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.
 */

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

/* Standard includes independent of library */

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

#include "math/qhull.hpp"

#ifdef HAVE_QHULL
using namespace std;
using namespace OpenMD;

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

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

void AlphaHull::computeHull(vector<StuntDouble*> bodydoubles) { 
 
  int numpoints = bodydoubles.size();
  
  Triangles_.clear();
  
  vertexT *vertex;
  facetT *facet, *neighbor;
  pointT *interiorPoint;
  int curlong, totlong;
  
  
  vector<double> ptArray(numpoints*dim_);
  
  // Copy the positon vector into a points vector for qhull.
  vector<StuntDouble*>::iterator SD;
  int i = 0;
  for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
    Vector3d pos = (*SD)->getPos();      
    ptArray[dim_ * i] = pos.x();
    ptArray[dim_ * i + 1] = pos.y();
    ptArray[dim_ * i + 2] = pos.z();
    i++;
  }
  
  /* Clean up memory from previous convex hull calculations*/
  boolT ismalloc = False;
  
  /* compute the hull for our local points (or all the points for single
     processor versions) */
  if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
                   const_cast<char *>(options_.c_str()), NULL, stderr)) {
    
    sprintf(painCave.errMsg, "AlphaHull: Qhull failed to compute convex hull");
    painCave.isFatal = 1;
    simError();
    
  } //qh_new_qhull
  
  
#ifdef IS_MPI
  //If we are doing the mpi version, set up some vectors for data communication
  
  int nproc;
  int myrank;
  MPI_Comm_size( MPI_COMM_WORLD, &nproc);
  MPI_Comm_rank( MPI_COMM_WORLD, &myrank);

  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_Allgather(&localHullSites, 1, MPI_INT, &hullSitesOnProc[0],
                1, MPI_INT, MPI_COMM_WORLD);

  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_Allgatherv(&coords[0], count, MPI_DOUBLE, &globalCoords[0],
                 &coordsOnProc[0], &vectorDisplacements[0], 
                 MPI_DOUBLE, MPI_COMM_WORLD);
  
  MPI_Allgatherv(&vels[0], count, MPI_DOUBLE, &globalVels[0], 
                 &coordsOnProc[0], &vectorDisplacements[0],
                 MPI_DOUBLE, MPI_COMM_WORLD);
  
  MPI_Allgatherv(&masses[0], localHullSites, MPI_DOUBLE,
                 &globalMasses[0], &hullSitesOnProc[0], 
                 &displacements[0], MPI_DOUBLE, MPI_COMM_WORLD);
  
  // Free previous hull
  qh_freeqhull(!qh_ALL);
  qh_memfreeshort(&curlong, &totlong);
  if (curlong || totlong) {
    sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n"
            "\tdid not free %d bytes of long memory (%d pieces)", 
            totlong, curlong);
    painCave.isFatal = 1;
    simError();
  }
  
  if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
                   const_cast<char *>(options_.c_str()), NULL, stderr)){
    
    sprintf(painCave.errMsg, 
            "AlphaHull: Qhull failed to compute global convex hull");
    painCave.isFatal = 1;
    simError();
        
  } //qh_new_qhull

#endif

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

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

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

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

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

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


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

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

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

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

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


/*  
  FORALLfacets {  
    Triangle face;

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

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

    int ver = 0;

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

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

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

      int localID = id - displacements[myrank];

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

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

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

  qh_freeqhull(!qh_ALL);
  qh_memfreeshort(&curlong, &totlong);
  if (curlong || totlong) {
    sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n"
            "\tdid not free %d bytes of long memory (%d pieces)", 
            totlong, curlong);
    painCave.isFatal = 1;
    simError();
  }
}

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

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

#endif //QHULL
Revision:	1969
Committed:	Wed Feb 26 14:14:50 2014 UTC (11 years, 2 months ago) by gezelter
File size:	16380 byte(s)
Log Message:	Fixes to deal with deprecation of MPI C++ bindings. We've reverted back to the C calls.
#	User	Rev	Content
1	gezelter	1879	/* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
2	chuckv	1402	*
3			* The University of Notre Dame grants you ("Licensee") a
4			* non-exclusive, royalty free, license to use, modify and
5			* redistribute this software in source and binary code form, provided
6			* that the following conditions are met:
7			*
8			* 1. Redistributions of source code must retain the above copyright
9			* notice, this list of conditions and the following disclaimer.
10			*
11			* 2. Redistributions in binary form must reproduce the above copyright
12			* notice, this list of conditions and the following disclaimer in the
13			* documentation and/or other materials provided with the
14			* distribution.
15			*
16			* This software is provided "AS IS," without a warranty of any
17			* kind. All express or implied conditions, representations and
18			* warranties, including any implied warranty of merchantability,
19			* fitness for a particular purpose or non-infringement, are hereby
20			* excluded. The University of Notre Dame and its licensors shall not
21			* be liable for any damages suffered by licensee as a result of
22			* using, modifying or distributing the software or its
23			* derivatives. In no event will the University of Notre Dame or its
24			* licensors be liable for any lost revenue, profit or data, or for
25			* direct, indirect, special, consequential, incidental or punitive
26			* damages, however caused and regardless of the theory of liability,
27			* arising out of the use of or inability to use software, even if the
28			* University of Notre Dame has been advised of the possibility of
29			* such damages.
30			*
31			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32			* research, please cite the appropriate papers when you publish your
33			* work. Good starting points are:
34			*
35	gezelter	1879	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39	gezelter	1879	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
40	chuckv	1402	*
41			* AlphaHull.cpp
42			*
43	gezelter	1879	* Purpose: To calculate an alpha-shape hull.
44	chuckv	1402	*/
45
46	gezelter	1938	#ifdef IS_MPI
47			#include <mpi.h>
48			#endif
49
50	chuckv	1402	/* Standard includes independent of library */
51
52			#include <iostream>
53			#include <fstream>
54			#include <list>
55			#include <algorithm>
56			#include <iterator>
57			#include "math/AlphaHull.hpp"
58			#include "utils/simError.h"
59	gezelter	1879
60	gezelter	1782	#include "math/qhull.hpp"
61	chuckv	1402
62	gezelter	1879	#ifdef HAVE_QHULL
63			using namespace std;
64	chuckv	1402	using namespace OpenMD;
65
66	gezelter	1879	double calculate_circumradius(pointT* p0, pointT* p1, pointT* p2, int dim);
67	chuckv	1402
68	gezelter	1879	AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha),
69			options_("qhull d QJ Tcv Pp") {
70	chuckv	1402	}
71
72	gezelter	1879	void AlphaHull::computeHull(vector<StuntDouble*> bodydoubles) {
73	chuckv	1402
74			int numpoints = bodydoubles.size();
75
76			Triangles_.clear();
77
78	gezelter	1879	vertexT *vertex;
79	chuckv	1402	facetT facet, neighbor;
80	gezelter	1879	pointT *interiorPoint;
81	chuckv	1402	int curlong, totlong;
82
83	gezelter	1879
84			vector<double> ptArray(numpoints*dim_);
85
86	chuckv	1402	// Copy the positon vector into a points vector for qhull.
87	gezelter	1879	vector<StuntDouble*>::iterator SD;
88	chuckv	1402	int i = 0;
89			for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
90			Vector3d pos = (*SD)->getPos();
91			ptArray[dim_ * i] = pos.x();
92			ptArray[dim_ * i + 1] = pos.y();
93			ptArray[dim_ * i + 2] = pos.z();
94			i++;
95			}
96	gezelter	1879
97			/* Clean up memory from previous convex hull calculations*/
98	chuckv	1402	boolT ismalloc = False;
99	gezelter	1879
100			/* compute the hull for our local points (or all the points for single
101			processor versions) */
102	chuckv	1402	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
103			const_cast<char *>(options_.c_str()), NULL, stderr)) {
104	gezelter	1879
105	chuckv	1402	sprintf(painCave.errMsg, "AlphaHull: Qhull failed to compute convex hull");
106			painCave.isFatal = 1;
107			simError();
108
109			} //qh_new_qhull
110	gezelter	1879
111
112	chuckv	1402	#ifdef IS_MPI
113			//If we are doing the mpi version, set up some vectors for data communication
114
115	gezelter	1969	int nproc;
116			int myrank;
117			MPI_Comm_size( MPI_COMM_WORLD, &nproc);
118			MPI_Comm_rank( MPI_COMM_WORLD, &myrank);
119
120	chuckv	1402	int localHullSites = 0;
121
122	gezelter	1879	vector<int> hullSitesOnProc(nproc, 0);
123			vector<int> coordsOnProc(nproc, 0);
124			vector<int> displacements(nproc, 0);
125			vector<int> vectorDisplacements(nproc, 0);
126	chuckv	1402
127	gezelter	1879	vector<double> coords;
128			vector<double> vels;
129			vector<int> indexMap;
130			vector<double> masses;
131	chuckv	1402
132			FORALLvertices{
133			localHullSites++;
134
135			int idx = qh_pointid(vertex->point);
136
137			indexMap.push_back(idx);
138
139			coords.push_back(ptArray[dim_ * idx]);
140			coords.push_back(ptArray[dim_ * idx + 1]);
141			coords.push_back(ptArray[dim_ * idx + 2]);
142
143			StuntDouble* sd = bodydoubles[idx];
144
145			Vector3d vel = sd->getVel();
146			vels.push_back(vel.x());
147			vels.push_back(vel.y());
148			vels.push_back(vel.z());
149
150			masses.push_back(sd->getMass());
151			}
152
153	gezelter	1969	MPI_Allgather(&localHullSites, 1, MPI_INT, &hullSitesOnProc[0],
154			1, MPI_INT, MPI_COMM_WORLD);
155	chuckv	1402
156			int globalHullSites = 0;
157			for (int iproc = 0; iproc < nproc; iproc++){
158			globalHullSites += hullSitesOnProc[iproc];
159			coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
160			}
161
162			displacements[0] = 0;
163			vectorDisplacements[0] = 0;
164
165			for (int iproc = 1; iproc < nproc; iproc++){
166			displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
167			vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
168			}
169
170	gezelter	1879	vector<double> globalCoords(dim_ * globalHullSites);
171			vector<double> globalVels(dim_ * globalHullSites);
172			vector<double> globalMasses(globalHullSites);
173	chuckv	1402
174			int count = coordsOnProc[myrank];
175
176	gezelter	1969	MPI_Allgatherv(&coords[0], count, MPI_DOUBLE, &globalCoords[0],
177			&coordsOnProc[0], &vectorDisplacements[0],
178			MPI_DOUBLE, MPI_COMM_WORLD);
179
180			MPI_Allgatherv(&vels[0], count, MPI_DOUBLE, &globalVels[0],
181			&coordsOnProc[0], &vectorDisplacements[0],
182			MPI_DOUBLE, MPI_COMM_WORLD);
183
184			MPI_Allgatherv(&masses[0], localHullSites, MPI_DOUBLE,
185			&globalMasses[0], &hullSitesOnProc[0],
186			&displacements[0], MPI_DOUBLE, MPI_COMM_WORLD);
187
188	chuckv	1402	// Free previous hull
189			qh_freeqhull(!qh_ALL);
190			qh_memfreeshort(&curlong, &totlong);
191	gezelter	1879	if (curlong \|\| totlong) {
192			sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n"
193			"\tdid not free %d bytes of long memory (%d pieces)",
194			totlong, curlong);
195			painCave.isFatal = 1;
196			simError();
197			}
198	chuckv	1402
199			if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
200			const_cast<char *>(options_.c_str()), NULL, stderr)){
201
202	gezelter	1879	sprintf(painCave.errMsg,
203			"AlphaHull: Qhull failed to compute global convex hull");
204	chuckv	1402	painCave.isFatal = 1;
205			simError();
206	gezelter	1879
207	chuckv	1402	} //qh_new_qhull
208
209			#endif
210
211			//Set facet->center as the Voronoi center
212			qh_setvoronoi_all();
213
214
215			int convexNumVert = qh_setsize(qh_facetvertices (qh facet_list, NULL, false));
216			//Insert all the sample points, because, even with alpha=0, the alpha shape/alpha complex will
217			//contain them.
218
219			// tri::Allocator<CMeshO>::AddVertices(pm.cm,convexNumVert);
220
221			/*ivp length is 'qh num_vertices' because each vertex is accessed through its ID whose range is
222			0<=qh_pointid(vertex->point)<qh num_vertices*/
223			// vector<tri::Allocator<CMeshO>::VertexPointer> ivp(qh num_vertices);
224			/*i=0;
225			FORALLvertices{
226			if ((*vertex).point){
227			// pm.cm.vert[i].P()[0] = (*vertex).point[0];
228			// pm.cm.vert[i].P()[1] = (*vertex).point[1];
229			//pm.cm.vert[i].P()[2] = (*vertex).point[2];
230			// ivp[qh_pointid(vertex->point)] = &pm.cm.vert[i];
231			i++;
232			}
233			}
234			*/
235			//Set of alpha complex triangles for alphashape filtering
236			setT* set= qh_settemp(4* qh num_facets);
237
238			qh visit_id++;
239			int numFacets=0;
240	gezelter	1879	vector<vector <int> > facetlist;
241	chuckv	1404	interiorPoint = qh interior_point;
242	chuckv	1402	FORALLfacet_(qh facet_list) {
243			numFacets++;
244			if (!facet->upperdelaunay) {
245			//For all facets (that are tetrahedrons)calculate the radius of the empty circumsphere considering
246			//the distance between the circumcenter and a vertex of the facet
247			vertexT* vertex = (vertexT *)(facet->vertices->e[0].p);
248			double* center = facet->center;
249			double radius = qh_pointdist(vertex->point,center,dim_);
250
251			if (radius>alpha_) // if the facet is not good consider the ridges
252			{
253			//if calculating the alphashape, unmark the facet ('good' is used as 'marked').
254			facet->good=false;
255
256			//Compute each ridge (triangle) once and test the cironference radius with alpha
257			facet->visitid= qh visit_id;
258			qh_makeridges(facet);
259			ridgeT ridge, *ridgep;
260			int goodTriangles=0;
261			FOREACHridge_(facet->ridges) {
262			neighbor= otherfacet_(ridge, facet);
263			if (( neighbor->visitid != qh visit_id)){
264			//Calculate the radius of the circumference
265			pointT* p0 = ((vertexT*) (ridge->vertices->e[0].p))->point;
266			pointT* p1 = ((vertexT*) (ridge->vertices->e[1].p))->point;
267			pointT* p2 = ((vertexT*) (ridge->vertices->e[2].p))->point;
268
269			radius = calculate_circumradius(p0,p1,p2, dim_);
270
271			if(radius <=alpha_){
272			goodTriangles++;
273			//save the triangle (ridge) for subsequent filtering
274			qh_setappend(&set, ridge);
275			}
276			}
277			}
278
279			//If calculating the alphashape, mark the facet('good' is used as 'marked').
280			//This facet will have some triangles hidden by the facet's neighbor.
281			if(goodTriangles==4)
282			facet->good=true;
283
284			}
285			else //the facet is good. Put all the triangles of the tetrahedron in the mesh
286			{
287			//Compute each ridge (triangle) once
288			facet->visitid= qh visit_id;
289			//If calculating the alphashape, mark the facet('good' is used as 'marked').
290			//This facet will have some triangles hidden by the facet's neighbor.
291			facet->good=true;
292			qh_makeridges(facet);
293			ridgeT ridge, *ridgep;
294			FOREACHridge_(facet->ridges) {
295			neighbor= otherfacet_(ridge, facet);
296			if ((neighbor->visitid != qh visit_id)){
297			qh_setappend(&set, ridge);
298			}
299			}
300			}
301			}
302			}
303			//assert(numFacets== qh num_facets);
304
305			//Filter the triangles (only the ones on the boundary of the alpha complex) and build the mesh
306	chuckv	1404
307	gezelter	1879	int ridgesCount=0;
308	chuckv	1402
309			ridgeT ridge, *ridgep;
310			FOREACHridge_(set) {
311			if ((!ridge->top->good \|\| !ridge->bottom->good \|\| ridge->top->upperdelaunay \|\| ridge->bottom->upperdelaunay)){
312			// tri::Allocator<CMeshO>::FaceIterator fi=tri::Allocator<CMeshO>::AddFaces(pm.cm,1);
313			ridgesCount++;
314			int vertex_n, vertex_i;
315			Triangle face;
316
317			// Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
318			//face.setNormal(V3dNormal);
319
320
321	chuckv	1404	//coordT *center = qh_getcenter(ridge->vertices);
322	gezelter	1879	//cout << "Centers are " << center[0] << " " <<center[1] << " " << center[2] << endl;
323	chuckv	1402	//Vector3d V3dCentroid(center[0], center[1], center[2]);
324			//face.setCentroid(V3dCentroid);
325	chuckv	1404
326	chuckv	1402
327	chuckv	1404	Vector3d faceVel = V3Zero;
328	chuckv	1402	Vector3d p[3];
329	chuckv	1404	RealType faceMass = 0.0;
330	chuckv	1402
331			int ver = 0;
332	gezelter	1879	vector<int> virtexlist;
333	chuckv	1402	FOREACHvertex_i_(ridge->vertices){
334			int id = qh_pointid(vertex->point);
335			p[ver][0] = vertex->point[0];
336			p[ver][1] = vertex->point[1];
337			p[ver][2] = vertex->point[2];
338			Vector3d vel;
339			RealType mass;
340			ver++;
341			virtexlist.push_back(id);
342	gezelter	1879	// cout << "Ridge: " << ridgesCount << " Vertex " << id << endl;
343	chuckv	1404
344			vel = bodydoubles[id]->getVel();
345			mass = bodydoubles[id]->getMass();
346			face.addVertexSD(bodydoubles[id]);
347
348
349			faceVel = faceVel + vel;
350			faceMass = faceMass + mass;
351			} //FOREACH Vertex
352	chuckv	1402	facetlist.push_back(virtexlist);
353	chuckv	1404	face.addVertices(p[0],p[1],p[2]);
354			face.setFacetMass(faceMass);
355	gezelter	1782	face.setFacetVelocity(faceVel / RealType(3.0));
356	chuckv	1404
357			RealType area = face.getArea();
358			area_ += area;
359			Vector3d normal = face.getUnitNormal();
360			RealType offset = ((0.0-p[0][0])normal[0] + (0.0-p[0][1])normal[1] + (0.0-p[0][2])*normal[2]);
361			RealType dist = normal[0] * interiorPoint[0] + normal[1]interiorPoint[1] + normal[2]interiorPoint[2];
362	gezelter	1879	cout << "Dist and normal and area are: " << normal << endl;
363	chuckv	1404	volume_ += dist *area/qh hull_dim;
364
365			Triangles_.push_back(face);
366	chuckv	1402	}
367			}
368
369	gezelter	1879	cout << "Volume is: " << volume_ << endl;
370	chuckv	1404
371	chuckv	1402	//assert(pm.cm.fn == ridgesCount);
372	chuckv	1404	/*
373	chuckv	1402	std::cout <<"OFF"<<std::endl;
374			std::cout << bodydoubles.size() << " " << facetlist.size() << " " << 3*facetlist.size() << std::endl;
375			for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
376			Vector3d pos = (*SD)->getPos();
377			std::cout << pos.x() << " " << pos.y() << " " << pos.z() << std::endl;
378			}
379
380
381			std::vector<std::vector<int> >::iterator thisfacet;
382			std::vector<int>::iterator thisvertex;
383
384			for (thisfacet = facetlist.begin(); thisfacet != facetlist.end(); thisfacet++){
385			std::cout << (*thisfacet).size();
386			for (thisvertex = (thisfacet).begin(); thisvertex != (thisfacet).end(); thisvertex++){
387			std::cout << " " << *thisvertex;
388			}
389			std::cout << std::endl;
390			}
391	chuckv	1404	*/
392	chuckv	1402
393
394
395			/*
396			FORALLfacets {
397			Triangle face;
398
399			Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
400			face.setNormal(V3dNormal);
401
402			RealType faceArea = qh_facetarea(facet);
403			face.setArea(faceArea);
404
405			vertices = qh_facet3vertex(facet);
406
407			coordT *center = qh_getcenter(vertices);
408			Vector3d V3dCentroid(center[0], center[1], center[2]);
409			face.setCentroid(V3dCentroid);
410
411			Vector3d faceVel = V3Zero;
412			Vector3d p[3];
413			RealType faceMass = 0.0;
414
415			int ver = 0;
416
417			FOREACHvertex_(vertices){
418			int id = qh_pointid(vertex->point);
419			p[ver][0] = vertex->point[0];
420			p[ver][1] = vertex->point[1];
421			p[ver][2] = vertex->point[2];
422
423			Vector3d vel;
424			RealType mass;
425
426			#ifdef IS_MPI
427			vel = Vector3d(globalVels[dim_ * id],
428			globalVels[dim_ * id + 1],
429			globalVels[dim_ * id + 2]);
430			mass = globalMasses[id];
431
432			// localID will be between 0 and hullSitesOnProc[myrank] if we
433			// own this guy.
434
435			int localID = id - displacements[myrank];
436
437			if (localID >= 0 && localID < hullSitesOnProc[myrank])
438			face.addVertexSD(bodydoubles[indexMap[localID]]);
439
440			#else
441			vel = bodydoubles[id]->getVel();
442			mass = bodydoubles[id]->getMass();
443			face.addVertexSD(bodydoubles[id]);
444			#endif
445
446			faceVel = faceVel + vel;
447			faceMass = faceMass + mass;
448			ver++;
449			} //Foreachvertex
450
451			face.addVertices(p[0], p[1], p[2]);
452			face.setFacetMass(faceMass);
453			face.setFacetVelocity(faceVel/3.0);
454			Triangles_.push_back(face);
455			qh_settempfree(&vertices);
456
457			} //FORALLfacets
458			*/
459	chuckv	1404	// qh_getarea(qh facet_list);
460			//volume_ = qh totvol;
461			// area_ = qh totarea;
462	chuckv	1402
463			qh_freeqhull(!qh_ALL);
464			qh_memfreeshort(&curlong, &totlong);
465	gezelter	1879	if (curlong \|\| totlong) {
466			sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n"
467			"\tdid not free %d bytes of long memory (%d pieces)",
468			totlong, curlong);
469			painCave.isFatal = 1;
470			simError();
471			}
472	chuckv	1402	}
473
474	gezelter	1879	void AlphaHull::printHull(const string& geomFileName) {
475
476	chuckv	1402	#ifdef IS_MPI
477			if (worldRank == 0) {
478			#endif
479	gezelter	1879	FILE *newGeomFile;
480
481			//create new .md file based on old .md file
482			newGeomFile = fopen(geomFileName.c_str(), "w");
483			qh_findgood_all(qh facet_list);
484			for (int i = 0; i < qh_PRINTEND; i++)
485			qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
486
487			fclose(newGeomFile);
488	chuckv	1402	#ifdef IS_MPI
489			}
490			#endif
491			}
492
493			double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim){
494			coordT a = qh_pointdist(p0,p1,dim);
495			coordT b = qh_pointdist(p1,p2,dim);
496			coordT c = qh_pointdist(p2,p0,dim);
497
498			coordT sum =(a + b + c)*0.5;
499			coordT area = sum(a+b-sum)(a+c-sum)*(b+c-sum);
500			return (double) (abc)/(4*sqrt(area));
501			}
502
503			#endif //QHULL