src/math/ConvexHull.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). 
 *
 *  ConvexHull.cpp
 *
 *  Purpose: To calculate a convex hull.
 */

/* Standard includes independent of library */

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

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

#include "math/qhull.hpp"

#ifdef HAVE_QHULL
using namespace OpenMD;
using namespace std;

ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") {
}

void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) { 
  
  int numpoints = bodydoubles.size();
  
  Triangles_.clear();
  
  vertexT *vertex, **vertexp;
  facetT *facet;
  setT *vertices;
  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, "ConvexHull: 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, "ConvexHull: 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, 
            "ConvexHull: Qhull failed to compute global convex hull");
    painCave.isFatal = 1;
    simError();
    
  } //qh_new_qhull

#endif
  // commented out below, so comment out here also.
  // intPoint = qh interior_point;
  // RealType calcvol = 0.0;
  
  qh_triangulate ();
  int num_facets = qh num_facets;
  int num_vertices = qh num_vertices;

  FORALLfacets {  
    Triangle face;
    //Qhull sets the unit normal in facet->normal
    Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
    face.setUnitNormal(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{
        face.addVertexSD(NULL);
      }
#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 / RealType(3.0));
    /*
    RealType comparea = face.computeArea();
    realT calcarea = qh_facetarea (facet);
    Vector3d V3dCompNorm = -face.computeUnitNormal();
    RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
    RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
    cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  endl;
    calcvol +=  -dist*comparea/qh hull_dim;
    */
    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, "ConvexHull: qhull internal warning:\n"
            "\tdid not free %d bytes of long memory (%d pieces)", 
            totlong, curlong);
    painCave.isFatal = 1;
    simError();
  }
}

void ConvexHull::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
}
#endif //QHULL
Revision:	1866
Committed:	Thu Apr 25 14:32:56 2013 UTC (12 years ago) by gezelter
File size:	10610 byte(s)
Log Message:	Fixes for Qhull static build strangeness
#	User	Rev	Content
1	gezelter	1411	/* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
2	chuckv	1097	*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
9	chuckv	1097	* notice, this list of conditions and the following disclaimer.
10			*
11	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
12	chuckv	1097	* 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	gezelter	1390	* 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	1097	*
41			* ConvexHull.cpp
42			*
43	gezelter	1858	* Purpose: To calculate a convex hull.
44	chuckv	1097	*/
45
46	chuckv	1242	/* Standard includes independent of library */
47	chuckv	1374
48	chuckv	1097	#include <iostream>
49			#include <fstream>
50	chuckv	1188	#include <list>
51			#include <algorithm>
52			#include <iterator>
53	chuckv	1141	#include "math/ConvexHull.hpp"
54	chuckv	1188	#include "utils/simError.h"
55	chuckv	1293
56			#ifdef IS_MPI
57	chuckv	1374	#include <mpi.h>
58	chuckv	1293	#endif
59
60	gezelter	1704	#include "math/qhull.hpp"
61	chuckv	1293
62	chuckv	1374	#ifdef HAVE_QHULL
63	gezelter	1704	using namespace OpenMD;
64	gezelter	1858	using namespace std;
65	chuckv	1293
66	gezelter	1866	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") {
67	chuckv	1374	}
68	chuckv	1293
69	gezelter	1858	void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) {
70
71	chuckv	1374	int numpoints = bodydoubles.size();
72	gezelter	1858
73	chuckv	1374	Triangles_.clear();
74	chuckv	1242
75	chuckv	1293	vertexT vertex, *vertexp;
76			facetT *facet;
77			setT *vertices;
78	chuckv	1374	int curlong, totlong;
79	gezelter	1858
80			Vector3d boxMax;
81			Vector3d boxMin;
82	chuckv	1242
83	gezelter	1858	vector<double> ptArray(numpoints*dim_);
84	chuckv	1293
85			// Copy the positon vector into a points vector for qhull.
86	gezelter	1858	vector<StuntDouble*>::iterator SD;
87	chuckv	1293	int i = 0;
88	gezelter	1866
89	chuckv	1374	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	chuckv	1242
97	gezelter	1411	/* Clean up memory from previous convex hull calculations */
98	chuckv	1293	boolT ismalloc = False;
99	chuckv	1308
100	gezelter	1411	/* compute the hull for our local points (or all the points for single
101			processor versions) */
102	chuckv	1302	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
103	chuckv	1374	const_cast<char *>(options_.c_str()), NULL, stderr)) {
104	gezelter	1411
105	chuckv	1374	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
106			painCave.isFatal = 1;
107			simError();
108
109	chuckv	1293	} //qh_new_qhull
110
111
112			#ifdef IS_MPI
113	chuckv	1374	//If we are doing the mpi version, set up some vectors for data communication
114	chuckv	1242
115	chuckv	1374	int nproc = MPI::COMM_WORLD.Get_size();
116			int myrank = MPI::COMM_WORLD.Get_rank();
117			int localHullSites = 0;
118	chuckv	1293
119	gezelter	1858	vector<int> hullSitesOnProc(nproc, 0);
120			vector<int> coordsOnProc(nproc, 0);
121			vector<int> displacements(nproc, 0);
122			vector<int> vectorDisplacements(nproc, 0);
123	gezelter	1384
124	gezelter	1858	vector<double> coords;
125			vector<double> vels;
126			vector<int> indexMap;
127			vector<double> masses;
128	chuckv	1374
129			FORALLvertices{
130			localHullSites++;
131	chuckv	1242
132	chuckv	1374	int idx = qh_pointid(vertex->point);
133	gezelter	1378
134			indexMap.push_back(idx);
135
136	chuckv	1374	coords.push_back(ptArray[dim_ * idx]);
137			coords.push_back(ptArray[dim_ * idx + 1]);
138			coords.push_back(ptArray[dim_ * idx + 2]);
139	chuckv	1293
140	chuckv	1374	StuntDouble* sd = bodydoubles[idx];
141	chuckv	1188
142	chuckv	1374	Vector3d vel = sd->getVel();
143			vels.push_back(vel.x());
144			vels.push_back(vel.y());
145			vels.push_back(vel.z());
146	chuckv	1188
147	chuckv	1374	masses.push_back(sd->getMass());
148			}
149	chuckv	1188
150	chuckv	1374	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
151			1, MPI::INT);
152	chuckv	1307
153	chuckv	1374	int globalHullSites = 0;
154	gezelter	1376	for (int iproc = 0; iproc < nproc; iproc++){
155	chuckv	1374	globalHullSites += hullSitesOnProc[iproc];
156			coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
157	chuckv	1302	}
158	chuckv	1293
159	chuckv	1374	displacements[0] = 0;
160			vectorDisplacements[0] = 0;
161	chuckv	1316
162	gezelter	1376	for (int iproc = 1; iproc < nproc; iproc++){
163	chuckv	1374	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
164			vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
165	chuckv	1293	}
166
167	gezelter	1858	vector<double> globalCoords(dim_ * globalHullSites);
168			vector<double> globalVels(dim_ * globalHullSites);
169			vector<double> globalMasses(globalHullSites);
170	gezelter	1377
171	chuckv	1374	int count = coordsOnProc[myrank];
172	chuckv	1365
173	gezelter	1377	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
174			&coordsOnProc[0], &vectorDisplacements[0],
175	chuckv	1374	MPI::DOUBLE);
176	chuckv	1302
177	gezelter	1377	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
178			&coordsOnProc[0], &vectorDisplacements[0],
179	chuckv	1374	MPI::DOUBLE);
180	chuckv	1302
181	chuckv	1374	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
182	gezelter	1377	&globalMasses[0], &hullSitesOnProc[0],
183			&displacements[0], MPI::DOUBLE);
184	chuckv	1365
185	chuckv	1293	// Free previous hull
186	chuckv	1242	qh_freeqhull(!qh_ALL);
187			qh_memfreeshort(&curlong, &totlong);
188	gezelter	1411	if (curlong \|\| totlong) {
189			sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
190			"\tdid not free %d bytes of long memory (%d pieces)",
191			totlong, curlong);
192			painCave.isFatal = 1;
193			simError();
194			}
195	chuckv	1374
196			if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
197			const_cast<char *>(options_.c_str()), NULL, stderr)){
198
199	gezelter	1858	sprintf(painCave.errMsg,
200			"ConvexHull: Qhull failed to compute global convex hull");
201	chuckv	1374	painCave.isFatal = 1;
202			simError();
203
204	chuckv	1293	} //qh_new_qhull
205
206			#endif
207	gezelter	1825	// commented out below, so comment out here also.
208			// intPoint = qh interior_point;
209			// RealType calcvol = 0.0;
210	gezelter	1866
211			qh_triangulate ();
212			int num_facets = qh num_facets;
213			int num_vertices = qh num_vertices;
214
215	chuckv	1374	FORALLfacets {
216			Triangle face;
217	chuckv	1404	//Qhull sets the unit normal in facet->normal
218	chuckv	1374	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
219	chuckv	1404	face.setUnitNormal(V3dNormal);
220	chuckv	1371
221	chuckv	1374	RealType faceArea = qh_facetarea(facet);
222			face.setArea(faceArea);
223
224			vertices = qh_facet3vertex(facet);
225	chuckv	1293
226	chuckv	1374	coordT *center = qh_getcenter(vertices);
227			Vector3d V3dCentroid(center[0], center[1], center[2]);
228			face.setCentroid(V3dCentroid);
229	chuckv	1304
230	chuckv	1374	Vector3d faceVel = V3Zero;
231			Vector3d p[3];
232			RealType faceMass = 0.0;
233	gezelter	1377
234	chuckv	1374	int ver = 0;
235	chuckv	1293
236	chuckv	1374	FOREACHvertex_(vertices){
237			int id = qh_pointid(vertex->point);
238			p[ver][0] = vertex->point[0];
239			p[ver][1] = vertex->point[1];
240			p[ver][2] = vertex->point[2];
241			Vector3d vel;
242			RealType mass;
243	chuckv	1293
244	chuckv	1302	#ifdef IS_MPI
245	chuckv	1374	vel = Vector3d(globalVels[dim_ * id],
246			globalVels[dim_ * id + 1],
247			globalVels[dim_ * id + 2]);
248			mass = globalMasses[id];
249
250	gezelter	1377	// localID will be between 0 and hullSitesOnProc[myrank] if we
251			// own this guy.
252
253	chuckv	1374	int localID = id - displacements[myrank];
254	gezelter	1377
255	chuckv	1410
256			if (localID >= 0 && localID < hullSitesOnProc[myrank]){
257	gezelter	1378	face.addVertexSD(bodydoubles[indexMap[localID]]);
258	chuckv	1410	}else{
259			face.addVertexSD(NULL);
260			}
261	chuckv	1307	#else
262	chuckv	1374	vel = bodydoubles[id]->getVel();
263			mass = bodydoubles[id]->getMass();
264			face.addVertexSD(bodydoubles[id]);
265	gezelter	1411	#endif
266	chuckv	1374	faceVel = faceVel + vel;
267			faceMass = faceMass + mass;
268			ver++;
269			} //Foreachvertex
270	chuckv	1302
271	chuckv	1374	face.addVertices(p[0], p[1], p[2]);
272			face.setFacetMass(faceMass);
273	gezelter	1668	face.setFacetVelocity(faceVel / RealType(3.0));
274	chuckv	1404	/*
275			RealType comparea = face.computeArea();
276			realT calcarea = qh_facetarea (facet);
277			Vector3d V3dCompNorm = -face.computeUnitNormal();
278			RealType thisOffset = ((0.0-p[0][0])V3dCompNorm[0] + (0.0-p[0][1])V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
279			RealType dist = facet->offset + intPoint[0]V3dNormal[0] + intPoint[1]V3dNormal[1] + intPoint[2]*V3dNormal[2];
280	gezelter	1858	cout << "facet offset and computed offset: " << facet->offset << " " << thisOffset << endl;
281	chuckv	1404	calcvol += -dist*comparea/qh hull_dim;
282			*/
283	chuckv	1374	Triangles_.push_back(face);
284			qh_settempfree(&vertices);
285
286			} //FORALLfacets
287
288			qh_getarea(qh facet_list);
289			volume_ = qh totvol;
290			area_ = qh totarea;
291	gezelter	1858
292			int index = 0;
293			FORALLvertices {
294			Vector3d point(vertex->point[0], vertex->point[1], vertex->point[2]);
295			if (index == 0) {
296			boxMax = point;
297			boxMin = point;
298			} else {
299			for (int i = 0; i < 3; i++) {
300			boxMax[i] = max(boxMax[i], point[i]);
301			boxMin[i] = min(boxMin[i], point[i]);
302			}
303			}
304			index++;
305			}
306			boundingBox_ = Mat3x3d(0.0);
307			boundingBox_(0,0) = boxMax[0] - boxMin[0];
308			boundingBox_(1,1) = boxMax[1] - boxMin[1];
309			boundingBox_(2,2) = boxMax[2] - boxMin[2];
310
311	chuckv	1374	qh_freeqhull(!qh_ALL);
312			qh_memfreeshort(&curlong, &totlong);
313	gezelter	1411	if (curlong \|\| totlong) {
314			sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
315			"\tdid not free %d bytes of long memory (%d pieces)",
316			totlong, curlong);
317			painCave.isFatal = 1;
318			simError();
319			}
320	chuckv	1097	}
321
322	gezelter	1858	void ConvexHull::printHull(const string& geomFileName) {
323
324	gezelter	1384	#ifdef IS_MPI
325			if (worldRank == 0) {
326			#endif
327	gezelter	1858	FILE *newGeomFile;
328
329			//create new .md file based on old .md file
330			newGeomFile = fopen(geomFileName.c_str(), "w");
331			qh_findgood_all(qh facet_list);
332			for (int i = 0; i < qh_PRINTEND; i++)
333			qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
334
335			fclose(newGeomFile);
336	gezelter	1384	#ifdef IS_MPI
337			}
338			#endif
339	chuckv	1097	}
340	chuckv	1242	#endif //QHULL