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root/OpenMD/branches/development/src/math/ConvexHull.cpp

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trunk/src/math/ConvexHull.cpp (file contents), Revision 1302 by chuckv, Tue Oct 7 17:12:48 2008 UTC vs.
branches/development/src/math/ConvexHull.cpp (file contents), Revision 1704 by gezelter, Tue Apr 24 20:40:04 2012 UTC

#	Line 1 | Line 1
1	<	/* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved.
1	>	/* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
2		*
3		* The University of Notre Dame grants you ("Licensee") a
4		* non-exclusive, royalty free, license to use, modify and
5		* redistribute this software in source and binary code form, provided
6		* that the following conditions are met:
7		*
8	<	* 1. Acknowledgement of the program authors must be made in any
9	<	*    publication of scientific results based in part on use of the
10	<	*    program.  An acceptable form of acknowledgement is citation of
11	<	*    the article in which the program was described (Matthew
12	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
13	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
14	<	*    Parallel Simulation Engine for Molecular Dynamics,"
15	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
16	<	*
17	<	* 2. Redistributions of source code must retain the above copyright
8	>	* 1. Redistributions of source code must retain the above copyright
9		*    notice, this list of conditions and the following disclaimer.
10		*
11	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
28		* University of Notre Dame has been advised of the possibility of
29		* such damages.
30		*
31	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
32	+	* research, please cite the appropriate papers when you publish your
33	+	* work.  Good starting points are:
34	+	*
35	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	+	* [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
39	+	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40		*
41		*  ConvexHull.cpp
42		*
#	Line 44 | Line 44
44		*
45		*  Created by Charles F. Vardeman II on 11 Dec 2006.
46		*  @author  Charles F. Vardeman II
47	<	*  @version $Id: ConvexHull.cpp,v 1.9 2008-10-07 17:12:48 chuckv Exp $
47	>	*  @version $Id$
48		*
49		*/
50
51		/* Standard includes independent of library */
52	+
53		#include <iostream>
54		#include <fstream>
55		#include <list>
#	Line 57 | Line 58
58		#include "math/ConvexHull.hpp"
59		#include "utils/simError.h"
60
61	+	#ifdef IS_MPI
62	+	#include <mpi.h>
63	+	#endif
64
65	<	using namespace oopse;
65	>	#include "math/qhull.hpp"
66
67	<	/* CGAL version of convex hull first then QHULL */
68	<	#ifdef HAVE_CGAL
65	<	//#include <CGAL/Homogeneous.h>
66	<	#include <CGAL/basic.h>
67	<	//#include <CGAL/Simple_cartesian.h>
68	<	#include <CGAL/Cartesian.h>
69	<	#include <CGAL/Origin.h>
70	<	#include <CGAL/Exact_predicates_exact_constructions_kernel.h>
71	<	#include <CGAL/Convex_hull_traits_3.h>
72	<	#include <CGAL/convex_hull_3.h>
73	<	#include <CGAL/Polyhedron_traits_with_normals_3.h>
74	<	#include <CGAL/Polyhedron_3.h>
75	<	#include <CGAL/double.h>
76	<	#include <CGAL/number_utils.h>
67	>	#ifdef HAVE_QHULL
68	>	using namespace OpenMD;
69
70	+	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
71	+	}
72
73	<	//#include <CGAL/Quotient.h>
74	<	#include <CGAL/MP_Float.h>
75	<	//#include <CGAL/Lazy_exact_nt.h>
73	>	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
74	>
75	>	int numpoints = bodydoubles.size();
76
77	+	Triangles_.clear();
78	+
79	+	vertexT *vertex, **vertexp;
80	+	facetT *facet;
81	+	setT *vertices;
82	+	int curlong, totlong;
83	+	pointT *intPoint;
84	+
85	+	std::vector<double> ptArray(numpoints*dim_);
86
87	+	// Copy the positon vector into a points vector for qhull.
88	+	std::vector<StuntDouble*>::iterator SD;
89	+	int i = 0;
90	+	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
91	+	Vector3d pos = (*SD)->getPos();
92	+	ptArray[dim_ * i] = pos.x();
93	+	ptArray[dim_ * i + 1] = pos.y();
94	+	ptArray[dim_ * i + 2] = pos.z();
95	+	i++;
96	+	}
97	+
98	+	/* Clean up memory from previous convex hull calculations */
99	+	boolT ismalloc = False;
100	+
101	+	/* compute the hull for our local points (or all the points for single
102	+	processor versions) */
103	+	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
104	+	const_cast<char *>(options_.c_str()), NULL, stderr)) {
105	+
106	+	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
107	+	painCave.isFatal = 1;
108	+	simError();
109	+
110	+	} //qh_new_qhull
111
85	–	typedef CGAL::MP_Float RT;
86	–	//typedef double RT;
87	–	//typedef CGAL::Homogeneous<RT>                     K;
88	–	typedef CGAL::Exact_predicates_exact_constructions_kernel K;
89	–	typedef K::Vector_3                               Vector_3;
90	–	//typedef CGAL::Convex_hull_traits_3<K>             Traits;
91	–	typedef CGAL::Polyhedron_traits_with_normals_3<K> Traits;
92	–	//typedef Traits::Polyhedron_3                      Polyhedron_3;
93	–	typedef CGAL::Polyhedron_3<Traits>                     Polyhedron_3;
94	–	typedef K::Point_3                                Point_3;
112
113	+	#ifdef IS_MPI
114	+	//If we are doing the mpi version, set up some vectors for data communication
115	+
116	+	int nproc = MPI::COMM_WORLD.Get_size();
117	+	int myrank = MPI::COMM_WORLD.Get_rank();
118	+	int localHullSites = 0;
119
120	<	typedef Polyhedron_3::HalfedgeDS             HalfedgeDS;
121	<	typedef Polyhedron_3::Facet_iterator                   Facet_iterator;
122	<	typedef Polyhedron_3::Halfedge_around_facet_circulator Halfedge_facet_circulator;
123	<	typedef Polyhedron_3::Halfedge_handle Halfedge_handle;
101	<	typedef Polyhedron_3::Facet_iterator Facet_iterator;
102	<	typedef Polyhedron_3::Plane_iterator Plane_iterator;
103	<	typedef Polyhedron_3::Vertex_iterator Vertex_iterator;
104	<	typedef Polyhedron_3::Vertex_handle Vertex_handle;
105	<	typedef Polyhedron_3::Point_iterator Point_iterator;
106	<
120	>	std::vector<int> hullSitesOnProc(nproc, 0);
121	>	std::vector<int> coordsOnProc(nproc, 0);
122	>	std::vector<int> displacements(nproc, 0);
123	>	std::vector<int> vectorDisplacements(nproc, 0);
124
125	+	std::vector<double> coords;
126	+	std::vector<double> vels;
127	+	std::vector<int> indexMap;
128	+	std::vector<double> masses;
129
130	<	class Enriched_Point_3 : public K::Point_3{
131	<	public:
132	<	Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
130	>	FORALLvertices{
131	>	localHullSites++;
132	>
133	>	int idx = qh_pointid(vertex->point);
134
135	<	bool isMyPoint() const{ return yupMyPoint; }
114	<	void myPoint(){ yupMyPoint = true; }
115	<	void setSD(StuntDouble* SD){mySD = SD;}
116	<	StuntDouble* getStuntDouble(){return mySD;}
117	<	private:
118	<	bool yupMyPoint;
119	<	StuntDouble* mySD;
135	>	indexMap.push_back(idx);
136
137	<	};
137	>	coords.push_back(ptArray[dim_  * idx]);
138	>	coords.push_back(ptArray[dim_  * idx + 1]);
139	>	coords.push_back(ptArray[dim_  * idx + 2]);
140
141	+	StuntDouble* sd = bodydoubles[idx];
142
143	+	Vector3d vel = sd->getVel();
144	+	vels.push_back(vel.x());
145	+	vels.push_back(vel.y());
146	+	vels.push_back(vel.z());
147
148	+	masses.push_back(sd->getMass());
149	+	}
150
151	+	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
152	+	1, MPI::INT);
153
154	<	// compare Point_3's... used in setting up the STL map from points to indices
155	<	template <typename Pt3>
156	<	struct Point_3_comp {
157	<	bool operator() (const Pt3 & p, const Pt3 & q) const {
131	<	return CGAL::lexicographically_xyz_smaller(p,q); // this is defined inline & hence we had to create fn object & not ptrfun
154	>	int globalHullSites = 0;
155	>	for (int iproc = 0; iproc < nproc; iproc++){
156	>	globalHullSites += hullSitesOnProc[iproc];
157	>	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
158		}
133	–	};
159
160	<	// coordinate-based hashing inefficient but can we do better if pts are copied?
161	<	typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
160	>	displacements[0] = 0;
161	>	vectorDisplacements[0] = 0;
162	>
163	>	for (int iproc = 1; iproc < nproc; iproc++){
164	>	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
165	>	vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
166	>	}
167
168	<	#ifdef IS_MPI
169	<	struct {
170	<	double x,y,z;
141	<	} surfacePt;
142	<	#endif
168	>	std::vector<double> globalCoords(dim_ * globalHullSites);
169	>	std::vector<double> globalVels(dim_ * globalHullSites);
170	>	std::vector<double> globalMasses(globalHullSites);
171
172	<	ConvexHull::ConvexHull() : Hull(){
145	<	//If we are doing the mpi version, set up some vectors for data communication
146	<	#ifdef IS_MPI
147	<
148	<
149	<	nproc_ = MPI::COMM_WORLD.Get_size();
150	<	myrank_ = MPI::COMM_WORLD.Get_rank();
151	<	NstoProc_ = new int[nproc_];
152	<	displs_   = new int[nproc_];
153	<
154	<	// Create a surface point type in MPI to send
155	<	surfacePtType = MPI::DOUBLE.Create_contiguous(3);
156	<	surfacePtType.Commit();
157	<
158	<
159	<	#endif
160	<	}
161	<
162	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
163	<	{
164	<
165	<	std::vector<Enriched_Point_3> points;
166	<	ptMapType myMap;
167	<	Point_iterator   hc;
172	>	int count = coordsOnProc[myrank];
173
174	<	// Copy the positon vector into a points vector for cgal.
175	<	std::vector<StuntDouble*>::iterator SD;
174	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
175	>	&coordsOnProc[0], &vectorDisplacements[0],
176	>	MPI::DOUBLE);
177
178	<	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
179	<	{
180	<	Vector3d pos = (*SD)->getPos();
175	<	Enriched_Point_3* pt = new Enriched_Point_3(pos.x(),pos.y(),pos.z());
176	<	pt->setSD(*SD);
177	<	points.push_back(*pt);
178	<	// myMap[pt]=(*SD);
179	<	}
180	<
181	<	// define object to hold convex hull
182	<	CGAL::Object ch_object_;
183	<	Polyhedron_3 polyhedron;
178	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
179	>	&coordsOnProc[0], &vectorDisplacements[0],
180	>	MPI::DOUBLE);
181
182	<	// compute convex hull
183	<
184	<	std::vector<Enriched_Point_3>::iterator testpt;
188	<
189	<
190	<
191	<	CGAL::convex_hull_3(points.begin(), points.end(), polyhedron);
192	<
193	<
194	<
195	<	Ns_ = polyhedron.size_of_vertices();
196	<
197	<	#ifdef IS_MPI
198	<	/* Gather an array of the number of verticies on each processor */
199	<
200	<
201	<	surfacePtsGlobal_.clear();
202	<	surfacePtsLocal_.clear();
203	<
204	<	MPI::COMM_WORLD.Allgather(&Ns_,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
205	<
206	<	for (int i = 0; i < nproc_; i++){
207	<	Nsglobal_ += NstoProc_[i];
208	<	}
209	<	/*Reminder ideally, we would like to reserve size for the vectors here*/
210	<	surfacePtsLocal_.reserve(Ns_);
211	<	surfacePtsGlobal_.resize(Nsglobal_);
212	<	//  std::fill(surfacePtsGlobal_.begin(),surfacePtsGlobal_.end(),0);
213	<
214	<	/* Build a displacements array */
215	<	for (int i = 1; i < nproc_; i++){
216	<	displs_[i] = displs_[i-1] + NstoProc_[i-1];
217	<	}
218	<
219	<	int noffset = displs_[myrank_];
220	<	/* gather the potential hull */
221	<
222	<
223	<	for (hc =polyhedron.points_begin();hc != polyhedron.points_end(); ++hc){
224	<	Point_3 mypoint = *hc;
225	<	surfacePt_ mpiSurfacePt;
226	<	mpiSurfacePt.x = CGAL::to_double(mypoint.x());
227	<	mpiSurfacePt.y = CGAL::to_double(mypoint.y());
228	<	mpiSurfacePt.z = CGAL::to_double(mypoint.z());
229	<	surfacePtsLocal_.push_back(mpiSurfacePt);
230	<	}
231	<
232	<	MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,displs_,surfacePtType);
233	<	std::vector<surfacePt_>::iterator spt;
234	<	std::vector<Enriched_Point_3> gblpoints;
235	<
236	<	int mine = 0;
237	<	int pointidx = 0;
238	<	for (spt = surfacePtsGlobal_.begin(); spt != surfacePtsGlobal_.end(); ++spt)
239	<	{
240	<	surfacePt_ thispos = *spt;
241	<	Enriched_Point_3 ept(thispos.x,thispos.y,thispos.z);
242	<	if (mine >= noffset && mine < noffset + Ns_){
243	<	ept.myPoint();
244	<	ept.setSD(points[pointidx].getStuntDouble());
245	<	pointidx++;
246	<	}
247	<	gblpoints.push_back(ept);
248	<
249	<	mine++;
250	<	}
251	<
252	<	/* Compute the global hull */
253	<	polyhedron.clear();
254	<	CGAL::convex_hull_3(gblpoints.begin(), gblpoints.end(), polyhedron);
255	<
256	<
257	<	#endif
258	<
259	<
260	<
261	<	/* Loop over all of the surface triangles and build data structures for atoms and normals*/
262	<	Facet_iterator j;
263	<	area_ = 0;
264	<	for ( j = polyhedron.facets_begin(); j !=polyhedron.facets_end(); ++j) {
265	<	Halfedge_handle h = j->halfedge();
266	<
267	<	Point_3 r0=h->vertex()->point();
268	<	Point_3 r1=h->next()->vertex()->point();
269	<	Point_3 r2=h->next()->next()->vertex()->point();
270	<
271	<	Point_3* pr0 = &r0;
272	<	Point_3* pr1 = &r1;
273	<	Point_3* pr2 = &r2;
274	<
275	<	Enriched_Point_3* er0 = static_cast<Enriched_Point_3*>(pr0);
276	<	Enriched_Point_3* er1 = static_cast<Enriched_Point_3*>(pr1);
277	<	Enriched_Point_3* er2 = static_cast<Enriched_Point_3*>(pr2);
278	<
279	<	// StuntDouble* sd = er0->getStuntDouble();
280	<	std::cerr << "sd globalIndex = " << to_double(er0->x()) << "\n";
281	<
282	<	Point_3 thisCentroid = CGAL::centroid(r0,r1,r2);
283	<
284	<	Vector_3 normal = CGAL::cross_product(r1-r0,r2-r0);
285	<
286	<	Triangle* face = new Triangle();
287	<	Vector3d V3dNormal(CGAL::to_double(normal.x()),CGAL::to_double(normal.y()),CGAL::to_double(normal.z()));
288	<	Vector3d V3dCentroid(CGAL::to_double(thisCentroid.x()),CGAL::to_double(thisCentroid.y()),CGAL::to_double(thisCentroid.z()));
289	<	face->setNormal(V3dNormal);
290	<	face->setCentroid(V3dCentroid);
291	<	RealType faceArea = 0.5*V3dNormal.length();
292	<	face->setArea(faceArea);
293	<	area_ += faceArea;
294	<	Triangles_.push_back(face);
295	<	//    ptMapType::const_iterator locn=myMap.find(mypoint);
296	<	//    int myIndex = locn->second;
297	<
298	<	}
299	<
300	<	std::cout << "Number of surface atoms is: " << Ns_ << std::endl;
301	<
302	<
303	<
304	<	}
305	<	void ConvexHull::printHull(const std::string& geomFileName)
306	<	{
307	<	/*
308	<	std::ofstream newGeomFile;
309	<
310	<	//create new .md file based on old .md file
311	<	newGeomFile.open("testhull.off");
312	<
313	<	// Write polyhedron in Object File Format (OFF).
314	<	CGAL::set_ascii_mode( std::cout);
315	<	newGeomFile << "OFF" << std::endl << polyhedron.size_of_vertices() << ' '
316	<	<< polyhedron.size_of_facets() << " 0" << std::endl;
317	<	std::copy( polyhedron.points_begin(), polyhedron.points_end(),
318	<	std::ostream_iterator<Point_3>( newGeomFile, "\n"));
319	<	for (  Facet_iterator i = polyhedron.facets_begin(); i != polyhedron.facets_end(); ++i) {
320	<	Halfedge_facet_circulator j = i->facet_begin();
321	<	// Facets in polyhedral surfaces are at least triangles.
322	<	CGAL_assertion( CGAL::circulator_size(j) >= 3);
323	<	newGeomFile << CGAL::circulator_size(j) << ' ';
324	<	do {
325	<	newGeomFile << ' ' << std::distance(polyhedron.vertices_begin(), j->vertex());
326	<	} while ( ++j != i->facet_begin());
327	<	newGeomFile << std::endl;
328	<	}
329	<
330	<	newGeomFile.close();
331	<	*/
332	<	/*
333	<	std::ofstream newGeomFile;
334	<
335	<	//create new .md file based on old .md file
336	<	newGeomFile.open(geomFileName.c_str());
337	<
338	<	// Write polyhedron in Object File Format (OFF).
339	<	CGAL::set_ascii_mode( std::cout);
340	<	newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' '
341	<	<< ch_polyhedron.size_of_facets() << " 0" << std::endl;
342	<	std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(),
343	<	std::ostream_iterator<Point_3>( newGeomFile, "\n"));
344	<	for (  Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i)
345	<	{
346	<	Halfedge_facet_circulator j = i->facet_begin();
347	<	// Facets in polyhedral surfaces are at least triangles.
348	<	CGAL_assertion( CGAL::circulator_size(j) >= 3);
349	<	newGeomFile << CGAL::circulator_size(j) << ' ';
350	<	do
351	<	{
352	<	newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex());
353	<	}
354	<	while ( ++j != i->facet_begin());
355	<	newGeomFile << std::endl;
356	<	}
357	<
358	<	newGeomFile.close();
359	<	*/
360	<
361	<	}
362	<
182	>	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
183	>	&globalMasses[0], &hullSitesOnProc[0],
184	>	&displacements[0], MPI::DOUBLE);
185
186	<
187	<
188	<
189	<
190	<
191	<	#else
192	<	#ifdef HAVE_QHULL
193	<	/* Old options Qt Qu Qg QG0 FA */
194	<	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt  Qci Tcv Pp"), Ns_(200) {
195	<	//If we are doing the mpi version, set up some vectors for data communication
374	<	#ifdef IS_MPI
375	<
376	<
377	<	nproc_ = MPI::COMM_WORLD.Get_size();
378	<	myrank_ = MPI::COMM_WORLD.Get_rank();
379	<	NstoProc_ = new int[nproc_];
380	<	displs_   = new int[nproc_];
381	<
382	<	// Create a surface point type in MPI to send
383	<	//surfacePtType = MPI::DOUBLE.Create_contiguous(3);
384	<	// surfacePtType.Commit();
385	<
386	<
387	<	#endif
388	<	}
389	<
390	<
391	<
392	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
393	<	{
186	>	// Free previous hull
187	>	qh_freeqhull(!qh_ALL);
188	>	qh_memfreeshort(&curlong, &totlong);
189	>	if (curlong || totlong) {
190	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
191	>	"\tdid not free %d bytes of long memory (%d pieces)",
192	>	totlong, curlong);
193	>	painCave.isFatal = 1;
194	>	simError();
195	>	}
196
197	<	std::vector<int> surfaceIDs;
198	<	std::vector<int> surfaceIDsGlobal;
199	<	std::vector<int> localPtsMap;
200	<	int numpoints = bodydoubles.size();
201	<
202	<	//coordT* pt_array;
203	<	coordT* surfpt_array;
402	<	vertexT *vertex, **vertexp;
403	<	facetT *facet;
404	<	setT *vertices;
405	<	int curlong,totlong;
406	<	int id;
407	<
408	<	coordT *point,**pointp;
409	<
410	<
411	<	FILE *outdummy = NULL;
412	<	FILE *errdummy = NULL;
413	<
414	<	//pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
415	<
416	<	//  double* ptArray = new double[numpoints * 3];
417	<	std::vector<double> ptArray(numpoints*3);
418	<	std::vector<bool> isSurfaceID(numpoints);
419	<
420	<	// Copy the positon vector into a points vector for qhull.
421	<	std::vector<StuntDouble*>::iterator SD;
422	<	int i = 0;
423	<	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
424	<	{
425	<	Vector3d pos = (*SD)->getPos();
426	<
427	<	ptArray[dim_ * i] = pos.x();
428	<	ptArray[dim_ * i + 1] = pos.y();
429	<	ptArray[dim_ * i + 2] = pos.z();
430	<	i++;
431	<	}
432	<
433	<
434	<
435	<
436	<
437	<
438	<	boolT ismalloc = False;
439	<	/* Clean up memory from previous convex hull calculations*/
440	<	Triangles_.clear();
441	<	surfaceSDs_.clear();
442	<	surfaceSDs_.reserve(Ns_);
443	<
444	<	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
445	<	const_cast<char *>(options_.c_str()), NULL, stderr)) {
446	<
447	<	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
448	<	painCave.isFatal = 0;
449	<	simError();
450	<
197	>	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
198	>	const_cast<char *>(options_.c_str()), NULL, stderr)){
199	>
200	>	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
201	>	painCave.isFatal = 1;
202	>	simError();
203	>
204		} //qh_new_qhull
205
206	<
207	<	#ifdef IS_MPI
208	<	std::vector<double> localPts;
209	<	int localPtArraySize;
210	<
211	<
212	<	std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
213	<
461	<
462	<	FORALLfacets {
206	>	#endif
207	>	intPoint = qh interior_point;
208	>	RealType calcvol = 0.0;
209	>	FORALLfacets {
210	>	Triangle face;
211	>	//Qhull sets the unit normal in facet->normal
212	>	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
213	>	face.setUnitNormal(V3dNormal);
214
215	<	if (!facet->simplicial){
216	<	// should never happen with Qt
466	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
467	<	painCave.isFatal = 0;
468	<	simError();
469	<	}
215	>	RealType faceArea = qh_facetarea(facet);
216	>	face.setArea(faceArea);
217
471	–
218		vertices = qh_facet3vertex(facet);
473	–	FOREACHvertex_(vertices){
474	–	id = qh_pointid(vertex->point);
475	–
476	–	if( !isSurfaceID[id] ){
477	–	isSurfaceID[id] = true;
478	–	}
479	–	}
480	–	qh_settempfree(&vertices);
219
220	<	} //FORALLfacets
220	>	coordT *center = qh_getcenter(vertices);
221	>	Vector3d V3dCentroid(center[0], center[1], center[2]);
222	>	face.setCentroid(V3dCentroid);
223
224	<
224	>	Vector3d faceVel = V3Zero;
225	>	Vector3d p[3];
226	>	RealType faceMass = 0.0;
227
228	<	/*
487	<	std::sort(surfaceIDs.begin(),surfaceIDs.end());
488	<	surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
489	<	int localPtArraySize = surfaceIDs.size() * 3;
490	<	*/
228	>	int ver = 0;
229
230	<	//localPts.resize(localPtArraySize);
231	<	//std::fill(localPts.begin(),localPts.end(),0.0);
230	>	FOREACHvertex_(vertices){
231	>	int id = qh_pointid(vertex->point);
232	>	p[ver][0] = vertex->point[0];
233	>	p[ver][1] = vertex->point[1];
234	>	p[ver][2] = vertex->point[2];
235	>	Vector3d vel;
236	>	RealType mass;
237
495	–
496	–	int idx = 0;
497	–	int nIsIts = 0;
498	–	/*
499	–	// Copy the surface points into an array.
500	–	for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
501	–	list_iter != isSurfaceID.end(); list_iter++)
502	–	{
503	–	bool isIt = *list_iter;
504	–	if (isIt){
505	–	localPts.push_back(ptArray[dim_ * idx]);
506	–	localPts.push_back(ptArray[dim_ * idx + 1]);
507	–	localPts.push_back(ptArray[dim_ * idx + 2]);
508	–	localPtsMap.push_back(idx);
509	–	nIsIts++;
510	–	} //Isit
511	–	idx++;
512	–	} //isSurfaceID
513	–	*/
514	–	FORALLvertices {
515	–	idx = qh_pointid(vertex->point);
516	–	localPts.push_back(ptArray[dim_ * idx]);
517	–	localPts.push_back(ptArray[dim_ * idx + 1]);
518	–	localPts.push_back(ptArray[dim_ * idx + 2]);
519	–	localPtsMap.push_back(idx);
520	–	}
521	–
522	–
523	–	localPtArraySize = localPts.size();
524	–
525	–
526	–	MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
527	–
528	–	Nsglobal_=0;
529	–	for (int i = 0; i < nproc_; i++){
530	–	Nsglobal_ += NstoProc_[i];
531	–	}
532	–
533	–
534	–	int nglobalPts = int(Nsglobal_/3);
535	–
536	–
537	–	std::vector<double> globalPts;
538	–	globalPts.resize(Nsglobal_);
539	–
540	–	isSurfaceID.resize(nglobalPts);
541	–
542	–
543	–	std::fill(globalPts.begin(),globalPts.end(),0.0);
544	–
545	–	displs_[0] = 0;
546	–	/* Build a displacements array */
547	–	for (int i = 1; i < nproc_; i++){
548	–	displs_[i] = displs_[i-1] + NstoProc_[i-1];
549	–	}
550	–
551	–
552	–	int noffset = displs_[myrank_];
553	–	/* gather the potential hull */
554	–
555	–	MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
556	–
557	–	/*
558	–	if (myrank_ == 0){
559	–	for (i = 0; i < globalPts.size(); i++){
560	–	std::cout << globalPts[i] << std::endl;
561	–	}
562	–	}
563	–	*/
564	–	// Free previous hull
565	–	qh_freeqhull(!qh_ALL);
566	–	qh_memfreeshort(&curlong, &totlong);
567	–	if (curlong || totlong)
568	–	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
569	–	<< totlong << curlong << std::endl;
570	–
571	–	if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
572	–	const_cast<char *>(options_.c_str()), NULL, stderr)){
573	–
574	–	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
575	–	painCave.isFatal = 1;
576	–	simError();
577	–
578	–	} //qh_new_qhull
579	–
580	–	#endif
581	–
582	–
583	–
584	–
585	–
586	–
587	–	unsigned int nf = qh num_facets;
588	–
589	–	/* Build Surface SD list first */
590	–
591	–	std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
592	–
593	–	FORALLfacets {
594	–
595	–	if (!facet->simplicial){
596	–	// should never happen with Qt
597	–	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
598	–	painCave.isFatal = 1;
599	–	simError();
600	–	} //simplicical
601	–
602	–	Triangle* face = new Triangle();
603	–	Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
604	–	face->setNormal(V3dNormal);
605	–	//face->setCentroid(V3dCentroid);
606	–	RealType faceArea = 0.5*V3dNormal.length();
607	–	//face->setArea(faceArea);
608	–
609	–
610	–	vertices = qh_facet3vertex(facet);
611	–	FOREACHvertex_(vertices){
612	–	id = qh_pointid(vertex->point);
613	–	int localindex = id;
238		#ifdef IS_MPI
239	<
240	<	if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
241	<	localindex = localPtsMap[id-noffset/3];
242	<	#endif
619	<	face->addVertex(bodydoubles[localindex]);
620	<	if( !isSurfaceID[id] ){
621	<	isSurfaceID[id] = true;
622	<	#ifdef IS_MPI
623	<
624	<	#endif
625	<
626	<	surfaceSDs_.push_back(bodydoubles[localindex]);
627	<
628	<	} //IF isSurfaceID
239	>	vel = Vector3d(globalVels[dim_ * id],
240	>	globalVels[dim_ * id + 1],
241	>	globalVels[dim_ * id + 2]);
242	>	mass = globalMasses[id];
243
244	<	#ifdef IS_MPI
245	<
632	<	}else{
633	<	face->addVertex(NULL);
634	<	}
635	<	#endif
636	<	} //Foreachvertex
244	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
245	>	// own this guy.
246
247	<	Triangles_.push_back(face);
639	<	qh_settempfree(&vertices);
640	<
641	<	} //FORALLfacets
247	>	int localID = id - displacements[myrank];
248
643	–
249
250	<	Ns_ = surfaceSDs_.size();
250	>	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
251	>	face.addVertexSD(bodydoubles[indexMap[localID]]);
252	>	}else{
253	>	face.addVertexSD(NULL);
254	>	}
255	>	#else
256	>	vel = bodydoubles[id]->getVel();
257	>	mass = bodydoubles[id]->getMass();
258	>	face.addVertexSD(bodydoubles[id]);
259	>	#endif
260	>	faceVel = faceVel + vel;
261	>	faceMass = faceMass + mass;
262	>	ver++;
263	>	} //Foreachvertex
264
265	+	face.addVertices(p[0], p[1], p[2]);
266	+	face.setFacetMass(faceMass);
267	+	face.setFacetVelocity(faceVel / RealType(3.0));
268	+	/*
269	+	RealType comparea = face.computeArea();
270	+	realT calcarea = qh_facetarea (facet);
271	+	Vector3d V3dCompNorm = -face.computeUnitNormal();
272	+	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
273	+	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
274	+	std::cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  std::endl;
275	+	calcvol +=  -dist*comparea/qh hull_dim;
276	+	*/
277	+	Triangles_.push_back(face);
278	+	qh_settempfree(&vertices);
279
280	+	} //FORALLfacets
281	+
282		qh_getarea(qh facet_list);
283		volume_ = qh totvol;
284		area_ = qh totarea;
285	<
652	<
653	<
285	>	//  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl;
286		qh_freeqhull(!qh_ALL);
287		qh_memfreeshort(&curlong, &totlong);
288	<	if (curlong || totlong)
289	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
290	<	<< totlong << curlong << std::endl;
291	<
292	<
293	<
288	>	if (curlong || totlong) {
289	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
290	>	"\tdid not free %d bytes of long memory (%d pieces)",
291	>	totlong, curlong);
292	>	painCave.isFatal = 1;
293	>	simError();
294	>	}
295		}
296
297	+	void ConvexHull::printHull(const std::string& geomFileName) {
298
299	<
300	<	void ConvexHull::printHull(const std::string& geomFileName)
301	<	{
668	<
299	>	#ifdef IS_MPI
300	>	if (worldRank == 0)  {
301	>	#endif
302		FILE *newGeomFile;
303
304		//create new .md file based on old .md file
#	Line 675 | Line 308 | void ConvexHull::printHull(const std::string& geomFile
308		qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
309
310		fclose(newGeomFile);
311	+	#ifdef IS_MPI
312	+	}
313	+	#endif
314		}
315		#endif //QHULL
680	–	#endif //CGAL
681	–
682	–
683	–

Comparing:
trunk/src/math/ConvexHull.cpp (property svn:keywords), Revision 1302 by chuckv, Tue Oct 7 17:12:48 2008 UTC vs.
branches/development/src/math/ConvexHull.cpp (property svn:keywords), Revision 1704 by gezelter, Tue Apr 24 20:40:04 2012 UTC

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