src/math/AlphaHull.cpp

/* Copyright (c) 2008, 2009, 2010 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *
 *  AlphaHull.cpp
 *
 *  Purpose: To calculate Alpha hull, hull volume libqhull.
 *
 *  Created by Charles F. Vardeman II on 11 Dec 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id$
 *
 */

/* Standard includes independent of library */

#include <iostream>
#include <fstream>
#include <list>
#include <algorithm>
#include <iterator>
#include <utility>
#include "math/AlphaHull.hpp"
#include "utils/simError.h"
#ifdef IS_MPI
#include <mpi.h>
#endif
#include "math/qhull.hpp"

using namespace OpenMD;

#ifdef HAVE_QHULL
double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim);

AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha), options_("qhull d QJ Tcv Pp") {
}

void AlphaHull::computeHull(std::vector<StuntDouble*> bodydoubles) { 
 
  int numpoints = bodydoubles.size();
  bool alphashape=true;
  
  Triangles_.clear();
  
  vertexT *vertex, **vertexp;
  facetT *facet, *neighbor;
  setT *vertices, *verticestop, *verticesbottom;
  int curlong, totlong;
  pointT *interiorPoint;
  
  std::vector<double> ptArray(numpoints*dim_);

  // Copy the positon vector into a points vector for qhull.
  std::vector<StuntDouble*>::iterator SD;
  int i = 0;
  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
    Vector3d pos = (*SD)->getPos();      
    ptArray[dim_ * i] = pos.x();
    ptArray[dim_ * i + 1] = pos.y();
    ptArray[dim_ * i + 2] = pos.z();
    i++;
  }

    /* Clean up memory from previous convex hull calculations*/
  boolT ismalloc = False;

  int ridgesCount=0;
  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
                   const_cast<char *>(options_.c_str()), NULL, stderr)) {

    sprintf(painCave.errMsg, "AlphaHull: Qhull failed to compute convex hull");
    painCave.isFatal = 1;
    simError();
    
  } //qh_new_qhull


#ifdef IS_MPI
  //If we are doing the mpi version, set up some vectors for data communication
  
  int nproc = MPI::COMM_WORLD.Get_size();
  int myrank = MPI::COMM_WORLD.Get_rank();
  int localHullSites = 0;

  std::vector<int> hullSitesOnProc(nproc, 0);
  std::vector<int> coordsOnProc(nproc, 0);
  std::vector<int> displacements(nproc, 0);
  std::vector<int> vectorDisplacements(nproc, 0);

  std::vector<double> coords;
  std::vector<double> vels;
  std::vector<int> indexMap;
  std::vector<double> masses;

  FORALLvertices{
    localHullSites++;
    
    int idx = qh_pointid(vertex->point);

    indexMap.push_back(idx);

    coords.push_back(ptArray[dim_  * idx]);
    coords.push_back(ptArray[dim_  * idx + 1]);
    coords.push_back(ptArray[dim_  * idx + 2]);

    StuntDouble* sd = bodydoubles[idx];

    Vector3d vel = sd->getVel();
    vels.push_back(vel.x());
    vels.push_back(vel.y());
    vels.push_back(vel.z());

    masses.push_back(sd->getMass());
  }

  MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
                            1, MPI::INT);

  int globalHullSites = 0;
  for (int iproc = 0; iproc < nproc; iproc++){
    globalHullSites += hullSitesOnProc[iproc];
    coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
  }

  displacements[0] = 0;
  vectorDisplacements[0] = 0;
  
  for (int iproc = 1; iproc < nproc; iproc++){
    displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
    vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1]; 
  }

  std::vector<double> globalCoords(dim_ * globalHullSites);
  std::vector<double> globalVels(dim_ * globalHullSites);
  std::vector<double> globalMasses(globalHullSites);

  int count = coordsOnProc[myrank];
  
  MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
                             &coordsOnProc[0], &vectorDisplacements[0], 
                             MPI::DOUBLE);

  MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0], 
                             &coordsOnProc[0], &vectorDisplacements[0],
                             MPI::DOUBLE);

  MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
                             &globalMasses[0], &hullSitesOnProc[0], 
                             &displacements[0], MPI::DOUBLE);

  // Free previous hull
  qh_freeqhull(!qh_ALL);
  qh_memfreeshort(&curlong, &totlong);
  if (curlong || totlong)
    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
              << totlong << curlong << std::endl;
  
  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
                   const_cast<char *>(options_.c_str()), NULL, stderr)){
    
    sprintf(painCave.errMsg, "AlphaHull: Qhull failed to compute global convex hull");
    painCave.isFatal = 1;
    simError();
    
  } //qh_new_qhull


#endif

  //Set facet->center as the Voronoi center
  qh_setvoronoi_all();
  
  
  int convexNumVert = qh_setsize(qh_facetvertices (qh facet_list, NULL, false));
  //Insert all the sample points, because, even with alpha=0, the alpha shape/alpha complex will
  //contain them.

  //  tri::Allocator<CMeshO>::AddVertices(pm.cm,convexNumVert);
  
  /*ivp length is 'qh num_vertices' because each vertex is accessed through its ID whose range is 
    0<=qh_pointid(vertex->point)<qh num_vertices*/
  //  vector<tri::Allocator<CMeshO>::VertexPointer> ivp(qh num_vertices);
  /*i=0;
  FORALLvertices{       
    if ((*vertex).point){
      //  pm.cm.vert[i].P()[0] = (*vertex).point[0];
      // pm.cm.vert[i].P()[1] = (*vertex).point[1];
      //pm.cm.vert[i].P()[2] = (*vertex).point[2];
      // ivp[qh_pointid(vertex->point)] = &pm.cm.vert[i];
      i++;
    }
  }
  */
  //Set of alpha complex triangles for alphashape filtering
  setT* set= qh_settemp(4* qh num_facets); 
  
  qh visit_id++;
  int numFacets=0;
  std::vector<std::vector <int> > facetlist;
  interiorPoint = qh interior_point;
  FORALLfacet_(qh facet_list) {
    numFacets++;
    if (!facet->upperdelaunay) {
      //For all facets (that are tetrahedrons)calculate the radius of the empty circumsphere considering 
      //the distance between the circumcenter and a vertex of the facet
      vertexT* vertex = (vertexT *)(facet->vertices->e[0].p);
      double* center = facet->center;
      double radius =  qh_pointdist(vertex->point,center,dim_);
      
      if (radius>alpha_) // if the facet is not good consider the ridges
        {
          //if calculating the alphashape, unmark the facet ('good' is used as 'marked'). 
          facet->good=false;
          
          //Compute each ridge (triangle) once and test the cironference radius with alpha
          facet->visitid= qh visit_id;
          qh_makeridges(facet);
          ridgeT *ridge, **ridgep;
          int goodTriangles=0;
          FOREACHridge_(facet->ridges) {
            neighbor= otherfacet_(ridge, facet);
            if (( neighbor->visitid != qh visit_id)){                   
              //Calculate the radius of the circumference 
              pointT* p0 = ((vertexT*) (ridge->vertices->e[0].p))->point;
              pointT* p1 = ((vertexT*) (ridge->vertices->e[1].p))->point;
              pointT* p2 = ((vertexT*) (ridge->vertices->e[2].p))->point;
              
              radius = calculate_circumradius(p0,p1,p2, dim_);
              
              if(radius <=alpha_){
                goodTriangles++;
                //save the triangle (ridge) for subsequent filtering
                qh_setappend(&set, ridge); 
              }
            }
          }

          //If calculating the alphashape, mark the facet('good' is used as 'marked'). 
          //This facet will have some triangles hidden by the facet's neighbor.
          if(goodTriangles==4)
            facet->good=true;
          
        }
      else //the facet is good. Put all the triangles of the tetrahedron in the mesh
        {
          //Compute each ridge (triangle) once
          facet->visitid= qh visit_id;
          //If calculating the alphashape, mark the facet('good' is used as 'marked').
          //This facet will have some triangles hidden by the facet's neighbor.
          facet->good=true;
          qh_makeridges(facet);
          ridgeT *ridge, **ridgep;
          FOREACHridge_(facet->ridges) {
            neighbor= otherfacet_(ridge, facet);
            if ((neighbor->visitid != qh visit_id)){
                 qh_setappend(&set, ridge);
            }   
          }
        }
    }
  }
  //assert(numFacets== qh num_facets);
  
  //Filter the triangles (only the ones on the boundary of the alpha complex) and build the mesh


  ridgeT *ridge, **ridgep;
  FOREACHridge_(set) {
    if ((!ridge->top->good || !ridge->bottom->good || ridge->top->upperdelaunay || ridge->bottom->upperdelaunay)){
      //        tri::Allocator<CMeshO>::FaceIterator fi=tri::Allocator<CMeshO>::AddFaces(pm.cm,1);
      ridgesCount++;
      int vertex_n, vertex_i;
      Triangle face;
      
      // Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
      //face.setNormal(V3dNormal);
      
      
      //coordT *center = qh_getcenter(ridge->vertices);
      //std::cout << "Centers are " << center[0] << "  " <<center[1] << "  " << center[2] << std::endl;
      //Vector3d V3dCentroid(center[0], center[1], center[2]);
      //face.setCentroid(V3dCentroid);

      
      Vector3d faceVel = V3Zero;
      Vector3d p[3];
      RealType faceMass = 0.0;
      
      int ver = 0;
      std::vector<int> virtexlist;
      FOREACHvertex_i_(ridge->vertices){
        int id = qh_pointid(vertex->point);
        p[ver][0] = vertex->point[0];
        p[ver][1] = vertex->point[1];
        p[ver][2] = vertex->point[2];
        Vector3d vel;
        RealType mass;
        ver++;
        virtexlist.push_back(id);
        // std::cout << "Ridge: " << ridgesCount << " Vertex " << id << std::endl; 

        vel = bodydoubles[id]->getVel();
        mass = bodydoubles[id]->getMass();
        face.addVertexSD(bodydoubles[id]);


        faceVel = faceVel + vel;
        faceMass = faceMass + mass;
      } //FOREACH Vertex 
      facetlist.push_back(virtexlist);
      face.addVertices(p[0],p[1],p[2]);
      face.setFacetMass(faceMass);
      face.setFacetVelocity(faceVel / RealType(3.0));
      
      RealType area = face.getArea();
      area_ += area;
      Vector3d normal = face.getUnitNormal();
      RealType offset =  ((0.0-p[0][0])*normal[0] + (0.0-p[0][1])*normal[1] + (0.0-p[0][2])*normal[2]);
      RealType dist =  normal[0] * interiorPoint[0] + normal[1]*interiorPoint[1] + normal[2]*interiorPoint[2];
      std::cout << "Dist and normal and area are: " << normal << std::endl;
      volume_ += dist *area/qh hull_dim;
      
      Triangles_.push_back(face);
    }
  }

  std::cout << "Volume is: " << volume_ << std::endl; 

//assert(pm.cm.fn == ridgesCount);
/*
  std::cout <<"OFF"<<std::endl; 
  std::cout << bodydoubles.size() << "  " << facetlist.size() << "  " << 3*facetlist.size() << std::endl; 
  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
    Vector3d pos = (*SD)->getPos();      
    std::cout << pos.x() << "  " << pos.y() << "  " << pos.z() << std::endl; 
  }

  
  std::vector<std::vector<int> >::iterator thisfacet;
  std::vector<int>::iterator thisvertex;

  for (thisfacet = facetlist.begin(); thisfacet != facetlist.end(); thisfacet++){
    std::cout << (*thisfacet).size(); 
    for (thisvertex = (*thisfacet).begin(); thisvertex != (*thisfacet).end(); thisvertex++){
      std::cout << "  " <<  *thisvertex;
    }
    std::cout << std::endl; 
  }
*/


/*  
  FORALLfacets {  
    Triangle face;

    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
    face.setNormal(V3dNormal);
    
    RealType faceArea = qh_facetarea(facet);
    face.setArea(faceArea);
    
    vertices = qh_facet3vertex(facet);
      
    coordT *center = qh_getcenter(vertices);
    Vector3d V3dCentroid(center[0], center[1], center[2]);
    face.setCentroid(V3dCentroid);

    Vector3d faceVel = V3Zero;
    Vector3d p[3];
    RealType faceMass = 0.0;

    int ver = 0;

    FOREACHvertex_(vertices){
      int id = qh_pointid(vertex->point);
      p[ver][0] = vertex->point[0];
      p[ver][1] = vertex->point[1];
      p[ver][2] = vertex->point[2];
      
      Vector3d vel;
      RealType mass;

#ifdef IS_MPI
      vel = Vector3d(globalVels[dim_ * id],
                     globalVels[dim_ * id + 1], 
                     globalVels[dim_ * id + 2]);
      mass = globalMasses[id];

      // localID will be between 0 and hullSitesOnProc[myrank] if we
      // own this guy.

      int localID = id - displacements[myrank];

      if (localID >= 0 && localID < hullSitesOnProc[myrank])
        face.addVertexSD(bodydoubles[indexMap[localID]]);
      
#else
      vel = bodydoubles[id]->getVel();
      mass = bodydoubles[id]->getMass();
      face.addVertexSD(bodydoubles[id]);      
#endif
        
      faceVel = faceVel + vel;
      faceMass = faceMass + mass;
      ver++;      
    } //Foreachvertex

    face.addVertices(p[0], p[1], p[2]);
    face.setFacetMass(faceMass);
    face.setFacetVelocity(faceVel/3.0);
    Triangles_.push_back(face);
    qh_settempfree(&vertices);      

  } //FORALLfacets
*/
  // qh_getarea(qh facet_list);
  //volume_ = qh totvol;
  // area_ = qh totarea;

  qh_freeqhull(!qh_ALL);
  qh_memfreeshort(&curlong, &totlong);
  if (curlong || totlong)
    std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
              << totlong << curlong << std::endl;    
}

void AlphaHull::printHull(const std::string& geomFileName) {

#ifdef IS_MPI
  if (worldRank == 0)  {
#endif
  FILE *newGeomFile;
  
  //create new .md file based on old .md file
  newGeomFile = fopen(geomFileName.c_str(), "w");
  qh_findgood_all(qh facet_list);
  for (int i = 0; i < qh_PRINTEND; i++)
    qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
  
  fclose(newGeomFile);
#ifdef IS_MPI
  }
#endif  
}

  double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim){
    coordT a = qh_pointdist(p0,p1,dim);
    coordT b = qh_pointdist(p1,p2,dim);
    coordT c = qh_pointdist(p2,p0,dim);
    
    coordT sum =(a + b + c)*0.5;
    coordT area = sum*(a+b-sum)*(a+c-sum)*(b+c-sum);
    return (double) (a*b*c)/(4*sqrt(area));
  }

#endif //QHULL
Revision:	1782
Committed:	Wed Aug 22 02:28:28 2012 UTC (12 years, 8 months ago) by gezelter
File size:	16446 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	User	Rev	Content
1	chuckv	1402	/* Copyright (c) 2008, 2009, 2010 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
5			* redistribute this software in source and binary code form, provided
6			* that the following conditions are met:
7			*
8			* 1. Redistributions of source code must retain the above copyright
9			* notice, this list of conditions and the following disclaimer.
10			*
11			* 2. Redistributions in binary form must reproduce the above copyright
12			* notice, this list of conditions and the following disclaimer in the
13			* documentation and/or other materials provided with the
14			* distribution.
15			*
16			* This software is provided "AS IS," without a warranty of any
17			* kind. All express or implied conditions, representations and
18			* warranties, including any implied warranty of merchantability,
19			* fitness for a particular purpose or non-infringement, are hereby
20			* excluded. The University of Notre Dame and its licensors shall not
21			* be liable for any damages suffered by licensee as a result of
22			* using, modifying or distributing the software or its
23			* derivatives. In no event will the University of Notre Dame or its
24			* licensors be liable for any lost revenue, profit or data, or for
25			* direct, indirect, special, consequential, incidental or punitive
26			* damages, however caused and regardless of the theory of liability,
27			* arising out of the use of or inability to use software, even if the
28			* University of Notre Dame has been advised of the possibility of
29			* such damages.
30			*
31			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32			* research, please cite the appropriate papers when you publish your
33			* work. Good starting points are:
34			*
35			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40	chuckv	1402	*
41			* AlphaHull.cpp
42			*
43			* Purpose: To calculate Alpha hull, hull volume libqhull.
44			*
45			* Created by Charles F. Vardeman II on 11 Dec 2006.
46			* @author Charles F. Vardeman II
47	gezelter	1442	* @version $Id$
48	chuckv	1402	*
49			*/
50
51			/* Standard includes independent of library */
52
53			#include <iostream>
54			#include <fstream>
55			#include <list>
56			#include <algorithm>
57			#include <iterator>
58			#include <utility>
59			#include "math/AlphaHull.hpp"
60			#include "utils/simError.h"
61			#ifdef IS_MPI
62			#include <mpi.h>
63			#endif
64	gezelter	1782	#include "math/qhull.hpp"
65	chuckv	1402
66			using namespace OpenMD;
67
68			#ifdef HAVE_QHULL
69			double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim);
70
71	chuckv	1404	AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha), options_("qhull d QJ Tcv Pp") {
72	chuckv	1402	}
73
74			void AlphaHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
75
76			int numpoints = bodydoubles.size();
77			bool alphashape=true;
78
79			Triangles_.clear();
80
81			vertexT vertex, *vertexp;
82			facetT facet, neighbor;
83	chuckv	1404	setT vertices, verticestop, *verticesbottom;
84	chuckv	1402	int curlong, totlong;
85	chuckv	1404	pointT *interiorPoint;
86	chuckv	1402
87			std::vector<double> ptArray(numpoints*dim_);
88
89			// Copy the positon vector into a points vector for qhull.
90			std::vector<StuntDouble*>::iterator SD;
91			int i = 0;
92			for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
93			Vector3d pos = (*SD)->getPos();
94			ptArray[dim_ * i] = pos.x();
95			ptArray[dim_ * i + 1] = pos.y();
96			ptArray[dim_ * i + 2] = pos.z();
97			i++;
98			}
99
100			/* Clean up memory from previous convex hull calculations*/
101			boolT ismalloc = False;
102
103			int ridgesCount=0;
104			if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
105			const_cast<char *>(options_.c_str()), NULL, stderr)) {
106
107			sprintf(painCave.errMsg, "AlphaHull: Qhull failed to compute convex hull");
108			painCave.isFatal = 1;
109			simError();
110
111			} //qh_new_qhull
112
113
114			#ifdef IS_MPI
115			//If we are doing the mpi version, set up some vectors for data communication
116
117			int nproc = MPI::COMM_WORLD.Get_size();
118			int myrank = MPI::COMM_WORLD.Get_rank();
119			int localHullSites = 0;
120
121			std::vector<int> hullSitesOnProc(nproc, 0);
122			std::vector<int> coordsOnProc(nproc, 0);
123			std::vector<int> displacements(nproc, 0);
124			std::vector<int> vectorDisplacements(nproc, 0);
125
126			std::vector<double> coords;
127			std::vector<double> vels;
128			std::vector<int> indexMap;
129			std::vector<double> masses;
130
131			FORALLvertices{
132			localHullSites++;
133
134			int idx = qh_pointid(vertex->point);
135
136			indexMap.push_back(idx);
137
138			coords.push_back(ptArray[dim_ * idx]);
139			coords.push_back(ptArray[dim_ * idx + 1]);
140			coords.push_back(ptArray[dim_ * idx + 2]);
141
142			StuntDouble* sd = bodydoubles[idx];
143
144			Vector3d vel = sd->getVel();
145			vels.push_back(vel.x());
146			vels.push_back(vel.y());
147			vels.push_back(vel.z());
148
149			masses.push_back(sd->getMass());
150			}
151
152			MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
153			1, MPI::INT);
154
155			int globalHullSites = 0;
156			for (int iproc = 0; iproc < nproc; iproc++){
157			globalHullSites += hullSitesOnProc[iproc];
158			coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
159			}
160
161			displacements[0] = 0;
162			vectorDisplacements[0] = 0;
163
164			for (int iproc = 1; iproc < nproc; iproc++){
165			displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
166			vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
167			}
168
169			std::vector<double> globalCoords(dim_ * globalHullSites);
170			std::vector<double> globalVels(dim_ * globalHullSites);
171			std::vector<double> globalMasses(globalHullSites);
172
173			int count = coordsOnProc[myrank];
174
175			MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
176			&coordsOnProc[0], &vectorDisplacements[0],
177			MPI::DOUBLE);
178
179			MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
180			&coordsOnProc[0], &vectorDisplacements[0],
181			MPI::DOUBLE);
182
183			MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
184			&globalMasses[0], &hullSitesOnProc[0],
185			&displacements[0], MPI::DOUBLE);
186
187			// Free previous hull
188			qh_freeqhull(!qh_ALL);
189			qh_memfreeshort(&curlong, &totlong);
190			if (curlong \|\| totlong)
191			std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
192			<< totlong << curlong << std::endl;
193
194			if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
195			const_cast<char *>(options_.c_str()), NULL, stderr)){
196
197			sprintf(painCave.errMsg, "AlphaHull: Qhull failed to compute global convex hull");
198			painCave.isFatal = 1;
199			simError();
200
201			} //qh_new_qhull
202
203
204			#endif
205
206			//Set facet->center as the Voronoi center
207			qh_setvoronoi_all();
208
209
210			int convexNumVert = qh_setsize(qh_facetvertices (qh facet_list, NULL, false));
211			//Insert all the sample points, because, even with alpha=0, the alpha shape/alpha complex will
212			//contain them.
213
214			// tri::Allocator<CMeshO>::AddVertices(pm.cm,convexNumVert);
215
216			/*ivp length is 'qh num_vertices' because each vertex is accessed through its ID whose range is
217			0<=qh_pointid(vertex->point)<qh num_vertices*/
218			// vector<tri::Allocator<CMeshO>::VertexPointer> ivp(qh num_vertices);
219			/*i=0;
220			FORALLvertices{
221			if ((*vertex).point){
222			// pm.cm.vert[i].P()[0] = (*vertex).point[0];
223			// pm.cm.vert[i].P()[1] = (*vertex).point[1];
224			//pm.cm.vert[i].P()[2] = (*vertex).point[2];
225			// ivp[qh_pointid(vertex->point)] = &pm.cm.vert[i];
226			i++;
227			}
228			}
229			*/
230			//Set of alpha complex triangles for alphashape filtering
231			setT* set= qh_settemp(4* qh num_facets);
232
233			qh visit_id++;
234			int numFacets=0;
235			std::vector<std::vector <int> > facetlist;
236	chuckv	1404	interiorPoint = qh interior_point;
237	chuckv	1402	FORALLfacet_(qh facet_list) {
238			numFacets++;
239			if (!facet->upperdelaunay) {
240			//For all facets (that are tetrahedrons)calculate the radius of the empty circumsphere considering
241			//the distance between the circumcenter and a vertex of the facet
242			vertexT* vertex = (vertexT *)(facet->vertices->e[0].p);
243			double* center = facet->center;
244			double radius = qh_pointdist(vertex->point,center,dim_);
245
246			if (radius>alpha_) // if the facet is not good consider the ridges
247			{
248			//if calculating the alphashape, unmark the facet ('good' is used as 'marked').
249			facet->good=false;
250
251			//Compute each ridge (triangle) once and test the cironference radius with alpha
252			facet->visitid= qh visit_id;
253			qh_makeridges(facet);
254			ridgeT ridge, *ridgep;
255			int goodTriangles=0;
256			FOREACHridge_(facet->ridges) {
257			neighbor= otherfacet_(ridge, facet);
258			if (( neighbor->visitid != qh visit_id)){
259			//Calculate the radius of the circumference
260			pointT* p0 = ((vertexT*) (ridge->vertices->e[0].p))->point;
261			pointT* p1 = ((vertexT*) (ridge->vertices->e[1].p))->point;
262			pointT* p2 = ((vertexT*) (ridge->vertices->e[2].p))->point;
263
264			radius = calculate_circumradius(p0,p1,p2, dim_);
265
266			if(radius <=alpha_){
267			goodTriangles++;
268			//save the triangle (ridge) for subsequent filtering
269			qh_setappend(&set, ridge);
270			}
271			}
272			}
273
274			//If calculating the alphashape, mark the facet('good' is used as 'marked').
275			//This facet will have some triangles hidden by the facet's neighbor.
276			if(goodTriangles==4)
277			facet->good=true;
278
279			}
280			else //the facet is good. Put all the triangles of the tetrahedron in the mesh
281			{
282			//Compute each ridge (triangle) once
283			facet->visitid= qh visit_id;
284			//If calculating the alphashape, mark the facet('good' is used as 'marked').
285			//This facet will have some triangles hidden by the facet's neighbor.
286			facet->good=true;
287			qh_makeridges(facet);
288			ridgeT ridge, *ridgep;
289			FOREACHridge_(facet->ridges) {
290			neighbor= otherfacet_(ridge, facet);
291			if ((neighbor->visitid != qh visit_id)){
292			qh_setappend(&set, ridge);
293			}
294			}
295			}
296			}
297			}
298			//assert(numFacets== qh num_facets);
299
300			//Filter the triangles (only the ones on the boundary of the alpha complex) and build the mesh
301	chuckv	1404
302
303	chuckv	1402
304			ridgeT ridge, *ridgep;
305			FOREACHridge_(set) {
306			if ((!ridge->top->good \|\| !ridge->bottom->good \|\| ridge->top->upperdelaunay \|\| ridge->bottom->upperdelaunay)){
307			// tri::Allocator<CMeshO>::FaceIterator fi=tri::Allocator<CMeshO>::AddFaces(pm.cm,1);
308			ridgesCount++;
309			int vertex_n, vertex_i;
310			Triangle face;
311
312			// Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
313			//face.setNormal(V3dNormal);
314
315
316	chuckv	1404	//coordT *center = qh_getcenter(ridge->vertices);
317			//std::cout << "Centers are " << center[0] << " " <<center[1] << " " << center[2] << std::endl;
318	chuckv	1402	//Vector3d V3dCentroid(center[0], center[1], center[2]);
319			//face.setCentroid(V3dCentroid);
320	chuckv	1404
321	chuckv	1402
322	chuckv	1404	Vector3d faceVel = V3Zero;
323	chuckv	1402	Vector3d p[3];
324	chuckv	1404	RealType faceMass = 0.0;
325	chuckv	1402
326			int ver = 0;
327			std::vector<int> virtexlist;
328			FOREACHvertex_i_(ridge->vertices){
329			int id = qh_pointid(vertex->point);
330			p[ver][0] = vertex->point[0];
331			p[ver][1] = vertex->point[1];
332			p[ver][2] = vertex->point[2];
333			Vector3d vel;
334			RealType mass;
335			ver++;
336			virtexlist.push_back(id);
337	chuckv	1404	// std::cout << "Ridge: " << ridgesCount << " Vertex " << id << std::endl;
338
339			vel = bodydoubles[id]->getVel();
340			mass = bodydoubles[id]->getMass();
341			face.addVertexSD(bodydoubles[id]);
342
343
344			faceVel = faceVel + vel;
345			faceMass = faceMass + mass;
346			} //FOREACH Vertex
347	chuckv	1402	facetlist.push_back(virtexlist);
348	chuckv	1404	face.addVertices(p[0],p[1],p[2]);
349			face.setFacetMass(faceMass);
350	gezelter	1782	face.setFacetVelocity(faceVel / RealType(3.0));
351	chuckv	1404
352			RealType area = face.getArea();
353			area_ += area;
354			Vector3d normal = face.getUnitNormal();
355			RealType offset = ((0.0-p[0][0])normal[0] + (0.0-p[0][1])normal[1] + (0.0-p[0][2])*normal[2]);
356			RealType dist = normal[0] * interiorPoint[0] + normal[1]interiorPoint[1] + normal[2]interiorPoint[2];
357			std::cout << "Dist and normal and area are: " << normal << std::endl;
358			volume_ += dist *area/qh hull_dim;
359
360			Triangles_.push_back(face);
361	chuckv	1402	}
362			}
363
364	chuckv	1404	std::cout << "Volume is: " << volume_ << std::endl;
365
366	chuckv	1402	//assert(pm.cm.fn == ridgesCount);
367	chuckv	1404	/*
368	chuckv	1402	std::cout <<"OFF"<<std::endl;
369			std::cout << bodydoubles.size() << " " << facetlist.size() << " " << 3*facetlist.size() << std::endl;
370			for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
371			Vector3d pos = (*SD)->getPos();
372			std::cout << pos.x() << " " << pos.y() << " " << pos.z() << std::endl;
373			}
374
375
376			std::vector<std::vector<int> >::iterator thisfacet;
377			std::vector<int>::iterator thisvertex;
378
379			for (thisfacet = facetlist.begin(); thisfacet != facetlist.end(); thisfacet++){
380			std::cout << (*thisfacet).size();
381			for (thisvertex = (thisfacet).begin(); thisvertex != (thisfacet).end(); thisvertex++){
382			std::cout << " " << *thisvertex;
383			}
384			std::cout << std::endl;
385			}
386	chuckv	1404	*/
387	chuckv	1402
388
389
390			/*
391			FORALLfacets {
392			Triangle face;
393
394			Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
395			face.setNormal(V3dNormal);
396
397			RealType faceArea = qh_facetarea(facet);
398			face.setArea(faceArea);
399
400			vertices = qh_facet3vertex(facet);
401
402			coordT *center = qh_getcenter(vertices);
403			Vector3d V3dCentroid(center[0], center[1], center[2]);
404			face.setCentroid(V3dCentroid);
405
406			Vector3d faceVel = V3Zero;
407			Vector3d p[3];
408			RealType faceMass = 0.0;
409
410			int ver = 0;
411
412			FOREACHvertex_(vertices){
413			int id = qh_pointid(vertex->point);
414			p[ver][0] = vertex->point[0];
415			p[ver][1] = vertex->point[1];
416			p[ver][2] = vertex->point[2];
417
418			Vector3d vel;
419			RealType mass;
420
421			#ifdef IS_MPI
422			vel = Vector3d(globalVels[dim_ * id],
423			globalVels[dim_ * id + 1],
424			globalVels[dim_ * id + 2]);
425			mass = globalMasses[id];
426
427			// localID will be between 0 and hullSitesOnProc[myrank] if we
428			// own this guy.
429
430			int localID = id - displacements[myrank];
431
432			if (localID >= 0 && localID < hullSitesOnProc[myrank])
433			face.addVertexSD(bodydoubles[indexMap[localID]]);
434
435			#else
436			vel = bodydoubles[id]->getVel();
437			mass = bodydoubles[id]->getMass();
438			face.addVertexSD(bodydoubles[id]);
439			#endif
440
441			faceVel = faceVel + vel;
442			faceMass = faceMass + mass;
443			ver++;
444			} //Foreachvertex
445
446			face.addVertices(p[0], p[1], p[2]);
447			face.setFacetMass(faceMass);
448			face.setFacetVelocity(faceVel/3.0);
449			Triangles_.push_back(face);
450			qh_settempfree(&vertices);
451
452			} //FORALLfacets
453			*/
454	chuckv	1404	// qh_getarea(qh facet_list);
455			//volume_ = qh totvol;
456			// area_ = qh totarea;
457	chuckv	1402
458			qh_freeqhull(!qh_ALL);
459			qh_memfreeshort(&curlong, &totlong);
460			if (curlong \|\| totlong)
461			std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
462			<< totlong << curlong << std::endl;
463			}
464
465			void AlphaHull::printHull(const std::string& geomFileName) {
466
467			#ifdef IS_MPI
468			if (worldRank == 0) {
469			#endif
470			FILE *newGeomFile;
471
472			//create new .md file based on old .md file
473			newGeomFile = fopen(geomFileName.c_str(), "w");
474			qh_findgood_all(qh facet_list);
475			for (int i = 0; i < qh_PRINTEND; i++)
476			qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
477
478			fclose(newGeomFile);
479			#ifdef IS_MPI
480			}
481			#endif
482			}
483
484			double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim){
485			coordT a = qh_pointdist(p0,p1,dim);
486			coordT b = qh_pointdist(p1,p2,dim);
487			coordT c = qh_pointdist(p2,p0,dim);
488
489			coordT sum =(a + b + c)*0.5;
490			coordT area = sum(a+b-sum)(a+c-sum)*(b+c-sum);
491			return (double) (abc)/(4*sqrt(area));
492			}
493
494			#endif //QHULL