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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
Revision 1308 by chuckv, Tue Oct 21 16:44:00 2008 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
1 > /* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved.
2   *
3   * The University of Notre Dame grants you ("Licensee") a
4   * non-exclusive, royalty free, license to use, modify and
# Line 44 | Line 44
44   *
45   *  Created by Charles F. Vardeman II on 11 Dec 2006.
46   *  @author  Charles F. Vardeman II
47 < *  @version $Id: ConvexHull.cpp,v 1.8 2008-09-14 01:32:25 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.12 2008-10-21 16:44:00 chuckv Exp $
48   *
49   */
50  
# Line 369 | Line 369 | void ConvexHull::printHull(const std::string& geomFile
369   #else
370   #ifdef HAVE_QHULL
371   /* Old options Qt Qu Qg QG0 FA */
372 < ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt  Qci Tcv Pp") {
372 > /* More old opts Qc Qi Pp*/
373 > ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200), nTriangles_(0) {
374    //If we are doing the mpi version, set up some vectors for data communication
375   #ifdef IS_MPI
376  
# Line 380 | Line 381 | ConvexHull::ConvexHull() : Hull(), dim_(3), options_("
381   displs_   = new int[nproc_];
382  
383   // Create a surface point type in MPI to send
384 < surfacePtType = MPI::DOUBLE.Create_contiguous(3);
385 < surfacePtType.Commit();
384 > //surfacePtType = MPI::DOUBLE.Create_contiguous(3);
385 > // surfacePtType.Commit();
386  
387  
388   #endif
# Line 413 | Line 414 | void ConvexHull::computeHull(std::vector<StuntDouble*>
414    
415    //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
416  
417 <  double* ptArray = new double[numpoints * 3];
417 > //  double* ptArray = new double[numpoints * 3];
418 >  std::vector<double> ptArray(numpoints*3);
419    std::vector<bool> isSurfaceID(numpoints);
420  
421    // Copy the positon vector into a points vector for qhull.
# Line 435 | Line 437 | void ConvexHull::computeHull(std::vector<StuntDouble*>
437    
438    
439    boolT ismalloc = False;
440 +  /* Clean up memory from previous convex hull calculations*/
441 +  
442    Triangles_.clear();
443    surfaceSDs_.clear();
444 <  
445 <  if (qh_new_qhull(dim_, numpoints, ptArray, ismalloc,
444 >  surfaceSDs_.reserve(Ns_);
445 >
446 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
447                      const_cast<char *>(options_.c_str()), NULL, stderr)) {
448  
449        sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
450 <      painCave.isFatal = 0;
450 >      painCave.isFatal = 1;
451        simError();
452        
453    } //qh_new_qhull
# Line 450 | Line 455 | void ConvexHull::computeHull(std::vector<StuntDouble*>
455  
456   #ifdef IS_MPI
457    std::vector<double> localPts;
458 +  std::vector<double> localVel;
459    int localPtArraySize;
460    
461 +
462    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
463 +
464  
465    FORALLfacets {
466      
467      if (!facet->simplicial){
468        // should never happen with Qt
469        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
470 <      painCave.isFatal = 0;
470 >      painCave.isFatal = 1;
471        simError();
472      }
473      
# Line 484 | Line 492 | void ConvexHull::computeHull(std::vector<StuntDouble*>
492    int localPtArraySize = surfaceIDs.size() * 3;
493    */
494  
495 <  localPts.resize(localPtArraySize);
496 <  //  std::fill(localPts.begin(),globalPts.end(),0.0);
495 >  //localPts.resize(localPtArraySize);
496 >  //std::fill(localPts.begin(),localPts.end(),0.0);
497  
498  
499    int idx = 0;
500 +  int nIsIts = 0;
501 + /*
502    // Copy the surface points into an array.
503    for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
504        list_iter != isSurfaceID.end(); list_iter++)
# Line 499 | Line 509 | void ConvexHull::computeHull(std::vector<StuntDouble*>
509          localPts.push_back(ptArray[dim_ * idx + 1]);
510          localPts.push_back(ptArray[dim_ * idx + 2]);
511          localPtsMap.push_back(idx);
512 +        nIsIts++;
513        } //Isit
514        idx++;
515      } //isSurfaceID
516 <  
516 >  */
517 >  FORALLvertices {
518 >    idx = qh_pointid(vertex->point);
519 >    localPts.push_back(ptArray[dim_ * idx]);    
520 >    localPts.push_back(ptArray[dim_ * idx + 1]);
521 >    localPts.push_back(ptArray[dim_ * idx + 2]);
522  
523 +    Vector3d vel = bodydoubles[idx]->getVel();
524 +    localVel.push_back(vel.x());
525 +    localVel.push_back(vel.y());
526 +    localVel.push_back(vel.z());
527 +
528 +    localPtsMap.push_back(idx);
529 +  }
530 +
531 +
532    localPtArraySize = localPts.size();
533 +
534 +
535    MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
536  
537 +  Nsglobal_=0;
538    for (int i = 0; i < nproc_; i++){
539      Nsglobal_ += NstoProc_[i];
540    }
541 +  
542 +
543 +  int nglobalPts = int(Nsglobal_/3);
544 +
545  
546 <  std::vector<double> globalPts;
547 <  globalPts.resize(Nsglobal_);
548 <  isSurfaceID.resize(int(Nsglobal_/3));
546 >  std::vector<double> globalPts(Nsglobal_);
547 >  std::vector<double> globalVel(Nsglobal_);
548 >
549 >  isSurfaceID.resize(nglobalPts);
550 >
551 >
552    std::fill(globalPts.begin(),globalPts.end(),0.0);
553 +
554 +  displs_[0] = 0;
555    /* Build a displacements array */
556    for (int i = 1; i < nproc_; i++){
557      displs_[i] = displs_[i-1] + NstoProc_[i-1];
558    }
559    
560 +  
561    int noffset = displs_[myrank_];
562    /* gather the potential hull */
563    
564 <  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],NstoProc_,displs_,MPI::DOUBLE);
564 >  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
565 >  MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize,MPI::DOUBLE,&globalVel[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
566  
567 <
568 <
569 <
567 >  /*
568 >  if (myrank_ == 0){
569 >    for (i = 0; i < globalPts.size(); i++){
570 >      std::cout << globalPts[i] << std::endl;
571 >    }
572 >  }
573 >  */
574    // Free previous hull
575    qh_freeqhull(!qh_ALL);
576    qh_memfreeshort(&curlong, &totlong);
# Line 535 | Line 578 | void ConvexHull::computeHull(std::vector<StuntDouble*>
578      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
579                << totlong << curlong << std::endl;
580  
581 <  if (qh_new_qhull(dim_, numpoints, &globalPts[0], ismalloc,
581 >  if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
582                      const_cast<char *>(options_.c_str()), NULL, stderr)){
583  
584        sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
585 <      painCave.isFatal = 0;
585 >      painCave.isFatal = 1;
586        simError();
587        
588    } //qh_new_qhull
# Line 552 | Line 595 | void ConvexHull::computeHull(std::vector<StuntDouble*>
595  
596  
597      unsigned int nf = qh num_facets;
598 <    
598 >    
599      /* Build Surface SD list first */
600  
601      std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
# Line 562 | Line 605 | void ConvexHull::computeHull(std::vector<StuntDouble*>
605        if (!facet->simplicial){
606        // should never happen with Qt
607          sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
608 <        painCave.isFatal = 0;
608 >        painCave.isFatal = 1;
609          simError();
610        } //simplicical
611        
612 <      Triangle* face = new Triangle();
612 >      Triangle face;
613        Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
614 <      face->setNormal(V3dNormal);
615 <      //face->setCentroid(V3dCentroid);
614 >      face.setNormal(V3dNormal);
615 >
616 >      
617 >
618        RealType faceArea = 0.5*V3dNormal.length();
619 <      face->setArea(faceArea);
619 >      face.setArea(faceArea);
620  
621  
622        vertices = qh_facet3vertex(facet);
623 +      
624 +      coordT *center = qh_getcenter(vertices);
625 +      Vector3d V3dCentroid(center[0], center[1], center[2]);
626 +      face.setCentroid(V3dCentroid);
627 +      Vector3d faceVel = V3Zero;
628        FOREACHvertex_(vertices){
629          id = qh_pointid(vertex->point);
630 <        face->addVertex(bodydoubles[id]);
631 <        if( !isSurfaceID[id] ){
632 <          isSurfaceID[id] = true;
633 <          surfaceSDs_.push_back(bodydoubles[id]);
634 <        } //IF isSurfaceID
635 <      } //Foreachvertex
630 >        int localindex = id;
631 > #ifdef IS_MPI
632 >        Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 1]);
633 >        faceVel = faceVel + velVector;
634 >        if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
635 >          localindex = localPtsMap[id-noffset/3];
636 > #else
637 >          faceVel = faceVel + bodydoubles[localindex]->getVel();
638 > #endif
639 >          face.addVertex(bodydoubles[localindex]);
640 >          if( !isSurfaceID[id] ){
641 >            isSurfaceID[id] = true;
642 > #ifdef IS_MPI      
643 >            
644 > #endif
645 >            
646 >            surfaceSDs_.push_back(bodydoubles[localindex]);
647 >            
648 >          } //IF isSurfaceID
649  
650 <
650 > #ifdef IS_MPI
651 >        
652 >        }else{
653 >          face.addVertex(NULL);
654 >          }
655 > #endif
656 >      } //Foreachvertex
657 >      /*
658 >      if (!SETempty_(facet->coplanarset)){
659 >        FOREACHpoint_(facet->coplanarset){
660 >          id = qh_pointid(point);
661 >          surfaceSDs_.push_back(bodydoubles[id]);
662 >        }
663 >      }
664 >      */
665 >      face.setFacetVelocity(faceVel/3.0);
666        Triangles_.push_back(face);
667        qh_settempfree(&vertices);      
668 <      
668 >
669      } //FORALLfacets
592 –                
670  
594 –                
595 –                
671      /*
672 <  std::sort(surfaceIDs.begin(),surfaceIDs.end());
673 <  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
674 <  for(std::vector<int>::iterator list_iter = surfaceIDs.begin();
675 <      list_iter != surfaceIDs.end(); list_iter++)
601 <    {
602 <    int i = *list_iter;
603 <    surfaceSDs_.push_back(bodydoubles[i]);
672 >    std::cout << surfaceSDs_.size() << std::endl;
673 >    for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
674 >      Vector3d thisatom = (*SD)->getPos();
675 >      std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
676      }
677      */
678  
679  
680  
681 <
682 <
683 <
684 <  Ns_ = surfaceSDs_.size();
685 <
686 <
687 <  qh_getarea(qh facet_list);
688 <  volume_ = qh totvol;
689 <  area_ = qh totarea;
690 <
691 <  
692 <
693 <  qh_freeqhull(!qh_ALL);
694 <  qh_memfreeshort(&curlong, &totlong);
695 <  if (curlong || totlong)
696 <    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
697 <              << totlong << curlong << std::endl;
626 <  
627 <  
628 <  // free(pt_array);
629 <  
681 >    Ns_ = surfaceSDs_.size();
682 >    nTriangles_ = Triangles_.size();
683 >    
684 >    qh_getarea(qh facet_list);
685 >    volume_ = qh totvol;
686 >    area_ = qh totarea;
687 >    
688 >    
689 >    
690 >    qh_freeqhull(!qh_ALL);
691 >    qh_memfreeshort(&curlong, &totlong);
692 >    if (curlong || totlong)
693 >      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
694 >                << totlong << curlong << std::endl;
695 >    
696 >    
697 >    
698   }
699  
700  

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