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:	1704
Committed:	Tue Apr 24 20:40:04 2012 UTC (13 years, 6 months ago) by gezelter
File size:	16446 byte(s)
Log Message:	qhull modifications for compilation
#	Content
1	/* 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	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40	*
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	* @version $Id$
48	*
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	#include "math/qhull.hpp"
65
66	using namespace OpenMD;
67
68	#ifdef HAVE_QHULL
69	double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim);
70
71	AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha), options_("qhull d QJ Tcv Pp") {
72	}
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	setT vertices, verticestop, *verticesbottom;
84	int curlong, totlong;
85	pointT *interiorPoint;
86
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	interiorPoint = qh interior_point;
237	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
302
303
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	//coordT *center = qh_getcenter(ridge->vertices);
317	//std::cout << "Centers are " << center[0] << " " <<center[1] << " " << center[2] << std::endl;
318	//Vector3d V3dCentroid(center[0], center[1], center[2]);
319	//face.setCentroid(V3dCentroid);
320
321
322	Vector3d faceVel = V3Zero;
323	Vector3d p[3];
324	RealType faceMass = 0.0;
325
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	// 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	facetlist.push_back(virtexlist);
348	face.addVertices(p[0],p[1],p[2]);
349	face.setFacetMass(faceMass);
350	face.setFacetVelocity(faceVel / RealType(3.0));
351
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	}
362	}
363
364	std::cout << "Volume is: " << volume_ << std::endl;
365
366	//assert(pm.cm.fn == ridgesCount);
367	/*
368	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	*/
387
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	// qh_getarea(qh facet_list);
455	//volume_ = qh totvol;
456	// area_ = qh totarea;
457
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