2 2 0.00231 14.606705 4.173345 34.260021 0 0 0
|
||||
184 2 2 0.001481 12.520033 6.260016 34.260021 0 0 0
|
||||
185 2 2 0.014646 16.693378 4.173345 32.173344 0 0 0
|
||||
188 2 2 0.000878 16.693378 6.260016 34.260021 0 0 0
|
||||
145 2 2 0.019659 25.040066 0 32.173344 0 1 0
|
||||
148 2 2 0.00156 25.040066 2.086672 34.260021 0 0 0
|
||||
162 2 2 0.017746 18.780048 2.086672 32.173344 0 0 0
|
||||
163 2 2 0.001489 18.780048 0 34.260021 0 1 0
|
||||
165 2 2 0.034109 20.86672 0 32.173344 0 1 0
|
||||
166 2 2 0.031678 22.953394 2.086672 32.173344 0 0 0
|
||||
167 2 2 0.002473 22.953394 0 34.260021 0 1 0
|
||||
168 2 2 0.002352 20.86672 2.086672 34.260021 0 0 0
|
||||
169 2 2 0.014267 25.040066 4.173345 32.173344 0 0 0
|
||||
172 2 2 0.000168 25.040066 6.260016 34.260021 0 0 0
|
||||
186 2 2 0.008992 18.780048 6.260016 32.173344 0 0 0
|
||||
187 2 2 0.000504 18.780048 4.173345 34.260021 0 0 0
|
||||
189 2 2 0.021772 20.86672 4.173345 32.173344 0 0 0
|
||||
190 2 2 0.01304 22.953394 6.260016 32.173344 0 0 0
|
||||
191 2 2 0.00118 22.953394 4.173345 34.260021 0 0 0
|
||||
192 2 2 0.001457 20.86672 6.260016 34.260021 0 0 0
|
||||
194 2 2 0.025689 2.086672 10.433361 32.173344 0 0 0
|
||||
195 2 2 0.000649 2.086672 8.346689 34.260021 0 0 0
|
||||
197 2 2 0.015557 4.173345 8.346689 32.173344 0 0 0
|
||||
198 2 2 0.025584 6.260016 10.433361 32.173344 0 0 0
|
||||
199 2 2 0.002292 6.260016 8.346689 34.260021 0 0 0
|
||||
200 2 2 0.000819 4.173345 10.433361 34.260021 0 0 0
|
||||
201 2 2 0.035591 8.346689 8.346689 32.173344 0 0 0
|
||||
204 2 2 0.002678 8.346689 10.433361 34.260021 0 0 0
|
||||
218 2 2 0.021343 2.086672 14.606705 32.173344 0 0 0
|
||||
219 2 2 0.001799 2.086672 12.520033 34.260021 0 0 0
|
||||
221 2 2 0.022952 4.173345 12.520033 32.173344 0 0 0
|
||||
222 2 2 0.012325 6.260016 14.606705 32.173344 0 0 0
|
||||
223 2 2 0.001876 6.260016 12.520033 34.260021 0 0 0
|
||||
224 2 2 0.001718 4.173345 14.606705 34.260021 0 0 0
|
||||
225 2 2 0.023719 8.346689 12.520033 32.173344 0 0 0
|
||||
228 2 2 0.000744 8.346689 14.606705 34.260021 0 0 0
|
||||
202 2 2 0.015873 10.433361 10.433361 32.173344 0 0 0
|
||||
203 2 2 0.000758 10.433361 8.346689 34.260021 0 0 0
|
||||
205 2 2 0.008097 12.520033 8.346689 32.173344 0 0 0
|
||||
206 2 2 0.015646 14.606705 10.433361 32.173344 0 0 0
|
||||
207 2 2 0.001702 14.606705 8.346689 34.260021 0 0 0
|
||||
208 2 2 0.000994 12.520033 10.433361 34.260021 0 0 0
|
||||
209 2 2 0.017819 16.693378 8.346689 32.173344 0 0 0
|
||||
212 2 2 0.001677 16.693378 10.433361 34.260021 0 0 0
|
||||
226 2 2 0.004714 10.433361 14.606705 32.173344 0 0 0
|
||||
227 2 2 0.001251 10.433361 12.520033 34.260021 0 0 0
|
||||
229 2 2 0.018756 12.520033 12.520033 32.173344 0 0 0
|
||||
230 2 2 -0.00689 14.606705 14.606705 32.173344 0 0 0
|
||||
231 2 2 0.000922 14.606705 12.520033 34.260021 0 0 0
|
||||
232 2 2 -0.002432 12.520033 14.606705 34.260021 0 0 0
|
||||
233 2 2 0.015625 16.693378 12.520033 32.173344 0 0 0
|
||||
236 2 2 0.001044 16.693378 14.606705 34.260021 0 0 0
|
||||
193 2 2 0.001698 25.040066 8.346689 32.173344 0 0 0
|
||||
196 2 2 0.00215 25.040066 10.433361 34.260021 0 0 0
|
||||
210 2 2 0.029386 18.780048 10.433361 32.173344 0 0 0
|
||||
211 2 2 0.000676 18.780048 8.346689 34.260021 0 0 0
|
||||
213 2 2 0.020182 20.86672 8.346689 32.173344 0 0 0
|
||||
214 2 2 0.02881 22.953394 10.433361 32.173344 0 0 0
|
||||
215 2 2 0.002276 22.953394 8.346689 34.260021 0 0 0
|
||||
216 2 2 0.003118 20.86672 10.433361 34.260021 0 0 0
|
||||
217 2 2 0.012257 25.040066 12.520033 32.173344 0 0 0
|
||||
220 2 2 0.001591 25.040066 14.606705 34.260021 0 0 0
|
||||
234 2 2 -0.009585 18.780048 14.606705 32.173344 0 0 0
|
||||
235 2 2 0.001459 18.780048 12.520033 34.260021 0 0 0
|
||||
237 2 2 0.020359 20.86672 12.520033 32.173344 0 0 0
|
||||
238 2 2 0.004616 22.953394 14.606705 32.173344 0 0 0
|
||||
239 2 2 0.000697 22.953394 12.520033 34.260021 0 0 0
|
||||
240 2 2 5e-06 20.86672 14.606705 34.260021 0 0 0
|
||||
242 2 2 0.034403 2.086672 18.780048 32.173344 0 0 0
|
||||
243 2 2 0.002402 2.086672 16.693378 34.260021 0 0 0
|
||||
245 2 2 0.021827 4.173345 16.693378 32.173344 0 0 0
|
||||
246 2 2 0.011918 6.260016 18.780048 32.173344 0 0 0
|
||||
247 2 2 0.000792 6.260016 16.693378 34.260021 0 0 0
|
||||
248 2 2 0.002071 4.173345 18.780048 34.260021 0 0 0
|
||||
249 2 2 -0.002694 8.346689 16.693378 32.173344 0 0 0
|
||||
252 2 2 0.000351 8.346689 18.780048 34.260021 0 0 0
|
||||
266 2 2 0.037372 2.086672 22.953394 32.173344 0 0 0
|
||||
267 2 2 0.002492 2.086672 20.86672 34.260021 0 0 0
|
||||
269 2 2 0.03734 4.173345 20.86672 32.173344 0 0 0
|
||||
270 2 2 0.015818 6.260016 22.953394 32.173344 0 0 0
|
||||
271 2 2 -0.0001 6.260016 20.86672 34.260021 0 0 0
|
||||
272 2 2 0.002801 4.173345 22.953394 34.260021 0 0 0
|
||||
273 2 2 0.017084 8.346689 20.86672 32.173344 0 0 0
|
||||
276 2 2 0.001644 8.346689 22.953394 34.260021 0 0 0
|
||||
250 2 2 -0.000573 10.433361 18.780048 32.173344 0 0 0
|
||||
251 2 2 0.000448 10.433361 16.693378 34.260021 0 0 0
|
||||
253 2 2 0.001141 12.520033 16.693378 32.173344 0 0 0
|
||||
254 2 2 0.015575 14.606705 18.780048 32.173344 0 0 0
|
||||
255 2 2 0.000258 14.606705 16.693378 34.260021 0 0 0
|
||||
256 2 2 0.000372 12.520033 18.780048 34.260021 0 0 0
|
||||
257 2 2 0.011285 16.693378 16.693378 32.173344 0 0 0
|
||||
260 2 2 0.001199 16.693378 18.780048 34.260021 0 0 0
|
||||
274 2 2 0.031072 10.433361 22.953394 32.173344 0 0 0
|
||||
275 2 2 -0.00031 10.433361 20.86672 34.260021 0 0 0
|
||||
277 2 2 -0.004414 12.520033 20.86672 32.173344 0 0 0
|
||||
278 2 2 0.017397 14.606705 22.953394 32.173344 0 0 0
|
||||
279 2 2 0.001344 14.606705 20.86672 34.260021 0 0 0
|
||||
280 2 2 0.000672 12.520033 22.953394 34.260021 0 0 0
|
||||
281 2 2 0.0252 16.693378 20.86672 32.173344 0 0 0
|
||||
284 2 2 0.001824 16.693378 22.953394 34.260021 0 0 0
|
||||
241 2 2 0.029057 25.040066 16.693378 32.173344 0 0 0
|
||||
244 2 2 0.001076 25.040066 18.780048 34.260021 0 0 0
|
||||
258 2 2 0.035183 18.780048 18.780048 32.173344 0 0 0
|
||||
259 2 2 0.0002 18.780048 16.693378 34.260021 0 0 0
|
||||
261 2 2 0.034083 20.86672 16.693378 32.173344 0 0 0
|
||||
262 2 2 0.036995 22.953394 18.780048 32.173344 0 0 0
|
||||
263 2 2 0.001484 22.953394 16.693378 34.260021 0 0 0
|
||||
264 2 2 0.00377 20.86672 18.780048 34.260021 0 0 0
|
||||
265 2 2 0.024028 25.040066 20.86672 32.173344 0 0 0
|
||||
268 2 2 0.001334 25.040066 22.953394 34.260021 0 0 0
|
||||
282 2 2 0.030927 18.780048 22.953394 32.173344 0 0 0
|
||||
283 2 2 0.002185 18.780048 20.86672 34.260021 0 0 0
|
||||
285 2 2 0.043618 20.86672 20.86672 32.173344 0 0 0
|
||||
286 2 2 0.030615 22.953394 22.953394 32.173344 0 0 0
|
||||
287 2 2 0.001068 22.953394 20.86672 34.260021 0 0 0
|
||||
288 2 2 0.001887 20.86672 22.953394 34.260021 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
2 0 0 0
|
||||
3 0 0 0
|
||||
5 0 0 0
|
||||
6 0 0 0
|
||||
7 0 0 0
|
||||
8 0 0 0
|
||||
9 0 0 0
|
||||
12 0 0 0
|
||||
26 0 0 0
|
||||
27 0 0 0
|
||||
29 0 0 0
|
||||
30 0 0 0
|
||||
31 0 0 0
|
||||
32 0 0 0
|
||||
33 0 0 0
|
||||
36 0 0 0
|
||||
10 0 0 0
|
||||
11 0 0 0
|
||||
13 0 0 0
|
||||
14 0 0 0
|
||||
15 0 0 0
|
||||
16 0 0 0
|
||||
17 0 0 0
|
||||
20 0 0 0
|
||||
34 0 0 0
|
||||
35 0 0 0
|
||||
37 0 0 0
|
||||
38 0 0 0
|
||||
39 0 0 0
|
||||
40 0 0 0
|
||||
41 0 0 0
|
||||
44 0 0 0
|
||||
1 0 0 0
|
||||
4 0 0 0
|
||||
18 0 0 0
|
||||
19 0 0 0
|
||||
21 0 0 0
|
||||
22 0 0 0
|
||||
23 0 0 0
|
||||
24 0 0 0
|
||||
25 0 0 0
|
||||
28 0 0 0
|
||||
42 0 0 0
|
||||
43 0 0 0
|
||||
45 0 0 0
|
||||
46 0 0 0
|
||||
47 0 0 0
|
||||
48 0 0 0
|
||||
50 0 0 0
|
||||
51 0 0 0
|
||||
53 0 0 0
|
||||
54 0 0 0
|
||||
55 0 0 0
|
||||
56 0 0 0
|
||||
57 0 0 0
|
||||
60 0 0 0
|
||||
74 0 0 0
|
||||
75 0 0 0
|
||||
77 0 0 0
|
||||
78 0 0 0
|
||||
79 0 0 0
|
||||
80 0 0 0
|
||||
81 0 0 0
|
||||
84 0 0 0
|
||||
58 0 0 0
|
||||
59 0 0 0
|
||||
61 0 0 0
|
||||
62 0 0 0
|
||||
63 0 0 0
|
||||
64 0 0 0
|
||||
65 0 0 0
|
||||
68 0 0 0
|
||||
82 0 0 0
|
||||
83 0 0 0
|
||||
85 0 0 0
|
||||
86 0 0 0
|
||||
87 0 0 0
|
||||
88 0 0 0
|
||||
89 0 0 0
|
||||
92 0 0 0
|
||||
49 0 0 0
|
||||
52 0 0 0
|
||||
66 0 0 0
|
||||
67 0 0 0
|
||||
69 0 0 0
|
||||
70 0 0 0
|
||||
71 0 0 0
|
||||
72 0 0 0
|
||||
73 0 0 0
|
||||
76 0 0 0
|
||||
90 0 0 0
|
||||
91 0 0 0
|
||||
93 0 0 0
|
||||
94 0 0 0
|
||||
95 0 0 0
|
||||
96 0 0 0
|
||||
98 0 0 0
|
||||
99 0 0 0
|
||||
101 0 0 0
|
||||
102 0 0 0
|
||||
103 0 0 0
|
||||
104 0 0 0
|
||||
105 0 0 0
|
||||
108 0 0 0
|
||||
122 0 0 0
|
||||
123 0 0 0
|
||||
125 0 0 0
|
||||
126 0 0 0
|
||||
127 0 0 0
|
||||
128 0 0 0
|
||||
129 0 0 0
|
||||
132 0 0 0
|
||||
106 0 0 0
|
||||
107 0 0 0
|
||||
109 0 0 0
|
||||
110 0 0 0
|
||||
111 0 0 0
|
||||
112 0 0 0
|
||||
113 0 0 0
|
||||
116 0 0 0
|
||||
130 0 0 0
|
||||
131 0 0 0
|
||||
133 0 0 0
|
||||
134 0 0 0
|
||||
135 0 0 0
|
||||
136 0 0 0
|
||||
137 0 0 0
|
||||
140 0 0 0
|
||||
97 0 0 0
|
||||
100 0 0 0
|
||||
114 0 0 0
|
||||
115 0 0 0
|
||||
117 0 0 0
|
||||
118 0 0 0
|
||||
119 0 0 0
|
||||
120 0 0 0
|
||||
121 0 0 0
|
||||
124 0 0 0
|
||||
138 0 0 0
|
||||
139 0 0 0
|
||||
141 0 0 0
|
||||
142 0 0 0
|
||||
143 0 0 0
|
||||
144 0 0 0
|
||||
146 0 0 0
|
||||
147 0 0 0
|
||||
149 0 0 0
|
||||
150 0 0 0
|
||||
151 0 0 0
|
||||
152 0 0 0
|
||||
153 0 0 0
|
||||
156 0 0 0
|
||||
170 0 0 0
|
||||
171 0 0 0
|
||||
173 0 0 0
|
||||
174 0 0 0
|
||||
175 0 0 0
|
||||
176 0 0 0
|
||||
177 0 0 0
|
||||
180 0 0 0
|
||||
154 0 0 0
|
||||
155 0 0 0
|
||||
157 0 0 0
|
||||
158 0 0 0
|
||||
159 0 0 0
|
||||
160 0 0 0
|
||||
161 0 0 0
|
||||
164 0 0 0
|
||||
178 0 0 0
|
||||
179 0 0 0
|
||||
181 0 0 0
|
||||
182 0 0 0
|
||||
183 0 0 0
|
||||
184 0 0 0
|
||||
185 0 0 0
|
||||
188 0 0 0
|
||||
145 0 0 0
|
||||
148 0 0 0
|
||||
162 0 0 0
|
||||
163 0 0 0
|
||||
165 0 0 0
|
||||
166 0 0 0
|
||||
167 0 0 0
|
||||
168 0 0 0
|
||||
169 0 0 0
|
||||
172 0 0 0
|
||||
186 0 0 0
|
||||
187 0 0 0
|
||||
189 0 0 0
|
||||
190 0 0 0
|
||||
191 0 0 0
|
||||
192 0 0 0
|
||||
194 0 0 0
|
||||
195 0 0 0
|
||||
197 0 0 0
|
||||
198 0 0 0
|
||||
199 0 0 0
|
||||
200 0 0 0
|
||||
201 0 0 0
|
||||
204 0 0 0
|
||||
218 0 0 0
|
||||
219 0 0 0
|
||||
221 0 0 0
|
||||
222 0 0 0
|
||||
223 0 0 0
|
||||
224 0 0 0
|
||||
225 0 0 0
|
||||
228 0 0 0
|
||||
202 0 0 0
|
||||
203 0 0 0
|
||||
205 0 0 0
|
||||
206 0 0 0
|
||||
207 0 0 0
|
||||
208 0 0 0
|
||||
209 0 0 0
|
||||
212 0 0 0
|
||||
226 0 0 0
|
||||
227 0 0 0
|
||||
229 0 0 0
|
||||
230 0 0 0
|
||||
231 0 0 0
|
||||
232 0 0 0
|
||||
233 0 0 0
|
||||
236 0 0 0
|
||||
193 0 0 0
|
||||
196 0 0 0
|
||||
210 0 0 0
|
||||
211 0 0 0
|
||||
213 0 0 0
|
||||
214 0 0 0
|
||||
215 0 0 0
|
||||
216 0 0 0
|
||||
217 0 0 0
|
||||
220 0 0 0
|
||||
234 0 0 0
|
||||
235 0 0 0
|
||||
237 0 0 0
|
||||
238 0 0 0
|
||||
239 0 0 0
|
||||
240 0 0 0
|
||||
242 0 0 0
|
||||
243 0 0 0
|
||||
245 0 0 0
|
||||
246 0 0 0
|
||||
247 0 0 0
|
||||
248 0 0 0
|
||||
249 0 0 0
|
||||
252 0 0 0
|
||||
266 0 0 0
|
||||
267 0 0 0
|
||||
269 0 0 0
|
||||
270 0 0 0
|
||||
271 0 0 0
|
||||
272 0 0 0
|
||||
273 0 0 0
|
||||
276 0 0 0
|
||||
250 0 0 0
|
||||
251 0 0 0
|
||||
253 0 0 0
|
||||
254 0 0 0
|
||||
255 0 0 0
|
||||
256 0 0 0
|
||||
257 0 0 0
|
||||
260 0 0 0
|
||||
274 0 0 0
|
||||
275 0 0 0
|
||||
277 0 0 0
|
||||
278 0 0 0
|
||||
279 0 0 0
|
||||
280 0 0 0
|
||||
281 0 0 0
|
||||
284 0 0 0
|
||||
241 0 0 0
|
||||
244 0 0 0
|
||||
258 0 0 0
|
||||
259 0 0 0
|
||||
261 0 0 0
|
||||
262 0 0 0
|
||||
263 0 0 0
|
||||
264 0 0 0
|
||||
265 0 0 0
|
||||
268 0 0 0
|
||||
282 0 0 0
|
||||
283 0 0 0
|
||||
285 0 0 0
|
||||
286 0 0 0
|
||||
287 0 0 0
|
||||
288 0 0 0
|
||||
17
examples/PACKAGES/electrode/check_amat/charged.settings
Normal file
17
examples/PACKAGES/electrode/check_amat/charged.settings
Normal file
@ -0,0 +1,17 @@
|
||||
atom_style full
|
||||
units real
|
||||
kspace_style pppm/electrode 1.0e-8
|
||||
kspace_modify gewald 0.231
|
||||
kspace_modify mesh 8 8 16
|
||||
kspace_modify order 5
|
||||
|
||||
boundary p p f
|
||||
kspace_modify slab 3.0
|
||||
pair_style lj/cut/coul/long 12 12
|
||||
processors * * 1
|
||||
|
||||
|
||||
read_data "charged.data"
|
||||
|
||||
group ele type 1 2
|
||||
pair_coeff * * 0.0 0.0
|
||||
12
examples/PACKAGES/electrode/check_amat/check.py
Executable file
12
examples/PACKAGES/electrode/check_amat/check.py
Executable file
@ -0,0 +1,12 @@
|
||||
#!/bin/python3
|
||||
|
||||
import numpy as np
|
||||
|
||||
onestep = np.loadtxt("onestep.csv", skiprows=1)
|
||||
twostep = np.loadtxt("twostep.csv", skiprows=1)
|
||||
|
||||
for matrix in [onestep, twostep]:
|
||||
assert matrix.shape == (288, 288), matrix.shape
|
||||
|
||||
diff = abs(np.sum(onestep - twostep))
|
||||
assert diff < 1e-11, diff
|
||||
20
examples/PACKAGES/electrode/check_amat/check.sh
Executable file
20
examples/PACKAGES/electrode/check_amat/check.sh
Executable file
@ -0,0 +1,20 @@
|
||||
#!/bin/bash -e
|
||||
|
||||
lmpbin=$1
|
||||
if [ ! -f $lmpbin ]; then
|
||||
echo "LAMMPS binary '$lmpbin' is not a file"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
|
||||
rm -f *.csv
|
||||
$lmpbin < onestep.in > /dev/null
|
||||
$lmpbin < twostep.in > /dev/null
|
||||
for matrix in twostep.csv onestep.csv; do
|
||||
if [ ! -f $matrix ]; then
|
||||
echo "$matrix missing after running LAMMPS"
|
||||
exit 1
|
||||
fi
|
||||
done
|
||||
python3 check.py
|
||||
rm *.csv log.lammps
|
||||
6
examples/PACKAGES/electrode/check_amat/onestep.in
Normal file
6
examples/PACKAGES/electrode/check_amat/onestep.in
Normal file
@ -0,0 +1,6 @@
|
||||
include charged.settings
|
||||
|
||||
kspace_modify amat onestep
|
||||
|
||||
fix fxupdate ele electrode/conp 0.0 1.805 write_mat onestep.csv
|
||||
run 0
|
||||
6
examples/PACKAGES/electrode/check_amat/twostep.in
Normal file
6
examples/PACKAGES/electrode/check_amat/twostep.in
Normal file
@ -0,0 +1,6 @@
|
||||
include charged.settings
|
||||
|
||||
kspace_modify amat twostep
|
||||
|
||||
fix fxupdate ele electrode/conp 0.0 1.805 write_mat twostep.csv
|
||||
run 0
|
||||
2
examples/PACKAGES/electrode/check_conq/.gitignore
vendored
Normal file
2
examples/PACKAGES/electrode/check_conq/.gitignore
vendored
Normal file
@ -0,0 +1,2 @@
|
||||
log*
|
||||
*csv
|
||||
4766
examples/PACKAGES/electrode/check_conq/cap.data
Normal file
4766
examples/PACKAGES/electrode/check_conq/cap.data
Normal file
File diff suppressed because it is too large
Load Diff
19
examples/PACKAGES/electrode/check_conq/cgil.settings
Normal file
19
examples/PACKAGES/electrode/check_conq/cgil.settings
Normal file
@ -0,0 +1,19 @@
|
||||
#Roy-Maroncelli BMI-PF6 + carbon
|
||||
pair_modify mix arithmetic
|
||||
pair_coeff 1 1 0.61185 4.38
|
||||
pair_coeff 2 2 0.08604 3.41
|
||||
pair_coeff 3 3 0.43738 5.04
|
||||
pair_coeff 4 4 1.12572 5.06
|
||||
pair_coeff 5 5 0.05497 3.37
|
||||
|
||||
bond_coeff 1 200 2.7076
|
||||
bond_coeff 2 200 3.8213
|
||||
angle_coeff 1 200 116.035
|
||||
|
||||
group BMI type 1 2 3
|
||||
fix fx_rattle_BMI BMI shake 1e-4 20 0 b 1 2 a 1
|
||||
|
||||
group bot molecule 641
|
||||
group top molecule 642
|
||||
group ele union bot top
|
||||
group electrolyte type 1 2 3 4
|
||||
35
examples/PACKAGES/electrode/check_conq/equal.in
Normal file
35
examples/PACKAGES/electrode/check_conq/equal.in
Normal file
@ -0,0 +1,35 @@
|
||||
variable tag string equal
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 16 16
|
||||
processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
variable qtop equal 1.0
|
||||
variable qbot equal -v_qtop
|
||||
variable vbot internal 0.0
|
||||
variable vtop internal 0.0
|
||||
fix fxupdate bot electrode/conq v_qbot 1.979 couple top v_qtop symm on
|
||||
fix_modify fxupdate set v bot vbot
|
||||
fix_modify fxupdate set v top vtop
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e) $(v_vbot:%20.15e) $(v_vtop:%20.15e)" file ${tag}.csv screen no title "#Fix electrode conq test setting = equal"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall v_vbot v_vtop
|
||||
run 50
|
||||
39
examples/PACKAGES/electrode/check_conq/equal_intvars.in
Normal file
39
examples/PACKAGES/electrode/check_conq/equal_intvars.in
Normal file
@ -0,0 +1,39 @@
|
||||
variable tag string equal_intvars
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 16 16
|
||||
processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
variable qtop equal 1.0
|
||||
variable qbot equal -v_qtop
|
||||
|
||||
variable qsb_bot internal 0.0
|
||||
variable me00 internal 0.0
|
||||
variable vbot equal v_me00*(v_qbot-v_qsb_bot)
|
||||
variable vtop equal -v_vbot
|
||||
|
||||
fix fxupdate bot electrode/conp v_vbot 1.979 couple top v_vtop symm on
|
||||
fix_modify fxupdate set qsb bot qsb_bot
|
||||
fix_modify fxupdate set me bot bot me00
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e) $(v_vtop:%20.15e) $(v_vbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode conq test setting = equal, emulated with conp"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall v_vbot v_vtop
|
||||
run 50
|
||||
5
examples/PACKAGES/electrode/check_conq/p3m3dc.settings
Normal file
5
examples/PACKAGES/electrode/check_conq/p3m3dc.settings
Normal file
@ -0,0 +1,5 @@
|
||||
kspace_style pppm/electrode 1.0e-7
|
||||
#kspace_modify gewald 0.2311815
|
||||
kspace_modify slab 3.0
|
||||
#kspace_modify mesh 24 24 210
|
||||
#kspace_modify order 5
|
||||
31
examples/PACKAGES/electrode/check_conq/ramp.in
Normal file
31
examples/PACKAGES/electrode/check_conq/ramp.in
Normal file
@ -0,0 +1,31 @@
|
||||
variable tag string equal
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 16 16
|
||||
processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
variable vtop equal ramp(0,5)
|
||||
variable vbot equal -v_vtop
|
||||
fix fxupdate bot electrode/conq v_vbot 1.979 couple top v_vtop symm on
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode conq test setting = ramp"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
2
examples/PACKAGES/electrode/check_equalstyle/.gitignore
vendored
Normal file
2
examples/PACKAGES/electrode/check_equalstyle/.gitignore
vendored
Normal file
@ -0,0 +1,2 @@
|
||||
*.csv
|
||||
log.lammps_*
|
||||
4766
examples/PACKAGES/electrode/check_equalstyle/cap.data
Normal file
4766
examples/PACKAGES/electrode/check_equalstyle/cap.data
Normal file
File diff suppressed because it is too large
Load Diff
19
examples/PACKAGES/electrode/check_equalstyle/cgil.settings
Normal file
19
examples/PACKAGES/electrode/check_equalstyle/cgil.settings
Normal file
@ -0,0 +1,19 @@
|
||||
#Roy-Maroncelli BMI-PF6 + carbon
|
||||
pair_modify mix arithmetic
|
||||
pair_coeff 1 1 0.61185 4.38
|
||||
pair_coeff 2 2 0.08604 3.41
|
||||
pair_coeff 3 3 0.43738 5.04
|
||||
pair_coeff 4 4 1.12572 5.06
|
||||
pair_coeff 5 5 0.05497 3.37
|
||||
|
||||
bond_coeff 1 200 2.7076
|
||||
bond_coeff 2 200 3.8213
|
||||
angle_coeff 1 200 116.035
|
||||
|
||||
group BMI type 1 2 3
|
||||
fix fx_rattle_BMI BMI shake 1e-4 20 0 b 1 2 a 1
|
||||
|
||||
group bot molecule 641
|
||||
group top molecule 642
|
||||
group ele union bot top
|
||||
group electrolyte type 1 2 3 4
|
||||
20
examples/PACKAGES/electrode/check_equalstyle/check.py
Executable file
20
examples/PACKAGES/electrode/check_equalstyle/check.py
Executable file
@ -0,0 +1,20 @@
|
||||
#!/bin/python3
|
||||
|
||||
import numpy as np
|
||||
|
||||
const = np.loadtxt("const.csv", skiprows=1)
|
||||
equal = np.loadtxt("equal.csv", skiprows=1)
|
||||
ramp = np.loadtxt("ramp.csv", skiprows=1)
|
||||
|
||||
for matrix in [const, equal, ramp]:
|
||||
assert matrix.shape == (6, 3), matrix.shape
|
||||
|
||||
# equal follows const
|
||||
diff0 = abs(np.sum(const - equal))
|
||||
assert diff0 < 1e-8, diff0
|
||||
|
||||
# equal starts same as ramp but ends differently
|
||||
diff1 = abs(np.sum(equal[0] - ramp[0]))
|
||||
assert diff1 < 1e-8, diff1
|
||||
diff2 = np.sum(abs(equal[-1] - ramp[-1]))
|
||||
assert diff2 > 1e-8, diff2
|
||||
22
examples/PACKAGES/electrode/check_equalstyle/check.sh
Executable file
22
examples/PACKAGES/electrode/check_equalstyle/check.sh
Executable file
@ -0,0 +1,22 @@
|
||||
#!/bin/bash -e
|
||||
|
||||
lmpbin=$1
|
||||
if [ ! -f $lmpbin ]; then
|
||||
echo "LAMMPS binary '$lmpbin' is not a file"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
|
||||
rm -f *.csv
|
||||
$lmpbin < const.in > /dev/null
|
||||
$lmpbin < equal.in > /dev/null
|
||||
$lmpbin < ramp.in > /dev/null
|
||||
for printout in const.csv equal.csv ramp.csv; do
|
||||
if [ ! -f $printout ]; then
|
||||
echo "$printout missing after running LAMMPS"
|
||||
exit 1
|
||||
fi
|
||||
cat $printout
|
||||
done
|
||||
python3 check.py
|
||||
rm *.csv log.lammps*
|
||||
29
examples/PACKAGES/electrode/check_equalstyle/const.in
Normal file
29
examples/PACKAGES/electrode/check_equalstyle/const.in
Normal file
@ -0,0 +1,29 @@
|
||||
variable tag string const
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 16 16
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
fix fxupdate bot electrode/conp -1.0 1.979 couple top 1.0 symm on
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = const"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
31
examples/PACKAGES/electrode/check_equalstyle/equal.in
Normal file
31
examples/PACKAGES/electrode/check_equalstyle/equal.in
Normal file
@ -0,0 +1,31 @@
|
||||
variable tag string equal
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 16 16
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
variable vtop equal 1.0
|
||||
variable vbot equal -v_vtop
|
||||
fix fxupdate bot electrode/conp v_vbot 1.979 couple top v_vtop symm on
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = equal"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
@ -0,0 +1,5 @@
|
||||
kspace_style pppm/electrode 1.0e-7
|
||||
#kspace_modify gewald 0.2311815
|
||||
kspace_modify slab 3.0
|
||||
#kspace_modify mesh 24 24 210
|
||||
#kspace_modify order 5
|
||||
31
examples/PACKAGES/electrode/check_equalstyle/ramp.in
Normal file
31
examples/PACKAGES/electrode/check_equalstyle/ramp.in
Normal file
@ -0,0 +1,31 @@
|
||||
variable tag string ramp
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 16 16
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
variable vtop equal ramp(1.0,5.0)
|
||||
variable vbot equal -v_vtop
|
||||
fix fxupdate bot electrode/conp v_vbot 1.979 couple top v_vtop symm on
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = ramp"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
2
examples/PACKAGES/electrode/check_etypes/.gitignore
vendored
Normal file
2
examples/PACKAGES/electrode/check_etypes/.gitignore
vendored
Normal file
@ -0,0 +1,2 @@
|
||||
log*
|
||||
*csv
|
||||
4766
examples/PACKAGES/electrode/check_etypes/cap.data
Normal file
4766
examples/PACKAGES/electrode/check_etypes/cap.data
Normal file
File diff suppressed because it is too large
Load Diff
19
examples/PACKAGES/electrode/check_etypes/cgil.settings
Normal file
19
examples/PACKAGES/electrode/check_etypes/cgil.settings
Normal file
@ -0,0 +1,19 @@
|
||||
#Roy-Maroncelli BMI-PF6 + carbon
|
||||
pair_modify mix arithmetic
|
||||
pair_coeff 1 1 0.61185 4.38
|
||||
pair_coeff 2 2 0.08604 3.41
|
||||
pair_coeff 3 3 0.43738 5.04
|
||||
pair_coeff 4 4 1.12572 5.06
|
||||
pair_coeff 5 5 0.05497 3.37
|
||||
|
||||
bond_coeff 1 200 2.7076
|
||||
bond_coeff 2 200 3.8213
|
||||
angle_coeff 1 200 116.035
|
||||
|
||||
group BMI type 1 2 3
|
||||
fix fx_rattle_BMI BMI shake 1e-4 20 0 b 1 2 a 1
|
||||
|
||||
group bot molecule 641
|
||||
group top molecule 642
|
||||
group ele union bot top
|
||||
group electrolyte type 1 2 3 4
|
||||
12
examples/PACKAGES/electrode/check_etypes/check.py
Executable file
12
examples/PACKAGES/electrode/check_etypes/check.py
Executable file
@ -0,0 +1,12 @@
|
||||
#!/bin/python3
|
||||
|
||||
import numpy as np
|
||||
|
||||
ref = np.loadtxt("ref.csv", skiprows=1)
|
||||
etypes = np.loadtxt("etypes.csv", skiprows=1)
|
||||
|
||||
for matrix in [ref, etypes]:
|
||||
assert matrix.shape == (6, 3), matrix.shape
|
||||
|
||||
diff0 = abs(np.sum(ref - etypes))
|
||||
assert diff0 < 1e-8, diff0
|
||||
21
examples/PACKAGES/electrode/check_etypes/check.sh
Executable file
21
examples/PACKAGES/electrode/check_etypes/check.sh
Executable file
@ -0,0 +1,21 @@
|
||||
#!/bin/bash -e
|
||||
|
||||
lmpbin=$1
|
||||
if [ ! -f $lmpbin ]; then
|
||||
echo "LAMMPS binary '$lmpbin' is not a file"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
|
||||
rm -f *.csv
|
||||
$lmpbin -i ref.in > /dev/null
|
||||
$lmpbin -i etypes.in > /dev/null
|
||||
for printout in ref.csv etypes.csv; do
|
||||
if [ ! -f $printout ]; then
|
||||
echo "$printout missing after running LAMMPS"
|
||||
exit 1
|
||||
fi
|
||||
#cat $printout
|
||||
done
|
||||
python3 check.py
|
||||
rm *.csv log.lammps*
|
||||
31
examples/PACKAGES/electrode/check_etypes/etypes.in
Normal file
31
examples/PACKAGES/electrode/check_etypes/etypes.in
Normal file
@ -0,0 +1,31 @@
|
||||
variable tag string etypes
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 16 16
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
neigh_modify check no # force neighbor list rebuild for cost testing
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
fix fxupdate bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = etypes"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
5
examples/PACKAGES/electrode/check_etypes/p3m3dc.settings
Normal file
5
examples/PACKAGES/electrode/check_etypes/p3m3dc.settings
Normal file
@ -0,0 +1,5 @@
|
||||
kspace_style pppm/electrode 1.0e-7
|
||||
#kspace_modify gewald 0.2311815
|
||||
kspace_modify slab 3.0 amat onestep # default
|
||||
#kspace_modify mesh 24 24 210
|
||||
#kspace_modify order 5
|
||||
31
examples/PACKAGES/electrode/check_etypes/ref.in
Normal file
31
examples/PACKAGES/electrode/check_etypes/ref.in
Normal file
@ -0,0 +1,31 @@
|
||||
variable tag string ref
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 16 16
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
neigh_modify check no # force neighbor list rebuild for cost testing
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
fix fxupdate bot electrode/conp -1.0 1.979 couple top 1.0 symm on
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = ref"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
2
examples/PACKAGES/electrode/check_ffield/.gitignore
vendored
Normal file
2
examples/PACKAGES/electrode/check_ffield/.gitignore
vendored
Normal file
@ -0,0 +1,2 @@
|
||||
log*
|
||||
*csv
|
||||
4766
examples/PACKAGES/electrode/check_ffield/cap.data
Normal file
4766
examples/PACKAGES/electrode/check_ffield/cap.data
Normal file
File diff suppressed because it is too large
Load Diff
21
examples/PACKAGES/electrode/check_ffield/cgil.settings
Normal file
21
examples/PACKAGES/electrode/check_ffield/cgil.settings
Normal file
@ -0,0 +1,21 @@
|
||||
#Roy-Maroncelli BMI-PF6 + carbon
|
||||
pair_modify mix arithmetic
|
||||
pair_coeff 1 1 0.61185 4.38
|
||||
pair_coeff 2 2 0.08604 3.41
|
||||
pair_coeff 3 3 0.43738 5.04
|
||||
pair_coeff 4 4 1.12572 5.06
|
||||
pair_coeff 5 5 0.05497 3.37
|
||||
|
||||
bond_coeff 1 200 2.7076
|
||||
bond_coeff 2 200 3.8213
|
||||
angle_coeff 1 200 116.035
|
||||
|
||||
group BMI type 1 2 3
|
||||
fix fx_rattle_BMI BMI shake 1e-4 20 0 b 1 2 a 1
|
||||
|
||||
group bot molecule 641
|
||||
group top molecule 642
|
||||
group ele union bot top
|
||||
group electrolyte type 1 2 3 4
|
||||
|
||||
neigh_modify one 4000
|
||||
18
examples/PACKAGES/electrode/check_ffield/check.py
Executable file
18
examples/PACKAGES/electrode/check_ffield/check.py
Executable file
@ -0,0 +1,18 @@
|
||||
#!/bin/python3
|
||||
|
||||
import numpy as np
|
||||
|
||||
ref = np.loadtxt("ref.csv", skiprows=1)
|
||||
ffield = np.loadtxt("ffield.csv", skiprows=1)
|
||||
ffield_flip = np.loadtxt("ffield_flip.csv", skiprows=1)
|
||||
|
||||
for matrix in [ref, ffield, ffield_flip]:
|
||||
assert matrix.shape == (6, 3), matrix.shape
|
||||
|
||||
# ref is close to ffield
|
||||
diff = np.sum(np.abs(ref - ffield))
|
||||
assert diff < 3e-4, diff
|
||||
|
||||
# ffield and ffield_flip are identical
|
||||
diff = np.sum(np.abs(ffield_flip - ffield))
|
||||
assert diff < 1e-9, diff
|
||||
22
examples/PACKAGES/electrode/check_ffield/check.sh
Executable file
22
examples/PACKAGES/electrode/check_ffield/check.sh
Executable file
@ -0,0 +1,22 @@
|
||||
#!/bin/bash -e
|
||||
|
||||
lmpbin=$1
|
||||
if [ ! -f $lmpbin ]; then
|
||||
echo "LAMMPS binary '$lmpbin' is not a file"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
|
||||
rm -f *.csv
|
||||
$lmpbin < ref.in > /dev/null
|
||||
$lmpbin < ffield.in > /dev/null
|
||||
$lmpbin < ffield_flip.in > /dev/null
|
||||
for printout in ref.csv ffield.csv ffield_flip.csv; do
|
||||
if [ ! -f $printout ]; then
|
||||
echo "$printout missing after running LAMMPS"
|
||||
exit 1
|
||||
fi
|
||||
# cat $printout
|
||||
done
|
||||
python3 check.py
|
||||
rm *.csv log.lammps*
|
||||
29
examples/PACKAGES/electrode/check_ffield/ffield.in
Normal file
29
examples/PACKAGES/electrode/check_ffield/ffield.in
Normal file
@ -0,0 +1,29 @@
|
||||
variable tag string ffield
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m.settings"
|
||||
boundary p p p
|
||||
pair_style lj/cut/coul/long 14 14
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
fix fxupdate bot electrode/conp -1.0 1.979 couple top 1.0 symm on write_inv ${tag}_inv.csv ffield on
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = ffield"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
29
examples/PACKAGES/electrode/check_ffield/ffield_flip.in
Normal file
29
examples/PACKAGES/electrode/check_ffield/ffield_flip.in
Normal file
@ -0,0 +1,29 @@
|
||||
variable tag string ffield_flip
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m.settings"
|
||||
boundary p p p
|
||||
pair_style lj/cut/coul/long 14 14
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
fix fxupdate top electrode/conp 1.0 1.979 couple bot -1.0 symm on write_inv ${tag}_inv.csv ffield on
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = ffield"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
4
examples/PACKAGES/electrode/check_ffield/p3m.settings
Normal file
4
examples/PACKAGES/electrode/check_ffield/p3m.settings
Normal file
@ -0,0 +1,4 @@
|
||||
kspace_style pppm/electrode 1.0e-6
|
||||
#kspace_modify gewald 0.2311815
|
||||
#kspace_modify mesh 24 24 210
|
||||
#kspace_modify order 5
|
||||
5
examples/PACKAGES/electrode/check_ffield/p3m3dc.settings
Normal file
5
examples/PACKAGES/electrode/check_ffield/p3m3dc.settings
Normal file
@ -0,0 +1,5 @@
|
||||
kspace_style pppm/electrode 1.0e-6
|
||||
#kspace_modify gewald 0.2311815
|
||||
kspace_modify slab 3.0
|
||||
#kspace_modify mesh 24 24 210
|
||||
#kspace_modify order 5
|
||||
29
examples/PACKAGES/electrode/check_ffield/ref.in
Normal file
29
examples/PACKAGES/electrode/check_ffield/ref.in
Normal file
@ -0,0 +1,29 @@
|
||||
variable tag string ref
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 14 14
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
fix fxupdate bot electrode/conp -1.0 1.979 couple top 1.0 symm on write_inv ${tag}_inv.csv
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = ref"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
2
examples/PACKAGES/electrode/check_hybrid/.gitignore
vendored
Normal file
2
examples/PACKAGES/electrode/check_hybrid/.gitignore
vendored
Normal file
@ -0,0 +1,2 @@
|
||||
*.csv
|
||||
log.lammps*
|
||||
4766
examples/PACKAGES/electrode/check_hybrid/cap.data
Normal file
4766
examples/PACKAGES/electrode/check_hybrid/cap.data
Normal file
File diff suppressed because it is too large
Load Diff
17
examples/PACKAGES/electrode/check_hybrid/cgil.settings
Normal file
17
examples/PACKAGES/electrode/check_hybrid/cgil.settings
Normal file
@ -0,0 +1,17 @@
|
||||
#Roy-Maroncelli BMI-PF6 + carbon
|
||||
bond_coeff 1 200 2.7076
|
||||
bond_coeff 2 200 3.8213
|
||||
angle_coeff 1 200 116.035
|
||||
|
||||
group BMI type 1 2 3
|
||||
fix fx_rattle_BMI BMI shake 1e-4 20 0 b 1 2 a 1
|
||||
|
||||
group bot molecule 641
|
||||
group top molecule 642
|
||||
group ele union bot top
|
||||
group electrolyte type 1 2 3 4
|
||||
|
||||
set group bot charge 0
|
||||
set group top charge 0
|
||||
fix fxupdate bot electrode/conp -1.0 1.979 couple top 1.0 symm on
|
||||
|
||||
32
examples/PACKAGES/electrode/check_hybrid/coul.in
Normal file
32
examples/PACKAGES/electrode/check_hybrid/coul.in
Normal file
@ -0,0 +1,32 @@
|
||||
variable tag string coul
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style coul/long 16
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
|
||||
pair_modify mix arithmetic
|
||||
pair_coeff * *
|
||||
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = coul"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
37
examples/PACKAGES/electrode/check_hybrid/hybrid.in
Normal file
37
examples/PACKAGES/electrode/check_hybrid/hybrid.in
Normal file
@ -0,0 +1,37 @@
|
||||
variable tag string hybrid
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style hybrid/overlay lj/cut 16 coul/long 16
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
|
||||
pair_modify mix arithmetic
|
||||
pair_coeff 1 1 lj/cut 0.61185 4.38
|
||||
pair_coeff 2 2 lj/cut 0.08604 3.41
|
||||
pair_coeff 3 3 lj/cut 0.43738 5.04
|
||||
pair_coeff 4 4 lj/cut 1.12572 5.06
|
||||
pair_coeff 5 5 lj/cut 0.05497 3.37
|
||||
pair_coeff * * coul/long
|
||||
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = hybrid"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
36
examples/PACKAGES/electrode/check_hybrid/lj.in
Normal file
36
examples/PACKAGES/electrode/check_hybrid/lj.in
Normal file
@ -0,0 +1,36 @@
|
||||
variable tag string lj
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
#include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut 16
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
|
||||
pair_modify mix arithmetic
|
||||
pair_coeff 1 1 0.61185 4.38
|
||||
pair_coeff 2 2 0.08604 3.41
|
||||
pair_coeff 3 3 0.43738 5.04
|
||||
pair_coeff 4 4 1.12572 5.06
|
||||
pair_coeff 5 5 0.05497 3.37
|
||||
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = lj"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
5
examples/PACKAGES/electrode/check_hybrid/p3m3dc.settings
Normal file
5
examples/PACKAGES/electrode/check_hybrid/p3m3dc.settings
Normal file
@ -0,0 +1,5 @@
|
||||
kspace_style pppm/electrode 1.0e-7
|
||||
#kspace_modify gewald 0.2311815
|
||||
kspace_modify slab 3.0
|
||||
#kspace_modify mesh 24 24 210
|
||||
#kspace_modify order 5
|
||||
36
examples/PACKAGES/electrode/check_hybrid/ref.in
Normal file
36
examples/PACKAGES/electrode/check_hybrid/ref.in
Normal file
@ -0,0 +1,36 @@
|
||||
variable tag string ref
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 16 16
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
|
||||
pair_modify mix arithmetic
|
||||
pair_coeff 1 1 0.61185 4.38
|
||||
pair_coeff 2 2 0.08604 3.41
|
||||
pair_coeff 3 3 0.43738 5.04
|
||||
pair_coeff 4 4 1.12572 5.06
|
||||
pair_coeff 5 5 0.05497 3.37
|
||||
|
||||
include "cgil.settings"
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = ref"
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
2
examples/PACKAGES/electrode/check_intel/.gitignore
vendored
Normal file
2
examples/PACKAGES/electrode/check_intel/.gitignore
vendored
Normal file
@ -0,0 +1,2 @@
|
||||
log*
|
||||
*csv
|
||||
4766
examples/PACKAGES/electrode/check_intel/cap.data
Normal file
4766
examples/PACKAGES/electrode/check_intel/cap.data
Normal file
File diff suppressed because it is too large
Load Diff
23
examples/PACKAGES/electrode/check_intel/cgil.settings
Normal file
23
examples/PACKAGES/electrode/check_intel/cgil.settings
Normal file
@ -0,0 +1,23 @@
|
||||
#Roy-Maroncelli BMI-PF6 + carbon
|
||||
pair_modify mix arithmetic
|
||||
pair_coeff 1 1 0.61185 4.38
|
||||
pair_coeff 2 2 0.08604 3.41
|
||||
pair_coeff 3 3 0.43738 5.04
|
||||
pair_coeff 4 4 1.12572 5.06
|
||||
pair_coeff 5 5 0.05497 3.37
|
||||
|
||||
bond_coeff 1 200 2.7076
|
||||
bond_coeff 2 200 3.8213
|
||||
angle_coeff 1 200 116.035
|
||||
|
||||
group BMI type 1 2 3
|
||||
fix fx_rattle_BMI BMI shake 1e-4 20 0 b 1 2 a 1
|
||||
|
||||
group bot molecule 641
|
||||
group top molecule 642
|
||||
group ele union bot top
|
||||
group electrolyte type 1 2 3 4
|
||||
|
||||
group carbon type 5
|
||||
group carbon_neutral subtract carbon ele
|
||||
neigh_modify exclude group carbon carbon_neutral
|
||||
12
examples/PACKAGES/electrode/check_intel/check.py
Executable file
12
examples/PACKAGES/electrode/check_intel/check.py
Executable file
@ -0,0 +1,12 @@
|
||||
#!/bin/python3
|
||||
|
||||
import numpy as np
|
||||
|
||||
nointel = np.loadtxt("ref_nointel.csv", skiprows=1)
|
||||
intel = np.loadtxt("ref_intel.csv", skiprows=1)
|
||||
|
||||
for matrix in [nointel, intel]:
|
||||
assert matrix.shape == (6, 3), matrix.shape
|
||||
|
||||
diff0 = np.sum(np.abs(nointel - intel))
|
||||
assert diff0 < 5e-4, diff0
|
||||
17
examples/PACKAGES/electrode/check_intel/check.sh
Executable file
17
examples/PACKAGES/electrode/check_intel/check.sh
Executable file
@ -0,0 +1,17 @@
|
||||
#!/bin/bash -e
|
||||
|
||||
lmpbin=$1
|
||||
if [ ! -f $lmpbin ]; then
|
||||
echo "LAMMPS binary '$lmpbin' is not a file"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
|
||||
rm -f *.csv
|
||||
$lmpbin -i ref.in #> /dev/null
|
||||
mv ref.csv ref_nointel.csv
|
||||
$lmpbin -i ref.in -pk intel 0 omp 1 mode double -sf intel #> /dev/null
|
||||
mv ref.csv ref_intel.csv
|
||||
|
||||
python3 check.py
|
||||
#rm *.csv log.lammps*
|
||||
5
examples/PACKAGES/electrode/check_intel/p3m3dc.settings
Normal file
5
examples/PACKAGES/electrode/check_intel/p3m3dc.settings
Normal file
@ -0,0 +1,5 @@
|
||||
kspace_style pppm/electrode 1.0e-7
|
||||
kspace_modify gewald 0.21
|
||||
kspace_modify slab 3.0
|
||||
kspace_modify mesh 32 32 200
|
||||
kspace_modify order 5
|
||||
32
examples/PACKAGES/electrode/check_intel/ref.in
Normal file
32
examples/PACKAGES/electrode/check_intel/ref.in
Normal file
@ -0,0 +1,32 @@
|
||||
variable tag string ref
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
include "p3m3dc.settings"
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 16 16
|
||||
#processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
neigh_modify check no # force neighbor list rebuild for cost testing
|
||||
|
||||
#dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
fix fxupdate bot electrode/conp -1.0 1.979 couple top 1.0 symm on
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%20.15e) $(c_qbot:%20.15e)" file ${tag}.csv screen no title "#Fix electrode equal-style variable test setting = etypes"
|
||||
|
||||
thermo 10
|
||||
timestep 2.5
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 50
|
||||
26110
examples/PACKAGES/electrode/example/cap.data
Normal file
26110
examples/PACKAGES/electrode/example/cap.data
Normal file
File diff suppressed because it is too large
Load Diff
30
examples/PACKAGES/electrode/example/conp.in
Normal file
30
examples/PACKAGES/electrode/example/conp.in
Normal file
@ -0,0 +1,30 @@
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
# Select one file for kspace settings
|
||||
include "p3m3dc.settings"
|
||||
# include "ew3dc.settings"
|
||||
# include "ew2d.settings"
|
||||
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 15 12
|
||||
processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "mw.settings"
|
||||
|
||||
dump alldump all custom 1000 all.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 298.0 298.0 241
|
||||
fix fxupdate bot electrode/conp -1.0 1.805132 couple top 1.0 write_inv fix_inv.csv symm on
|
||||
compute q ele property/atom q
|
||||
compute qtop top reduce sum c_q
|
||||
compute qbot bot reduce sum c_q
|
||||
compute qall ele reduce sum c_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 200
|
||||
|
||||
4
examples/PACKAGES/electrode/example/ew2d.settings
Normal file
4
examples/PACKAGES/electrode/example/ew2d.settings
Normal file
@ -0,0 +1,4 @@
|
||||
kspace_style ewald/electrode 1.0e-6
|
||||
kspace_modify gewald 0.2311815
|
||||
kspace_modify kmax/ewald 10 10 29
|
||||
kspace_modify slab ew2d
|
||||
4
examples/PACKAGES/electrode/example/ew3dc.settings
Normal file
4
examples/PACKAGES/electrode/example/ew3dc.settings
Normal file
@ -0,0 +1,4 @@
|
||||
kspace_style ewald/electrode 1.0e-6
|
||||
kspace_modify gewald 0.2311815
|
||||
kspace_modify kmax/ewald 10 10 88
|
||||
kspace_modify slab 3.0
|
||||
17
examples/PACKAGES/electrode/example/mw.settings
Normal file
17
examples/PACKAGES/electrode/example/mw.settings
Normal file
@ -0,0 +1,17 @@
|
||||
pair_modify mix arithmetic
|
||||
pair_coeff 1 1 0.15540152963671128 3.166
|
||||
pair_coeff 4 4 0.09999999999999999 2.584
|
||||
pair_coeff 5 5 0.09999999999999999 4.401
|
||||
pair_coeff 6 6 5.29 2.951
|
||||
pair_coeff 7 7 5.29 2.951
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
pair_coeff 3 3 0.0 0.0
|
||||
bond_coeff 1 450 0.9999965664194801
|
||||
bond_coeff 2 450 0.9999965664194801
|
||||
angle_coeff 1 55 109.46937551578806
|
||||
group SPC type 1 2 3
|
||||
fix fx_rattle_SPC SPC shake 1.0e-4 20 0 b 1 2 a 1
|
||||
group bot type 6
|
||||
group top type 7
|
||||
group ele type 6 7
|
||||
group electrolyte type 1 2 3 4 5
|
||||
5
examples/PACKAGES/electrode/example/p3m3dc.settings
Normal file
5
examples/PACKAGES/electrode/example/p3m3dc.settings
Normal file
@ -0,0 +1,5 @@
|
||||
kspace_style pppm/electrode 1.0e-6
|
||||
kspace_modify gewald 0.2311815
|
||||
kspace_modify slab 3.0
|
||||
kspace_modify mesh 24 24 210
|
||||
kspace_modify order 5
|
||||
4
examples/PACKAGES/electrode/test_cgil_2d3d/.gitignore
vendored
Normal file
4
examples/PACKAGES/electrode/test_cgil_2d3d/.gitignore
vendored
Normal file
@ -0,0 +1,4 @@
|
||||
log.lammps*
|
||||
fix_inv*
|
||||
printout*
|
||||
*lammpstrj
|
||||
4766
examples/PACKAGES/electrode/test_cgil_2d3d/cap.data
Normal file
4766
examples/PACKAGES/electrode/test_cgil_2d3d/cap.data
Normal file
File diff suppressed because it is too large
Load Diff
19
examples/PACKAGES/electrode/test_cgil_2d3d/cgil.settings
Normal file
19
examples/PACKAGES/electrode/test_cgil_2d3d/cgil.settings
Normal file
@ -0,0 +1,19 @@
|
||||
#Roy-Maroncelli BMI-PF6 + carbon
|
||||
pair_modify mix arithmetic
|
||||
pair_coeff 1 1 0.61185 4.38
|
||||
pair_coeff 2 2 0.08604 3.41
|
||||
pair_coeff 3 3 0.43738 5.04
|
||||
pair_coeff 4 4 1.12572 5.06
|
||||
pair_coeff 5 5 0.05497 3.37
|
||||
|
||||
bond_coeff 1 200 2.7076
|
||||
bond_coeff 2 200 3.8213
|
||||
angle_coeff 1 200 116.035
|
||||
|
||||
group BMI type 1 2 3
|
||||
fix fx_rattle_BMI BMI shake 1e-4 20 0 b 1 2 a 1
|
||||
|
||||
group bot molecule 641
|
||||
group top molecule 642
|
||||
group ele union bot top
|
||||
group electrolyte type 1 2 3 4
|
||||
34
examples/PACKAGES/electrode/test_cgil_2d3d/conp.in
Normal file
34
examples/PACKAGES/electrode/test_cgil_2d3d/conp.in
Normal file
@ -0,0 +1,34 @@
|
||||
variable tag getenv TAG
|
||||
log log.lammps_${tag}
|
||||
atom_style full
|
||||
units real
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
# Select one file for kspace settings
|
||||
if "${tag} == p3m" then "include p3m3dc.settings" &
|
||||
elif "${tag} == ew3dc" "include ew3dc.settings" &
|
||||
elif "${tag} == ew2d" "include ew2d.settings"
|
||||
|
||||
boundary p p f
|
||||
pair_style lj/cut/coul/long 16 16
|
||||
processors * * 2
|
||||
|
||||
read_data "cap.data"
|
||||
include "cgil.settings"
|
||||
|
||||
dump alldump all custom 1000 all_${tag}.lammpstrj id mol type x y z q
|
||||
fix fxnvt electrolyte nvt temp 500.0 500.0 100.
|
||||
fix fxupdate bot electrode/conp -1.0 1.979 couple top 1.0 write_inv fix_inv_${tag}.csv symm on
|
||||
#fix conp bot conp 1 top 1.979 2 log_conp pppm
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qall ele reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix print all print 10 "$(step:%8.3g) $(c_qtop:%8.3e) $(c_qbot:%8.3e) $(c_ctemp:%8.3f) $(etotal:%12.3f)" file printout_${tag} screen no
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step c_ctemp epair etotal c_qtop c_qbot c_qall
|
||||
run 500
|
||||
4
examples/PACKAGES/electrode/test_cgil_2d3d/ew2d.settings
Normal file
4
examples/PACKAGES/electrode/test_cgil_2d3d/ew2d.settings
Normal file
@ -0,0 +1,4 @@
|
||||
kspace_style ewald/electrode 1.0e-6
|
||||
kspace_modify gewald 0.2311815
|
||||
kspace_modify kmax/ewald 10 10 29
|
||||
kspace_modify slab ew2d
|
||||
@ -0,0 +1,4 @@
|
||||
kspace_style ewald/electrode 1.0e-6
|
||||
#kspace_modify gewald 0.2311815
|
||||
#kspace_modify kmax/ewald 10 10 88
|
||||
kspace_modify slab 3.0
|
||||
@ -0,0 +1,5 @@
|
||||
kspace_style pppm/electrode 1.0e-7
|
||||
#kspace_modify gewald 0.2311815
|
||||
kspace_modify slab 3.0
|
||||
#kspace_modify mesh 24 24 210
|
||||
#kspace_modify order 5
|
||||
10
examples/PACKAGES/electrode/test_cgil_2d3d/runtests.sh
Normal file
10
examples/PACKAGES/electrode/test_cgil_2d3d/runtests.sh
Normal file
@ -0,0 +1,10 @@
|
||||
LMP_EXEC=lmp_electrode
|
||||
tags=(p3m ew3dc ew2d)
|
||||
|
||||
for t in ${tags[@]}
|
||||
do
|
||||
export TAG=$t
|
||||
mpirun -np 4 $LMP_EXEC -i conp.in
|
||||
done
|
||||
|
||||
paste printout_*
|
||||
7
examples/PACKAGES/electrode/thermo/.gitignore
vendored
Normal file
7
examples/PACKAGES/electrode/thermo/.gitignore
vendored
Normal file
@ -0,0 +1,7 @@
|
||||
*.dat
|
||||
*.xyz
|
||||
log.lammps
|
||||
mat.csv
|
||||
final.inp
|
||||
random.inp
|
||||
nohup.out
|
||||
131
examples/PACKAGES/electrode/thermo/conp/control.inp
Normal file
131
examples/PACKAGES/electrode/thermo/conp/control.inp
Normal file
@ -0,0 +1,131 @@
|
||||
|
||||
# Thermopotentiostat example calculation for nano-confined water
|
||||
# between two electrodes (Ne) with applied voltage. Simulation
|
||||
# can be performed with unmodified version of LAMMPS. Run as:
|
||||
#
|
||||
# lmp -in control.inp
|
||||
#
|
||||
# Output files:
|
||||
# temp.dat temperature
|
||||
# md.xyz trajectory
|
||||
# final.inp final configuration for restarting
|
||||
#
|
||||
# F. Deissenbeck, C. Freysoldt, M. Todorova, J. Neugebauer, S. Wippermann,
|
||||
# wippermann@mpie.de, 12.08.2020
|
||||
|
||||
|
||||
units real
|
||||
dimension 3
|
||||
atom_style full
|
||||
processors * * 2
|
||||
|
||||
kspace_style pppm/electrode 1.0e-5
|
||||
kspace_modify slab 4.0 # non-periodic electrostatic boundary conditions in z-direction
|
||||
kspace_modify gewald 0.2311815
|
||||
boundary p p f
|
||||
|
||||
read_data ../sample.inp
|
||||
include ../potential.inp
|
||||
neighbor 2.0 bin
|
||||
neigh_modify one 3000
|
||||
|
||||
|
||||
|
||||
# input parameters
|
||||
# ----------------
|
||||
|
||||
variable dt equal 0.967553728 # time step [fs],
|
||||
# 0.483776864 fs = 20 Hartree a.u.
|
||||
variable dumpsteps equal 1000 # dump trajectory every ${dumpsteps} steps
|
||||
|
||||
|
||||
|
||||
group moving_particles type 1 2
|
||||
group electrodes type 3 4
|
||||
|
||||
group Ne_left type 3
|
||||
group Ne_right type 4
|
||||
|
||||
|
||||
|
||||
|
||||
# NVE section (+ explicit thermostat if desired)
|
||||
# ----------------------------------------------
|
||||
|
||||
timestep ${dt}
|
||||
|
||||
# init velocities to setup new claculation,
|
||||
# not needed here since sample.inp is already equilibrated (at Phi0 = 0 V)
|
||||
|
||||
#velocity moving_particles create 350.0 4928459 rot yes dist gaussian
|
||||
|
||||
|
||||
# apply explicit thermostat if desired,
|
||||
# also not needed here since electrode charge distribution
|
||||
# of thermopotentiostat has an explicit temperature (charge fluctuations)
|
||||
# that actively controls the kinetic temperature
|
||||
|
||||
#fix 1 moving_particles temp/csvr 350.0 350.0 ${th_time} 54324
|
||||
#fix 1 moving_particles langevin 350.0 350.0 ${th_time} 699483
|
||||
|
||||
|
||||
# integrate Hamiltonian equations of motion -> pure NVE ensemble
|
||||
|
||||
fix 2 moving_particles nve
|
||||
|
||||
|
||||
# ensure electrodes are not moving
|
||||
|
||||
fix freeze1 Ne_left setforce 0.0 0.0 0.0
|
||||
fix freeze2 Ne_right setforce 0.0 0.0 0.0
|
||||
|
||||
|
||||
|
||||
# thermopotentiostat section
|
||||
# --------------------------
|
||||
|
||||
fix conpid Ne_left electrode/conp 1.0 1.805132 couple Ne_right -1.0 symm on write_mat mat.csv
|
||||
|
||||
# output section
|
||||
# --------------
|
||||
|
||||
dump 5 all custom ${dumpsteps} md.xyz id element xu yu zu q
|
||||
dump_modify 5 format float %20.15g element H O Ne_a Ne_b sort id
|
||||
|
||||
|
||||
# compute temperature
|
||||
|
||||
compute myTemp moving_particles temp
|
||||
compute movppe moving_particles pe/atom
|
||||
compute myPe moving_particles reduce sum c_movppe
|
||||
compute myKe moving_particles ke
|
||||
fix 6 moving_particles ave/time 1 1 1 c_myTemp c_myPe c_myKe file temp.dat format '%20.16f'
|
||||
|
||||
# compute charges
|
||||
compute q electrodes property/atom q
|
||||
compute q_left Ne_left reduce sum c_q
|
||||
compute q_right Ne_right reduce sum c_q
|
||||
compute q_all electrodes reduce sum c_q
|
||||
|
||||
thermo_style custom step etotal c_myTemp c_q_left c_q_right c_q_all f_conpid[1] f_conpid[2]
|
||||
thermo 100
|
||||
|
||||
|
||||
|
||||
fix 3 moving_particles shake 0.0001 20 0 b 1 a 1
|
||||
|
||||
|
||||
|
||||
# run simulation and write final configuration for restart
|
||||
# --------------------------------------------------------
|
||||
|
||||
# total number of timesteps
|
||||
|
||||
run 100000
|
||||
|
||||
|
||||
# write final coordinates and velocities,
|
||||
# nocoeff needed, or LAMMPS will not be able to restart from final.inp
|
||||
|
||||
write_data final.inp nocoeff
|
||||
|
||||
260
examples/PACKAGES/electrode/thermo/flat/control.inp
Normal file
260
examples/PACKAGES/electrode/thermo/flat/control.inp
Normal file
@ -0,0 +1,260 @@
|
||||
|
||||
# Thermopotentiostat example calculation for nano-confined water
|
||||
# between two electrodes (Ne) with applied voltage. Simulation
|
||||
# can be performed with unmodified version of LAMMPS. Run as:
|
||||
#
|
||||
# lmp -in control.inp
|
||||
#
|
||||
# Output files:
|
||||
# temp.dat temperature
|
||||
# traj_Phi.dat potential
|
||||
# traj_n.dat charge
|
||||
# md.xyz trajectory
|
||||
# final.inp final configuration for restarting
|
||||
#
|
||||
# F. Deissenbeck, C. Freysoldt, M. Todorova, J. Neugebauer, S. Wippermann,
|
||||
# wippermann@mpie.de, 12.08.2020
|
||||
|
||||
|
||||
units real
|
||||
dimension 3
|
||||
atom_style full
|
||||
|
||||
kspace_style pppm/electrode 1.0e-5
|
||||
kspace_modify slab 4.0 # non-periodic electrostatic boundary conditions in z-direction
|
||||
kspace_modify gewald 0.2311815
|
||||
boundary p p f
|
||||
|
||||
read_data ../sample.inp
|
||||
include ../potential.inp
|
||||
neighbor 2.0 bin
|
||||
neigh_modify one 3000
|
||||
|
||||
|
||||
|
||||
# input parameters
|
||||
# ----------------
|
||||
|
||||
variable dt equal 0.967553728 # time step [fs],
|
||||
# 0.483776864 fs = 20 Hartree a.u.
|
||||
|
||||
variable th_temp equal 350.0 # temperature [K]
|
||||
|
||||
variable phi0 equal 2.0 # external applied potential [V]
|
||||
variable po_time equal 100.0 # relaxation time potentiostat [fs]
|
||||
|
||||
variable dumpsteps equal 1000 # dump trajectory every ${dumpsteps} steps
|
||||
|
||||
|
||||
|
||||
# constants
|
||||
# ---------
|
||||
|
||||
variable eps0 equal 0.005526349358057108 # [e-/(V Angstrom)]
|
||||
variable kB equal 8.617333262145E-5 # [eV/K]
|
||||
variable C equal v_eps0*v_Area/v_distance # [e-/V]
|
||||
|
||||
|
||||
|
||||
# setup - do not change (unless lowest electrode is not at z=2.0)
|
||||
# ---------------------------------------------------------------
|
||||
|
||||
variable Area equal ($(xhi)-$(xlo))*($(yhi)-$(ylo)) # [A**2]
|
||||
|
||||
group moving_particles type 1 2
|
||||
group electrodes type 3 4
|
||||
|
||||
group Ne_left type 3
|
||||
group Ne_right type 4
|
||||
variable Neatoms equal count(Ne_left)
|
||||
|
||||
|
||||
# get electrode distance (to compute C) and
|
||||
# one electrode atom (Ne) id (to update charge during simulation)
|
||||
|
||||
variable r atom gmask(Ne_right)*sqrt((z-10.0)*(z-10.0))
|
||||
compute computedis all reduce max v_r # max dist between electrodes
|
||||
compute ne_left_id Ne_left property/atom id
|
||||
compute one_id_neleft Ne_left reduce min c_ne_left_id # get minimum id
|
||||
thermo_style custom c_computedis c_one_id_neleft # dump to check
|
||||
|
||||
run 0
|
||||
|
||||
variable distance equal c_computedis
|
||||
variable id_of_neleft equal c_one_id_neleft
|
||||
|
||||
|
||||
|
||||
# ----------------------- #
|
||||
# | simulation protocol | #
|
||||
# ----------------------- #
|
||||
|
||||
# compute dipole moments
|
||||
# ----------------------
|
||||
|
||||
# total dipole
|
||||
|
||||
compute waterNe all chunk/atom bin/1d z lower $(zhi)
|
||||
compute dip_tot all dipole/chunk waterNe
|
||||
fix 5 all ave/time 1 1 1 c_dip_tot[*] file dipole_total.dat mode vector
|
||||
|
||||
|
||||
# water-only dipole
|
||||
|
||||
compute onlywater moving_particles chunk/atom bin/1d z lower $(zhi)
|
||||
compute dip_water all dipole/chunk onlywater
|
||||
fix 43 all ave/time 1 1 1 c_dip_water[*] file dipole_water.dat mode vector
|
||||
|
||||
|
||||
# electrode-only dipole, needed to compute electrode charge without recursion
|
||||
|
||||
compute elcharge electrodes chunk/atom bin/1d z lower $(zhi)
|
||||
compute dip_elec all dipole/chunk elcharge
|
||||
fix 83 all ave/time 1 1 1 c_dip_elec[*] file dipole_electrode.dat mode vector
|
||||
|
||||
|
||||
|
||||
# NVE section (+ explicit thermostat if desired)
|
||||
# ----------------------------------------------
|
||||
|
||||
timestep ${dt}
|
||||
|
||||
# init velocities to setup new claculation,
|
||||
# not needed here since sample.inp is already equilibrated (at Phi0 = 0 V)
|
||||
|
||||
#velocity moving_particles create 350.0 4928459 rot yes dist gaussian
|
||||
|
||||
|
||||
# apply explicit thermostat if desired,
|
||||
# also not needed here since electrode charge distribution
|
||||
# of thermopotentiostat has an explicit temperature (charge fluctuations)
|
||||
# that actively controls the kinetic temperature
|
||||
|
||||
# integrate Hamiltonian equations of motion -> pure NVE ensemble
|
||||
|
||||
fix 2 moving_particles nve
|
||||
|
||||
|
||||
# ensure electrodes are not moving
|
||||
|
||||
fix freeze1 Ne_left setforce 0.0 0.0 0.0
|
||||
fix freeze2 Ne_right setforce 0.0 0.0 0.0
|
||||
|
||||
|
||||
|
||||
# thermopotentiostat section
|
||||
# --------------------------
|
||||
|
||||
# calculate electrode charge n from electrode-only dipole moment,
|
||||
# done in this way in order to avoid a recursive loop due to lammps
|
||||
# functional scripting language
|
||||
|
||||
variable charge_t1 equal -1*(c_dip_elec[1][3])/v_distance
|
||||
|
||||
|
||||
# obtain voltage Phi from total dipole moment
|
||||
# phi = -dip[3] / (eps0 * Area)
|
||||
|
||||
variable phi equal -1*c_dip_tot[1][3]/(v_eps0*v_Area)
|
||||
|
||||
# Ohm's Law potentiostat,
|
||||
# dissipative term of Eq. 7 without fluctuation, cools system,
|
||||
# only for testing purposes and by default deactivated
|
||||
|
||||
#variable phi_new equal v_phi0+(v_phi-v_phi0)*exp(-1*v_dt/v_po_time)
|
||||
|
||||
|
||||
# CANONICAL SAMPLING BY STOCHASTIC THERMOPOTENTIOSTAT,
|
||||
# equivalent to Eq. 7, just using Phi as the basic variable here,
|
||||
# phi_new = phi0 + (phi - phi0) * np.exp(-dt/po_time) \
|
||||
# + np.sqrt(kB*th_temp/C) * np.sqrt(1-np.exp(-2*dt/po_time))*np.random.normal(0.0,1.0),
|
||||
# random number is read from file here to ensure reproducibility
|
||||
# iterate random number every timestep with dummy fix
|
||||
|
||||
variable random file ../random.inp
|
||||
variable phi_new equal v_phi0+(v_phi-v_phi0)*exp(-1*v_dt/v_po_time)+sqrt((v_kB*v_th_temp/v_C)*(1.0-exp(-2*v_dt/v_po_time)))*v_random
|
||||
variable dummy equal next(random)
|
||||
fix fxdummy all ave/time 1 1 1 v_dummy
|
||||
|
||||
# compute new charges on left and right electrodes
|
||||
# dq = C * (phi_new - phi), q = q + dq
|
||||
# performed specifically in this way to access the charge and hence phi_new only once,
|
||||
# lammps scripting is functional, not imperative, and hence "reading" phi_new twice
|
||||
# would also evaluate phi_new twice with different random numbers N and update charges on left electrode -> must avoid!
|
||||
|
||||
variable c equal (v_charge_t1+v_C*(v_phi_new-v_phi))
|
||||
variable charge equal v_c/(1.0*v_Neatoms)
|
||||
variable charge_2 equal -1.0*q[v_id_of_neleft]
|
||||
|
||||
|
||||
# set charges on left and right electrodes,
|
||||
# warning about unit cell being not charge-neutral can be ignored:
|
||||
# after adapting left electrode first, unit cell is indeed non-neutral,
|
||||
# after adapting right electrode subsequently it is neutral again
|
||||
|
||||
fix potentio_left Ne_left adapt 1 atom charge v_charge
|
||||
fix potentio_right Ne_right adapt 1 atom charge v_charge_2
|
||||
|
||||
|
||||
|
||||
# output section
|
||||
# --------------
|
||||
|
||||
dump 5 all custom ${dumpsteps} md.xyz id element xu yu zu q
|
||||
dump_modify 5 format float %20.15g element H O Ne_a Ne_b sort id
|
||||
fix potential all ave/time 1 1 1 v_phi file traj_Phi.dat
|
||||
fix rho all ave/time 1 1 1 v_charge_t1 file traj_n.dat
|
||||
|
||||
|
||||
# compute temperature
|
||||
|
||||
compute myTemp moving_particles temp
|
||||
compute movppe moving_particles pe/atom
|
||||
compute myPe moving_particles reduce sum c_movppe
|
||||
compute myKe moving_particles ke
|
||||
fix 6 moving_particles ave/time 1 1 1 c_myTemp c_myPe c_myKe file temp.dat format '%20.16f'
|
||||
|
||||
# compute charges
|
||||
compute q electrodes property/atom q
|
||||
compute q_left Ne_left reduce sum c_q
|
||||
compute q_right Ne_right reduce sum c_q
|
||||
compute q_all electrodes reduce sum c_q
|
||||
|
||||
thermo_style custom step etotal c_myTemp c_q_left c_q_right c_q_all
|
||||
thermo 100
|
||||
|
||||
|
||||
# compute temperature individually for H and O atoms if desired
|
||||
|
||||
#group movingH type 1
|
||||
#group movingO type 2
|
||||
#compute myTempH movingH temp
|
||||
#compute myTempO movingO temp
|
||||
#fix 7 moving_particles ave/time 1 1 1 c_myTempH c_myTempO file tempOH.dat format '%20.16f'
|
||||
|
||||
|
||||
|
||||
# rigid water => use shake-algorithm
|
||||
# ----------------------------------
|
||||
|
||||
# must be at end of input file,
|
||||
# if deactivating shake remember to choose smaller timestep,
|
||||
# i.e. dt = 0.5 fs (or 20 Hartree atomic units) works fine
|
||||
|
||||
fix 3 moving_particles shake 0.0001 20 0 b 1 a 1
|
||||
|
||||
|
||||
|
||||
# run simulation and write final configuration for restart
|
||||
# --------------------------------------------------------
|
||||
|
||||
# total number of timesteps
|
||||
|
||||
run 100000
|
||||
|
||||
|
||||
# write final coordinates and velocities,
|
||||
# nocoeff needed, or LAMMPS will not be able to restart from final.inp
|
||||
|
||||
write_data final.inp nocoeff
|
||||
|
||||
27
examples/PACKAGES/electrode/thermo/potential.inp
Normal file
27
examples/PACKAGES/electrode/thermo/potential.inp
Normal file
@ -0,0 +1,27 @@
|
||||
# W.L. Jorgensen et.al., The Journal of Chemical Physics 79926 (1983);
|
||||
# https://doi.org/10.1063/1.44586
|
||||
|
||||
# create groups
|
||||
group H type 1
|
||||
group O type 2
|
||||
group Ne_a type 3
|
||||
group Ne_b type 4
|
||||
|
||||
# set charges
|
||||
set group O charge -0.830
|
||||
set group H charge 0.415
|
||||
set group Ne_a charge 0
|
||||
set group Ne_b charge 0
|
||||
|
||||
# TIP3P Potential Parameters
|
||||
pair_style lj/cut/coul/long 16.0
|
||||
pair_coeff * * 0.0 0.0
|
||||
pair_coeff 2 2 0.102 3.188
|
||||
bond_style harmonic
|
||||
bond_coeff 1 450 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 55 104.52
|
||||
|
||||
# O - electrode (Ne) interaction
|
||||
pair_coeff 2 3 0.102 3.188
|
||||
pair_coeff 2 4 0.102 3.188
|
||||
7
examples/PACKAGES/electrode/thermo/rng.py
Executable file
7
examples/PACKAGES/electrode/thermo/rng.py
Executable file
@ -0,0 +1,7 @@
|
||||
#!/usr/bin/env python3
|
||||
|
||||
import numpy as np
|
||||
|
||||
rng = np.random.default_rng(7)
|
||||
vals = rng.standard_normal(10 ** 6 + 1)
|
||||
np.savetxt("random.inp", vals)
|
||||
14853
examples/PACKAGES/electrode/thermo/sample.inp
Normal file
14853
examples/PACKAGES/electrode/thermo/sample.inp
Normal file
File diff suppressed because it is too large
Load Diff
131
examples/PACKAGES/electrode/thermo/thermo/control.inp
Normal file
131
examples/PACKAGES/electrode/thermo/thermo/control.inp
Normal file
@ -0,0 +1,131 @@
|
||||
|
||||
# Thermopotentiostat example calculation for nano-confined water
|
||||
# between two electrodes (Ne) with applied voltage. Simulation
|
||||
# can be performed with unmodified version of LAMMPS. Run as:
|
||||
#
|
||||
# lmp -in control.inp
|
||||
#
|
||||
# Output files:
|
||||
# temp.dat temperature
|
||||
# md.xyz trajectory
|
||||
# final.inp final configuration for restarting
|
||||
#
|
||||
# F. Deissenbeck, C. Freysoldt, M. Todorova, J. Neugebauer, S. Wippermann,
|
||||
# wippermann@mpie.de, 12.08.2020
|
||||
|
||||
|
||||
units real
|
||||
dimension 3
|
||||
atom_style full
|
||||
processors * * 2
|
||||
|
||||
kspace_style pppm/electrode 1.0e-5
|
||||
kspace_modify slab 4.0 # non-periodic electrostatic boundary conditions in z-direction
|
||||
kspace_modify gewald 0.2311815
|
||||
boundary p p f
|
||||
|
||||
read_data ../sample.inp
|
||||
include ../potential.inp
|
||||
neighbor 2.0 bin
|
||||
neigh_modify one 3000
|
||||
|
||||
|
||||
|
||||
# input parameters
|
||||
# ----------------
|
||||
|
||||
variable dt equal 0.967553728 # time step [fs],
|
||||
# 0.483776864 fs = 20 Hartree a.u.
|
||||
variable dumpsteps equal 1000 # dump trajectory every ${dumpsteps} steps
|
||||
|
||||
|
||||
|
||||
group moving_particles type 1 2
|
||||
group electrodes type 3 4
|
||||
|
||||
group Ne_left type 3
|
||||
group Ne_right type 4
|
||||
|
||||
|
||||
|
||||
|
||||
# NVE section (+ explicit thermostat if desired)
|
||||
# ----------------------------------------------
|
||||
|
||||
timestep ${dt}
|
||||
|
||||
# init velocities to setup new claculation,
|
||||
# not needed here since sample.inp is already equilibrated (at Phi0 = 0 V)
|
||||
|
||||
#velocity moving_particles create 350.0 4928459 rot yes dist gaussian
|
||||
|
||||
|
||||
# apply explicit thermostat if desired,
|
||||
# also not needed here since electrode charge distribution
|
||||
# of thermopotentiostat has an explicit temperature (charge fluctuations)
|
||||
# that actively controls the kinetic temperature
|
||||
|
||||
#fix 1 moving_particles temp/csvr 350.0 350.0 ${th_time} 54324
|
||||
#fix 1 moving_particles langevin 350.0 350.0 ${th_time} 699483
|
||||
|
||||
|
||||
# integrate Hamiltonian equations of motion -> pure NVE ensemble
|
||||
|
||||
fix 2 moving_particles nve
|
||||
|
||||
|
||||
# ensure electrodes are not moving
|
||||
|
||||
fix freeze1 Ne_left setforce 0.0 0.0 0.0
|
||||
fix freeze2 Ne_right setforce 0.0 0.0 0.0
|
||||
|
||||
|
||||
|
||||
# thermopotentiostat section
|
||||
# --------------------------
|
||||
|
||||
fix thermoid Ne_left electrode/thermo 1.0 1.805132 couple Ne_right -1.0 temp 350 100 write_mat mat.csv
|
||||
|
||||
# output section
|
||||
# --------------
|
||||
|
||||
dump 5 all custom ${dumpsteps} md.xyz id element xu yu zu q
|
||||
dump_modify 5 format float %20.15g element H O Ne_a Ne_b sort id
|
||||
|
||||
|
||||
# compute temperature
|
||||
|
||||
compute myTemp moving_particles temp
|
||||
compute movppe moving_particles pe/atom
|
||||
compute myPe moving_particles reduce sum c_movppe
|
||||
compute myKe moving_particles ke
|
||||
fix 6 moving_particles ave/time 1 1 1 c_myTemp c_myPe c_myKe file temp.dat format '%20.16f'
|
||||
|
||||
# compute charges
|
||||
compute q electrodes property/atom q
|
||||
compute q_left Ne_left reduce sum c_q
|
||||
compute q_right Ne_right reduce sum c_q
|
||||
compute q_all electrodes reduce sum c_q
|
||||
|
||||
thermo_style custom step etotal c_myTemp c_q_left c_q_right c_q_all f_thermoid[1] f_thermoid[2]
|
||||
thermo 100
|
||||
|
||||
|
||||
|
||||
fix 3 moving_particles shake 0.0001 20 0 b 1 a 1
|
||||
|
||||
|
||||
|
||||
# run simulation and write final configuration for restart
|
||||
# --------------------------------------------------------
|
||||
|
||||
# total number of timesteps
|
||||
|
||||
run 100000
|
||||
|
||||
|
||||
# write final coordinates and velocities,
|
||||
# nocoeff needed, or LAMMPS will not be able to restart from final.inp
|
||||
|
||||
write_data final.inp nocoeff
|
||||
|
||||
3
examples/PACKAGES/electrode/thoams-fermi/.gitignore
vendored
Normal file
3
examples/PACKAGES/electrode/thoams-fermi/.gitignore
vendored
Normal file
@ -0,0 +1,3 @@
|
||||
*.csv
|
||||
log.lammps_*
|
||||
tf.data
|
||||
600
examples/PACKAGES/electrode/thoams-fermi/charged.data
Normal file
600
examples/PACKAGES/electrode/thoams-fermi/charged.data
Normal file
@ -0,0 +1,600 @@
|
||||
LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0
|
||||
|
||||
288 atoms
|
||||
2 atom types
|
||||
|
||||
0.285001 25.325067 xlo xhi
|
||||
-0.368323 24.671743 ylo yhi
|
||||
-1.043333 43.303354 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 196.966553
|
||||
2 196.966553
|
||||
|
||||
Pair Coeffs # lj/cut/coul/long
|
||||
|
||||
1 0 0
|
||||
2 0 0
|
||||
|
||||
Atoms # full
|
||||
|
||||
1 1 1 -0.00023 25.040066 0 8 0 1 0
|
||||
2 1 1 -0.002921 2.086672 2.086672 8 0 0 0
|
||||
3 1 1 -0.04033 2.086672 0 10.086673 0 1 0
|
||||
4 1 1 -0.012754 25.040066 2.086672 10.086673 0 0 0
|
||||
5 1 1 -0.000757 4.173345 0 8 0 1 0
|
||||
6 1 1 -0.000483 6.260016 2.086672 8 0 0 0
|
||||
7 1 1 -0.02377 6.260016 0 10.086673 0 1 0
|
||||
8 1 1 -0.031311 4.173345 2.086672 10.086673 0 0 0
|
||||
9 1 1 -0.002302 8.346689 0 8 0 1 0
|
||||
10 1 1 -0.000534 10.433361 2.086672 8 0 0 0
|
||||
11 1 1 -0.006246 10.433361 0 10.086673 0 1 0
|
||||
12 1 1 -0.03014 8.346689 2.086672 10.086673 0 0 0
|
||||
13 1 1 0.000222 12.520033 0 8 0 1 0
|
||||
14 1 1 -0.000958 14.606705 2.086672 8 0 0 0
|
||||
15 1 1 -0.024586 14.606705 0 10.086673 0 1 0
|
||||
16 1 1 -0.032305 12.520033 2.086672 10.086673 0 0 0
|
||||
17 1 1 -0.001102 16.693378 0 8 0 1 0
|
||||
18 1 1 0.00046 18.780048 2.086672 8 0 0 0
|
||||
19 1 1 -0.011993 18.780048 0 10.086673 0 1 0
|
||||
20 1 1 -0.015815 16.693378 2.086672 10.086673 0 0 0
|
||||
21 1 1 0.001654 20.86672 0 8 0 1 0
|
||||
22 1 1 0.000999 22.953394 2.086672 8 0 0 0
|
||||
23 1 1 -0.010485 22.953394 0 10.086673 0 1 0
|
||||
24 1 1 -0.038444 20.86672 2.086672 10.086673 0 0 0
|
||||
25 1 1 3.8e-05 25.040066 4.173345 8 0 0 0
|
||||
26 1 1 -3e-05 2.086672 6.260016 8 0 0 0
|
||||
27 1 1 -0.011104 2.086672 4.173345 10.086673 0 0 0
|
||||
28 1 1 -0.032472 25.040066 6.260016 10.086673 0 0 0
|
||||
29 1 1 0.000807 4.173345 4.173345 8 0 0 0
|
||||
30 1 1 -0.000974 6.260016 6.260016 8 0 0 0
|
||||
31 1 1 -0.017105 6.260016 4.173345 10.086673 0 0 0
|
||||
32 1 1 -0.010937 4.173345 6.260016 10.086673 0 0 0
|
||||
33 1 1 0.001587 8.346689 4.173345 8 0 0 0
|
||||
34 1 1 0.001733 10.433361 6.260016 8 0 0 0
|
||||
35 1 1 -0.001065 10.433361 4.173345 10.086673 0 0 0
|
||||
36 1 1 0.004269 8.346689 6.260016 10.086673 0 0 0
|
||||
37 1 1 -0.000623 12.520033 4.173345 8 0 0 0
|
||||
38 1 1 -0.003876 14.606705 6.260016 8 0 0 0
|
||||
39 1 1 -0.030292 14.606705 4.173345 10.086673 0 0 0
|
||||
40 1 1 -0.024863 12.520033 6.260016 10.086673 0 0 0
|
||||
41 1 1 -0.000446 16.693378 4.173345 8 0 0 0
|
||||
42 1 1 -0.002036 18.780048 6.260016 8 0 0 0
|
||||
43 1 1 -0.031052 18.780048 4.173345 10.086673 0 0 0
|
||||
44 1 1 -0.044616 16.693378 6.260016 10.086673 0 0 0
|
||||
45 1 1 -0.001031 20.86672 4.173345 8 0 0 0
|
||||
46 1 1 -0.00021 22.953394 6.260016 8 0 0 0
|
||||
47 1 1 -0.004291 22.953394 4.173345 10.086673 0 0 0
|
||||
48 1 1 -0.020295 20.86672 6.260016 10.086673 0 0 0
|
||||
49 1 1 -0.006345 25.040066 8.346689 8 0 0 0
|
||||
50 1 1 -0.00328 2.086672 10.433361 8 0 0 0
|
||||
51 1 1 -0.037649 2.086672 8.346689 10.086673 0 0 0
|
||||
52 1 1 -0.05504 25.040066 10.433361 10.086673 0 0 0
|
||||
53 1 1 -0.000151 4.173345 8.346689 8 0 0 0
|
||||
54 1 1 -0.000508 6.260016 10.433361 8 0 0 0
|
||||
55 1 1 -0.014809 6.260016 8.346689 10.086673 0 0 0
|
||||
56 1 1 -0.016074 4.173345 10.433361 10.086673 0 0 0
|
||||
57 1 1 0.00092 8.346689 8.346689 8 0 0 0
|
||||
58 1 1 -0.003585 10.433361 10.433361 8 0 0 0
|
||||
59 1 1 -0.015447 10.433361 8.346689 10.086673 0 0 0
|
||||
60 1 1 -0.037118 8.346689 10.433361 10.086673 0 0 0
|
||||
61 1 1 -0.000856 12.520033 8.346689 8 0 0 0
|
||||
62 1 1 0.001309 14.606705 10.433361 8 0 0 0
|
||||
63 1 1 -0.034936 14.606705 8.346689 10.086673 0 0 0
|
||||
64 1 1 -0.022444 12.520033 10.433361 10.086673 0 0 0
|
||||
65 1 1 -0.00144 16.693378 8.346689 8 0 0 0
|
||||
66 1 1 -0.004359 18.780048 10.433361 8 0 0 0
|
||||
67 1 1 -0.02956 18.780048 8.346689 10.086673 0 0 0
|
||||
68 1 1 -0.008916 16.693378 10.433361 10.086673 0 0 0
|
||||
69 1 1 0.0004 20.86672 8.346689 8 0 0 0
|
||||
70 1 1 0.000209 22.953394 10.433361 8 0 0 0
|
||||
71 1 1 -0.017199 22.953394 8.346689 10.086673 0 0 0
|
||||
72 1 1 -0.03354 20.86672 10.433361 10.086673 0 0 0
|
||||
73 1 1 -8e-05 25.040066 12.520033 8 0 0 0
|
||||
74 1 1 -0.000342 2.086672 14.606705 8 0 0 0
|
||||
75 1 1 -0.027442 2.086672 12.520033 10.086673 0 0 0
|
||||
76 1 1 -0.025027 25.040066 14.606705 10.086673 0 0 0
|
||||
77 1 1 0.000536 4.173345 12.520033 8 0 0 0
|
||||
78 1 1 -0.000368 6.260016 14.606705 8 0 0 0
|
||||
79 1 1 -0.022015 6.260016 12.520033 10.086673 0 0 0
|
||||
80 1 1 0.003048 4.173345 14.606705 10.086673 0 0 0
|
||||
81 1 1 -0.002516 8.346689 12.520033 8 0 0 0
|
||||
82 1 1 0.002034 10.433361 14.606705 8 0 0 0
|
||||
83 1 1 -0.012341 10.433361 12.520033 10.086673 0 0 0
|
||||
84 1 1 -0.004673 8.346689 14.606705 10.086673 0 0 0
|
||||
85 1 1 0.000168 12.520033 12.520033 8 0 0 0
|
||||
86 1 1 0.000653 14.606705 14.606705 8 0 0 0
|
||||
87 1 1 0.007996 14.606705 12.520033 10.086673 0 0 0
|
||||
88 1 1 0.015522 12.520033 14.606705 10.086673 0 0 0
|
||||
89 1 1 -2.2e-05 16.693378 12.520033 8 0 0 0
|
||||
90 1 1 0.000716 18.780048 14.606705 8 0 0 0
|
||||
91 1 1 -0.013279 18.780048 12.520033 10.086673 0 0 0
|
||||
92 1 1 -0.001057 16.693378 14.606705 10.086673 0 0 0
|
||||
93 1 1 -0.000971 20.86672 12.520033 8 0 0 0
|
||||
94 1 1 -0.000871 22.953394 14.606705 8 0 0 0
|
||||
95 1 1 -0.014468 22.953394 12.520033 10.086673 0 0 0
|
||||
96 1 1 -0.028593 20.86672 14.606705 10.086673 0 0 0
|
||||
97 1 1 -0.000311 25.040066 16.693378 8 0 0 0
|
||||
98 1 1 -0.001941 2.086672 18.780048 8 0 0 0
|
||||
99 1 1 -0.015815 2.086672 16.693378 10.086673 0 0 0
|
||||
100 1 1 -0.012408 25.040066 18.780048 10.086673 0 0 0
|
||||
101 1 1 0.000289 4.173345 16.693378 8 0 0 0
|
||||
102 1 1 7.1e-05 6.260016 18.780048 8 0 0 0
|
||||
103 1 1 -0.03149 6.260016 16.693378 10.086673 0 0 0
|
||||
104 1 1 -0.033754 4.173345 18.780048 10.086673 0 0 0
|
||||
105 1 1 -0.003025 8.346689 16.693378 8 0 0 0
|
||||
106 1 1 -4.9e-05 10.433361 18.780048 8 0 0 0
|
||||
107 1 1 -0.026304 10.433361 16.693378 10.086673 0 0 0
|
||||
108 1 1 -0.025007 8.346689 18.780048 10.086673 0 0 0
|
||||
109 1 1 0.001185 12.520033 16.693378 8 0 0 0
|
||||
110 1 1 -0.000778 14.606705 18.780048 8 0 0 0
|
||||
111 1 1 -0.020266 14.606705 16.693378 10.086673 0 0 0
|
||||
112 1 1 -0.010312 12.520033 18.780048 10.086673 0 0 0
|
||||
113 1 1 -0.000613 16.693378 16.693378 8 0 0 0
|
||||
114 1 1 -0.000958 18.780048 18.780048 8 0 0 0
|
||||
115 1 1 -0.036602 18.780048 16.693378 10.086673 0 0 0
|
||||
116 1 1 -0.029068 16.693378 18.780048 10.086673 0 0 0
|
||||
117 1 1 -0.005554 20.86672 16.693378 8 0 0 0
|
||||
118 1 1 0.000738 22.953394 18.780048 8 0 0 0
|
||||
119 1 1 -0.027189 22.953394 16.693378 10.086673 0 0 0
|
||||
120 1 1 -0.023111 20.86672 18.780048 10.086673 0 0 0
|
||||
121 1 1 7.5e-05 25.040066 20.86672 8 0 0 0
|
||||
122 1 1 0.000623 2.086672 22.953394 8 0 0 0
|
||||
123 1 1 -0.007516 2.086672 20.86672 10.086673 0 0 0
|
||||
124 1 1 -0.014682 25.040066 22.953394 10.086673 0 0 0
|
||||
125 1 1 0.000878 4.173345 20.86672 8 0 0 0
|
||||
126 1 1 -0.001576 6.260016 22.953394 8 0 0 0
|
||||
127 1 1 -0.029629 6.260016 20.86672 10.086673 0 0 0
|
||||
128 1 1 0.004728 4.173345 22.953394 10.086673 0 0 0
|
||||
129 1 1 -0.003433 8.346689 20.86672 8 0 0 0
|
||||
130 1 1 -0.000577 10.433361 22.953394 8 0 0 0
|
||||
131 1 1 -0.026467 10.433361 20.86672 10.086673 0 0 0
|
||||
132 1 1 -0.043264 8.346689 22.953394 10.086673 0 0 0
|
||||
133 1 1 -0.000921 12.520033 20.86672 8 0 0 0
|
||||
134 1 1 -0.000361 14.606705 22.953394 8 0 0 0
|
||||
135 1 1 -0.017852 14.606705 20.86672 10.086673 0 0 0
|
||||
136 1 1 -0.021653 12.520033 22.953394 10.086673 0 0 0
|
||||
137 1 1 0.000268 16.693378 20.86672 8 0 0 0
|
||||
138 1 1 -0.000345 18.780048 22.953394 8 0 0 0
|
||||
139 1 1 -0.00903 18.780048 20.86672 10.086673 0 0 0
|
||||
140 1 1 -0.01542 16.693378 22.953394 10.086673 0 0 0
|
||||
141 1 1 0.000128 20.86672 20.86672 8 0 0 0
|
||||
142 1 1 0.000334 22.953394 22.953394 8 0 0 0
|
||||
143 1 1 -0.002285 22.953394 20.86672 10.086673 0 0 0
|
||||
144 1 1 -0.00745 20.86672 22.953394 10.086673 0 0 0
|
||||
145 2 2 0.019659 25.040066 0 32.173344 0 1 0
|
||||
146 2 2 0.022955 2.086672 2.086672 32.173344 0 0 0
|
||||
147 2 2 0.000876 2.086672 0 34.260021 0 1 0
|
||||
148 2 2 0.00156 25.040066 2.086672 34.260021 0 0 0
|
||||
149 2 2 0.027435 4.173345 0 32.173344 0 1 0
|
||||
150 2 2 0.020862 6.260016 2.086672 32.173344 0 0 0
|
||||
151 2 2 0.001578 6.260016 0 34.260021 0 1 0
|
||||
152 2 2 0.001014 4.173345 2.086672 34.260021 0 0 0
|
||||
153 2 2 0.021009 8.346689 0 32.173344 0 1 0
|
||||
154 2 2 0.01514 10.433361 2.086672 32.173344 0 0 0
|
||||
155 2 2 0.001872 10.433361 0 34.260021 0 1 0
|
||||
156 2 2 0.001184 8.346689 2.086672 34.260021 0 0 0
|
||||
157 2 2 0.004752 12.520033 0 32.173344 0 1 0
|
||||
158 2 2 0.005408 14.606705 2.086672 32.173344 0 0 0
|
||||
159 2 2 0.000237 14.606705 0 34.260021 0 1 0
|
||||
160 2 2 0.001509 12.520033 2.086672 34.260021 0 0 0
|
||||
161 2 2 0.012702 16.693378 0 32.173344 0 1 0
|
||||
162 2 2 0.017746 18.780048 2.086672 32.173344 0 0 0
|
||||
163 2 2 0.001489 18.780048 0 34.260021 0 1 0
|
||||
164 2 2 0.000611 16.693378 2.086672 34.260021 0 0 0
|
||||
165 2 2 0.034109 20.86672 0 32.173344 0 1 0
|
||||
166 2 2 0.031678 22.953394 2.086672 32.173344 0 0 0
|
||||
167 2 2 0.002473 22.953394 0 34.260021 0 1 0
|
||||
168 2 2 0.002352 20.86672 2.086672 34.260021 0 0 0
|
||||
169 2 2 0.014267 25.040066 4.173345 32.173344 0 0 0
|
||||
170 2 2 0.008185 2.086672 6.260016 32.173344 0 0 0
|
||||
171 2 2 0.001602 2.086672 4.173345 34.260021 0 0 0
|
||||
172 2 2 0.000168 25.040066 6.260016 34.260021 0 0 0
|
||||
173 2 2 0.022473 4.173345 4.173345 32.173344 0 0 0
|
||||
174 2 2 0.03292 6.260016 6.260016 32.173344 0 0 0
|
||||
175 2 2 0.002046 6.260016 4.173345 34.260021 0 0 0
|
||||
176 2 2 0.000803 4.173345 6.260016 34.260021 0 0 0
|
||||
177 2 2 0.032031 8.346689 4.173345 32.173344 0 0 0
|
||||
178 2 2 0.02783 10.433361 6.260016 32.173344 0 0 0
|
||||
179 2 2 0.001241 10.433361 4.173345 34.260021 0 0 0
|
||||
180 2 2 0.002258 8.346689 6.260016 34.260021 0 0 0
|
||||
181 2 2 0.019546 12.520033 4.173345 32.173344 0 0 0
|
||||
182 2 2 0.016796 14.606705 6.260016 32.173344 0 0 0
|
||||
183 2 2 0.00231 14.606705 4.173345 34.260021 0 0 0
|
||||
184 2 2 0.001481 12.520033 6.260016 34.260021 0 0 0
|
||||
185 2 2 0.014646 16.693378 4.173345 32.173344 0 0 0
|
||||
186 2 2 0.008992 18.780048 6.260016 32.173344 0 0 0
|
||||
187 2 2 0.000504 18.780048 4.173345 34.260021 0 0 0
|
||||
188 2 2 0.000878 16.693378 6.260016 34.260021 0 0 0
|
||||
189 2 2 0.021772 20.86672 4.173345 32.173344 0 0 0
|
||||
190 2 2 0.01304 22.953394 6.260016 32.173344 0 0 0
|
||||
191 2 2 0.00118 22.953394 4.173345 34.260021 0 0 0
|
||||
192 2 2 0.001457 20.86672 6.260016 34.260021 0 0 0
|
||||
193 2 2 0.001698 25.040066 8.346689 32.173344 0 0 0
|
||||
194 2 2 0.025689 2.086672 10.433361 32.173344 0 0 0
|
||||
195 2 2 0.000649 2.086672 8.346689 34.260021 0 0 0
|
||||
196 2 2 0.00215 25.040066 10.433361 34.260021 0 0 0
|
||||
197 2 2 0.015557 4.173345 8.346689 32.173344 0 0 0
|
||||
198 2 2 0.025584 6.260016 10.433361 32.173344 0 0 0
|
||||
199 2 2 0.002292 6.260016 8.346689 34.260021 0 0 0
|
||||
200 2 2 0.000819 4.173345 10.433361 34.260021 0 0 0
|
||||
201 2 2 0.035591 8.346689 8.346689 32.173344 0 0 0
|
||||
202 2 2 0.015873 10.433361 10.433361 32.173344 0 0 0
|
||||
203 2 2 0.000758 10.433361 8.346689 34.260021 0 0 0
|
||||
204 2 2 0.002678 8.346689 10.433361 34.260021 0 0 0
|
||||
205 2 2 0.008097 12.520033 8.346689 32.173344 0 0 0
|
||||
206 2 2 0.015646 14.606705 10.433361 32.173344 0 0 0
|
||||
207 2 2 0.001702 14.606705 8.346689 34.260021 0 0 0
|
||||
208 2 2 0.000994 12.520033 10.433361 34.260021 0 0 0
|
||||
209 2 2 0.017819 16.693378 8.346689 32.173344 0 0 0
|
||||
210 2 2 0.029386 18.780048 10.433361 32.173344 0 0 0
|
||||
211 2 2 0.000676 18.780048 8.346689 34.260021 0 0 0
|
||||
212 2 2 0.001677 16.693378 10.433361 34.260021 0 0 0
|
||||
213 2 2 0.020182 20.86672 8.346689 32.173344 0 0 0
|
||||
214 2 2 0.02881 22.953394 10.433361 32.173344 0 0 0
|
||||
215 2 2 0.002276 22.953394 8.346689 34.260021 0 0 0
|
||||
216 2 2 0.003118 20.86672 10.433361 34.260021 0 0 0
|
||||
217 2 2 0.012257 25.040066 12.520033 32.173344 0 0 0
|
||||
218 2 2 0.021343 2.086672 14.606705 32.173344 0 0 0
|
||||
219 2 2 0.001799 2.086672 12.520033 34.260021 0 0 0
|
||||
220 2 2 0.001591 25.040066 14.606705 34.260021 0 0 0
|
||||
221 2 2 0.022952 4.173345 12.520033 32.173344 0 0 0
|
||||
222 2 2 0.012325 6.260016 14.606705 32.173344 0 0 0
|
||||
223 2 2 0.001876 6.260016 12.520033 34.260021 0 0 0
|
||||
224 2 2 0.001718 4.173345 14.606705 34.260021 0 0 0
|
||||
225 2 2 0.023719 8.346689 12.520033 32.173344 0 0 0
|
||||
226 2 2 0.004714 10.433361 14.606705 32.173344 0 0 0
|
||||
227 2 2 0.001251 10.433361 12.520033 34.260021 0 0 0
|
||||
228 2 2 0.000744 8.346689 14.606705 34.260021 0 0 0
|
||||
229 2 2 0.018756 12.520033 12.520033 32.173344 0 0 0
|
||||
230 2 2 -0.00689 14.606705 14.606705 32.173344 0 0 0
|
||||
231 2 2 0.000922 14.606705 12.520033 34.260021 0 0 0
|
||||
232 2 2 -0.002432 12.520033 14.606705 34.260021 0 0 0
|
||||
233 2 2 0.015625 16.693378 12.520033 32.173344 0 0 0
|
||||
234 2 2 -0.009585 18.780048 14.606705 32.173344 0 0 0
|
||||
235 2 2 0.001459 18.780048 12.520033 34.260021 0 0 0
|
||||
236 2 2 0.001044 16.693378 14.606705 34.260021 0 0 0
|
||||
237 2 2 0.020359 20.86672 12.520033 32.173344 0 0 0
|
||||
238 2 2 0.004616 22.953394 14.606705 32.173344 0 0 0
|
||||
239 2 2 0.000697 22.953394 12.520033 34.260021 0 0 0
|
||||
240 2 2 5e-06 20.86672 14.606705 34.260021 0 0 0
|
||||
241 2 2 0.029057 25.040066 16.693378 32.173344 0 0 0
|
||||
242 2 2 0.034403 2.086672 18.780048 32.173344 0 0 0
|
||||
243 2 2 0.002402 2.086672 16.693378 34.260021 0 0 0
|
||||
244 2 2 0.001076 25.040066 18.780048 34.260021 0 0 0
|
||||
245 2 2 0.021827 4.173345 16.693378 32.173344 0 0 0
|
||||
246 2 2 0.011918 6.260016 18.780048 32.173344 0 0 0
|
||||
247 2 2 0.000792 6.260016 16.693378 34.260021 0 0 0
|
||||
248 2 2 0.002071 4.173345 18.780048 34.260021 0 0 0
|
||||
249 2 2 -0.002694 8.346689 16.693378 32.173344 0 0 0
|
||||
250 2 2 -0.000573 10.433361 18.780048 32.173344 0 0 0
|
||||
251 2 2 0.000448 10.433361 16.693378 34.260021 0 0 0
|
||||
252 2 2 0.000351 8.346689 18.780048 34.260021 0 0 0
|
||||
253 2 2 0.001141 12.520033 16.693378 32.173344 0 0 0
|
||||
254 2 2 0.015575 14.606705 18.780048 32.173344 0 0 0
|
||||
255 2 2 0.000258 14.606705 16.693378 34.260021 0 0 0
|
||||
256 2 2 0.000372 12.520033 18.780048 34.260021 0 0 0
|
||||
257 2 2 0.011285 16.693378 16.693378 32.173344 0 0 0
|
||||
258 2 2 0.035183 18.780048 18.780048 32.173344 0 0 0
|
||||
259 2 2 0.0002 18.780048 16.693378 34.260021 0 0 0
|
||||
260 2 2 0.001199 16.693378 18.780048 34.260021 0 0 0
|
||||
261 2 2 0.034083 20.86672 16.693378 32.173344 0 0 0
|
||||
262 2 2 0.036995 22.953394 18.780048 32.173344 0 0 0
|
||||
263 2 2 0.001484 22.953394 16.693378 34.260021 0 0 0
|
||||
264 2 2 0.00377 20.86672 18.780048 34.260021 0 0 0
|
||||
265 2 2 0.024028 25.040066 20.86672 32.173344 0 0 0
|
||||
266 2 2 0.037372 2.086672 22.953394 32.173344 0 0 0
|
||||
267 2 2 0.002492 2.086672 20.86672 34.260021 0 0 0
|
||||
268 2 2 0.001334 25.040066 22.953394 34.260021 0 0 0
|
||||
269 2 2 0.03734 4.173345 20.86672 32.173344 0 0 0
|
||||
270 2 2 0.015818 6.260016 22.953394 32.173344 0 0 0
|
||||
271 2 2 -0.0001 6.260016 20.86672 34.260021 0 0 0
|
||||
272 2 2 0.002801 4.173345 22.953394 34.260021 0 0 0
|
||||
273 2 2 0.017084 8.346689 20.86672 32.173344 0 0 0
|
||||
274 2 2 0.031072 10.433361 22.953394 32.173344 0 0 0
|
||||
275 2 2 -0.00031 10.433361 20.86672 34.260021 0 0 0
|
||||
276 2 2 0.001644 8.346689 22.953394 34.260021 0 0 0
|
||||
277 2 2 -0.004414 12.520033 20.86672 32.173344 0 0 0
|
||||
278 2 2 0.017397 14.606705 22.953394 32.173344 0 0 0
|
||||
279 2 2 0.001344 14.606705 20.86672 34.260021 0 0 0
|
||||
280 2 2 0.000672 12.520033 22.953394 34.260021 0 0 0
|
||||
281 2 2 0.0252 16.693378 20.86672 32.173344 0 0 0
|
||||
282 2 2 0.030927 18.780048 22.953394 32.173344 0 0 0
|
||||
283 2 2 0.002185 18.780048 20.86672 34.260021 0 0 0
|
||||
284 2 2 0.001824 16.693378 22.953394 34.260021 0 0 0
|
||||
285 2 2 0.043618 20.86672 20.86672 32.173344 0 0 0
|
||||
286 2 2 0.030615 22.953394 22.953394 32.173344 0 0 0
|
||||
287 2 2 0.001068 22.953394 20.86672 34.260021 0 0 0
|
||||
288 2 2 0.001887 20.86672 22.953394 34.260021 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
2 0 0 0
|
||||
3 0 0 0
|
||||
5 0 0 0
|
||||
6 0 0 0
|
||||
7 0 0 0
|
||||
8 0 0 0
|
||||
9 0 0 0
|
||||
12 0 0 0
|
||||
26 0 0 0
|
||||
27 0 0 0
|
||||
29 0 0 0
|
||||
30 0 0 0
|
||||
31 0 0 0
|
||||
32 0 0 0
|
||||
33 0 0 0
|
||||
36 0 0 0
|
||||
10 0 0 0
|
||||
11 0 0 0
|
||||
13 0 0 0
|
||||
14 0 0 0
|
||||
15 0 0 0
|
||||
16 0 0 0
|
||||
17 0 0 0
|
||||
20 0 0 0
|
||||
34 0 0 0
|
||||
35 0 0 0
|
||||
37 0 0 0
|
||||
38 0 0 0
|
||||
39 0 0 0
|
||||
40 0 0 0
|
||||
41 0 0 0
|
||||
44 0 0 0
|
||||
1 0 0 0
|
||||
4 0 0 0
|
||||
18 0 0 0
|
||||
19 0 0 0
|
||||
21 0 0 0
|
||||
22 0 0 0
|
||||
23 0 0 0
|
||||
24 0 0 0
|
||||
25 0 0 0
|
||||
28 0 0 0
|
||||
42 0 0 0
|
||||
43 0 0 0
|
||||
45 0 0 0
|
||||
46 0 0 0
|
||||
47 0 0 0
|
||||
48 0 0 0
|
||||
50 0 0 0
|
||||
51 0 0 0
|
||||
53 0 0 0
|
||||
54 0 0 0
|
||||
55 0 0 0
|
||||
56 0 0 0
|
||||
57 0 0 0
|
||||
60 0 0 0
|
||||
74 0 0 0
|
||||
75 0 0 0
|
||||
77 0 0 0
|
||||
78 0 0 0
|
||||
79 0 0 0
|
||||
80 0 0 0
|
||||
81 0 0 0
|
||||
84 0 0 0
|
||||
58 0 0 0
|
||||
59 0 0 0
|
||||
61 0 0 0
|
||||
62 0 0 0
|
||||
63 0 0 0
|
||||
64 0 0 0
|
||||
65 0 0 0
|
||||
68 0 0 0
|
||||
82 0 0 0
|
||||
83 0 0 0
|
||||
85 0 0 0
|
||||
86 0 0 0
|
||||
87 0 0 0
|
||||
88 0 0 0
|
||||
89 0 0 0
|
||||
92 0 0 0
|
||||
49 0 0 0
|
||||
52 0 0 0
|
||||
66 0 0 0
|
||||
67 0 0 0
|
||||
69 0 0 0
|
||||
70 0 0 0
|
||||
71 0 0 0
|
||||
72 0 0 0
|
||||
73 0 0 0
|
||||
76 0 0 0
|
||||
90 0 0 0
|
||||
91 0 0 0
|
||||
93 0 0 0
|
||||
94 0 0 0
|
||||
95 0 0 0
|
||||
96 0 0 0
|
||||
98 0 0 0
|
||||
99 0 0 0
|
||||
101 0 0 0
|
||||
102 0 0 0
|
||||
103 0 0 0
|
||||
104 0 0 0
|
||||
105 0 0 0
|
||||
108 0 0 0
|
||||
122 0 0 0
|
||||
123 0 0 0
|
||||
125 0 0 0
|
||||
126 0 0 0
|
||||
127 0 0 0
|
||||
128 0 0 0
|
||||
129 0 0 0
|
||||
132 0 0 0
|
||||
106 0 0 0
|
||||
107 0 0 0
|
||||
109 0 0 0
|
||||
110 0 0 0
|
||||
111 0 0 0
|
||||
112 0 0 0
|
||||
113 0 0 0
|
||||
116 0 0 0
|
||||
130 0 0 0
|
||||
131 0 0 0
|
||||
133 0 0 0
|
||||
134 0 0 0
|
||||
135 0 0 0
|
||||
136 0 0 0
|
||||
137 0 0 0
|
||||
140 0 0 0
|
||||
97 0 0 0
|
||||
100 0 0 0
|
||||
114 0 0 0
|
||||
115 0 0 0
|
||||
117 0 0 0
|
||||
118 0 0 0
|
||||
119 0 0 0
|
||||
120 0 0 0
|
||||
121 0 0 0
|
||||
124 0 0 0
|
||||
138 0 0 0
|
||||
139 0 0 0
|
||||
141 0 0 0
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||||
142 0 0 0
|
||||
143 0 0 0
|
||||
144 0 0 0
|
||||
146 0 0 0
|
||||
147 0 0 0
|
||||
149 0 0 0
|
||||
150 0 0 0
|
||||
151 0 0 0
|
||||
152 0 0 0
|
||||
153 0 0 0
|
||||
156 0 0 0
|
||||
170 0 0 0
|
||||
171 0 0 0
|
||||
173 0 0 0
|
||||
174 0 0 0
|
||||
175 0 0 0
|
||||
176 0 0 0
|
||||
177 0 0 0
|
||||
180 0 0 0
|
||||
154 0 0 0
|
||||
155 0 0 0
|
||||
157 0 0 0
|
||||
158 0 0 0
|
||||
159 0 0 0
|
||||
160 0 0 0
|
||||
161 0 0 0
|
||||
164 0 0 0
|
||||
178 0 0 0
|
||||
179 0 0 0
|
||||
181 0 0 0
|
||||
182 0 0 0
|
||||
183 0 0 0
|
||||
184 0 0 0
|
||||
185 0 0 0
|
||||
188 0 0 0
|
||||
145 0 0 0
|
||||
148 0 0 0
|
||||
162 0 0 0
|
||||
163 0 0 0
|
||||
165 0 0 0
|
||||
166 0 0 0
|
||||
167 0 0 0
|
||||
168 0 0 0
|
||||
169 0 0 0
|
||||
172 0 0 0
|
||||
186 0 0 0
|
||||
187 0 0 0
|
||||
189 0 0 0
|
||||
190 0 0 0
|
||||
191 0 0 0
|
||||
192 0 0 0
|
||||
194 0 0 0
|
||||
195 0 0 0
|
||||
197 0 0 0
|
||||
198 0 0 0
|
||||
199 0 0 0
|
||||
200 0 0 0
|
||||
201 0 0 0
|
||||
204 0 0 0
|
||||
218 0 0 0
|
||||
219 0 0 0
|
||||
221 0 0 0
|
||||
222 0 0 0
|
||||
223 0 0 0
|
||||
224 0 0 0
|
||||
225 0 0 0
|
||||
228 0 0 0
|
||||
202 0 0 0
|
||||
203 0 0 0
|
||||
205 0 0 0
|
||||
206 0 0 0
|
||||
207 0 0 0
|
||||
208 0 0 0
|
||||
209 0 0 0
|
||||
212 0 0 0
|
||||
226 0 0 0
|
||||
227 0 0 0
|
||||
229 0 0 0
|
||||
230 0 0 0
|
||||
231 0 0 0
|
||||
232 0 0 0
|
||||
233 0 0 0
|
||||
236 0 0 0
|
||||
193 0 0 0
|
||||
196 0 0 0
|
||||
210 0 0 0
|
||||
211 0 0 0
|
||||
213 0 0 0
|
||||
214 0 0 0
|
||||
215 0 0 0
|
||||
216 0 0 0
|
||||
217 0 0 0
|
||||
220 0 0 0
|
||||
234 0 0 0
|
||||
235 0 0 0
|
||||
237 0 0 0
|
||||
238 0 0 0
|
||||
239 0 0 0
|
||||
240 0 0 0
|
||||
242 0 0 0
|
||||
243 0 0 0
|
||||
245 0 0 0
|
||||
246 0 0 0
|
||||
247 0 0 0
|
||||
248 0 0 0
|
||||
249 0 0 0
|
||||
252 0 0 0
|
||||
266 0 0 0
|
||||
267 0 0 0
|
||||
269 0 0 0
|
||||
270 0 0 0
|
||||
271 0 0 0
|
||||
272 0 0 0
|
||||
273 0 0 0
|
||||
276 0 0 0
|
||||
250 0 0 0
|
||||
251 0 0 0
|
||||
253 0 0 0
|
||||
254 0 0 0
|
||||
255 0 0 0
|
||||
256 0 0 0
|
||||
257 0 0 0
|
||||
260 0 0 0
|
||||
274 0 0 0
|
||||
275 0 0 0
|
||||
277 0 0 0
|
||||
278 0 0 0
|
||||
279 0 0 0
|
||||
280 0 0 0
|
||||
281 0 0 0
|
||||
284 0 0 0
|
||||
241 0 0 0
|
||||
244 0 0 0
|
||||
258 0 0 0
|
||||
259 0 0 0
|
||||
261 0 0 0
|
||||
262 0 0 0
|
||||
263 0 0 0
|
||||
264 0 0 0
|
||||
265 0 0 0
|
||||
268 0 0 0
|
||||
282 0 0 0
|
||||
283 0 0 0
|
||||
285 0 0 0
|
||||
286 0 0 0
|
||||
287 0 0 0
|
||||
288 0 0 0
|
||||
19
examples/PACKAGES/electrode/thoams-fermi/charged.settings
Normal file
19
examples/PACKAGES/electrode/thoams-fermi/charged.settings
Normal file
@ -0,0 +1,19 @@
|
||||
atom_style full
|
||||
units real
|
||||
kspace_style pppm/electrode 1.0e-8
|
||||
kspace_modify gewald 0.231
|
||||
kspace_modify mesh 8 8 16
|
||||
kspace_modify order 5
|
||||
|
||||
boundary p p f
|
||||
kspace_modify slab 3.0
|
||||
pair_style lj/cut/coul/long 12 12
|
||||
processors * * 1
|
||||
|
||||
|
||||
read_data "charged.data"
|
||||
|
||||
group ele type 1 2
|
||||
group bot type 1
|
||||
group top type 2
|
||||
pair_coeff * * 0.0 0.0
|
||||
10
examples/PACKAGES/electrode/thoams-fermi/tf.in
Normal file
10
examples/PACKAGES/electrode/thoams-fermi/tf.in
Normal file
@ -0,0 +1,10 @@
|
||||
include charged.settings
|
||||
|
||||
kspace_modify amat onestep
|
||||
|
||||
fix fxupdate bot electrode/conp -1.0 1.805 couple top 1.0 write_mat tf.csv
|
||||
fix_modify fxupdate tf 1 1.0 18.1715745
|
||||
fix_modify fxupdate tf 2 1.0 18.1715745
|
||||
run 0
|
||||
|
||||
write_data tf.data
|
||||
Reference in New Issue
Block a user