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root/OpenMD/trunk/src/math/ConvexHull.cpp
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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1304 by chuckv, Wed Oct 15 18:26:01 2008 UTC vs.
Revision 1365 by chuckv, Mon Oct 12 20:11:29 2009 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved.
1 > /* Copyright (c) 2008, 2009 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 1.10 2008-10-15 18:26:01 chuckv Exp $
47 > *  @version $Id: ConvexHull.cpp,v 1.14 2009-10-12 20:11:29 chuckv Exp $
48   *
49   */
50  
# Line 149 | Line 149 | ConvexHull::ConvexHull() : Hull(){
149   nproc_ = MPI::COMM_WORLD.Get_size();
150   myrank_ = MPI::COMM_WORLD.Get_rank();
151   NstoProc_ = new int[nproc_];
152 < displs_   = new int[nproc_];
153 <
152 > vecdispls_   = new int[nproc_];
153 > displs_ = new int[nproc_];
154   // Create a surface point type in MPI to send
155   surfacePtType = MPI::DOUBLE.Create_contiguous(3);
156   surfacePtType.Commit();
# Line 213 | Line 213 | void ConvexHull::computeHull(std::vector<StuntDouble*>
213  
214    /* Build a displacements array */
215    for (int i = 1; i < nproc_; i++){
216 <    displs_[i] = displs_[i-1] + NstoProc_[i-1];
216 >    vecdispls_[i] = vecdispls_[i-1] + NstoProc_[i-1];
217    }
218    
219 <  int noffset = displs_[myrank_];
219 >  int noffset = vecdispls_[myrank_];
220    /* gather the potential hull */
221    
222    
# Line 229 | Line 229 | void ConvexHull::computeHull(std::vector<StuntDouble*>
229      surfacePtsLocal_.push_back(mpiSurfacePt);
230    }
231  
232 <  MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,displs_,surfacePtType);
232 >  MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,vecdispls_,surfacePtType);
233    std::vector<surfacePt_>::iterator spt;
234    std::vector<Enriched_Point_3> gblpoints;
235  
# Line 297 | Line 297 | void ConvexHull::computeHull(std::vector<StuntDouble*>
297  
298    }
299    
300 –  std::cout << "Number of surface atoms is: " << Ns_ << std::endl;
300    
301  
302  
# Line 370 | Line 369 | void ConvexHull::printHull(const std::string& geomFile
369   #ifdef HAVE_QHULL
370   /* Old options Qt Qu Qg QG0 FA */
371   /* More old opts Qc Qi Pp*/
372 < ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200) {
372 > ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200), nTriangles_(0) {
373    //If we are doing the mpi version, set up some vectors for data communication
374   #ifdef IS_MPI
375  
# Line 378 | Line 377 | ConvexHull::ConvexHull() : Hull(), dim_(3), options_("
377   nproc_ = MPI::COMM_WORLD.Get_size();
378   myrank_ = MPI::COMM_WORLD.Get_rank();
379   NstoProc_ = new int[nproc_];
380 < displs_   = new int[nproc_];
380 > vecdispls_   = new int[nproc_];
381 > vecNstoProc_ = new int[nproc_];
382 > displs_ = new int[nproc_];
383  
384   // Create a surface point type in MPI to send
385   //surfacePtType = MPI::DOUBLE.Create_contiguous(3);
# Line 438 | Line 439 | void ConvexHull::computeHull(std::vector<StuntDouble*>
439    
440    boolT ismalloc = False;
441    /* Clean up memory from previous convex hull calculations*/
442 +  
443    Triangles_.clear();
444    surfaceSDs_.clear();
445    surfaceSDs_.reserve(Ns_);
# Line 446 | Line 448 | void ConvexHull::computeHull(std::vector<StuntDouble*>
448                      const_cast<char *>(options_.c_str()), NULL, stderr)) {
449  
450        sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
451 <      painCave.isFatal = 0;
451 >      painCave.isFatal = 1;
452        simError();
453        
454    } //qh_new_qhull
# Line 454 | Line 456 | void ConvexHull::computeHull(std::vector<StuntDouble*>
456  
457   #ifdef IS_MPI
458    std::vector<double> localPts;
459 +  std::vector<double> localVel;
460 +  std::vector<double> localMass;
461    int localPtArraySize;
462    
463  
# Line 465 | Line 469 | void ConvexHull::computeHull(std::vector<StuntDouble*>
469      if (!facet->simplicial){
470        // should never happen with Qt
471        sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
472 <      painCave.isFatal = 0;
472 >      painCave.isFatal = 1;
473        simError();
474      }
475      
# Line 483 | Line 487 | void ConvexHull::computeHull(std::vector<StuntDouble*>
487    } //FORALLfacets
488  
489  
486 –
487 –  /*
488 –  std::sort(surfaceIDs.begin(),surfaceIDs.end());
489 –  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
490 –  int localPtArraySize = surfaceIDs.size() * 3;
491 –  */
492 –
493 –  //localPts.resize(localPtArraySize);
494 –  //std::fill(localPts.begin(),localPts.end(),0.0);
490  
491  
492    int idx = 0;
493    int nIsIts = 0;
499 – /*
500 –  // Copy the surface points into an array.
501 –  for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
502 –      list_iter != isSurfaceID.end(); list_iter++)
503 –    {
504 –      bool isIt = *list_iter;
505 –      if (isIt){
506 –        localPts.push_back(ptArray[dim_ * idx]);    
507 –        localPts.push_back(ptArray[dim_ * idx + 1]);
508 –        localPts.push_back(ptArray[dim_ * idx + 2]);
509 –        localPtsMap.push_back(idx);
510 –        nIsIts++;
511 –      } //Isit
512 –      idx++;
513 –    } //isSurfaceID
514 –  */
494    FORALLvertices {
495      idx = qh_pointid(vertex->point);
496      localPts.push_back(ptArray[dim_ * idx]);    
497      localPts.push_back(ptArray[dim_ * idx + 1]);
498      localPts.push_back(ptArray[dim_ * idx + 2]);
499 +
500 +    Vector3d vel = bodydoubles[idx]->getVel();
501 +    localVel.push_back(vel.x());
502 +    localVel.push_back(vel.y());
503 +    localVel.push_back(vel.z());
504 +
505 +
506 +    RealType bdmass = bodydoubles[idx]->getMass();
507 +    localMass.push_back(bdmass);
508 +
509      localPtsMap.push_back(idx);
510 +
511    }
512  
513  
514 <  localPtArraySize = localPts.size();
525 <
514 >  localPtArraySize = int(localPts.size()/3.0);
515  
516    MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
517 <
517 >  
518    Nsglobal_=0;
519    for (int i = 0; i < nproc_; i++){
520      Nsglobal_ += NstoProc_[i];
521 +    vecNstoProc_[i] = NstoProc_[i]*3;
522    }
523    
524  
525 <  int nglobalPts = int(Nsglobal_/3);
525 >  int nglobalPts = Nsglobal_*3;
526  
527  
528 <  std::vector<double> globalPts;
529 <  globalPts.resize(Nsglobal_);
528 >  std::vector<double> globalPts(nglobalPts);
529 >  std::vector<double> globalVel(nglobalPts);
530 >  std::vector<double> globalMass(Nsglobal_);
531  
532 +
533 +  
534    isSurfaceID.resize(nglobalPts);
535  
536  
537    std::fill(globalPts.begin(),globalPts.end(),0.0);
538  
539 <  displs_[0] = 0;
539 >  vecdispls_[0] = 0;
540    /* Build a displacements array */
541    for (int i = 1; i < nproc_; i++){
542 <    displs_[i] = displs_[i-1] + NstoProc_[i-1];
542 >    vecdispls_[i] = vecdispls_[i-1] + vecNstoProc_[i-1];
543    }
544    
545 +  displs_[0] = 0;
546 +  for (int i = 1; i < nproc_; i++){
547 +    displs_[i] = displs_[i-1] + NstoProc_[i-1];
548 +  }
549    
550 <  int noffset = displs_[myrank_];
550 >  int noffset = vecdispls_[myrank_];
551    /* gather the potential hull */
552    
553 <  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
553 >  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize*3,MPI::DOUBLE,&globalPts[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
554 >  MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize*3,MPI::DOUBLE,&globalVel[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
555 >  MPI::COMM_WORLD.Allgatherv(&localMass[0],localPtArraySize,MPI::DOUBLE,&globalMass[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
556  
557    /*
558 +  int tmpidx = 0;
559 +  
560    if (myrank_ == 0){
561 <    for (i = 0; i < globalPts.size(); i++){
562 <      std::cout << globalPts[i] << std::endl;
561 >    for (i = 0; i < nglobalPts-3; i++){      
562 >      std::cout << "Au   " << globalPts[tmpidx] << "  " << globalPts[tmpidx+1] << "  " << globalPts[tmpidx +2] << std::endl;
563 >      tmpidx = tmpidx + 3;
564      }
565    }
566    */
567 +  
568    // Free previous hull
569    qh_freeqhull(!qh_ALL);
570    qh_memfreeshort(&curlong, &totlong);
# Line 569 | Line 572 | void ConvexHull::computeHull(std::vector<StuntDouble*>
572      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
573                << totlong << curlong << std::endl;
574  
575 <  if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
575 >  if (qh_new_qhull(dim_, Nsglobal_, &globalPts[0], ismalloc,
576                      const_cast<char *>(options_.c_str()), NULL, stderr)){
577  
578        sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
# Line 600 | Line 603 | void ConvexHull::computeHull(std::vector<StuntDouble*>
603          simError();
604        } //simplicical
605        
606 <      Triangle* face = new Triangle();
606 >      Triangle face;
607        Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
608 <      face->setNormal(V3dNormal);
608 >      face.setNormal(V3dNormal);
609  
610        
611  
612 <      RealType faceArea = 0.5*V3dNormal.length();
613 <      face->setArea(faceArea);
612 >      //RealType faceArea = 0.5*V3dNormal.length();
613 >      RealType faceArea = qh_facetarea(facet);
614 >      face.setArea(faceArea);
615  
616  
617        vertices = qh_facet3vertex(facet);
618        
619        coordT *center = qh_getcenter(vertices);
620        Vector3d V3dCentroid(center[0], center[1], center[2]);
621 <      face->setCentroid(V3dCentroid);
622 <
621 >      face.setCentroid(V3dCentroid);
622 >      Vector3d faceVel = V3Zero;
623 >      Vector3d p[3];
624 >      RealType faceMass = 0.0;
625 >      int ver = 0;
626        FOREACHvertex_(vertices){
627          id = qh_pointid(vertex->point);
628 +        p[ver][0] = vertex->point[0];
629 +        p[ver][1] = vertex->point[1];
630 +        p[ver][2] = vertex->point[2];
631          int localindex = id;
632   #ifdef IS_MPI
633 +        Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 1]);
634          
635 +        faceVel = faceVel + velVector;
636 +        faceMass = faceMass + globalMass[id];
637          if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
638            localindex = localPtsMap[id-noffset/3];
639 + #else
640 +          faceVel = faceVel + bodydoubles[localindex]->getVel();
641 +          faceMass = faceMass + bodydoubles[localindex]->getMass();
642   #endif
643 <          face->addVertex(bodydoubles[localindex]);
643 >          face.addVertexSD(bodydoubles[localindex]);
644            if( !isSurfaceID[id] ){
645              isSurfaceID[id] = true;
646   #ifdef IS_MPI      
# Line 638 | Line 654 | void ConvexHull::computeHull(std::vector<StuntDouble*>
654   #ifdef IS_MPI
655          
656          }else{
657 <          face->addVertex(NULL);
657 >          face.addVertexSD(NULL);
658            }
659   #endif
660 +        ver++;
661        } //Foreachvertex
662        /*
663        if (!SETempty_(facet->coplanarset)){
# Line 649 | Line 666 | void ConvexHull::computeHull(std::vector<StuntDouble*>
666            surfaceSDs_.push_back(bodydoubles[id]);
667          }
668        }
669 <
669 >      */
670 >      face.addVertices(p[0],p[1],p[2]);
671 >      face.setFacetMass(faceMass);
672 >      face.setFacetVelocity(faceVel/3.0);
673        Triangles_.push_back(face);
674        qh_settempfree(&vertices);      
675 <      */
675 >
676      } //FORALLfacets
677  
678 <    /*
678 >    /*    
679      std::cout << surfaceSDs_.size() << std::endl;
680      for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
681        Vector3d thisatom = (*SD)->getPos();
# Line 666 | Line 686 | void ConvexHull::computeHull(std::vector<StuntDouble*>
686  
687  
688      Ns_ = surfaceSDs_.size();
689 +    nTriangles_ = Triangles_.size();
690      
670 –    
691      qh_getarea(qh facet_list);
692      volume_ = qh totvol;
693      area_ = qh totarea;

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