ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/math/ConvexHull.cpp
(Generate patch)

Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
Revision 1365 by chuckv, Mon Oct 12 20:11:29 2009 UTC

# Line 1 | Line 1
1 < /* Copyright (c) 2006 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 1.8 2008-09-14 01:32:25 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 369 | Line 368 | void ConvexHull::printHull(const std::string& geomFile
368   #else
369   #ifdef HAVE_QHULL
370   /* Old options Qt Qu Qg QG0 FA */
371 < ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt  Qci Tcv Pp") {
371 > /* More old opts Qc Qi Pp*/
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 377 | 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);
386 < surfacePtType.Commit();
385 > //surfacePtType = MPI::DOUBLE.Create_contiguous(3);
386 > // surfacePtType.Commit();
387  
388  
389   #endif
# Line 413 | Line 415 | void ConvexHull::computeHull(std::vector<StuntDouble*>
415    
416    //pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
417  
418 <  double* ptArray = new double[numpoints * 3];
418 > //  double* ptArray = new double[numpoints * 3];
419 >  std::vector<double> ptArray(numpoints*3);
420    std::vector<bool> isSurfaceID(numpoints);
421  
422    // Copy the positon vector into a points vector for qhull.
# Line 435 | Line 438 | void ConvexHull::computeHull(std::vector<StuntDouble*>
438    
439    
440    boolT ismalloc = False;
441 +  /* Clean up memory from previous convex hull calculations*/
442 +  
443    Triangles_.clear();
444    surfaceSDs_.clear();
445 <  
446 <  if (qh_new_qhull(dim_, numpoints, ptArray, ismalloc,
445 >  surfaceSDs_.reserve(Ns_);
446 >
447 >  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
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 450 | 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 +
464    std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
465 +
466  
467    FORALLfacets {
468      
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 478 | Line 488 | void ConvexHull::computeHull(std::vector<StuntDouble*>
488  
489  
490  
481 –  /*
482 –  std::sort(surfaceIDs.begin(),surfaceIDs.end());
483 –  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
484 –  int localPtArraySize = surfaceIDs.size() * 3;
485 –  */
491  
487 –  localPts.resize(localPtArraySize);
488 –  //  std::fill(localPts.begin(),globalPts.end(),0.0);
489 –
490 –
492    int idx = 0;
493 <  // Copy the surface points into an array.
494 <  for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
495 <      list_iter != isSurfaceID.end(); list_iter++)
496 <    {
497 <      bool isIt = *list_iter;
498 <      if (isIt){
498 <        localPts.push_back(ptArray[dim_ * idx]);    
499 <        localPts.push_back(ptArray[dim_ * idx + 1]);
500 <        localPts.push_back(ptArray[dim_ * idx + 2]);
501 <        localPtsMap.push_back(idx);
502 <      } //Isit
503 <      idx++;
504 <    } //isSurfaceID
505 <  
506 <
507 <  localPtArraySize = localPts.size();
508 <  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
493 >  int nIsIts = 0;
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 = int(localPts.size()/3.0);
515 +
516 +  MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
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 = Nsglobal_*3;
526 +
527  
528 <  std::vector<double> globalPts;
529 <  globalPts.resize(Nsglobal_);
530 <  isSurfaceID.resize(int(Nsglobal_/3));
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 +  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 <  int noffset = displs_[myrank_];
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 = vecdispls_[myrank_];
551    /* gather the potential hull */
552    
553 <  MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],NstoProc_,displs_,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 <
559 <
557 >  /*
558 >  int tmpidx = 0;
559 >  
560 >  if (myrank_ == 0){
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 535 | 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_, numpoints, &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");
579 <      painCave.isFatal = 0;
579 >      painCave.isFatal = 1;
580        simError();
581        
582    } //qh_new_qhull
# Line 552 | Line 589 | void ConvexHull::computeHull(std::vector<StuntDouble*>
589  
590  
591      unsigned int nf = qh num_facets;
592 <    
592 >    
593      /* Build Surface SD list first */
594  
595      std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
# Line 562 | Line 599 | void ConvexHull::computeHull(std::vector<StuntDouble*>
599        if (!facet->simplicial){
600        // should never happen with Qt
601          sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
602 <        painCave.isFatal = 0;
602 >        painCave.isFatal = 1;
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);
609 <      //face->setCentroid(V3dCentroid);
610 <      RealType faceArea = 0.5*V3dNormal.length();
574 <      face->setArea(faceArea);
608 >      face.setNormal(V3dNormal);
609 >
610 >      
611  
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 +      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 <        face->addVertex(bodydoubles[id]);
629 <        if( !isSurfaceID[id] ){
630 <          isSurfaceID[id] = true;
631 <          surfaceSDs_.push_back(bodydoubles[id]);
632 <        } //IF isSurfaceID
633 <      } //Foreachvertex
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.addVertexSD(bodydoubles[localindex]);
644 >          if( !isSurfaceID[id] ){
645 >            isSurfaceID[id] = true;
646 > #ifdef IS_MPI      
647 >            
648 > #endif
649 >            
650 >            surfaceSDs_.push_back(bodydoubles[localindex]);
651 >            
652 >          } //IF isSurfaceID
653  
654 <
654 > #ifdef IS_MPI
655 >        
656 >        }else{
657 >          face.addVertexSD(NULL);
658 >          }
659 > #endif
660 >        ver++;
661 >      } //Foreachvertex
662 >      /*
663 >      if (!SETempty_(facet->coplanarset)){
664 >        FOREACHpoint_(facet->coplanarset){
665 >          id = qh_pointid(point);
666 >          surfaceSDs_.push_back(bodydoubles[id]);
667 >        }
668 >      }
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
592 –                
677  
678 <                
679 <                
680 <    /*
681 <  std::sort(surfaceIDs.begin(),surfaceIDs.end());
682 <  surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
599 <  for(std::vector<int>::iterator list_iter = surfaceIDs.begin();
600 <      list_iter != surfaceIDs.end(); list_iter++)
601 <    {
602 <    int i = *list_iter;
603 <    surfaceSDs_.push_back(bodydoubles[i]);
678 >    /*    
679 >    std::cout << surfaceSDs_.size() << std::endl;
680 >    for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
681 >      Vector3d thisatom = (*SD)->getPos();
682 >      std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
683      }
684      */
685  
686  
687  
688 <
689 <
690 <
691 <  Ns_ = surfaceSDs_.size();
692 <
693 <
694 <  qh_getarea(qh facet_list);
695 <  volume_ = qh totvol;
696 <  area_ = qh totarea;
697 <
698 <  
699 <
700 <  qh_freeqhull(!qh_ALL);
701 <  qh_memfreeshort(&curlong, &totlong);
702 <  if (curlong || totlong)
703 <    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
704 <              << totlong << curlong << std::endl;
626 <  
627 <  
628 <  // free(pt_array);
629 <  
688 >    Ns_ = surfaceSDs_.size();
689 >    nTriangles_ = Triangles_.size();
690 >    
691 >    qh_getarea(qh facet_list);
692 >    volume_ = qh totvol;
693 >    area_ = qh totarea;
694 >    
695 >    
696 >    
697 >    qh_freeqhull(!qh_ALL);
698 >    qh_memfreeshort(&curlong, &totlong);
699 >    if (curlong || totlong)
700 >      std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
701 >                << totlong << curlong << std::endl;
702 >    
703 >    
704 >    
705   }
706  
707  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines