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root/OpenMD/trunk/src/math/ConvexHull.cpp

Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 1 | Line 1
1	<	/* Copyright (c) 2006 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 1.8 2008-09-14 01:32:25 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(){
173	<	//If we are doing the mpi version, set up some vectors for data communication
174	<	#ifdef IS_MPI
172	>	int count = coordsOnProc[myrank];
173	>
174	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
175	>	&coordsOnProc[0], &vectorDisplacements[0],
176	>	MPI::DOUBLE);
177
178	<
179	<	nproc_ = MPI::COMM_WORLD.Get_size();
180	<	myrank_ = MPI::COMM_WORLD.Get_rank();
151	<	NstoProc_ = new int[nproc_];
152	<	displs_   = new int[nproc_];
178	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
179	>	&coordsOnProc[0], &vectorDisplacements[0],
180	>	MPI::DOUBLE);
181
182	<	// Create a surface point type in MPI to send
183	<	surfacePtType = MPI::DOUBLE.Create_contiguous(3);
184	<	surfacePtType.Commit();
157	<
182	>	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
183	>	&globalMasses[0], &hullSitesOnProc[0],
184	>	&displacements[0], MPI::DOUBLE);
185
186	<	#endif
187	<	}
188	<
189	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
190	<	{
191	<
192	<	std::vector<Enriched_Point_3> points;
193	<	ptMapType myMap;
194	<	Point_iterator   hc;
168	<
169	<	// Copy the positon vector into a points vector for cgal.
170	<	std::vector<StuntDouble*>::iterator SD;
171	<
172	<	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
173	<	{
174	<	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;
184	<
185	<	// compute convex hull
186	<
187	<	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];
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		}
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	–	}
196
197	<	int noffset = displs_[myrank_];
198	<	/* gather the potential hull */
199	<
200	<
201	<	for (hc =polyhedron.points_begin();hc != polyhedron.points_end(); ++hc){
202	<	Point_3 mypoint = *hc;
203	<	surfacePt_ mpiSurfacePt;
204	<	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	<	}
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
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	–
206		#endif
207
208	+	intPoint = qh interior_point;
209	+	RealType calcvol = 0.0;
210	+	FORALLfacets {
211	+	Triangle face;
212	+	//Qhull sets the unit normal in facet->normal
213	+	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
214	+	face.setUnitNormal(V3dNormal);
215	+
216	+	RealType faceArea = qh_facetarea(facet);
217	+	face.setArea(faceArea);
218	+
219	+	vertices = qh_facet3vertex(facet);
220	+
221	+	coordT *center = qh_getcenter(vertices);
222	+	Vector3d V3dCentroid(center[0], center[1], center[2]);
223	+	face.setCentroid(V3dCentroid);
224
225	<
226	<	/* Loop over all of the surface triangles and build data structures for atoms and normals*/
227	<	Facet_iterator j;
263	<	area_ = 0;
264	<	for ( j = polyhedron.facets_begin(); j !=polyhedron.facets_end(); ++j) {
265	<	Halfedge_handle h = j->halfedge();
225	>	Vector3d faceVel = V3Zero;
226	>	Vector3d p[3];
227	>	RealType faceMass = 0.0;
228
229	<	Point_3 r0=h->vertex()->point();
268	<	Point_3 r1=h->next()->vertex()->point();
269	<	Point_3 r2=h->next()->next()->vertex()->point();
229	>	int ver = 0;
230
231	<	Point_3* pr0 = &r0;
232	<	Point_3* pr1 = &r1;
233	<	Point_3* pr2 = &r2;
234	<
235	<	Enriched_Point_3* er0 = static_cast<Enriched_Point_3*>(pr0);
236	<	Enriched_Point_3* er1 = static_cast<Enriched_Point_3*>(pr1);
237	<	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;
231	>	FOREACHvertex_(vertices){
232	>	int id = qh_pointid(vertex->point);
233	>	p[ver][0] = vertex->point[0];
234	>	p[ver][1] = vertex->point[1];
235	>	p[ver][2] = vertex->point[2];
236	>	Vector3d vel;
237	>	RealType mass;
238
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	–
363	–
364	–
365	–
366	–
367	–
368	–
369	–	#else
370	–	#ifdef HAVE_QHULL
371	–	/* Old options Qt Qu Qg QG0 FA */
372	–	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt  Qci Tcv Pp") {
373	–	//If we are doing the mpi version, set up some vectors for data communication
239		#ifdef IS_MPI
240	+	vel = Vector3d(globalVels[dim_ * id],
241	+	globalVels[dim_ * id + 1],
242	+	globalVels[dim_ * id + 2]);
243	+	mass = globalMasses[id];
244
245	+	// localID will be between 0 and hullSitesOnProc[myrank] if we
246	+	// own this guy.
247
248	<	nproc_ = MPI::COMM_WORLD.Get_size();
378	<	myrank_ = MPI::COMM_WORLD.Get_rank();
379	<	NstoProc_ = new int[nproc_];
380	<	displs_   = new int[nproc_];
248	>	int localID = id - displacements[myrank];
249
382	–	// Create a surface point type in MPI to send
383	–	surfacePtType = MPI::DOUBLE.Create_contiguous(3);
384	–	surfacePtType.Commit();
385	–
250
251	<	#endif
252	<	}
253	<
254	<
391	<
392	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
393	<	{
394	<
395	<	std::vector<int> surfaceIDs;
396	<	std::vector<int> surfaceIDsGlobal;
397	<	std::vector<int> localPtsMap;
398	<	int numpoints = bodydoubles.size();
399	<
400	<	//coordT* pt_array;
401	<	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<bool> isSurfaceID(numpoints);
418	<
419	<	// Copy the positon vector into a points vector for qhull.
420	<	std::vector<StuntDouble*>::iterator SD;
421	<	int i = 0;
422	<	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
423	<	{
424	<	Vector3d pos = (*SD)->getPos();
425	<
426	<	ptArray[dim_ * i] = pos.x();
427	<	ptArray[dim_ * i + 1] = pos.y();
428	<	ptArray[dim_ * i + 2] = pos.z();
429	<	i++;
430	<	}
431	<
432	<
433	<
434	<
435	<
436	<
437	<	boolT ismalloc = False;
438	<	Triangles_.clear();
439	<	surfaceSDs_.clear();
440	<
441	<	if (qh_new_qhull(dim_, numpoints, ptArray, ismalloc,
442	<	const_cast<char *>(options_.c_str()), NULL, stderr)) {
443	<
444	<	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
445	<	painCave.isFatal = 0;
446	<	simError();
447	<
448	<	} //qh_new_qhull
449	<
450	<
451	<	#ifdef IS_MPI
452	<	std::vector<double> localPts;
453	<	int localPtArraySize;
454	<
455	<	std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
456	<
457	<	FORALLfacets {
458	<
459	<	if (!facet->simplicial){
460	<	// should never happen with Qt
461	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
462	<	painCave.isFatal = 0;
463	<	simError();
464	<	}
465	<
466	<
467	<	vertices = qh_facet3vertex(facet);
468	<	FOREACHvertex_(vertices){
469	<	id = qh_pointid(vertex->point);
470	<
471	<	if( !isSurfaceID[id] ){
472	<	isSurfaceID[id] = true;
251	>	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
252	>	face.addVertexSD(bodydoubles[indexMap[localID]]);
253	>	}else{
254	>	face.addVertexSD(NULL);
255		}
256	<	}
257	<	qh_settempfree(&vertices);
258	<
259	<	} //FORALLfacets
256	>	#else
257	>	vel = bodydoubles[id]->getVel();
258	>	mass = bodydoubles[id]->getMass();
259	>	face.addVertexSD(bodydoubles[id]);
260	>	#endif
261	>	faceVel = faceVel + vel;
262	>	faceMass = faceMass + mass;
263	>	ver++;
264	>	} //Foreachvertex
265
266	<
267	<
268	<	/*
482	<	std::sort(surfaceIDs.begin(),surfaceIDs.end());
483	<	surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
484	<	int localPtArraySize = surfaceIDs.size() * 3;
485	<	*/
486	<
487	<	localPts.resize(localPtArraySize);
488	<	//  std::fill(localPts.begin(),globalPts.end(),0.0);
489	<
490	<
491	<	int idx = 0;
492	<	// Copy the surface points into an array.
493	<	for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
494	<	list_iter != isSurfaceID.end(); list_iter++)
495	<	{
496	<	bool isIt = *list_iter;
497	<	if (isIt){
498	<	localPts.push_back(ptArray[dim_ * idx]);
499	<	localPts.push_back(ptArray[dim_ * idx + 1]);
500	<	localPts.push_back(ptArray[dim_ * idx + 2]);
501	<	localPtsMap.push_back(idx);
502	<	} //Isit
503	<	idx++;
504	<	} //isSurfaceID
505	<
506	<
507	<	localPtArraySize = localPts.size();
508	<	MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
509	<
510	<	for (int i = 0; i < nproc_; i++){
511	<	Nsglobal_ += NstoProc_[i];
512	<	}
513	<
514	<	std::vector<double> globalPts;
515	<	globalPts.resize(Nsglobal_);
516	<	isSurfaceID.resize(int(Nsglobal_/3));
517	<	std::fill(globalPts.begin(),globalPts.end(),0.0);
518	<	/* Build a displacements array */
519	<	for (int i = 1; i < nproc_; i++){
520	<	displs_[i] = displs_[i-1] + NstoProc_[i-1];
521	<	}
522	<
523	<	int noffset = displs_[myrank_];
524	<	/* gather the potential hull */
525	<
526	<	MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],NstoProc_,displs_,MPI::DOUBLE);
527	<
528	<
529	<
530	<
531	<	// Free previous hull
532	<	qh_freeqhull(!qh_ALL);
533	<	qh_memfreeshort(&curlong, &totlong);
534	<	if (curlong || totlong)
535	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
536	<	<< totlong << curlong << std::endl;
537	<
538	<	if (qh_new_qhull(dim_, numpoints, &globalPts[0], ismalloc,
539	<	const_cast<char *>(options_.c_str()), NULL, stderr)){
540	<
541	<	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
542	<	painCave.isFatal = 0;
543	<	simError();
544	<
545	<	} //qh_new_qhull
546	<
547	<	#endif
548	<
549	<
550	<
551	<
552	<
553	<
554	<	unsigned int nf = qh num_facets;
555	<
556	<	/* Build Surface SD list first */
557	<
558	<	std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
559	<
560	<	FORALLfacets {
561	<
562	<	if (!facet->simplicial){
563	<	// should never happen with Qt
564	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
565	<	painCave.isFatal = 0;
566	<	simError();
567	<	} //simplicical
568	<
569	<	Triangle* face = new Triangle();
570	<	Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
571	<	face->setNormal(V3dNormal);
572	<	//face->setCentroid(V3dCentroid);
573	<	RealType faceArea = 0.5*V3dNormal.length();
574	<	face->setArea(faceArea);
575	<
576	<
577	<	vertices = qh_facet3vertex(facet);
578	<	FOREACHvertex_(vertices){
579	<	id = qh_pointid(vertex->point);
580	<	face->addVertex(bodydoubles[id]);
581	<	if( !isSurfaceID[id] ){
582	<	isSurfaceID[id] = true;
583	<	surfaceSDs_.push_back(bodydoubles[id]);
584	<	} //IF isSurfaceID
585	<	} //Foreachvertex
586	<
587	<
588	<	Triangles_.push_back(face);
589	<	qh_settempfree(&vertices);
590	<
591	<	} //FORALLfacets
592	<
593	<
594	<
595	<
266	>	face.addVertices(p[0], p[1], p[2]);
267	>	face.setFacetMass(faceMass);
268	>	face.setFacetVelocity(faceVel / RealType(3.0));
269		/*
270	<	std::sort(surfaceIDs.begin(),surfaceIDs.end());
271	<	surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
272	<	for(std::vector<int>::iterator list_iter = surfaceIDs.begin();
273	<	list_iter != surfaceIDs.end(); list_iter++)
274	<	{
275	<	int i = *list_iter;
276	<	surfaceSDs_.push_back(bodydoubles[i]);
604	<	}
270	>	RealType comparea = face.computeArea();
271	>	realT calcarea = qh_facetarea (facet);
272	>	Vector3d V3dCompNorm = -face.computeUnitNormal();
273	>	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
274	>	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
275	>	std::cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  std::endl;
276	>	calcvol +=  -dist*comparea/qh hull_dim;
277		*/
278	+	Triangles_.push_back(face);
279	+	qh_settempfree(&vertices);
280
281	<
282	<
609	<
610	<
611	<
612	<	Ns_ = surfaceSDs_.size();
613	<
614	<
281	>	} //FORALLfacets
282	>
283		qh_getarea(qh facet_list);
284		volume_ = qh totvol;
285		area_ = qh totarea;
286	<
619	<
620	<
286	>	//  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl;
287		qh_freeqhull(!qh_ALL);
288		qh_memfreeshort(&curlong, &totlong);
289	<	if (curlong || totlong)
290	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
291	<	<< totlong << curlong << std::endl;
292	<
293	<
294	<	// free(pt_array);
295	<
289	>	if (curlong || totlong) {
290	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
291	>	"\tdid not free %d bytes of long memory (%d pieces)",
292	>	totlong, curlong);
293	>	painCave.isFatal = 1;
294	>	simError();
295	>	}
296		}
297
298	+	void ConvexHull::printHull(const std::string& geomFileName) {
299
300	<
301	<	void ConvexHull::printHull(const std::string& geomFileName)
302	<	{
636	<
300	>	#ifdef IS_MPI
301	>	if (worldRank == 0)  {
302	>	#endif
303		FILE *newGeomFile;
304
305		//create new .md file based on old .md file
#	Line 643 | Line 309 | void ConvexHull::printHull(const std::string& geomFile
309		qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
310
311		fclose(newGeomFile);
312	+	#ifdef IS_MPI
313	+	}
314	+	#endif
315		}
316		#endif //QHULL
648	–	#endif //CGAL
649	–
650	–
651	–

Comparing trunk/src/math/ConvexHull.cpp (property svn:keywords):
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 | Line 1
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