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trunk/src/math/ConvexHull.cpp (file contents), Revision 1307 by chuckv, Mon Oct 20 19:36:32 2008 UTC vs.
branches/development/src/math/ConvexHull.cpp (file contents), Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 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 1.11 2008-10-20 19:36:32 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>
80	<	#include <CGAL/MP_Float.h>
81	<	//#include <CGAL/Lazy_exact_nt.h>
82	<
83	<
84	<
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;
95	<
96	<
97	<	typedef Polyhedron_3::HalfedgeDS             HalfedgeDS;
98	<	typedef Polyhedron_3::Facet_iterator                   Facet_iterator;
99	<	typedef Polyhedron_3::Halfedge_around_facet_circulator Halfedge_facet_circulator;
100	<	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;
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	<	class Enriched_Point_3 : public K::Point_3{
88	<	public:
89	<	Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
87	>	// Copy the positon vector into a points vector for qhull.
88	>	std::vector<StuntDouble*>::iterator SD;
89	>	int i = 0;
90
91	<	bool isMyPoint() const{ return yupMyPoint; }
92	<	void myPoint(){ yupMyPoint = true; }
93	<	void setSD(StuntDouble* SD){mySD = SD;}
94	<	StuntDouble* getStuntDouble(){return mySD;}
95	<	private:
96	<	bool yupMyPoint;
119	<	StuntDouble* mySD;
120	<
121	<	};
122	<
123	<
124	<
125	<
126	<
127	<	// compare Point_3's... used in setting up the STL map from points to indices
128	<	template <typename Pt3>
129	<	struct Point_3_comp {
130	<	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
91	>	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
92	>	Vector3d pos = (*SD)->getPos();
93	>	ptArray[dim_ * i] = pos.x();
94	>	ptArray[dim_ * i + 1] = pos.y();
95	>	ptArray[dim_ * i + 2] = pos.z();
96	>	i++;
97		}
98	<	};
98	>
99	>	/* Clean up memory from previous convex hull calculations */
100	>	boolT ismalloc = False;
101	>
102	>	/* compute the hull for our local points (or all the points for single
103	>	processor versions) */
104	>	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
105	>	const_cast<char *>(options_.c_str()), NULL, stderr)) {
106	>
107	>	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
108	>	painCave.isFatal = 1;
109	>	simError();
110	>
111	>	} //qh_new_qhull
112
135	–	// coordinate-based hashing inefficient but can we do better if pts are copied?
136	–	typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
113
114		#ifdef IS_MPI
139	–	struct {
140	–	double x,y,z;
141	–	} surfacePt;
142	–	#endif
143	–
144	–	ConvexHull::ConvexHull() : Hull(){
115		//If we are doing the mpi version, set up some vectors for data communication
116	<	#ifdef IS_MPI
116	>
117	>	int nproc = MPI::COMM_WORLD.Get_size();
118	>	int myrank = MPI::COMM_WORLD.Get_rank();
119	>	int localHullSites = 0;
120
121	+	std::vector<int> hullSitesOnProc(nproc, 0);
122	+	std::vector<int> coordsOnProc(nproc, 0);
123	+	std::vector<int> displacements(nproc, 0);
124	+	std::vector<int> vectorDisplacements(nproc, 0);
125
126	<	nproc_ = MPI::COMM_WORLD.Get_size();
127	<	myrank_ = MPI::COMM_WORLD.Get_rank();
128	<	NstoProc_ = new int[nproc_];
129	<	displs_   = new int[nproc_];
126	>	std::vector<double> coords;
127	>	std::vector<double> vels;
128	>	std::vector<int> indexMap;
129	>	std::vector<double> masses;
130
131	<	// Create a surface point type in MPI to send
132	<	surfacePtType = MPI::DOUBLE.Create_contiguous(3);
133	<	surfacePtType.Commit();
134	<
131	>	FORALLvertices{
132	>	localHullSites++;
133	>
134	>	int idx = qh_pointid(vertex->point);
135
136	<	#endif
160	<	}
136	>	indexMap.push_back(idx);
137
138	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
139	<	{
140	<
165	<	std::vector<Enriched_Point_3> points;
166	<	ptMapType myMap;
167	<	Point_iterator   hc;
168	<
169	<	// Copy the positon vector into a points vector for cgal.
170	<	std::vector<StuntDouble*>::iterator SD;
138	>	coords.push_back(ptArray[dim_  * idx]);
139	>	coords.push_back(ptArray[dim_  * idx + 1]);
140	>	coords.push_back(ptArray[dim_  * idx + 2]);
141
142	<	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;
142	>	StuntDouble* sd = bodydoubles[idx];
143
144	<	// compute convex hull
145	<
146	<	std::vector<Enriched_Point_3>::iterator testpt;
147	<
189	<
190	<
191	<	CGAL::convex_hull_3(points.begin(), points.end(), polyhedron);
192	<
193	<
194	<
195	<	Ns_ = polyhedron.size_of_vertices();
144	>	Vector3d vel = sd->getVel();
145	>	vels.push_back(vel.x());
146	>	vels.push_back(vel.y());
147	>	vels.push_back(vel.z());
148
149	<	#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];
149	>	masses.push_back(sd->getMass());
150		}
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);
151
152	<	/* Build a displacements array */
153	<	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	<	}
152	>	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
153	>	1, MPI::INT);
154
155	<	MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,displs_,surfacePtType);
156	<	std::vector<surfacePt_>::iterator spt;
157	<	std::vector<Enriched_Point_3> gblpoints;
158	<
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	<
155	>	int globalHullSites = 0;
156	>	for (int iproc = 0; iproc < nproc; iproc++){
157	>	globalHullSites += hullSitesOnProc[iproc];
158	>	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
159		}
299	–
300	–	std::cout << "Number of surface atoms is: " << Ns_ << std::endl;
301	–
160
161	<
162	<	}
305	<	void ConvexHull::printHull(const std::string& geomFileName)
306	<	{
307	<	/*
308	<	std::ofstream newGeomFile;
161	>	displacements[0] = 0;
162	>	vectorDisplacements[0] = 0;
163
164	<	//create new .md file based on old .md file
165	<	newGeomFile.open("testhull.off");
166	<
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;
164	>	for (int iproc = 1; iproc < nproc; iproc++){
165	>	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
166	>	vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
167		}
329	–
330	–	newGeomFile.close();
331	–	*/
332	–	/*
333	–	std::ofstream newGeomFile;
168
169	<	//create new .md file based on old .md file
170	<	newGeomFile.open(geomFileName.c_str());
169	>	std::vector<double> globalCoords(dim_ * globalHullSites);
170	>	std::vector<double> globalVels(dim_ * globalHullSites);
171	>	std::vector<double> globalMasses(globalHullSites);
172
173	<	// 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	<	/* More old opts Qc Qi Pp*/
373	<	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200), nTriangles_(0) {
374	<	//If we are doing the mpi version, set up some vectors for data communication
375	<	#ifdef IS_MPI
376	<
377	<
378	<	nproc_ = MPI::COMM_WORLD.Get_size();
379	<	myrank_ = MPI::COMM_WORLD.Get_rank();
380	<	NstoProc_ = new int[nproc_];
381	<	displs_   = new int[nproc_];
382	<
383	<	// Create a surface point type in MPI to send
384	<	//surfacePtType = MPI::DOUBLE.Create_contiguous(3);
385	<	// surfacePtType.Commit();
386	<
387	<
388	<	#endif
389	<	}
390	<
391	<
392	<
393	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
394	<	{
173	>	int count = coordsOnProc[myrank];
174
175	<	std::vector<int> surfaceIDs;
176	<	std::vector<int> surfaceIDsGlobal;
177	<	std::vector<int> localPtsMap;
399	<	int numpoints = bodydoubles.size();
175	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
176	>	&coordsOnProc[0], &vectorDisplacements[0],
177	>	MPI::DOUBLE);
178
179	<	//coordT* pt_array;
180	<	coordT* surfpt_array;
181	<	vertexT *vertex, **vertexp;
404	<	facetT *facet;
405	<	setT *vertices;
406	<	int curlong,totlong;
407	<	int id;
408	<
409	<	coordT *point,**pointp;
179	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
180	>	&coordsOnProc[0], &vectorDisplacements[0],
181	>	MPI::DOUBLE);
182
183	+	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
184	+	&globalMasses[0], &hullSitesOnProc[0],
185	+	&displacements[0], MPI::DOUBLE);
186
187	<	FILE *outdummy = NULL;
188	<	FILE *errdummy = NULL;
187	>	// Free previous hull
188	>	qh_freeqhull(!qh_ALL);
189	>	qh_memfreeshort(&curlong, &totlong);
190	>	if (curlong || totlong) {
191	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
192	>	"\tdid not free %d bytes of long memory (%d pieces)",
193	>	totlong, curlong);
194	>	painCave.isFatal = 1;
195	>	simError();
196	>	}
197
198	<	//pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
199	<
200	<	//  double* ptArray = new double[numpoints * 3];
201	<	std::vector<double> ptArray(numpoints*3);
202	<	std::vector<bool> isSurfaceID(numpoints);
203	<
204	<	// Copy the positon vector into a points vector for qhull.
422	<	std::vector<StuntDouble*>::iterator SD;
423	<	int i = 0;
424	<	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
425	<	{
426	<	Vector3d pos = (*SD)->getPos();
427	<
428	<	ptArray[dim_ * i] = pos.x();
429	<	ptArray[dim_ * i + 1] = pos.y();
430	<	ptArray[dim_ * i + 2] = pos.z();
431	<	i++;
432	<	}
433	<
434	<
435	<
436	<
437	<
438	<
439	<	boolT ismalloc = False;
440	<	/* Clean up memory from previous convex hull calculations*/
441	<	Triangles_.clear();
442	<	surfaceSDs_.clear();
443	<	surfaceSDs_.reserve(Ns_);
444	<
445	<	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
446	<	const_cast<char *>(options_.c_str()), NULL, stderr)) {
447	<
448	<	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
449	<	painCave.isFatal = 1;
450	<	simError();
451	<
198	>	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
199	>	const_cast<char *>(options_.c_str()), NULL, stderr)){
200	>
201	>	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
202	>	painCave.isFatal = 1;
203	>	simError();
204	>
205		} //qh_new_qhull
206
207	<
208	<	#ifdef IS_MPI
209	<	std::vector<double> localPts;
210	<	std::vector<double> localVel;
211	<	int localPtArraySize;
212	<
213	<
214	<	std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
215	<
463	<
464	<	FORALLfacets {
207	>	#endif
208	>	// commented out below, so comment out here also.
209	>	// intPoint = qh interior_point;
210	>	// RealType calcvol = 0.0;
211	>	FORALLfacets {
212	>	Triangle face;
213	>	//Qhull sets the unit normal in facet->normal
214	>	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
215	>	face.setUnitNormal(V3dNormal);
216
217	<	if (!facet->simplicial){
218	<	// should never happen with Qt
468	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
469	<	painCave.isFatal = 1;
470	<	simError();
471	<	}
217	>	RealType faceArea = qh_facetarea(facet);
218	>	face.setArea(faceArea);
219
473	–
220		vertices = qh_facet3vertex(facet);
475	–	FOREACHvertex_(vertices){
476	–	id = qh_pointid(vertex->point);
477	–
478	–	if( !isSurfaceID[id] ){
479	–	isSurfaceID[id] = true;
480	–	}
481	–	}
482	–	qh_settempfree(&vertices);
221
222	<	} //FORALLfacets
222	>	coordT *center = qh_getcenter(vertices);
223	>	Vector3d V3dCentroid(center[0], center[1], center[2]);
224	>	face.setCentroid(V3dCentroid);
225
226	<
226	>	Vector3d faceVel = V3Zero;
227	>	Vector3d p[3];
228	>	RealType faceMass = 0.0;
229
230	<	/*
489	<	std::sort(surfaceIDs.begin(),surfaceIDs.end());
490	<	surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
491	<	int localPtArraySize = surfaceIDs.size() * 3;
492	<	*/
230	>	int ver = 0;
231
232	<	//localPts.resize(localPtArraySize);
233	<	//std::fill(localPts.begin(),localPts.end(),0.0);
232	>	FOREACHvertex_(vertices){
233	>	int id = qh_pointid(vertex->point);
234	>	p[ver][0] = vertex->point[0];
235	>	p[ver][1] = vertex->point[1];
236	>	p[ver][2] = vertex->point[2];
237	>	Vector3d vel;
238	>	RealType mass;
239
240	+	#ifdef IS_MPI
241	+	vel = Vector3d(globalVels[dim_ * id],
242	+	globalVels[dim_ * id + 1],
243	+	globalVels[dim_ * id + 2]);
244	+	mass = globalMasses[id];
245
246	<	int idx = 0;
247	<	int nIsIts = 0;
500	<	/*
501	<	// Copy the surface points into an array.
502	<	for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
503	<	list_iter != isSurfaceID.end(); list_iter++)
504	<	{
505	<	bool isIt = *list_iter;
506	<	if (isIt){
507	<	localPts.push_back(ptArray[dim_ * idx]);
508	<	localPts.push_back(ptArray[dim_ * idx + 1]);
509	<	localPts.push_back(ptArray[dim_ * idx + 2]);
510	<	localPtsMap.push_back(idx);
511	<	nIsIts++;
512	<	} //Isit
513	<	idx++;
514	<	} //isSurfaceID
515	<	*/
516	<	FORALLvertices {
517	<	idx = qh_pointid(vertex->point);
518	<	localPts.push_back(ptArray[dim_ * idx]);
519	<	localPts.push_back(ptArray[dim_ * idx + 1]);
520	<	localPts.push_back(ptArray[dim_ * idx + 2]);
246	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
247	>	// own this guy.
248
249	<	Vector3d vel = bodydoubles[idx]->getVel();
523	<	localVel.push_back(vel.x());
524	<	localVel.push_back(vel.y());
525	<	localVel.push_back(vel.z());
249	>	int localID = id - displacements[myrank];
250
527	–	localPtsMap.push_back(idx);
528	–	}
251
252	+	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
253	+	face.addVertexSD(bodydoubles[indexMap[localID]]);
254	+	}else{
255	+	face.addVertexSD(NULL);
256	+	}
257	+	#else
258	+	vel = bodydoubles[id]->getVel();
259	+	mass = bodydoubles[id]->getMass();
260	+	face.addVertexSD(bodydoubles[id]);
261	+	#endif
262	+	faceVel = faceVel + vel;
263	+	faceMass = faceMass + mass;
264	+	ver++;
265	+	} //Foreachvertex
266
267	<	localPtArraySize = localPts.size();
267	>	face.addVertices(p[0], p[1], p[2]);
268	>	face.setFacetMass(faceMass);
269	>	face.setFacetVelocity(faceVel / RealType(3.0));
270	>	/*
271	>	RealType comparea = face.computeArea();
272	>	realT calcarea = qh_facetarea (facet);
273	>	Vector3d V3dCompNorm = -face.computeUnitNormal();
274	>	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
275	>	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
276	>	std::cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  std::endl;
277	>	calcvol +=  -dist*comparea/qh hull_dim;
278	>	*/
279	>	Triangles_.push_back(face);
280	>	qh_settempfree(&vertices);
281
282	<
534	<	MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
535	<
536	<	Nsglobal_=0;
537	<	for (int i = 0; i < nproc_; i++){
538	<	Nsglobal_ += NstoProc_[i];
539	<	}
282	>	} //FORALLfacets
283
284	<
285	<	int nglobalPts = int(Nsglobal_/3);
286	<
287	<
545	<	std::vector<double> globalPts(Nsglobal_);
546	<	std::vector<double> globalVel(Nsglobal_);
547	<
548	<	isSurfaceID.resize(nglobalPts);
549	<
550	<
551	<	std::fill(globalPts.begin(),globalPts.end(),0.0);
552	<
553	<	displs_[0] = 0;
554	<	/* Build a displacements array */
555	<	for (int i = 1; i < nproc_; i++){
556	<	displs_[i] = displs_[i-1] + NstoProc_[i-1];
557	<	}
558	<
559	<
560	<	int noffset = displs_[myrank_];
561	<	/* gather the potential hull */
562	<
563	<	MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
564	<	MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize,MPI::DOUBLE,&globalVel[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
565	<
566	<	/*
567	<	if (myrank_ == 0){
568	<	for (i = 0; i < globalPts.size(); i++){
569	<	std::cout << globalPts[i] << std::endl;
570	<	}
571	<	}
572	<	*/
573	<	// Free previous hull
284	>	qh_getarea(qh facet_list);
285	>	volume_ = qh totvol;
286	>	area_ = qh totarea;
287	>	//  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl;
288		qh_freeqhull(!qh_ALL);
289		qh_memfreeshort(&curlong, &totlong);
290	<	if (curlong || totlong)
291	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
292	<	<< totlong << curlong << std::endl;
290	>	if (curlong || totlong) {
291	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
292	>	"\tdid not free %d bytes of long memory (%d pieces)",
293	>	totlong, curlong);
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	}
298
299	<	if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
581	<	const_cast<char *>(options_.c_str()), NULL, stderr)){
299	>	void ConvexHull::printHull(const std::string& geomFileName) {
300
583	–	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
584	–	painCave.isFatal = 1;
585	–	simError();
586	–
587	–	} //qh_new_qhull
588	–
589	–	#endif
590	–
591	–
592	–
593	–
594	–
595	–
596	–	unsigned int nf = qh num_facets;
597	–
598	–	/* Build Surface SD list first */
599	–
600	–	std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
601	–
602	–	FORALLfacets {
603	–
604	–	if (!facet->simplicial){
605	–	// should never happen with Qt
606	–	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
607	–	painCave.isFatal = 1;
608	–	simError();
609	–	} //simplicical
610	–
611	–	Triangle* face = new Triangle();
612	–	Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
613	–	face->setNormal(V3dNormal);
614	–
615	–
616	–
617	–	RealType faceArea = 0.5*V3dNormal.length();
618	–	face->setArea(faceArea);
619	–
620	–
621	–	vertices = qh_facet3vertex(facet);
622	–
623	–	coordT *center = qh_getcenter(vertices);
624	–	Vector3d V3dCentroid(center[0], center[1], center[2]);
625	–	face->setCentroid(V3dCentroid);
626	–	Vector3d faceVel = V3Zero;
627	–	FOREACHvertex_(vertices){
628	–	id = qh_pointid(vertex->point);
629	–	int localindex = id;
301		#ifdef IS_MPI
302	<	Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 1]);
632	<	faceVel = faceVel + velVector;
633	<	if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
634	<	localindex = localPtsMap[id-noffset/3];
635	<	#else
636	<	faceVel = faceVel + bodydoubles[localindex]->getVel();
302	>	if (worldRank == 0)  {
303		#endif
638	–	face->addVertex(bodydoubles[localindex]);
639	–	if( !isSurfaceID[id] ){
640	–	isSurfaceID[id] = true;
641	–	#ifdef IS_MPI
642	–
643	–	#endif
644	–
645	–	surfaceSDs_.push_back(bodydoubles[localindex]);
646	–
647	–	} //IF isSurfaceID
648	–
649	–	#ifdef IS_MPI
650	–
651	–	}else{
652	–	face->addVertex(NULL);
653	–	}
654	–	#endif
655	–	} //Foreachvertex
656	–	/*
657	–	if (!SETempty_(facet->coplanarset)){
658	–	FOREACHpoint_(facet->coplanarset){
659	–	id = qh_pointid(point);
660	–	surfaceSDs_.push_back(bodydoubles[id]);
661	–	}
662	–	}
663	–	*/
664	–	face->setFacetVelocity(faceVel/3.0);
665	–	Triangles_.push_back(face);
666	–	qh_settempfree(&vertices);
667	–
668	–	} //FORALLfacets
669	–
670	–	/*
671	–	std::cout << surfaceSDs_.size() << std::endl;
672	–	for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
673	–	Vector3d thisatom = (*SD)->getPos();
674	–	std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
675	–	}
676	–	*/
677	–
678	–
679	–
680	–	Ns_ = surfaceSDs_.size();
681	–	nTriangles_ = Triangles_.size();
682	–
683	–	qh_getarea(qh facet_list);
684	–	volume_ = qh totvol;
685	–	area_ = qh totarea;
686	–
687	–
688	–
689	–	qh_freeqhull(!qh_ALL);
690	–	qh_memfreeshort(&curlong, &totlong);
691	–	if (curlong || totlong)
692	–	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
693	–	<< totlong << curlong << std::endl;
694	–
695	–
696	–
697	–	}
698	–
699	–
700	–
701	–	void ConvexHull::printHull(const std::string& geomFileName)
702	–	{
703	–
304		FILE *newGeomFile;
305
306		//create new .md file based on old .md file
#	Line 710 | Line 310 | void ConvexHull::printHull(const std::string& geomFile
310		qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
311
312		fclose(newGeomFile);
313	+	#ifdef IS_MPI
314	+	}
315	+	#endif
316		}
317		#endif //QHULL
715	–	#endif //CGAL
716	–
717	–
718	–

Comparing:
trunk/src/math/ConvexHull.cpp (property svn:keywords), Revision 1307 by chuckv, Mon Oct 20 19:36:32 2008 UTC vs.
branches/development/src/math/ConvexHull.cpp (property svn:keywords), Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

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