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Revision 3259 - (show annotations)
Mon Oct 11 01:48:14 2010 UTC (8 years, 11 months ago) by jfenwick
File MIME type: text/plain
File size: 19302 byte(s)
Merging dudley and scons updates from branches

1
2 /*******************************************************
3 *
4 * Copyright (c) 2003-2010 by University of Queensland
5 * Earth Systems Science Computational Center (ESSCC)
6 * http://www.uq.edu.au/esscc
7 *
8 * Primary Business: Queensland, Australia
9 * Licensed under the Open Software License version 3.0
10 * http://www.opensource.org/licenses/osl-3.0.php
11 *
12 *******************************************************/
13
14
15 /**************************************************************/
16
17 /* Some utility routines: */
18
19 /**************************************************************/
20
21 #include "Finley.h"
22 #include "Util.h"
23
24 #ifdef _OPENMP
25 #include <omp.h>
26 #endif
27
28 #include "esysUtils/mem.h"
29 #include "esysUtils/index.h"
30 #include <string.h> /* for memcpy */
31
32
33 /**************************************************************/
34
35 /* returns true if any of the values in the short array values is not equalt to Zero */
36
37 bool_t Finley_Util_anyNonZeroDouble(dim_t N, double* values) {
38 dim_t q;
39 for (q=0;q<N;++q) if (ABS(values[q])>0) return TRUE;
40 return FALSE;
41 }
42 /**************************************************************/
43
44 /* gathers double values out from in by index: */
45
46 /* out(1:numData,1:len)=in(1:numData,index(1:len)) */
47
48 void Finley_Util_Gather_double(dim_t len,index_t* index,dim_t numData,double* in, double * out){
49 dim_t s,i;
50 for (s=0;s<len;s++) {
51 for (i=0;i<numData;i++) {
52 out[INDEX2(i,s,numData)]=in[INDEX2(i,index[s],numData)];
53 }
54 }
55 }
56
57 /**************************************************************/
58
59
60 /* gathers maybelong values out from in by index: */
61
62 /* out(1:numData,1:len)=in(1:numData,index(1:len)) */
63
64 void Finley_Util_Gather_int(dim_t len,index_t* index,dim_t numData, index_t* in, index_t * out){
65 dim_t s,i;
66 for (s=0;s<len;s++) {
67 for (i=0;i<numData;i++) {
68 out[INDEX2(i,s,numData)]=in[INDEX2(i,index[s],numData)];
69 }
70 }
71 }
72
73 /**************************************************************/
74
75 /* adds a vector in into out using and index. */
76
77 /* out(1:numData,index[p])+=in(1:numData,p) where p = {k=1...len , index[k]<upperBound}*/
78
79
80 void Finley_Util_AddScatter(dim_t len,index_t* index,dim_t numData,double* in,double * out, index_t upperBound){
81 dim_t i,s;
82 for (s=0;s<len;s++) {
83 for(i=0;i<numData;i++) {
84 if( index[s]<upperBound ) {
85 out[INDEX2(i,index[s],numData)]+=in[INDEX2(i,s,numData)];
86 }
87 }
88 }
89 }
90
91 /* multiplies two matrices */
92
93 /* A(1:A1,1:A2)=B(1:A1,1:B2)*C(1:B2,1:A2) */
94
95 void Finley_Util_SmallMatMult(dim_t A1,dim_t A2, double* A, dim_t B2, double*B, double* C) {
96 dim_t i,j,s;
97 register double rtmp;
98 for (i=0;i<A1;i++) {
99 for (j=0;j<A2;j++) {
100 rtmp=0;
101 for (s=0;s<B2;s++) rtmp+=B[INDEX2(i,s,A1)]*C[INDEX2(s,j,B2)];
102 A[INDEX2(i,j,A1)]=rtmp;
103 }
104 }
105 }
106
107 /* multiplies a two sets of matries: */
108
109 /* A(1:A1,1:A2,i)=B(1:A1,1:B2,i)*C(1:B2,1:A2,i) i=1,len */
110
111 void Finley_Util_SmallMatSetMult(dim_t len,dim_t A1,dim_t A2, double* A, dim_t B2, double*B, double* C) {
112 dim_t q,i,j,s;
113 register double rtmp;
114 for (q=0;q<len;q++) {
115 for (i=0;i<A1;i++) {
116 for (j=0;j<A2;j++) {
117 rtmp=0;
118 for (s=0;s<B2;s++) rtmp+=B[INDEX3(i,s,q,A1,B2)]*C[INDEX3(s,j,q,B2,A2)];
119 A[INDEX3(i,j,q, A1,A2)]=rtmp;
120 }
121 }
122 }
123 }
124 /* multiplies a set of matries with a single matrix: */
125
126 /* A(1:A1,1:A2,i)=B(1:A1,1:B2,i)*C(1:B2,1:A2) i=1,len */
127
128 void Finley_Util_SmallMatSetMult1(dim_t len,dim_t A1,dim_t A2, double* A, dim_t B2, double*B, double* C) {
129 dim_t q,i,j,s;
130 register double rtmp;
131 for (q=0;q<len;q++) {
132 for (i=0;i<A1;i++) {
133 for (j=0;j<A2;j++) {
134 rtmp=0;
135 for (s=0;s<B2;s++) rtmp+=B[INDEX3(i,s,q, A1,B2)]*C[INDEX2(s,j,B2)];
136 A[INDEX3(i,j,q,A1,A2)]=rtmp;
137 }
138 }
139 }
140 }
141 /* inverts the set of dim x dim matrices A(:,:,1:len) with dim=1,2,3 */
142 /* the determinante is returned. */
143
144 void Finley_Util_InvertSmallMat(dim_t len,dim_t dim,double* A,double *invA, double* det){
145 dim_t q;
146 register double D,A11,A12,A13,A21,A22,A23,A31,A32,A33;
147
148 switch(dim) {
149 case 1:
150 for (q=0;q<len;q++) {
151 D=A[q];
152 if (ABS(D) > 0 ){
153 det[q]=D;
154 D=1./D;
155 invA[q]=D;
156 } else {
157 Finley_setError(ZERO_DIVISION_ERROR,"__FILE__: Non-regular matrix");
158 return;
159 }
160 }
161 break;
162
163 case 2:
164 for (q=0;q<len;q++) {
165 A11=A[INDEX3(0,0,q,2,2)];
166 A12=A[INDEX3(0,1,q,2,2)];
167 A21=A[INDEX3(1,0,q,2,2)];
168 A22=A[INDEX3(1,1,q,2,2)];
169
170 D = A11*A22-A12*A21;
171 if (ABS(D) > 0 ){
172 det[q]=D;
173 D=1./D;
174 invA[INDEX3(0,0,q,2,2)]= A22*D;
175 invA[INDEX3(1,0,q,2,2)]=-A21*D;
176 invA[INDEX3(0,1,q,2,2)]=-A12*D;
177 invA[INDEX3(1,1,q,2,2)]= A11*D;
178 } else {
179 Finley_setError(ZERO_DIVISION_ERROR,"__FILE__: Non-regular matrix");
180 return;
181 }
182 }
183 break;
184
185 case 3:
186 for (q=0;q<len;q++) {
187 A11=A[INDEX3(0,0,q,3,3)];
188 A21=A[INDEX3(1,0,q,3,3)];
189 A31=A[INDEX3(2,0,q,3,3)];
190 A12=A[INDEX3(0,1,q,3,3)];
191 A22=A[INDEX3(1,1,q,3,3)];
192 A32=A[INDEX3(2,1,q,3,3)];
193 A13=A[INDEX3(0,2,q,3,3)];
194 A23=A[INDEX3(1,2,q,3,3)];
195 A33=A[INDEX3(2,2,q,3,3)];
196
197 D = A11*(A22*A33-A23*A32)+ A12*(A31*A23-A21*A33)+A13*(A21*A32-A31*A22);
198 if (ABS(D) > 0 ){
199 det[q] =D;
200 D=1./D;
201 invA[INDEX3(0,0,q,3,3)]=(A22*A33-A23*A32)*D;
202 invA[INDEX3(1,0,q,3,3)]=(A31*A23-A21*A33)*D;
203 invA[INDEX3(2,0,q,3,3)]=(A21*A32-A31*A22)*D;
204 invA[INDEX3(0,1,q,3,3)]=(A13*A32-A12*A33)*D;
205 invA[INDEX3(1,1,q,3,3)]=(A11*A33-A31*A13)*D;
206 invA[INDEX3(2,1,q,3,3)]=(A12*A31-A11*A32)*D;
207 invA[INDEX3(0,2,q,3,3)]=(A12*A23-A13*A22)*D;
208 invA[INDEX3(1,2,q,3,3)]=(A13*A21-A11*A23)*D;
209 invA[INDEX3(2,2,q,3,3)]=(A11*A22-A12*A21)*D;
210 } else {
211 Finley_setError(ZERO_DIVISION_ERROR,"__FILE__: Non-regular matrix");
212 return;
213 }
214 }
215 break;
216
217 }
218 return;
219 }
220
221 /* sets the derterminate of a set of dim x dim matrices A(:,:,1:len) with dim=1,2,3 */
222
223 void Finley_Util_DetOfSmallMat(dim_t len,dim_t dim,double* A, double* det){
224 dim_t q;
225 register double A11,A12,A13,A21,A22,A23,A31,A32,A33;
226
227 switch(dim) {
228 case 1:
229 for (q=0;q<len;q++) {
230 det[q]=A[q];
231 }
232 break;
233
234 case 2:
235 for (q=0;q<len;q++) {
236 A11=A[INDEX3(0,0,q,2,2)];
237 A12=A[INDEX3(0,1,q,2,2)];
238 A21=A[INDEX3(1,0,q,2,2)];
239 A22=A[INDEX3(1,1,q,2,2)];
240
241 det[q] = A11*A22-A12*A21;
242 }
243 break;
244
245 case 3:
246 for (q=0;q<len;q++) {
247 A11=A[INDEX3(0,0,q,3,3)];
248 A21=A[INDEX3(1,0,q,3,3)];
249 A31=A[INDEX3(2,0,q,3,3)];
250 A12=A[INDEX3(0,1,q,3,3)];
251 A22=A[INDEX3(1,1,q,3,3)];
252 A32=A[INDEX3(2,1,q,3,3)];
253 A13=A[INDEX3(0,2,q,3,3)];
254 A23=A[INDEX3(1,2,q,3,3)];
255 A33=A[INDEX3(2,2,q,3,3)];
256
257 det[q] = A11*(A22*A33-A23*A32)+ A12*(A31*A23-A21*A33)+A13*(A21*A32-A31*A22);
258 }
259 break;
260
261 }
262 return;
263 }
264 /* returns the normalized vector Normal[dim,len] orthogonal to A(:,0,q) and A(:,1,q) in the case of dim=3 */
265 /* or the vector A(:,0,q) in the case of dim=2 */
266
267 void Finley_NormalVector(dim_t len, dim_t dim, dim_t dim1, double* A,double* Normal) {
268 dim_t q;
269 register double A11,A12,CO_A13,A21,A22,CO_A23,A31,A32,CO_A33,length,invlength;
270
271 switch(dim) {
272 case 1:
273 for (q=0;q<len;q++) Normal[q] =1;
274 break;
275 case 2:
276 for (q=0;q<len;q++) {
277 A11=A[INDEX3(0,0,q,2,dim1)];
278 A21=A[INDEX3(1,0,q,2,dim1)];
279 length = sqrt(A11*A11+A21*A21);
280 if (! length>0) {
281 Finley_setError(ZERO_DIVISION_ERROR,"__FILE__: area equals zero.");
282 return;
283 } else {
284 invlength=1./length;
285 Normal[INDEX2(0,q,2)]=A21*invlength;
286 Normal[INDEX2(1,q,2)]=-A11*invlength;
287 }
288 }
289 break;
290 case 3:
291 for (q=0;q<len;q++) {
292 A11=A[INDEX3(0,0,q,3,dim1)];
293 A21=A[INDEX3(1,0,q,3,dim1)];
294 A31=A[INDEX3(2,0,q,3,dim1)];
295 A12=A[INDEX3(0,1,q,3,dim1)];
296 A22=A[INDEX3(1,1,q,3,dim1)];
297 A32=A[INDEX3(2,1,q,3,dim1)];
298 CO_A13=A21*A32-A31*A22;
299 CO_A23=A31*A12-A11*A32;
300 CO_A33=A11*A22-A21*A12;
301 length=sqrt(CO_A13*CO_A13+CO_A23*CO_A23+CO_A33*CO_A33);
302 if (! length>0) {
303 Finley_setError(ZERO_DIVISION_ERROR,"__FILE__: area equals zero.");
304 return;
305 } else {
306 invlength=1./length;
307 Normal[INDEX2(0,q,3)]=CO_A13*invlength;
308 Normal[INDEX2(1,q,3)]=CO_A23*invlength;
309 Normal[INDEX2(2,q,3)]=CO_A33*invlength;
310 }
311
312 }
313 break;
314
315 }
316 return;
317 }
318
319 /* return the length of the vector which is orthogonal to the vectors A(:,0,q) and A(:,1,q) in the case of dim=3 */
320 /* or the vector A(:,0,q) in the case of dim=2 */
321
322 void Finley_LengthOfNormalVector(dim_t len, dim_t dim, dim_t dim1, double* A,double* length) {
323 dim_t q;
324 double A11,A12,CO_A13,A21,A22,CO_A23,A31,A32,CO_A33;
325
326 switch(dim) {
327 case 1:
328 for (q=0;q<len;q++) length[q] =1;
329 break;
330 case 2:
331 for (q=0;q<len;q++) {
332 A11=A[INDEX3(0,0,q,2,dim1)];
333 A21=A[INDEX3(1,0,q,2,dim1)];
334 length[q] = sqrt(A11*A11+A21*A21);
335 }
336 break;
337 case 3:
338 for (q=0;q<len;q++) {
339 A11=A[INDEX3(0,0,q,3,dim1)];
340 A21=A[INDEX3(1,0,q,3,dim1)];
341 A31=A[INDEX3(2,0,q,3,dim1)];
342 A12=A[INDEX3(0,1,q,3,dim1)];
343 A22=A[INDEX3(1,1,q,3,dim1)];
344 A32=A[INDEX3(2,1,q,3,dim1)];
345 CO_A13=A21*A32-A31*A22;
346 CO_A23=A31*A12-A11*A32;
347 CO_A33=A11*A22-A21*A12;
348 length[q]=sqrt(CO_A13*CO_A13+CO_A23*CO_A23+CO_A33*CO_A33);
349 }
350 break;
351
352 }
353 return;
354 }
355
356 /* inverts the map map of length len */
357 /* there is no range checking! */
358 /* at output Map[invMap[i]]=i for i=0:lenInvMap */
359
360 void Finley_Util_InvertMap(dim_t lenInvMap, index_t* invMap,dim_t lenMap, index_t* Map) {
361 dim_t i;
362 for (i=0;i<lenInvMap;i++) invMap[i]=0;
363 for (i=0;i<lenMap;i++) {
364 if (Map[i]>=0) invMap[Map[i]]=i;
365 }
366 }
367
368 /* orders a Finley_Util_ValueAndIndex array by value */
369 /* it is assumed that n is large */
370
371 int Finley_Util_ValueAndIndex_compar(const void *arg1 , const void *arg2 ) {
372 Finley_Util_ValueAndIndex *e1,*e2;
373 e1=(Finley_Util_ValueAndIndex*) arg1;
374 e2=(Finley_Util_ValueAndIndex*) arg2;
375 if (e1->value < e2->value) return -1;
376 if (e1->value > e2->value) return 1;
377 if (e1->index < e2->index) return -1;
378 if (e1->index > e2->index) return 1;
379 return 0;
380 }
381
382 void Finley_Util_sortValueAndIndex(dim_t n,Finley_Util_ValueAndIndex* array) {
383 /* OMP : needs parallelization !*/
384 qsort(array,n,sizeof(Finley_Util_ValueAndIndex),Finley_Util_ValueAndIndex_compar);
385 }
386
387
388 /**************************************************************/
389
390 /* calculates the minimum value from a dim X N integer array */
391
392 index_t Finley_Util_getMinInt(dim_t dim,dim_t N,index_t* values) {
393 dim_t i,j;
394 index_t out,out_local;
395 out=INDEX_T_MAX;
396 if (values!=NULL && dim*N>0 ) {
397 out=values[0];
398 #pragma omp parallel private(out_local)
399 {
400 out_local=out;
401 #pragma omp for private(i,j) schedule(static)
402 for (j=0;j<N;j++) {
403 for (i=0;i<dim;i++) out_local=MIN(out_local,values[INDEX2(i,j,dim)]);
404 }
405 #pragma omp critical
406 out=MIN(out_local,out);
407 }
408 }
409 return out;
410 }
411
412 /* calculates the maximum value from a dim X N integer array */
413
414 index_t Finley_Util_getMaxInt(dim_t dim,dim_t N,index_t* values) {
415 dim_t i,j;
416 index_t out,out_local;
417 out=-INDEX_T_MAX;
418 if (values!=NULL && dim*N>0 ) {
419 out=values[0];
420 #pragma omp parallel private(out_local)
421 {
422 out_local=out;
423 #pragma omp for private(i,j) schedule(static)
424 for (j=0;j<N;j++) {
425 for (i=0;i<dim;i++) out_local=MAX(out_local,values[INDEX2(i,j,dim)]);
426 }
427 #pragma omp critical
428 out=MAX(out_local,out);
429 }
430 }
431 return out;
432 }
433 /**************************************************************/
434
435 /* calculates the minimum value from a dim X N integer array */
436
437 index_t Finley_Util_getFlaggedMinInt(dim_t dim,dim_t N,index_t* values, index_t ignore) {
438 dim_t i,j;
439 index_t out,out_local;
440 out=INDEX_T_MAX;
441 if (values!=NULL && dim*N>0 ) {
442 out=values[0];
443 #pragma omp parallel private(out_local)
444 {
445 out_local=out;
446 #pragma omp for private(i,j) schedule(static)
447 for (j=0;j<N;j++) {
448 for (i=0;i<dim;i++) if (values[INDEX2(i,j,dim)]!=ignore) out_local=MIN(out_local,values[INDEX2(i,j,dim)]);
449 }
450 #pragma omp critical
451 out=MIN(out_local,out);
452 }
453 }
454 return out;
455 }
456
457 /* calculates the maximum value from a dim X N integer array */
458
459 index_t Finley_Util_getFlaggedMaxInt(dim_t dim,dim_t N,index_t* values, index_t ignore) {
460 dim_t i,j;
461 index_t out,out_local;
462 out=-INDEX_T_MAX;
463 if (values!=NULL && dim*N>0 ) {
464 out=values[0];
465 #pragma omp parallel private(out_local)
466 {
467 out_local=out;
468 #pragma omp for private(i,j) schedule(static)
469 for (j=0;j<N;j++) {
470 for (i=0;i<dim;i++) if (values[INDEX2(i,j,dim)]!=ignore) out_local=MAX(out_local,values[INDEX2(i,j,dim)]);
471 }
472 #pragma omp critical
473 out=MAX(out_local,out);
474 }
475 }
476 return out;
477 }
478
479 /* set the index of the positive entries in mask. The length of index is returned. */
480
481 dim_t Finley_Util_packMask(dim_t N,index_t* mask,index_t* index) {
482 dim_t out,k;
483 out=0;
484 /*OMP */
485 for (k=0;k<N;k++) {
486 if (mask[k]>=0) {
487 index[out]=k;
488 out++;
489 }
490 }
491 return out;
492 }
493
494 /* returns true if array contains value */
495 bool_t Finley_Util_isAny(dim_t N,index_t* array,index_t value) {
496 bool_t out=FALSE;
497 dim_t i;
498 #pragma omp parallel for private(i) schedule(static) reduction(||:out)
499 for (i=0;i<N;i++) out = out || (array[i]==value);
500 return out;
501 }
502 /* calculates the cummultative sum in array and returns the total sum */
503 index_t Finley_Util_cumsum(dim_t N,index_t* array) {
504 index_t out=0,tmp;
505 dim_t i;
506 #ifdef _OPENMP
507 index_t *partial_sums=NULL, sum;
508 partial_sums=TMPMEMALLOC(omp_get_max_threads(),index_t);
509 #pragma omp parallel private(sum,i,tmp)
510 {
511 sum=0;
512 #pragma omp for schedule(static)
513 for (i=0;i<N;++i) sum+=array[i];
514 partial_sums[omp_get_thread_num()]=sum;
515 #pragma omp barrier
516 #pragma omp master
517 {
518 out=0;
519 for (i=0;i<omp_get_max_threads();++i) {
520 tmp=out;
521 out+=partial_sums[i];
522 partial_sums[i]=tmp;
523 }
524 }
525 #pragma omp barrier
526 sum=partial_sums[omp_get_thread_num()];
527 #pragma omp for schedule(static)
528 for (i=0;i<N;++i) {
529 tmp=sum;
530 sum+=array[i];
531 array[i]=tmp;
532 }
533 }
534 TMPMEMFREE(partial_sums);
535 #else
536 for (i=0;i<N;++i) {
537 tmp=out;
538 out+=array[i];
539 array[i]=tmp;
540 }
541 #endif
542 return out;
543 }
544 void Finley_Util_setValuesInUse(const index_t *values, const dim_t numValues, dim_t *numValuesInUse, index_t **valuesInUse, Esys_MPIInfo* mpiinfo)
545 {
546 dim_t i;
547 index_t lastFoundValue=INDEX_T_MIN, minFoundValue, local_minFoundValue, *newValuesInUse=NULL;
548 register index_t itmp;
549 bool_t allFound=FALSE;
550 dim_t nv=0;
551
552 while (! allFound) {
553 /*
554 * find smallest value bigger than lastFoundValue
555 */
556 minFoundValue=INDEX_T_MAX;
557 #pragma omp parallel private(local_minFoundValue)
558 {
559 local_minFoundValue=minFoundValue;
560 #pragma omp for private(i,itmp) schedule(static)
561 for (i=0;i< numValues;i++) {
562 itmp=values[i];
563 if ((itmp>lastFoundValue) && (itmp<local_minFoundValue)) local_minFoundValue=itmp;
564 }
565 #pragma omp critical
566 {
567 if (local_minFoundValue<minFoundValue) minFoundValue=local_minFoundValue;
568 }
569
570 }
571 #ifdef ESYS_MPI
572 local_minFoundValue=minFoundValue;
573 MPI_Allreduce(&local_minFoundValue,&minFoundValue, 1, MPI_INT, MPI_MIN, mpiinfo->comm );
574 #endif
575 /* if we found a new tag we need to add this too the valuesInUseList */
576
577 if (minFoundValue < INDEX_T_MAX) {
578 newValuesInUse=MEMALLOC(nv+1,index_t);
579 if (*valuesInUse!=NULL) {
580 memcpy(newValuesInUse,*valuesInUse,sizeof(index_t)*nv);
581 MEMFREE(*valuesInUse);
582 }
583 newValuesInUse[nv]=minFoundValue;
584 *valuesInUse=newValuesInUse;
585 newValuesInUse=NULL;
586 nv++;
587 lastFoundValue=minFoundValue;
588 } else {
589 allFound=TRUE;
590 }
591 }
592 *numValuesInUse=nv;
593 }
594
595
596 #ifdef ESYS_MPI
597 void Finley_printDoubleArray( FILE *fid, dim_t n, double *array, char *name )
598 {
599 index_t i;
600
601 if( name )
602 fprintf( fid, "%s [ ", name );
603 else
604 fprintf( fid, "[ " );
605 for( i=0; i<(n<60 ? n : 60); i++ )
606 fprintf( fid, "%g ", array[i] );
607 if( n>=30 )
608 fprintf( fid, "... " );
609 fprintf( fid, "]\n" );
610 }
611 void Finley_printIntArray( FILE *fid, dim_t n, int *array, char *name )
612 {
613 index_t i;
614
615 if( name )
616 fprintf( fid, "%s [ ", name );
617 else
618 fprintf( fid, "[ " );
619 for( i=0; i<(n<60 ? n : 60); i++ )
620 fprintf( fid, "%d ", array[i] );
621 if( n>=30 )
622 fprintf( fid, "... " );
623 fprintf( fid, "]\n" );
624 }
625 void Finley_printMaskArray( FILE *fid, dim_t n, int *array, char *name )
626 {
627 index_t i;
628
629 if( name )
630 fprintf( fid, "%s [ ", name );
631 else
632 fprintf( fid, "[ " );
633 for( i=0; i<(n<60 ? n : 60); i++ )
634 if( array[i]!=-1 )
635 fprintf( fid, "%3d ", array[i] );
636 else
637 fprintf( fid, " * " );
638 if( n>=30 )
639 fprintf( fid, "... " );
640 fprintf( fid, "]\n" );
641 }
642 #endif

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