Error "source type value could not be interpreted as target" about graphene mapping
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mengyy zhou
Apr 19, 2021, 12:14:24 PM4/19/21
to votca
Hi !
I have another problem, and looking forward to your answer. Four atoms
of graphene
need to be mapping
into a bead, but the system reports an error every time“source type value could not be interpreted as target"，this problem has been bothering me for a week，Thanks！
mengyy zhou
Apr 19, 2021, 12:17:40 PM4/19/21
to votca
The trajectory file cannot be uploaded normally, so I paste the text
，thanks！
0
ITEM: NUMBER OF ATOMS
420
ITEM: BOX BOUNDS pp pp pp
-8.1913882339999997e+00 4.6483830779000002e+01
-6.4119649000000001e+00 4.9306763662000002e+01
-1.0036178788000001e+01 6.3180167243000000e+01
ITEM: ATOMS id type xu yu zu
1 1 5.07717 1.82999 25.4
2 1 5.78731 3.05999 25.4
5 1 7.20759 3.05999 25.4
7 1 10.0482 3.05999 25.4
8 1 12.1786 1.82999 25.4
15 1 11.4684 3.05999 25.4
17 1 13.5989 1.82999 25.4
18 1 14.309 3.05999 25.4
29 1 15.7293 3.05999 25.4
31 1 18.5698 3.05999 25.4
3 1 5.07717 4.28999 25.4
4 1 5.78731 5.51999 25.4
6 1 7.91773 4.28999 25.4
9 1 5.07717 6.74999 25.4
10 1 5.78731 7.97999 25.4
11 1 7.20759 5.51999 25.4
12 1 7.91773 6.74999 25.4
19 1 5.07717 9.20999 25.4
21 1 7.20759 7.97999 25.4
22 1 7.91773 9.20999 25.4
13 1 9.33801 4.28999 25.4
14 1 10.0482 5.51999 25.4
16 1 12.1786 4.28999 25.4
23 1 9.33801 6.74999 25.4
24 1 10.0482 7.97999 25.4
25 1 11.4684 5.51999 25.4
26 1 12.1786 6.74999 25.4
27 1 13.5989 4.28999 25.4
37 1 9.33801 9.20999 25.4
39 1 11.4684 7.97999 25.4
40 1 12.1786 9.20999 25.4
41 1 13.5989 6.74999 25.4
59 1 13.5989 9.20999 25.4
28 1 14.309 5.51999 25.4
30 1 16.4394 4.28999 25.4
42 1 14.309 7.97999 25.4
43 1 15.7293 5.51999 25.4
44 1 16.4394 6.74999 25.4
45 1 17.8597 4.28999 25.4
46 1 18.5698 5.51999 25.4
61 1 15.7293 7.97999 25.4
62 1 16.4394 9.20999 25.4
63 1 17.8597 6.74999 25.4
64 1 18.5698 7.97999 25.4
85 1 17.8597 9.20999 25.4
20 1 5.78731 10.44 25.4
33 1 5.07717 11.67 25.4
35 1 7.20759 10.44 25.4
36 1 7.91773 11.67 25.4
54 1 7.91773 14.13 25.4
53 1 7.20759 12.9 25.4
51 1 5.07717 14.13 25.4
34 1 5.78731 12.9 25.4
38 1 10.0482 10.44 25.4
55 1 9.33801 11.67 25.4
57 1 11.4684 10.44 25.4
58 1 12.1786 11.67 25.4
81 1 13.5989 11.67 25.4
107 1 13.5989 14.13 25.4
80 1 12.1786 14.13 25.4
79 1 11.4684 12.9 25.4
77 1 9.33801 14.13 25.4
56 1 10.0482 12.9 25.4
60 1 14.309 10.44 25.4
83 1 15.7293 10.44 25.4
84 1 16.4394 11.67 25.4
86 1 18.5698 10.44 25.4
111 1 17.8597 11.67 25.4
139 1 17.8597 14.13 25.4
112 1 18.5698 12.9 25.4
110 1 16.4394 14.13 25.4
109 1 15.7293 12.9 25.4
82 1 14.309 12.9 25.4
52 1 5.78731 15.36 25.4
73 1 5.07717 16.59 25.4
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75 1 7.20759 15.36 25.4
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99 1 5.07717 19.05 25.4
100 1 5.78731 20.28 25.4
101 1 7.20759 17.82 25.4
102 1 7.91773 19.05 25.4
129 1 7.20759 20.28 25.4
78 1 10.0482 15.36 25.4
103 1 9.33801 16.59 25.4
104 1 10.0482 17.82 25.4
105 1 11.4684 15.36 25.4
106 1 12.1786 16.59 25.4
131 1 9.33801 19.05 25.4
132 1 10.0482 20.28 25.4
133 1 11.4684 17.82 25.4
134 1 12.1786 19.05 25.4
135 1 13.5989 16.59 25.4
161 1 11.4684 20.28 25.4
163 1 13.5989 19.05 25.4
108 1 14.309 15.36 25.4
136 1 14.309 17.82 25.4
137 1 15.7293 15.36 25.4
138 1 16.4394 16.59 25.4
140 1 18.5698 15.36 25.4
164 1 14.309 20.28 25.4
165 1 15.7293 17.82 25.4
166 1 16.4394 19.05 25.4
167 1 17.8597 16.59 25.4
168 1 18.5698 17.82 25.4
193 1 15.7293 20.28 25.4
195 1 17.8597 19.05 25.4
196 1 18.5698 20.28 25.4
127 1 5.07717 21.51 25.4
128 1 5.78731 22.74 25.4
130 1 7.91773 21.51 25.4
155 1 5.07717 23.97 25.4
156 1 5.78731 25.2 25.4
157 1 7.20759 22.74 25.4
158 1 7.91773 23.97 25.4
183 1 5.07717 26.43 25.4
185 1 7.20759 25.2 25.4
186 1 7.91773 26.43 25.4
159 1 9.33801 21.51 25.4
160 1 10.0482 22.74 25.4
162 1 12.1786 21.51 25.4
187 1 9.33801 23.97 25.4
188 1 10.0482 25.2 25.4
189 1 11.4684 22.74 25.4
190 1 12.1786 23.97 25.4
191 1 13.5989 21.51 25.4
215 1 9.33801 26.43 25.4
217 1 11.4684 25.2 25.4
218 1 12.1786 26.43 25.4
219 1 13.5989 23.97 25.4
247 1 13.5989 26.43 25.4
192 1 14.309 22.74 25.4
194 1 16.4394 21.51 25.4
220 1 14.309 25.2 25.4
221 1 15.7293 22.74 25.4
222 1 16.4394 23.97 25.4
223 1 17.8597 21.51 25.4
224 1 18.5698 22.74 25.4
249 1 15.7293 25.2 25.4
250 1 16.4394 26.43 25.4
251 1 17.8597 23.97 25.4
252 1 18.5698 25.2 25.4
279 1 17.8597 26.43 25.4
239 1 5.07717 31.35 25.4
240 1 5.78731 32.58 25.4
242 1 7.91773 31.35 25.4
269 1 7.20759 32.58 25.4
241 1 7.20759 30.12 25.4
214 1 7.91773 28.89 25.4
213 1 7.20759 27.66 25.4
212 1 5.78731 30.12 25.4
211 1 5.07717 28.89 25.4
184 1 5.78731 27.66 25.4
271 1 9.33801 31.35 25.4
272 1 10.0482 32.58 25.4
274 1 12.1786 31.35 25.4
301 1 11.4684 32.58 25.4
303 1 13.5989 31.35 25.4
275 1 13.5989 28.89 25.4
273 1 11.4684 30.12 25.4
246 1 12.1786 28.89 25.4
245 1 11.4684 27.66 25.4
244 1 10.0482 30.12 25.4
243 1 9.33801 28.89 25.4
216 1 10.0482 27.66 25.4
304 1 14.309 32.58 25.4
306 1 16.4394 31.35 25.4
331 1 15.7293 32.58 25.4
333 1 17.8597 31.35 25.4
334 1 18.5698 32.58 25.4
308 1 18.5698 30.12 25.4
307 1 17.8597 28.89 25.4
305 1 15.7293 30.12 25.4
280 1 18.5698 27.66 25.4
278 1 16.4394 28.89 25.4
277 1 15.7293 27.66 25.4
276 1 14.309 30.12 25.4
248 1 14.309 27.66 25.4
267 1 5.07717 33.81 25.4
268 1 5.78731 35.04 25.4
270 1 7.91773 33.81 25.4
295 1 5.07717 36.27 25.4
296 1 5.78731 37.5 25.4
297 1 7.20759 35.04 25.4
298 1 7.91773 36.27 25.4
324 1 7.20759 37.5 25.4
299 1 9.33801 33.81 25.4
300 1 10.0482 35.04 25.4
302 1 12.1786 33.81 25.4
325 1 9.33801 36.27 25.4
326 1 10.0482 37.5 25.4
327 1 11.4684 35.04 25.4
328 1 12.1786 36.27 25.4
329 1 13.5989 33.81 25.4
349 1 11.4684 37.5 25.4
351 1 13.5989 36.27 25.4
330 1 14.309 35.04 25.4
332 1 16.4394 33.81 25.4
352 1 14.309 37.5 25.4
353 1 15.7293 35.04 25.4
354 1 16.4394 36.27 25.4
355 1 17.8597 33.81 25.4
356 1 18.5698 35.04 25.4
372 1 15.7293 37.5 25.4
373 1 17.8597 36.27 25.4
374 1 18.5698 37.5 25.4
323 1 5.07717 38.73 25.4
350 1 12.1786 38.73 25.4
371 1 13.5989 38.73 25.4
32 1 20.7003 1.82999 25.4
47 1 19.9901 3.05999 25.4
49 1 22.1205 1.82999 25.4
50 1 22.8307 3.05999 25.4
69 1 24.251 3.05999 25.4
71 1 27.0915 3.05999 25.4
72 1 29.2219 1.82999 25.4
95 1 28.5118 3.05999 25.4
97 1 30.6422 1.82999 25.4
98 1 31.3524 3.05999 25.4
125 1 32.7727 3.05999 25.4
48 1 20.7003 4.28999 25.4
65 1 19.9901 5.51999 25.4
66 1 20.7003 6.74999 25.4
67 1 22.1205 4.28999 25.4
68 1 22.8307 5.51999 25.4
70 1 24.9611 4.28999 25.4
87 1 19.9901 7.97999 25.4
88 1 20.7003 9.20999 25.4
89 1 22.1205 6.74999 25.4
90 1 22.8307 7.97999 25.4
91 1 24.251 5.51999 25.4
92 1 24.9611 6.74999 25.4
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93 1 26.3814 4.28999 25.4
94 1 27.0915 5.51999 25.4
96 1 29.2219 4.28999 25.4
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121 1 28.5118 5.51999 25.4
122 1 29.2219 6.74999 25.4
147 1 26.3814 9.20999 25.4
149 1 28.5118 7.97999 25.4
150 1 29.2219 9.20999 25.4
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152 1 31.3524 7.97999 25.4
153 1 32.7727 5.51999 25.4
154 1 33.4828 6.74999 25.4
179 1 30.6422 9.20999 25.4
181 1 32.7727 7.97999 25.4
182 1 33.4828 9.20999 25.4
113 1 19.9901 10.44 25.4
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143 1 22.1205 11.67 25.4
145 1 24.251 10.44 25.4
146 1 24.9611 11.67 25.4
174 1 24.9611 14.13 25.4
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171 1 22.1205 14.13 25.4
144 1 22.8307 12.9 25.4
142 1 20.7003 14.13 25.4
141 1 19.9901 12.9 25.4
148 1 27.0915 10.44 25.4
175 1 26.3814 11.67 25.4
177 1 28.5118 10.44 25.4
178 1 29.2219 11.67 25.4
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203 1 26.3814 14.13 25.4
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180 1 31.3524 10.44 25.4
207 1 30.6422 11.67 25.4
209 1 32.7727 10.44 25.4
210 1 33.4828 11.67 25.4
238 1 33.4828 14.13 25.4
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235 1 30.6422 14.13 25.4
208 1 31.3524 12.9 25.4
169 1 19.9901 15.36 25.4
170 1 20.7003 16.59 25.4
172 1 22.8307 15.36 25.4
197 1 19.9901 17.82 25.4
198 1 20.7003 19.05 25.4
199 1 22.1205 16.59 25.4
200 1 22.8307 17.82 25.4
201 1 24.251 15.36 25.4
202 1 24.9611 16.59 25.4
225 1 19.9901 20.28 25.4
227 1 22.1205 19.05 25.4
228 1 22.8307 20.28 25.4
229 1 24.251 17.82 25.4
230 1 24.9611 19.05 25.4
257 1 24.251 20.28 25.4
204 1 27.0915 15.36 25.4
231 1 26.3814 16.59 25.4
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233 1 28.5118 15.36 25.4
234 1 29.2219 16.59 25.4
259 1 26.3814 19.05 25.4
260 1 27.0915 20.28 25.4
261 1 28.5118 17.82 25.4
262 1 29.2219 19.05 25.4
289 1 28.5118 20.28 25.4
236 1 31.3524 15.36 25.4
263 1 30.6422 16.59 25.4
264 1 31.3524 17.82 25.4
265 1 32.7727 15.36 25.4
266 1 33.4828 16.59 25.4
291 1 30.6422 19.05 25.4
292 1 31.3524 20.28 25.4
293 1 32.7727 17.82 25.4
294 1 33.4828 19.05 25.4
321 1 32.7727 20.28 25.4
226 1 20.7003 21.51 25.4
253 1 19.9901 22.74 25.4
254 1 20.7003 23.97 25.4
255 1 22.1205 21.51 25.4
256 1 22.8307 22.74 25.4
258 1 24.9611 21.51 25.4
281 1 19.9901 25.2 25.4
282 1 20.7003 26.43 25.4
283 1 22.1205 23.97 25.4
284 1 22.8307 25.2 25.4
285 1 24.251 22.74 25.4
286 1 24.9611 23.97 25.4
311 1 22.1205 26.43 25.4
313 1 24.251 25.2 25.4
314 1 24.9611 26.43 25.4
287 1 26.3814 21.51 25.4
288 1 27.0915 22.74 25.4
290 1 29.2219 21.51 25.4
315 1 26.3814 23.97 25.4
316 1 27.0915 25.2 25.4
317 1 28.5118 22.74 25.4
318 1 29.2219 23.97 25.4
341 1 26.3814 26.43 25.4
343 1 28.5118 25.2 25.4
344 1 29.2219 26.43 25.4
319 1 30.6422 21.51 25.4
320 1 31.3524 22.74 25.4
322 1 33.4828 21.51 25.4
345 1 30.6422 23.97 25.4
346 1 31.3524 25.2 25.4
347 1 32.7727 22.74 25.4
348 1 33.4828 23.97 25.4
367 1 30.6422 26.43 25.4
369 1 32.7727 25.2 25.4
370 1 33.4828 26.43 25.4
336 1 20.7003 31.35 25.4
357 1 19.9901 32.58 25.4
359 1 22.1205 31.35 25.4
360 1 22.8307 32.58 25.4
362 1 24.9611 31.35 25.4
379 1 24.251 32.58 25.4
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340 1 24.9611 28.89 25.4
339 1 24.251 27.66 25.4
338 1 22.8307 30.12 25.4
337 1 22.1205 28.89 25.4
335 1 19.9901 30.12 25.4
312 1 22.8307 27.66 25.4
310 1 20.7003 28.89 25.4
309 1 19.9901 27.66 25.4
381 1 26.3814 31.35 25.4
382 1 27.0915 32.58 25.4
384 1 29.2219 31.35 25.4
397 1 28.5118 32.58 25.4
383 1 28.5118 30.12 25.4
366 1 29.2219 28.89 25.4
365 1 28.5118 27.66 25.4
364 1 27.0915 30.12 25.4
363 1 26.3814 28.89 25.4
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399 1 30.6422 31.35 25.4
400 1 31.3524 32.58 25.4
402 1 33.4828 31.35 25.4
411 1 32.7727 32.58 25.4
401 1 32.7727 30.12 25.4
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387 1 32.7727 27.66 25.4
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385 1 30.6422 28.89 25.4
368 1 31.3524 27.66 25.4
358 1 20.7003 33.81 25.4
375 1 19.9901 35.04 25.4
376 1 20.7003 36.27 25.4
377 1 22.1205 33.81 25.4
378 1 22.8307 35.04 25.4
380 1 24.9611 33.81 25.4
389 1 19.9901 37.5 25.4
391 1 22.1205 36.27 25.4
392 1 22.8307 37.5 25.4
393 1 24.251 35.04 25.4
394 1 24.9611 36.27 25.4
404 1 24.251 37.5 25.4
395 1 26.3814 33.81 25.4
396 1 27.0915 35.04 25.4
398 1 29.2219 33.81 25.4
405 1 26.3814 36.27 25.4
406 1 27.0915 37.5 25.4
407 1 28.5118 35.04 25.4
408 1 29.2219 36.27 25.4
413 1 28.5118 37.5 25.4
409 1 30.6422 33.81 25.4
410 1 31.3524 35.04 25.4
412 1 33.4828 33.81 25.4
415 1 30.6422 36.27 25.4
416 1 31.3524 37.5 25.4
417 1 32.7727 35.04 25.4
418 1 33.4828 36.27 25.4
420 1 32.7727 37.5 25.4
390 1 20.7003 38.73 25.4
403 1 22.1205 38.73 25.4
414 1 29.2219 38.73 25.4
419 1 30.6422 38.73 25.4
The track file cannot be uploaded normally, so I paste the text
Christoph Junghans
Apr 19, 2021, 5:42:42 PM4/19/21
to vo...@googlegroups.com
Can you attach your inverse.log?
Thanks,
Christoph
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mengyy zhou
Apr 19, 2021, 9:07:49 PM4/19/21
to votca
Sorry there is no inverse.log file generated.
Christoph Junghans
Apr 19, 2021, 9:30:00 PM4/19/21
to vo...@googlegroups.com
What command are you running exactly?
And can you zip up all the inputs and attach?
Also from looking at this block:
Christoph
> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/8dbb6cf7-eab2-4ffc-ab36-d87d453e5f5cn%40googlegroups.com.
And can you zip up all the inputs and attach?
Also from looking at this block:
ITEM: BOX BOUNDS pp pp pp
-8.1913882339999997e+00 4.6483830779000002e+01
-6.4119649000000001e+00 4.9306763662000002e+01
-1.0036178788000001e+01 6.3180167243000000e+01
aren't there supposed to be 3 numbers?
-8.1913882339999997e+00 4.6483830779000002e+01
-6.4119649000000001e+00 4.9306763662000002e+01
-1.0036178788000001e+01 6.3180167243000000e+01
Christoph
mengyy zhou
Apr 19, 2021, 11:25:04 PM4/19/21
to votca
Thank you for your quick response!
1.csg_dump --top topol.xml
2.csg_dump --top topol.xml --excl
3.csg_map --top PI2.xml --no-map --trj xyz.dump --out out1.pdb
4.csg_map --top topol.xml --out out.pdb --cg mapping.xml --trj traj.dump
The above 4 commands was used to expect to get a coarse-grained model of graphene. The first and second commands can run normally and the results obtained was right. The third and fourth commands report an error"source type value could not be interpreted as target". Regarding the lammps trajectory file you mentioned, the dump file I used to run is also in this format, and it can run normally.
Thanks!
mengyy zhou
Apr 20, 2021, 10:48:51 AM4/20/21
to votca
I have solved the above problem, thank you again！
在2021年4月20日星期二 UTC+8 上午9:30:00<Christoph Junghans> 写道：
Christoph Junghans
Apr 20, 2021, 12:23:40 PM4/20/21
to vo...@googlegroups.com
On Tue, Apr 20, 2021 at 8:48 AM mengyy zhou <zhoumen...@gmail.com> wrote:
>
> I have solved the above problem, thank you again！
Can you let us know what the problem was? That will help other users!
>
> I have solved the above problem, thank you again！
Thanks,
Christoph
mengyy zhou
Apr 20, 2021, 10:30:45 PM4/20/21
to votca
Hi
Christoph
!
I prepared new all files,and I am sorry I did not figure out the specific reason,maybe there are something wrong about atomic mapping!
Thanks!
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