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;
  
  Vector3d boxMax;
  Vector3d boxMin;
  
  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;


  int index = 0;
  FORALLvertices {
    Vector3d point(vertex->point[0], vertex->point[1], vertex->point[2]);
    if (index == 0) {
      boxMax = point;
      boxMin = point;
    } else {
      for (int i = 0; i < 3; i++) {
        boxMax[i] = max(boxMax[i], point[i]);
        boxMin[i] = min(boxMin[i], point[i]);
      }
    }
    index++;
  }
  boundingBox_ = Mat3x3d(0.0);
  boundingBox_(0,0) = boxMax[0] - boxMin[0];
  boundingBox_(1,1) = boxMax[1] - boxMin[1];
  boundingBox_(2,2) = boxMax[2] - boxMin[2];

  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:	1858
Committed:	Wed Apr 3 21:32:13 2013 UTC (12 years ago) by gezelter
File size:	16976 byte(s)
Log Message:	Some bugfixes for cell-linked-list-style neighbor lists when the simulation doesn't use periodic boundary conditions. Cleaning up some of the Hull stuff while we're in there.
#	Content
1	/* Copyright (c) 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, 234107 (2008).
38	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
40	*
41	* AlphaHull.cpp
42	*
43	* Purpose: To calculate an alpha-shape hull.
44	*/
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
56	#ifdef IS_MPI
57	#include <mpi.h>
58	#endif
59
60	#include "math/qhull.hpp"
61
62	#ifdef HAVE_QHULL
63	using namespace std;
64	using namespace OpenMD;
65
66	double calculate_circumradius(pointT* p0, pointT* p1, pointT* p2, int dim);
67
68	AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha),
69	options_("qhull d QJ Tcv Pp") {
70	}
71
72	void AlphaHull::computeHull(vector<StuntDouble*> bodydoubles) {
73
74	int numpoints = bodydoubles.size();
75
76	Triangles_.clear();
77
78	vertexT *vertex;
79	facetT facet, neighbor;
80	pointT *interiorPoint;
81	int curlong, totlong;
82
83	Vector3d boxMax;
84	Vector3d boxMin;
85
86	vector<double> ptArray(numpoints*dim_);
87
88	// Copy the positon vector into a points vector for qhull.
89	vector<StuntDouble*>::iterator SD;
90	int i = 0;
91	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
92	Vector3d pos = (*SD)->getPos();
93	ptArray[dim_ * i] = pos.x();
94	ptArray[dim_ * i + 1] = pos.y();
95	ptArray[dim_ * i + 2] = pos.z();
96	i++;
97	}
98
99	/* Clean up memory from previous convex hull calculations*/
100	boolT ismalloc = False;
101
102	/* compute the hull for our local points (or all the points for single
103	processor versions) */
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	vector<int> hullSitesOnProc(nproc, 0);
122	vector<int> coordsOnProc(nproc, 0);
123	vector<int> displacements(nproc, 0);
124	vector<int> vectorDisplacements(nproc, 0);
125
126	vector<double> coords;
127	vector<double> vels;
128	vector<int> indexMap;
129	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	vector<double> globalCoords(dim_ * globalHullSites);
170	vector<double> globalVels(dim_ * globalHullSites);
171	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	sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n"
192	"\tdid not free %d bytes of long memory (%d pieces)",
193	totlong, curlong);
194	painCave.isFatal = 1;
195	simError();
196	}
197
198	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
199	const_cast<char *>(options_.c_str()), NULL, stderr)){
200
201	sprintf(painCave.errMsg,
202	"AlphaHull: Qhull failed to compute global convex hull");
203	painCave.isFatal = 1;
204	simError();
205
206	} //qh_new_qhull
207
208	#endif
209
210	//Set facet->center as the Voronoi center
211	qh_setvoronoi_all();
212
213
214	int convexNumVert = qh_setsize(qh_facetvertices (qh facet_list, NULL, false));
215	//Insert all the sample points, because, even with alpha=0, the alpha shape/alpha complex will
216	//contain them.
217
218	// tri::Allocator<CMeshO>::AddVertices(pm.cm,convexNumVert);
219
220	/*ivp length is 'qh num_vertices' because each vertex is accessed through its ID whose range is
221	0<=qh_pointid(vertex->point)<qh num_vertices*/
222	// vector<tri::Allocator<CMeshO>::VertexPointer> ivp(qh num_vertices);
223	/*i=0;
224	FORALLvertices{
225	if ((*vertex).point){
226	// pm.cm.vert[i].P()[0] = (*vertex).point[0];
227	// pm.cm.vert[i].P()[1] = (*vertex).point[1];
228	//pm.cm.vert[i].P()[2] = (*vertex).point[2];
229	// ivp[qh_pointid(vertex->point)] = &pm.cm.vert[i];
230	i++;
231	}
232	}
233	*/
234	//Set of alpha complex triangles for alphashape filtering
235	setT* set= qh_settemp(4* qh num_facets);
236
237	qh visit_id++;
238	int numFacets=0;
239	vector<vector <int> > facetlist;
240	interiorPoint = qh interior_point;
241	FORALLfacet_(qh facet_list) {
242	numFacets++;
243	if (!facet->upperdelaunay) {
244	//For all facets (that are tetrahedrons)calculate the radius of the empty circumsphere considering
245	//the distance between the circumcenter and a vertex of the facet
246	vertexT* vertex = (vertexT *)(facet->vertices->e[0].p);
247	double* center = facet->center;
248	double radius = qh_pointdist(vertex->point,center,dim_);
249
250	if (radius>alpha_) // if the facet is not good consider the ridges
251	{
252	//if calculating the alphashape, unmark the facet ('good' is used as 'marked').
253	facet->good=false;
254
255	//Compute each ridge (triangle) once and test the cironference radius with alpha
256	facet->visitid= qh visit_id;
257	qh_makeridges(facet);
258	ridgeT ridge, *ridgep;
259	int goodTriangles=0;
260	FOREACHridge_(facet->ridges) {
261	neighbor= otherfacet_(ridge, facet);
262	if (( neighbor->visitid != qh visit_id)){
263	//Calculate the radius of the circumference
264	pointT* p0 = ((vertexT*) (ridge->vertices->e[0].p))->point;
265	pointT* p1 = ((vertexT*) (ridge->vertices->e[1].p))->point;
266	pointT* p2 = ((vertexT*) (ridge->vertices->e[2].p))->point;
267
268	radius = calculate_circumradius(p0,p1,p2, dim_);
269
270	if(radius <=alpha_){
271	goodTriangles++;
272	//save the triangle (ridge) for subsequent filtering
273	qh_setappend(&set, ridge);
274	}
275	}
276	}
277
278	//If calculating the alphashape, mark the facet('good' is used as 'marked').
279	//This facet will have some triangles hidden by the facet's neighbor.
280	if(goodTriangles==4)
281	facet->good=true;
282
283	}
284	else //the facet is good. Put all the triangles of the tetrahedron in the mesh
285	{
286	//Compute each ridge (triangle) once
287	facet->visitid= qh visit_id;
288	//If calculating the alphashape, mark the facet('good' is used as 'marked').
289	//This facet will have some triangles hidden by the facet's neighbor.
290	facet->good=true;
291	qh_makeridges(facet);
292	ridgeT ridge, *ridgep;
293	FOREACHridge_(facet->ridges) {
294	neighbor= otherfacet_(ridge, facet);
295	if ((neighbor->visitid != qh visit_id)){
296	qh_setappend(&set, ridge);
297	}
298	}
299	}
300	}
301	}
302	//assert(numFacets== qh num_facets);
303
304	//Filter the triangles (only the ones on the boundary of the alpha complex) and build the mesh
305
306	int ridgesCount=0;
307
308	ridgeT ridge, *ridgep;
309	FOREACHridge_(set) {
310	if ((!ridge->top->good \|\| !ridge->bottom->good \|\| ridge->top->upperdelaunay \|\| ridge->bottom->upperdelaunay)){
311	// tri::Allocator<CMeshO>::FaceIterator fi=tri::Allocator<CMeshO>::AddFaces(pm.cm,1);
312	ridgesCount++;
313	int vertex_n, vertex_i;
314	Triangle face;
315
316	// Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
317	//face.setNormal(V3dNormal);
318
319
320	//coordT *center = qh_getcenter(ridge->vertices);
321	//cout << "Centers are " << center[0] << " " <<center[1] << " " << center[2] << endl;
322	//Vector3d V3dCentroid(center[0], center[1], center[2]);
323	//face.setCentroid(V3dCentroid);
324
325
326	Vector3d faceVel = V3Zero;
327	Vector3d p[3];
328	RealType faceMass = 0.0;
329
330	int ver = 0;
331	vector<int> virtexlist;
332	FOREACHvertex_i_(ridge->vertices){
333	int id = qh_pointid(vertex->point);
334	p[ver][0] = vertex->point[0];
335	p[ver][1] = vertex->point[1];
336	p[ver][2] = vertex->point[2];
337	Vector3d vel;
338	RealType mass;
339	ver++;
340	virtexlist.push_back(id);
341	// cout << "Ridge: " << ridgesCount << " Vertex " << id << endl;
342
343	vel = bodydoubles[id]->getVel();
344	mass = bodydoubles[id]->getMass();
345	face.addVertexSD(bodydoubles[id]);
346
347
348	faceVel = faceVel + vel;
349	faceMass = faceMass + mass;
350	} //FOREACH Vertex
351	facetlist.push_back(virtexlist);
352	face.addVertices(p[0],p[1],p[2]);
353	face.setFacetMass(faceMass);
354	face.setFacetVelocity(faceVel / RealType(3.0));
355
356	RealType area = face.getArea();
357	area_ += area;
358	Vector3d normal = face.getUnitNormal();
359	RealType offset = ((0.0-p[0][0])normal[0] + (0.0-p[0][1])normal[1] + (0.0-p[0][2])*normal[2]);
360	RealType dist = normal[0] * interiorPoint[0] + normal[1]interiorPoint[1] + normal[2]interiorPoint[2];
361	cout << "Dist and normal and area are: " << normal << endl;
362	volume_ += dist *area/qh hull_dim;
363
364	Triangles_.push_back(face);
365	}
366	}
367
368	cout << "Volume is: " << volume_ << endl;
369
370	//assert(pm.cm.fn == ridgesCount);
371	/*
372	std::cout <<"OFF"<<std::endl;
373	std::cout << bodydoubles.size() << " " << facetlist.size() << " " << 3*facetlist.size() << std::endl;
374	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
375	Vector3d pos = (*SD)->getPos();
376	std::cout << pos.x() << " " << pos.y() << " " << pos.z() << std::endl;
377	}
378
379
380	std::vector<std::vector<int> >::iterator thisfacet;
381	std::vector<int>::iterator thisvertex;
382
383	for (thisfacet = facetlist.begin(); thisfacet != facetlist.end(); thisfacet++){
384	std::cout << (*thisfacet).size();
385	for (thisvertex = (thisfacet).begin(); thisvertex != (thisfacet).end(); thisvertex++){
386	std::cout << " " << *thisvertex;
387	}
388	std::cout << std::endl;
389	}
390	*/
391
392
393
394	/*
395	FORALLfacets {
396	Triangle face;
397
398	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
399	face.setNormal(V3dNormal);
400
401	RealType faceArea = qh_facetarea(facet);
402	face.setArea(faceArea);
403
404	vertices = qh_facet3vertex(facet);
405
406	coordT *center = qh_getcenter(vertices);
407	Vector3d V3dCentroid(center[0], center[1], center[2]);
408	face.setCentroid(V3dCentroid);
409
410	Vector3d faceVel = V3Zero;
411	Vector3d p[3];
412	RealType faceMass = 0.0;
413
414	int ver = 0;
415
416	FOREACHvertex_(vertices){
417	int id = qh_pointid(vertex->point);
418	p[ver][0] = vertex->point[0];
419	p[ver][1] = vertex->point[1];
420	p[ver][2] = vertex->point[2];
421
422	Vector3d vel;
423	RealType mass;
424
425	#ifdef IS_MPI
426	vel = Vector3d(globalVels[dim_ * id],
427	globalVels[dim_ * id + 1],
428	globalVels[dim_ * id + 2]);
429	mass = globalMasses[id];
430
431	// localID will be between 0 and hullSitesOnProc[myrank] if we
432	// own this guy.
433
434	int localID = id - displacements[myrank];
435
436	if (localID >= 0 && localID < hullSitesOnProc[myrank])
437	face.addVertexSD(bodydoubles[indexMap[localID]]);
438
439	#else
440	vel = bodydoubles[id]->getVel();
441	mass = bodydoubles[id]->getMass();
442	face.addVertexSD(bodydoubles[id]);
443	#endif
444
445	faceVel = faceVel + vel;
446	faceMass = faceMass + mass;
447	ver++;
448	} //Foreachvertex
449
450	face.addVertices(p[0], p[1], p[2]);
451	face.setFacetMass(faceMass);
452	face.setFacetVelocity(faceVel/3.0);
453	Triangles_.push_back(face);
454	qh_settempfree(&vertices);
455
456	} //FORALLfacets
457	*/
458	// qh_getarea(qh facet_list);
459	//volume_ = qh totvol;
460	// area_ = qh totarea;
461
462
463	int index = 0;
464	FORALLvertices {
465	Vector3d point(vertex->point[0], vertex->point[1], vertex->point[2]);
466	if (index == 0) {
467	boxMax = point;
468	boxMin = point;
469	} else {
470	for (int i = 0; i < 3; i++) {
471	boxMax[i] = max(boxMax[i], point[i]);
472	boxMin[i] = min(boxMin[i], point[i]);
473	}
474	}
475	index++;
476	}
477	boundingBox_ = Mat3x3d(0.0);
478	boundingBox_(0,0) = boxMax[0] - boxMin[0];
479	boundingBox_(1,1) = boxMax[1] - boxMin[1];
480	boundingBox_(2,2) = boxMax[2] - boxMin[2];
481
482	qh_freeqhull(!qh_ALL);
483	qh_memfreeshort(&curlong, &totlong);
484	if (curlong \|\| totlong) {
485	sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n"
486	"\tdid not free %d bytes of long memory (%d pieces)",
487	totlong, curlong);
488	painCave.isFatal = 1;
489	simError();
490	}
491	}
492
493	void AlphaHull::printHull(const string& geomFileName) {
494
495	#ifdef IS_MPI
496	if (worldRank == 0) {
497	#endif
498	FILE *newGeomFile;
499
500	//create new .md file based on old .md file
501	newGeomFile = fopen(geomFileName.c_str(), "w");
502	qh_findgood_all(qh facet_list);
503	for (int i = 0; i < qh_PRINTEND; i++)
504	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
505
506	fclose(newGeomFile);
507	#ifdef IS_MPI
508	}
509	#endif
510	}
511
512	double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim){
513	coordT a = qh_pointdist(p0,p1,dim);
514	coordT b = qh_pointdist(p1,p2,dim);
515	coordT c = qh_pointdist(p2,p0,dim);
516
517	coordT sum =(a + b + c)*0.5;
518	coordT area = sum(a+b-sum)(a+c-sum)*(b+c-sum);
519	return (double) (abc)/(4*sqrt(area));
520	}
521
522	#endif //QHULL