src/math/AlphaHull.cpp

/* Copyright (c) 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, 234107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 *
 *  AlphaHull.cpp
 *
 *  Purpose: To calculate an alpha-shape hull.
 */

/* Standard includes independent of library */

#include <iostream>
#include <fstream>
#include <list>
#include <algorithm>
#include <iterator>
#include "math/AlphaHull.hpp"
#include "utils/simError.h"

#ifdef IS_MPI
#include <mpi.h>
#endif

#include "math/qhull.hpp"

#ifdef HAVE_QHULL
using namespace std;
using namespace OpenMD;

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(vector<StuntDouble*> bodydoubles) { 
 
  int numpoints = bodydoubles.size();
  
  Triangles_.clear();
  
  vertexT *vertex;
  facetT *facet, *neighbor;
  pointT *interiorPoint;
  int curlong, totlong;
  
  
  vector<double> ptArray(numpoints*dim_);
  
  // Copy the positon vector into a points vector for qhull.
  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;
  
  /* compute the hull for our local points (or all the points for single
     processor versions) */
  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;

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

  vector<double> coords;
  vector<double> vels;
  vector<int> indexMap;
  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]; 
  }

  vector<double> globalCoords(dim_ * globalHullSites);
  vector<double> globalVels(dim_ * globalHullSites);
  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) {
    sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n"
            "\tdid not free %d bytes of long memory (%d pieces)", 
            totlong, curlong);
    painCave.isFatal = 1;
    simError();
  }
  
  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;
  vector<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

  int ridgesCount=0;
  
  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);
      //cout << "Centers are " << center[0] << "  " <<center[1] << "  " << center[2] << 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;
      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);
        // cout << "Ridge: " << ridgesCount << " Vertex " << id << 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];
     cout << "Dist and normal and area are: " << normal << endl;
      volume_ += dist *area/qh hull_dim;
      
      Triangles_.push_back(face);
    }
  }

  cout << "Volume is: " << volume_ << 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) {
    sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n"
            "\tdid not free %d bytes of long memory (%d pieces)", 
            totlong, curlong);
    painCave.isFatal = 1;
    simError();
  }
}

void AlphaHull::printHull(const 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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	16422 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	User	Rev	Content
1	gezelter	1879	/* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
2	chuckv	1402	*
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	gezelter	1879	* [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, 234107 (2008).
38	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39	gezelter	1879	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
40	chuckv	1402	*
41			* AlphaHull.cpp
42			*
43	gezelter	1879	* Purpose: To calculate an alpha-shape hull.
44	chuckv	1402	*/
45
46			/* Standard includes independent of library */
47
48			#include <iostream>
49			#include <fstream>
50			#include <list>
51			#include <algorithm>
52			#include <iterator>
53			#include "math/AlphaHull.hpp"
54			#include "utils/simError.h"
55	gezelter	1879
56	chuckv	1402	#ifdef IS_MPI
57			#include <mpi.h>
58			#endif
59	gezelter	1879
60	gezelter	1782	#include "math/qhull.hpp"
61	chuckv	1402
62	gezelter	1879	#ifdef HAVE_QHULL
63			using namespace std;
64	chuckv	1402	using namespace OpenMD;
65
66	gezelter	1879	double calculate_circumradius(pointT* p0, pointT* p1, pointT* p2, int dim);
67	chuckv	1402
68	gezelter	1879	AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha),
69			options_("qhull d QJ Tcv Pp") {
70	chuckv	1402	}
71
72	gezelter	1879	void AlphaHull::computeHull(vector<StuntDouble*> bodydoubles) {
73	chuckv	1402
74			int numpoints = bodydoubles.size();
75
76			Triangles_.clear();
77
78	gezelter	1879	vertexT *vertex;
79	chuckv	1402	facetT facet, neighbor;
80	gezelter	1879	pointT *interiorPoint;
81	chuckv	1402	int curlong, totlong;
82
83	gezelter	1879
84			vector<double> ptArray(numpoints*dim_);
85
86	chuckv	1402	// Copy the positon vector into a points vector for qhull.
87	gezelter	1879	vector<StuntDouble*>::iterator SD;
88	chuckv	1402	int i = 0;
89			for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
90			Vector3d pos = (*SD)->getPos();
91			ptArray[dim_ * i] = pos.x();
92			ptArray[dim_ * i + 1] = pos.y();
93			ptArray[dim_ * i + 2] = pos.z();
94			i++;
95			}
96	gezelter	1879
97			/* Clean up memory from previous convex hull calculations*/
98	chuckv	1402	boolT ismalloc = False;
99	gezelter	1879
100			/* compute the hull for our local points (or all the points for single
101			processor versions) */
102	chuckv	1402	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
103			const_cast<char *>(options_.c_str()), NULL, stderr)) {
104	gezelter	1879
105	chuckv	1402	sprintf(painCave.errMsg, "AlphaHull: Qhull failed to compute convex hull");
106			painCave.isFatal = 1;
107			simError();
108
109			} //qh_new_qhull
110	gezelter	1879
111
112	chuckv	1402	#ifdef IS_MPI
113			//If we are doing the mpi version, set up some vectors for data communication
114
115			int nproc = MPI::COMM_WORLD.Get_size();
116			int myrank = MPI::COMM_WORLD.Get_rank();
117			int localHullSites = 0;
118
119	gezelter	1879	vector<int> hullSitesOnProc(nproc, 0);
120			vector<int> coordsOnProc(nproc, 0);
121			vector<int> displacements(nproc, 0);
122			vector<int> vectorDisplacements(nproc, 0);
123	chuckv	1402
124	gezelter	1879	vector<double> coords;
125			vector<double> vels;
126			vector<int> indexMap;
127			vector<double> masses;
128	chuckv	1402
129			FORALLvertices{
130			localHullSites++;
131
132			int idx = qh_pointid(vertex->point);
133
134			indexMap.push_back(idx);
135
136			coords.push_back(ptArray[dim_ * idx]);
137			coords.push_back(ptArray[dim_ * idx + 1]);
138			coords.push_back(ptArray[dim_ * idx + 2]);
139
140			StuntDouble* sd = bodydoubles[idx];
141
142			Vector3d vel = sd->getVel();
143			vels.push_back(vel.x());
144			vels.push_back(vel.y());
145			vels.push_back(vel.z());
146
147			masses.push_back(sd->getMass());
148			}
149
150			MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
151			1, MPI::INT);
152
153			int globalHullSites = 0;
154			for (int iproc = 0; iproc < nproc; iproc++){
155			globalHullSites += hullSitesOnProc[iproc];
156			coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
157			}
158
159			displacements[0] = 0;
160			vectorDisplacements[0] = 0;
161
162			for (int iproc = 1; iproc < nproc; iproc++){
163			displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
164			vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
165			}
166
167	gezelter	1879	vector<double> globalCoords(dim_ * globalHullSites);
168			vector<double> globalVels(dim_ * globalHullSites);
169			vector<double> globalMasses(globalHullSites);
170	chuckv	1402
171			int count = coordsOnProc[myrank];
172
173			MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
174			&coordsOnProc[0], &vectorDisplacements[0],
175			MPI::DOUBLE);
176
177			MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
178			&coordsOnProc[0], &vectorDisplacements[0],
179			MPI::DOUBLE);
180
181			MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
182			&globalMasses[0], &hullSitesOnProc[0],
183			&displacements[0], MPI::DOUBLE);
184
185			// Free previous hull
186			qh_freeqhull(!qh_ALL);
187			qh_memfreeshort(&curlong, &totlong);
188	gezelter	1879	if (curlong \|\| totlong) {
189			sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n"
190			"\tdid not free %d bytes of long memory (%d pieces)",
191			totlong, curlong);
192			painCave.isFatal = 1;
193			simError();
194			}
195	chuckv	1402
196			if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
197			const_cast<char *>(options_.c_str()), NULL, stderr)){
198
199	gezelter	1879	sprintf(painCave.errMsg,
200			"AlphaHull: Qhull failed to compute global convex hull");
201	chuckv	1402	painCave.isFatal = 1;
202			simError();
203	gezelter	1879
204	chuckv	1402	} //qh_new_qhull
205
206			#endif
207
208			//Set facet->center as the Voronoi center
209			qh_setvoronoi_all();
210
211
212			int convexNumVert = qh_setsize(qh_facetvertices (qh facet_list, NULL, false));
213			//Insert all the sample points, because, even with alpha=0, the alpha shape/alpha complex will
214			//contain them.
215
216			// tri::Allocator<CMeshO>::AddVertices(pm.cm,convexNumVert);
217
218			/*ivp length is 'qh num_vertices' because each vertex is accessed through its ID whose range is
219			0<=qh_pointid(vertex->point)<qh num_vertices*/
220			// vector<tri::Allocator<CMeshO>::VertexPointer> ivp(qh num_vertices);
221			/*i=0;
222			FORALLvertices{
223			if ((*vertex).point){
224			// pm.cm.vert[i].P()[0] = (*vertex).point[0];
225			// pm.cm.vert[i].P()[1] = (*vertex).point[1];
226			//pm.cm.vert[i].P()[2] = (*vertex).point[2];
227			// ivp[qh_pointid(vertex->point)] = &pm.cm.vert[i];
228			i++;
229			}
230			}
231			*/
232			//Set of alpha complex triangles for alphashape filtering
233			setT* set= qh_settemp(4* qh num_facets);
234
235			qh visit_id++;
236			int numFacets=0;
237	gezelter	1879	vector<vector <int> > facetlist;
238	chuckv	1404	interiorPoint = qh interior_point;
239	chuckv	1402	FORALLfacet_(qh facet_list) {
240			numFacets++;
241			if (!facet->upperdelaunay) {
242			//For all facets (that are tetrahedrons)calculate the radius of the empty circumsphere considering
243			//the distance between the circumcenter and a vertex of the facet
244			vertexT* vertex = (vertexT *)(facet->vertices->e[0].p);
245			double* center = facet->center;
246			double radius = qh_pointdist(vertex->point,center,dim_);
247
248			if (radius>alpha_) // if the facet is not good consider the ridges
249			{
250			//if calculating the alphashape, unmark the facet ('good' is used as 'marked').
251			facet->good=false;
252
253			//Compute each ridge (triangle) once and test the cironference radius with alpha
254			facet->visitid= qh visit_id;
255			qh_makeridges(facet);
256			ridgeT ridge, *ridgep;
257			int goodTriangles=0;
258			FOREACHridge_(facet->ridges) {
259			neighbor= otherfacet_(ridge, facet);
260			if (( neighbor->visitid != qh visit_id)){
261			//Calculate the radius of the circumference
262			pointT* p0 = ((vertexT*) (ridge->vertices->e[0].p))->point;
263			pointT* p1 = ((vertexT*) (ridge->vertices->e[1].p))->point;
264			pointT* p2 = ((vertexT*) (ridge->vertices->e[2].p))->point;
265
266			radius = calculate_circumradius(p0,p1,p2, dim_);
267
268			if(radius <=alpha_){
269			goodTriangles++;
270			//save the triangle (ridge) for subsequent filtering
271			qh_setappend(&set, ridge);
272			}
273			}
274			}
275
276			//If calculating the alphashape, mark the facet('good' is used as 'marked').
277			//This facet will have some triangles hidden by the facet's neighbor.
278			if(goodTriangles==4)
279			facet->good=true;
280
281			}
282			else //the facet is good. Put all the triangles of the tetrahedron in the mesh
283			{
284			//Compute each ridge (triangle) once
285			facet->visitid= qh visit_id;
286			//If calculating the alphashape, mark the facet('good' is used as 'marked').
287			//This facet will have some triangles hidden by the facet's neighbor.
288			facet->good=true;
289			qh_makeridges(facet);
290			ridgeT ridge, *ridgep;
291			FOREACHridge_(facet->ridges) {
292			neighbor= otherfacet_(ridge, facet);
293			if ((neighbor->visitid != qh visit_id)){
294			qh_setappend(&set, ridge);
295			}
296			}
297			}
298			}
299			}
300			//assert(numFacets== qh num_facets);
301
302			//Filter the triangles (only the ones on the boundary of the alpha complex) and build the mesh
303	chuckv	1404
304	gezelter	1879	int ridgesCount=0;
305	chuckv	1402
306			ridgeT ridge, *ridgep;
307			FOREACHridge_(set) {
308			if ((!ridge->top->good \|\| !ridge->bottom->good \|\| ridge->top->upperdelaunay \|\| ridge->bottom->upperdelaunay)){
309			// tri::Allocator<CMeshO>::FaceIterator fi=tri::Allocator<CMeshO>::AddFaces(pm.cm,1);
310			ridgesCount++;
311			int vertex_n, vertex_i;
312			Triangle face;
313
314			// Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
315			//face.setNormal(V3dNormal);
316
317
318	chuckv	1404	//coordT *center = qh_getcenter(ridge->vertices);
319	gezelter	1879	//cout << "Centers are " << center[0] << " " <<center[1] << " " << center[2] << endl;
320	chuckv	1402	//Vector3d V3dCentroid(center[0], center[1], center[2]);
321			//face.setCentroid(V3dCentroid);
322	chuckv	1404
323	chuckv	1402
324	chuckv	1404	Vector3d faceVel = V3Zero;
325	chuckv	1402	Vector3d p[3];
326	chuckv	1404	RealType faceMass = 0.0;
327	chuckv	1402
328			int ver = 0;
329	gezelter	1879	vector<int> virtexlist;
330	chuckv	1402	FOREACHvertex_i_(ridge->vertices){
331			int id = qh_pointid(vertex->point);
332			p[ver][0] = vertex->point[0];
333			p[ver][1] = vertex->point[1];
334			p[ver][2] = vertex->point[2];
335			Vector3d vel;
336			RealType mass;
337			ver++;
338			virtexlist.push_back(id);
339	gezelter	1879	// cout << "Ridge: " << ridgesCount << " Vertex " << id << endl;
340	chuckv	1404
341			vel = bodydoubles[id]->getVel();
342			mass = bodydoubles[id]->getMass();
343			face.addVertexSD(bodydoubles[id]);
344
345
346			faceVel = faceVel + vel;
347			faceMass = faceMass + mass;
348			} //FOREACH Vertex
349	chuckv	1402	facetlist.push_back(virtexlist);
350	chuckv	1404	face.addVertices(p[0],p[1],p[2]);
351			face.setFacetMass(faceMass);
352	gezelter	1782	face.setFacetVelocity(faceVel / RealType(3.0));
353	chuckv	1404
354			RealType area = face.getArea();
355			area_ += area;
356			Vector3d normal = face.getUnitNormal();
357			RealType offset = ((0.0-p[0][0])normal[0] + (0.0-p[0][1])normal[1] + (0.0-p[0][2])*normal[2]);
358			RealType dist = normal[0] * interiorPoint[0] + normal[1]interiorPoint[1] + normal[2]interiorPoint[2];
359	gezelter	1879	cout << "Dist and normal and area are: " << normal << endl;
360	chuckv	1404	volume_ += dist *area/qh hull_dim;
361
362			Triangles_.push_back(face);
363	chuckv	1402	}
364			}
365
366	gezelter	1879	cout << "Volume is: " << volume_ << endl;
367	chuckv	1404
368	chuckv	1402	//assert(pm.cm.fn == ridgesCount);
369	chuckv	1404	/*
370	chuckv	1402	std::cout <<"OFF"<<std::endl;
371			std::cout << bodydoubles.size() << " " << facetlist.size() << " " << 3*facetlist.size() << std::endl;
372			for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
373			Vector3d pos = (*SD)->getPos();
374			std::cout << pos.x() << " " << pos.y() << " " << pos.z() << std::endl;
375			}
376
377
378			std::vector<std::vector<int> >::iterator thisfacet;
379			std::vector<int>::iterator thisvertex;
380
381			for (thisfacet = facetlist.begin(); thisfacet != facetlist.end(); thisfacet++){
382			std::cout << (*thisfacet).size();
383			for (thisvertex = (thisfacet).begin(); thisvertex != (thisfacet).end(); thisvertex++){
384			std::cout << " " << *thisvertex;
385			}
386			std::cout << std::endl;
387			}
388	chuckv	1404	*/
389	chuckv	1402
390
391
392			/*
393			FORALLfacets {
394			Triangle face;
395
396			Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
397			face.setNormal(V3dNormal);
398
399			RealType faceArea = qh_facetarea(facet);
400			face.setArea(faceArea);
401
402			vertices = qh_facet3vertex(facet);
403
404			coordT *center = qh_getcenter(vertices);
405			Vector3d V3dCentroid(center[0], center[1], center[2]);
406			face.setCentroid(V3dCentroid);
407
408			Vector3d faceVel = V3Zero;
409			Vector3d p[3];
410			RealType faceMass = 0.0;
411
412			int ver = 0;
413
414			FOREACHvertex_(vertices){
415			int id = qh_pointid(vertex->point);
416			p[ver][0] = vertex->point[0];
417			p[ver][1] = vertex->point[1];
418			p[ver][2] = vertex->point[2];
419
420			Vector3d vel;
421			RealType mass;
422
423			#ifdef IS_MPI
424			vel = Vector3d(globalVels[dim_ * id],
425			globalVels[dim_ * id + 1],
426			globalVels[dim_ * id + 2]);
427			mass = globalMasses[id];
428
429			// localID will be between 0 and hullSitesOnProc[myrank] if we
430			// own this guy.
431
432			int localID = id - displacements[myrank];
433
434			if (localID >= 0 && localID < hullSitesOnProc[myrank])
435			face.addVertexSD(bodydoubles[indexMap[localID]]);
436
437			#else
438			vel = bodydoubles[id]->getVel();
439			mass = bodydoubles[id]->getMass();
440			face.addVertexSD(bodydoubles[id]);
441			#endif
442
443			faceVel = faceVel + vel;
444			faceMass = faceMass + mass;
445			ver++;
446			} //Foreachvertex
447
448			face.addVertices(p[0], p[1], p[2]);
449			face.setFacetMass(faceMass);
450			face.setFacetVelocity(faceVel/3.0);
451			Triangles_.push_back(face);
452			qh_settempfree(&vertices);
453
454			} //FORALLfacets
455			*/
456	chuckv	1404	// qh_getarea(qh facet_list);
457			//volume_ = qh totvol;
458			// area_ = qh totarea;
459	chuckv	1402
460			qh_freeqhull(!qh_ALL);
461			qh_memfreeshort(&curlong, &totlong);
462	gezelter	1879	if (curlong \|\| totlong) {
463			sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n"
464			"\tdid not free %d bytes of long memory (%d pieces)",
465			totlong, curlong);
466			painCave.isFatal = 1;
467			simError();
468			}
469	chuckv	1402	}
470
471	gezelter	1879	void AlphaHull::printHull(const string& geomFileName) {
472
473	chuckv	1402	#ifdef IS_MPI
474			if (worldRank == 0) {
475			#endif
476	gezelter	1879	FILE *newGeomFile;
477
478			//create new .md file based on old .md file
479			newGeomFile = fopen(geomFileName.c_str(), "w");
480			qh_findgood_all(qh facet_list);
481			for (int i = 0; i < qh_PRINTEND; i++)
482			qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
483
484			fclose(newGeomFile);
485	chuckv	1402	#ifdef IS_MPI
486			}
487			#endif
488			}
489
490			double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim){
491			coordT a = qh_pointdist(p0,p1,dim);
492			coordT b = qh_pointdist(p1,p2,dim);
493			coordT c = qh_pointdist(p2,p0,dim);
494
495			coordT sum =(a + b + c)*0.5;
496			coordT area = sum(a+b-sum)(a+c-sum)*(b+c-sum);
497			return (double) (abc)/(4*sqrt(area));
498			}
499
500			#endif //QHULL