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.
#	User	Rev	Content
1	gezelter	1858	/* 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	1858	* [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	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39	gezelter	1858	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
40	chuckv	1402	*
41			* AlphaHull.cpp
42			*
43	gezelter	1858	* 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	1858
56	chuckv	1402	#ifdef IS_MPI
57			#include <mpi.h>
58			#endif
59	gezelter	1858
60	gezelter	1704	#include "math/qhull.hpp"
61	chuckv	1402
62	gezelter	1858	#ifdef HAVE_QHULL
63			using namespace std;
64	chuckv	1402	using namespace OpenMD;
65
66	gezelter	1858	double calculate_circumradius(pointT* p0, pointT* p1, pointT* p2, int dim);
67	chuckv	1402
68	gezelter	1858	AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha),
69			options_("qhull d QJ Tcv Pp") {
70	chuckv	1402	}
71
72	gezelter	1858	void AlphaHull::computeHull(vector<StuntDouble*> bodydoubles) {
73	chuckv	1402
74			int numpoints = bodydoubles.size();
75
76			Triangles_.clear();
77
78	gezelter	1825	vertexT *vertex;
79	chuckv	1402	facetT facet, neighbor;
80	gezelter	1858	pointT *interiorPoint;
81	chuckv	1402	int curlong, totlong;
82
83	gezelter	1858	Vector3d boxMax;
84			Vector3d boxMin;
85
86			vector<double> ptArray(numpoints*dim_);
87
88	chuckv	1402	// Copy the positon vector into a points vector for qhull.
89	gezelter	1858	vector<StuntDouble*>::iterator SD;
90	chuckv	1402	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	gezelter	1858
99			/* Clean up memory from previous convex hull calculations*/
100	chuckv	1402	boolT ismalloc = False;
101	gezelter	1858
102			/* compute the hull for our local points (or all the points for single
103			processor versions) */
104	chuckv	1402	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
105			const_cast<char *>(options_.c_str()), NULL, stderr)) {
106	gezelter	1858
107	chuckv	1402	sprintf(painCave.errMsg, "AlphaHull: Qhull failed to compute convex hull");
108			painCave.isFatal = 1;
109			simError();
110
111			} //qh_new_qhull
112	gezelter	1858
113
114	chuckv	1402	#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	gezelter	1858	vector<int> hullSitesOnProc(nproc, 0);
122			vector<int> coordsOnProc(nproc, 0);
123			vector<int> displacements(nproc, 0);
124			vector<int> vectorDisplacements(nproc, 0);
125	chuckv	1402
126	gezelter	1858	vector<double> coords;
127			vector<double> vels;
128			vector<int> indexMap;
129			vector<double> masses;
130	chuckv	1402
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	gezelter	1858	vector<double> globalCoords(dim_ * globalHullSites);
170			vector<double> globalVels(dim_ * globalHullSites);
171			vector<double> globalMasses(globalHullSites);
172	chuckv	1402
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	gezelter	1858	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	chuckv	1402
198			if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
199			const_cast<char *>(options_.c_str()), NULL, stderr)){
200
201	gezelter	1858	sprintf(painCave.errMsg,
202			"AlphaHull: Qhull failed to compute global convex hull");
203	chuckv	1402	painCave.isFatal = 1;
204			simError();
205	gezelter	1858
206	chuckv	1402	} //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	gezelter	1858	vector<vector <int> > facetlist;
240	chuckv	1404	interiorPoint = qh interior_point;
241	chuckv	1402	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	chuckv	1404
306	gezelter	1858	int ridgesCount=0;
307	chuckv	1402
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	chuckv	1404	//coordT *center = qh_getcenter(ridge->vertices);
321	gezelter	1858	//cout << "Centers are " << center[0] << " " <<center[1] << " " << center[2] << endl;
322	chuckv	1402	//Vector3d V3dCentroid(center[0], center[1], center[2]);
323			//face.setCentroid(V3dCentroid);
324	chuckv	1404
325	chuckv	1402
326	chuckv	1404	Vector3d faceVel = V3Zero;
327	chuckv	1402	Vector3d p[3];
328	chuckv	1404	RealType faceMass = 0.0;
329	chuckv	1402
330			int ver = 0;
331	gezelter	1858	vector<int> virtexlist;
332	chuckv	1402	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	gezelter	1858	// cout << "Ridge: " << ridgesCount << " Vertex " << id << endl;
342	chuckv	1404
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	chuckv	1402	facetlist.push_back(virtexlist);
352	chuckv	1404	face.addVertices(p[0],p[1],p[2]);
353			face.setFacetMass(faceMass);
354	gezelter	1668	face.setFacetVelocity(faceVel / RealType(3.0));
355	chuckv	1404
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	gezelter	1858	cout << "Dist and normal and area are: " << normal << endl;
362	chuckv	1404	volume_ += dist *area/qh hull_dim;
363
364			Triangles_.push_back(face);
365	chuckv	1402	}
366			}
367
368	gezelter	1858	cout << "Volume is: " << volume_ << endl;
369	chuckv	1404
370	chuckv	1402	//assert(pm.cm.fn == ridgesCount);
371	chuckv	1404	/*
372	chuckv	1402	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	chuckv	1404	*/
391	chuckv	1402
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	chuckv	1404	// qh_getarea(qh facet_list);
459			//volume_ = qh totvol;
460			// area_ = qh totarea;
461	chuckv	1402
462	gezelter	1858
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	chuckv	1402	qh_freeqhull(!qh_ALL);
483			qh_memfreeshort(&curlong, &totlong);
484	gezelter	1858	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	chuckv	1402	}
492
493	gezelter	1858	void AlphaHull::printHull(const string& geomFileName) {
494
495	chuckv	1402	#ifdef IS_MPI
496			if (worldRank == 0) {
497			#endif
498	gezelter	1858	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	chuckv	1402	#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