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This commit is contained in:
Ludwig Ahrens-Iwers
2022-02-20 07:47:28 +00:00
committed by Shern Tee
parent efa5db4c58
commit c04f4a913f
8 changed files with 714 additions and 5 deletions
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3
examples/electrode/thoams-fermi/.gitignore vendored Normal file
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*.csv
log.lammps_*
tf.data

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examples/electrode/thoams-fermi/charged.data Normal file
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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
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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
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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
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236 0 0 0
193 0 0 0
196 0 0 0
210 0 0 0
211 0 0 0
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214 0 0 0
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217 0 0 0
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234 0 0 0
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239 0 0 0
240 0 0 0
242 0 0 0
243 0 0 0
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248 0 0 0
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252 0 0 0
266 0 0 0
267 0 0 0
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270 0 0 0
271 0 0 0
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276 0 0 0
250 0 0 0
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256 0 0 0
257 0 0 0
260 0 0 0
274 0 0 0
275 0 0 0
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278 0 0 0
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280 0 0 0
281 0 0 0
284 0 0 0
241 0 0 0
244 0 0 0
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287 0 0 0
288 0 0 0

19
examples/electrode/thoams-fermi/charged.settings Normal file
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@ -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/electrode/thoams-fermi/tf.in Normal file
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@ -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