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

Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1304 by chuckv, Wed Oct 15 18:26:01 2008 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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, 234107 (2008).
38	+	* [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
39	+	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
40		*
41		*  ConvexHull.cpp
42		*
43	<	*  Purpose: To calculate convexhull, hull volume libqhull.
44	<	*
45	<	*  Created by Charles F. Vardeman II on 11 Dec 2006.
46	<	*  @author  Charles F. Vardeman II
47	<	*  @version $Id: ConvexHull.cpp,v 1.10 2008-10-15 18:26:01 chuckv Exp $
48	<	*
43	>	*  Purpose: To calculate a convex hull.
44		*/
45
46	+	#ifdef IS_MPI
47	+	#include <mpi.h>
48	+	#endif
49	+
50		/* Standard includes independent of library */
51	+
52		#include <iostream>
53		#include <fstream>
54		#include <list>
#	Line 57 | Line 57
57		#include "math/ConvexHull.hpp"
58		#include "utils/simError.h"
59
60	+	#include "math/qhull.hpp"
61
62	<	using namespace oopse;
62	>	#ifdef HAVE_QHULL
63	>	using namespace OpenMD;
64	>	using namespace std;
65
66	<	/* CGAL version of convex hull first then QHULL */
67	<	#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>
66	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") {
67	>	}
68
69	+	void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) {
70	+
71	+	int numpoints = bodydoubles.size();
72	+
73	+	Triangles_.clear();
74	+
75	+	vertexT *vertex, **vertexp;
76	+	facetT *facet;
77	+	setT *vertices;
78	+	int curlong, totlong;
79
80	<	//#include <CGAL/Quotient.h>
80	<	#include <CGAL/MP_Float.h>
81	<	//#include <CGAL/Lazy_exact_nt.h>
80	>	vector<double> ptArray(numpoints*dim_);
81
82	<
83	<
84	<	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;
82	>	// Copy the positon vector into a points vector for qhull.
83	>	vector<StuntDouble*>::iterator SD;
84	>	int i = 0;
85
86	<
87	<
88	<	class Enriched_Point_3 : public K::Point_3{
89	<	public:
90	<	Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
91	<
113	<	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;
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
86	>	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
87	>	Vector3d pos = (*SD)->getPos();
88	>	ptArray[dim_ * i] = pos.x();
89	>	ptArray[dim_ * i + 1] = pos.y();
90	>	ptArray[dim_ * i + 2] = pos.z();
91	>	i++;
92		}
93	<	};
93	>
94	>	/* Clean up memory from previous convex hull calculations */
95	>	boolT ismalloc = False;
96	>
97	>	/* compute the hull for our local points (or all the points for single
98	>	processor versions) */
99	>	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
100	>	const_cast<char *>(options_.c_str()), NULL, stderr)) {
101	>
102	>	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
103	>	painCave.isFatal = 1;
104	>	simError();
105	>
106	>	} //qh_new_qhull
107
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;
108
109		#ifdef IS_MPI
139	–	struct {
140	–	double x,y,z;
141	–	} surfacePt;
142	–	#endif
143	–
144	–	ConvexHull::ConvexHull() : Hull(){
110		//If we are doing the mpi version, set up some vectors for data communication
111	<	#ifdef IS_MPI
111	>
112	>	int nproc;
113	>	int myrank;
114	>
115	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
116	>	MPI_Comm_rank( MPI_COMM_WORLD, &myrank);
117
118	+	int localHullSites = 0;
119
120	<	nproc_ = MPI::COMM_WORLD.Get_size();
121	<	myrank_ = MPI::COMM_WORLD.Get_rank();
122	<	NstoProc_ = new int[nproc_];
123	<	displs_   = new int[nproc_];
120	>	vector<int> hullSitesOnProc(nproc, 0);
121	>	vector<int> coordsOnProc(nproc, 0);
122	>	vector<int> displacements(nproc, 0);
123	>	vector<int> vectorDisplacements(nproc, 0);
124
125	<	// Create a surface point type in MPI to send
126	<	surfacePtType = MPI::DOUBLE.Create_contiguous(3);
127	<	surfacePtType.Commit();
128	<
125	>	vector<double> coords;
126	>	vector<double> vels;
127	>	vector<int> indexMap;
128	>	vector<double> masses;
129
130	<	#endif
131	<	}
130	>	FORALLvertices{
131	>	localHullSites++;
132	>
133	>	int idx = qh_pointid(vertex->point);
134
135	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
163	<	{
164	<
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;
135	>	indexMap.push_back(idx);
136
137	<	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
138	<	{
139	<	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	<
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	<
195	<	Ns_ = polyhedron.size_of_vertices();
141	>	StuntDouble* sd = bodydoubles[idx];
142
143	<	#ifdef IS_MPI
144	<	/* Gather an array of the number of verticies on each processor */
145	<
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	<	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];
148	>	masses.push_back(sd->getMass());
149		}
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);
150
151	<	/* Build a displacements array */
152	<	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	<	}
151	>	MPI_Allgather(&localHullSites, 1, MPI_INT, &hullSitesOnProc[0],
152	>	1, MPI_INT, MPI_COMM_WORLD);
153
154	<	MPI::COMM_WORLD.Allgatherv(&surfacePtsLocal_[0],Ns_,surfacePtType,&surfacePtsGlobal_[0],NstoProc_,displs_,surfacePtType);
155	<	std::vector<surfacePt_>::iterator spt;
156	<	std::vector<Enriched_Point_3> gblpoints;
157	<
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	<
154	>	int globalHullSites = 0;
155	>	for (int iproc = 0; iproc < nproc; iproc++){
156	>	globalHullSites += hullSitesOnProc[iproc];
157	>	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
158		}
299	–
300	–	std::cout << "Number of surface atoms is: " << Ns_ << std::endl;
301	–
159
160	<
161	<	}
305	<	void ConvexHull::printHull(const std::string& geomFileName)
306	<	{
307	<	/*
308	<	std::ofstream newGeomFile;
160	>	displacements[0] = 0;
161	>	vectorDisplacements[0] = 0;
162
163	<	//create new .md file based on old .md file
164	<	newGeomFile.open("testhull.off");
165	<
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;
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		}
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	–
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) {
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	–
167
168	+	vector<double> globalCoords(dim_ * globalHullSites);
169	+	vector<double> globalVels(dim_ * globalHullSites);
170	+	vector<double> globalMasses(globalHullSites);
171
172	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
394	<	{
172	>	int count = coordsOnProc[myrank];
173
174	<	std::vector<int> surfaceIDs;
175	<	std::vector<int> surfaceIDsGlobal;
176	<	std::vector<int> localPtsMap;
399	<	int numpoints = bodydoubles.size();
400	<
401	<	//coordT* pt_array;
402	<	coordT* surfpt_array;
403	<	vertexT *vertex, **vertexp;
404	<	facetT *facet;
405	<	setT *vertices;
406	<	int curlong,totlong;
407	<	int id;
174	>	MPI_Allgatherv(&coords[0], count, MPI_DOUBLE, &globalCoords[0],
175	>	&coordsOnProc[0], &vectorDisplacements[0],
176	>	MPI_DOUBLE, MPI_COMM_WORLD);
177
178	<	coordT *point,**pointp;
179	<
180	<
412	<	FILE *outdummy = NULL;
413	<	FILE *errdummy = NULL;
178	>	MPI_Allgatherv(&vels[0], count, MPI_DOUBLE, &globalVels[0],
179	>	&coordsOnProc[0], &vectorDisplacements[0],
180	>	MPI_DOUBLE, MPI_COMM_WORLD);
181
182	<	//pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
183	<
184	<	//  double* ptArray = new double[numpoints * 3];
418	<	std::vector<double> ptArray(numpoints*3);
419	<	std::vector<bool> isSurfaceID(numpoints);
420	<
421	<	// 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	<	}
182	>	MPI_Allgatherv(&masses[0], localHullSites, MPI_DOUBLE,
183	>	&globalMasses[0], &hullSitesOnProc[0],
184	>	&displacements[0], MPI_DOUBLE, MPI_COMM_WORLD);
185
186	<
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	<
198	<
199	<
200	<	boolT ismalloc = False;
201	<	/* Clean up memory from previous convex hull calculations*/
202	<	Triangles_.clear();
203	<	surfaceSDs_.clear();
204	<	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 = 0;
450	<	simError();
451	<
197	>	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
198	>	const_cast<char *>(options_.c_str()), NULL, stderr)){
199	>
200	>	sprintf(painCave.errMsg,
201	>	"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	<	int localPtArraySize;
207	>	#endif
208	>	// commented out below, so comment out here also.
209	>	// intPoint = qh interior_point;
210	>	// RealType calcvol = 0.0;
211
212	<
460	<	std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
461	<
212	>	qh_triangulate ();
213
214	<	FORALLfacets {
214	>	FORALLfacets {
215	>	Triangle face;
216	>	//Qhull sets the unit normal in facet->normal
217	>	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
218	>	face.setUnitNormal(V3dNormal);
219
220	<	if (!facet->simplicial){
221	<	// should never happen with Qt
467	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
468	<	painCave.isFatal = 0;
469	<	simError();
470	<	}
220	>	RealType faceArea = qh_facetarea(facet);
221	>	face.setArea(faceArea);
222
472	–
223		vertices = qh_facet3vertex(facet);
474	–	FOREACHvertex_(vertices){
475	–	id = qh_pointid(vertex->point);
476	–
477	–	if( !isSurfaceID[id] ){
478	–	isSurfaceID[id] = true;
479	–	}
480	–	}
481	–	qh_settempfree(&vertices);
224
225	<	} //FORALLfacets
225	>	coordT *center = qh_getcenter(vertices);
226	>	Vector3d V3dCentroid(center[0], center[1], center[2]);
227	>	face.setCentroid(V3dCentroid);
228
229	<
229	>	Vector3d faceVel = V3Zero;
230	>	Vector3d p[3];
231	>	RealType faceMass = 0.0;
232
233	<	/*
488	<	std::sort(surfaceIDs.begin(),surfaceIDs.end());
489	<	surfaceIDs.erase(std::unique(surfaceIDs.begin(), surfaceIDs.end()), surfaceIDs.end());
490	<	int localPtArraySize = surfaceIDs.size() * 3;
491	<	*/
233	>	int ver = 0;
234
235	<	//localPts.resize(localPtArraySize);
236	<	//std::fill(localPts.begin(),localPts.end(),0.0);
235	>	FOREACHvertex_(vertices){
236	>	int id = qh_pointid(vertex->point);
237	>	p[ver][0] = vertex->point[0];
238	>	p[ver][1] = vertex->point[1];
239	>	p[ver][2] = vertex->point[2];
240	>	Vector3d vel;
241	>	RealType mass;
242
243	+	#ifdef IS_MPI
244	+	vel = Vector3d(globalVels[dim_ * id],
245	+	globalVels[dim_ * id + 1],
246	+	globalVels[dim_ * id + 2]);
247	+	mass = globalMasses[id];
248
249	<	int idx = 0;
250	<	int nIsIts = 0;
499	<	/*
500	<	// Copy the surface points into an array.
501	<	for(std::vector<bool>::iterator list_iter = isSurfaceID.begin();
502	<	list_iter != isSurfaceID.end(); list_iter++)
503	<	{
504	<	bool isIt = *list_iter;
505	<	if (isIt){
506	<	localPts.push_back(ptArray[dim_ * idx]);
507	<	localPts.push_back(ptArray[dim_ * idx + 1]);
508	<	localPts.push_back(ptArray[dim_ * idx + 2]);
509	<	localPtsMap.push_back(idx);
510	<	nIsIts++;
511	<	} //Isit
512	<	idx++;
513	<	} //isSurfaceID
514	<	*/
515	<	FORALLvertices {
516	<	idx = qh_pointid(vertex->point);
517	<	localPts.push_back(ptArray[dim_ * idx]);
518	<	localPts.push_back(ptArray[dim_ * idx + 1]);
519	<	localPts.push_back(ptArray[dim_ * idx + 2]);
520	<	localPtsMap.push_back(idx);
521	<	}
249	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
250	>	// own this guy.
251
252	+	int localID = id - displacements[myrank];
253
524	–	localPtArraySize = localPts.size();
254
255	<
256	<	MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
255	>	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
256	>	face.addVertexSD(bodydoubles[indexMap[localID]]);
257	>	}else{
258	>	face.addVertexSD(NULL);
259	>	}
260	>	#else
261	>	vel = bodydoubles[id]->getVel();
262	>	mass = bodydoubles[id]->getMass();
263	>	face.addVertexSD(bodydoubles[id]);
264	>	#endif
265	>	faceVel = faceVel + vel;
266	>	faceMass = faceMass + mass;
267	>	ver++;
268	>	} //Foreachvertex
269
270	<	Nsglobal_=0;
271	<	for (int i = 0; i < nproc_; i++){
272	<	Nsglobal_ += NstoProc_[i];
273	<	}
274	<
275	<
276	<	int nglobalPts = int(Nsglobal_/3);
277	<
270	>	face.addVertices(p[0], p[1], p[2]);
271	>	face.setFacetMass(faceMass);
272	>	face.setFacetVelocity(faceVel / RealType(3.0));
273	>	/*
274	>	RealType comparea = face.computeArea();
275	>	realT calcarea = qh_facetarea (facet);
276	>	Vector3d V3dCompNorm = -face.computeUnitNormal();
277	>	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
278	>	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
279	>	cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  endl;
280	>	calcvol +=  -dist*comparea/qh hull_dim;
281	>	*/
282	>	Triangles_.push_back(face);
283	>	qh_settempfree(&vertices);
284
285	<	std::vector<double> globalPts;
539	<	globalPts.resize(Nsglobal_);
540	<
541	<	isSurfaceID.resize(nglobalPts);
542	<
543	<
544	<	std::fill(globalPts.begin(),globalPts.end(),0.0);
545	<
546	<	displs_[0] = 0;
547	<	/* Build a displacements array */
548	<	for (int i = 1; i < nproc_; i++){
549	<	displs_[i] = displs_[i-1] + NstoProc_[i-1];
550	<	}
285	>	} //FORALLfacets
286
287	<
288	<	int noffset = displs_[myrank_];
289	<	/* gather the potential hull */
290	<
556	<	MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
557	<
558	<	/*
559	<	if (myrank_ == 0){
560	<	for (i = 0; i < globalPts.size(); i++){
561	<	std::cout << globalPts[i] << std::endl;
562	<	}
563	<	}
564	<	*/
565	<	// Free previous hull
287	>	qh_getarea(qh facet_list);
288	>	volume_ = qh totvol;
289	>	area_ = qh totarea;
290	>
291		qh_freeqhull(!qh_ALL);
292		qh_memfreeshort(&curlong, &totlong);
293	<	if (curlong || totlong)
294	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
295	<	<< totlong << curlong << std::endl;
293	>	if (curlong || totlong) {
294	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
295	>	"\tdid not free %d bytes of long memory (%d pieces)",
296	>	totlong, curlong);
297	>	painCave.isFatal = 1;
298	>	simError();
299	>	}
300	>	}
301
302	<	if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
303	<	const_cast<char *>(options_.c_str()), NULL, stderr)){
574	<
575	<	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
576	<	painCave.isFatal = 1;
577	<	simError();
578	<
579	<	} //qh_new_qhull
580	<
581	<	#endif
582	<
583	<
584	<
585	<
586	<
587	<
588	<	unsigned int nf = qh num_facets;
589	<
590	<	/* Build Surface SD list first */
591	<
592	<	std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
593	<
594	<	FORALLfacets {
595	<
596	<	if (!facet->simplicial){
597	<	// should never happen with Qt
598	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
599	<	painCave.isFatal = 1;
600	<	simError();
601	<	} //simplicical
602	<
603	<	Triangle* face = new Triangle();
604	<	Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
605	<	face->setNormal(V3dNormal);
606	<
607	<
608	<
609	<	RealType faceArea = 0.5*V3dNormal.length();
610	<	face->setArea(faceArea);
611	<
612	<
613	<	vertices = qh_facet3vertex(facet);
614	<
615	<	coordT *center = qh_getcenter(vertices);
616	<	Vector3d V3dCentroid(center[0], center[1], center[2]);
617	<	face->setCentroid(V3dCentroid);
618	<
619	<	FOREACHvertex_(vertices){
620	<	id = qh_pointid(vertex->point);
621	<	int localindex = id;
302	>	void ConvexHull::printHull(const string& geomFileName) {
303	>
304		#ifdef IS_MPI
305	<
624	<	if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
625	<	localindex = localPtsMap[id-noffset/3];
305	>	if (worldRank == 0)  {
306		#endif
307	<	face->addVertex(bodydoubles[localindex]);
628	<	if( !isSurfaceID[id] ){
629	<	isSurfaceID[id] = true;
630	<	#ifdef IS_MPI
631	<
632	<	#endif
633	<
634	<	surfaceSDs_.push_back(bodydoubles[localindex]);
635	<
636	<	} //IF isSurfaceID
637	<
638	<	#ifdef IS_MPI
639	<
640	<	}else{
641	<	face->addVertex(NULL);
642	<	}
643	<	#endif
644	<	} //Foreachvertex
645	<	/*
646	<	if (!SETempty_(facet->coplanarset)){
647	<	FOREACHpoint_(facet->coplanarset){
648	<	id = qh_pointid(point);
649	<	surfaceSDs_.push_back(bodydoubles[id]);
650	<	}
651	<	}
652	<
653	<	Triangles_.push_back(face);
654	<	qh_settempfree(&vertices);
655	<	*/
656	<	} //FORALLfacets
657	<
658	<	/*
659	<	std::cout << surfaceSDs_.size() << std::endl;
660	<	for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
661	<	Vector3d thisatom = (*SD)->getPos();
662	<	std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
663	<	}
664	<	*/
665	<
666	<
667	<
668	<	Ns_ = surfaceSDs_.size();
307	>	FILE *newGeomFile;
308
309	+	//create new .md file based on old .md file
310	+	newGeomFile = fopen(geomFileName.c_str(), "w");
311	+	qh_findgood_all(qh facet_list);
312	+	for (int i = 0; i < qh_PRINTEND; i++)
313	+	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
314
315	<	qh_getarea(qh facet_list);
316	<	volume_ = qh totvol;
317	<	area_ = qh totarea;
318	<
675	<
676	<
677	<	qh_freeqhull(!qh_ALL);
678	<	qh_memfreeshort(&curlong, &totlong);
679	<	if (curlong || totlong)
680	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
681	<	<< totlong << curlong << std::endl;
682	<
683	<
684	<
315	>	fclose(newGeomFile);
316	>	#ifdef IS_MPI
317	>	}
318	>	#endif
319		}
686	–
687	–
688	–
689	–	void ConvexHull::printHull(const std::string& geomFileName)
690	–	{
691	–
692	–	FILE *newGeomFile;
693	–
694	–	//create new .md file based on old .md file
695	–	newGeomFile = fopen(geomFileName.c_str(), "w");
696	–	qh_findgood_all(qh facet_list);
697	–	for (int i = 0; i < qh_PRINTEND; i++)
698	–	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
699	–
700	–	fclose(newGeomFile);
701	–	}
320		#endif //QHULL
703	–	#endif //CGAL
704	–
705	–
706	–

Comparing trunk/src/math/ConvexHull.cpp (property svn:keywords):
Revision 1304 by chuckv, Wed Oct 15 18:26:01 2008 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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