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

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trunk/src/math/ConvexHull.cpp (file contents), Revision 1316 by chuckv, Fri Nov 14 15:44:34 2008 UTC vs.
branches/development/src/math/ConvexHull.cpp (file contents), Revision 1866 by gezelter, Thu Apr 25 14:32:56 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, 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 1.13 2008-11-14 15:44:34 chuckv Exp $
48	<	*
43	>	*  Purpose: To calculate a convex hull.
44		*/
45
46		/* Standard includes independent of library */
47	+
48		#include <iostream>
49		#include <fstream>
50		#include <list>
#	Line 57 | Line 53
53		#include "math/ConvexHull.hpp"
54		#include "utils/simError.h"
55
56	+	#ifdef IS_MPI
57	+	#include <mpi.h>
58	+	#endif
59
60	<	using namespace oopse;
60	>	#include "math/qhull.hpp"
61
62	<	/* CGAL version of convex hull first then QHULL */
63	<	#ifdef HAVE_CGAL
64	<	//#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>
62	>	#ifdef HAVE_QHULL
63	>	using namespace OpenMD;
64	>	using namespace std;
65
66	+	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") {
67	+	}
68
69	<	//#include <CGAL/Quotient.h>
70	<	#include <CGAL/MP_Float.h>
71	<	//#include <CGAL/Lazy_exact_nt.h>
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	+	Vector3d boxMax;
81	+	Vector3d boxMin;
82	+
83	+	vector<double> ptArray(numpoints*dim_);
84
85	+	// Copy the positon vector into a points vector for qhull.
86	+	vector<StuntDouble*>::iterator SD;
87	+	int i = 0;
88	+
89	+	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
90	+	Vector3d pos = (*SD)->getPos();
91	+	ptArray[dim_ * i] = pos.x();
92	+	ptArray[dim_ * i + 1] = pos.y();
93	+	ptArray[dim_ * i + 2] = pos.z();
94	+	i++;
95	+	}
96	+
97	+	/* Clean up memory from previous convex hull calculations */
98	+	boolT ismalloc = False;
99	+
100	+	/* compute the hull for our local points (or all the points for single
101	+	processor versions) */
102	+	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
103	+	const_cast<char *>(options_.c_str()), NULL, stderr)) {
104	+
105	+	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
106	+	painCave.isFatal = 1;
107	+	simError();
108	+
109	+	} //qh_new_qhull
110
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;
111
112	+	#ifdef IS_MPI
113	+	//If we are doing the mpi version, set up some vectors for data communication
114	+
115	+	int nproc = MPI::COMM_WORLD.Get_size();
116	+	int myrank = MPI::COMM_WORLD.Get_rank();
117	+	int localHullSites = 0;
118
119	<	typedef Polyhedron_3::HalfedgeDS             HalfedgeDS;
120	<	typedef Polyhedron_3::Facet_iterator                   Facet_iterator;
121	<	typedef Polyhedron_3::Halfedge_around_facet_circulator Halfedge_facet_circulator;
122	<	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	<
119	>	vector<int> hullSitesOnProc(nproc, 0);
120	>	vector<int> coordsOnProc(nproc, 0);
121	>	vector<int> displacements(nproc, 0);
122	>	vector<int> vectorDisplacements(nproc, 0);
123
124	+	vector<double> coords;
125	+	vector<double> vels;
126	+	vector<int> indexMap;
127	+	vector<double> masses;
128
129	<	class Enriched_Point_3 : public K::Point_3{
130	<	public:
131	<	Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
129	>	FORALLvertices{
130	>	localHullSites++;
131	>
132	>	int idx = qh_pointid(vertex->point);
133
134	<	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;
134	>	indexMap.push_back(idx);
135
136	<	};
136	>	coords.push_back(ptArray[dim_  * idx]);
137	>	coords.push_back(ptArray[dim_  * idx + 1]);
138	>	coords.push_back(ptArray[dim_  * idx + 2]);
139
140	+	StuntDouble* sd = bodydoubles[idx];
141
142	+	Vector3d vel = sd->getVel();
143	+	vels.push_back(vel.x());
144	+	vels.push_back(vel.y());
145	+	vels.push_back(vel.z());
146
147	+	masses.push_back(sd->getMass());
148	+	}
149
150	+	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
151	+	1, MPI::INT);
152
153	<	// compare Point_3's... used in setting up the STL map from points to indices
154	<	template <typename Pt3>
155	<	struct Point_3_comp {
156	<	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
153	>	int globalHullSites = 0;
154	>	for (int iproc = 0; iproc < nproc; iproc++){
155	>	globalHullSites += hullSitesOnProc[iproc];
156	>	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
157		}
133	–	};
158
159	<	// coordinate-based hashing inefficient but can we do better if pts are copied?
160	<	typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
159	>	displacements[0] = 0;
160	>	vectorDisplacements[0] = 0;
161	>
162	>	for (int iproc = 1; iproc < nproc; iproc++){
163	>	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
164	>	vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
165	>	}
166
167	<	#ifdef IS_MPI
168	<	struct {
169	<	double x,y,z;
141	<	} surfacePt;
142	<	#endif
167	>	vector<double> globalCoords(dim_ * globalHullSites);
168	>	vector<double> globalVels(dim_ * globalHullSites);
169	>	vector<double> globalMasses(globalHullSites);
170
171	<	ConvexHull::ConvexHull() : Hull(){
172	<	//If we are doing the mpi version, set up some vectors for data communication
173	<	#ifdef IS_MPI
171	>	int count = coordsOnProc[myrank];
172	>
173	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
174	>	&coordsOnProc[0], &vectorDisplacements[0],
175	>	MPI::DOUBLE);
176
177	+	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
178	+	&coordsOnProc[0], &vectorDisplacements[0],
179	+	MPI::DOUBLE);
180
181	<	nproc_ = MPI::COMM_WORLD.Get_size();
182	<	myrank_ = MPI::COMM_WORLD.Get_rank();
183	<	NstoProc_ = new int[nproc_];
152	<	vecdispls_   = new int[nproc_];
153	<	displs_ = new int[nproc_];
154	<	// Create a surface point type in MPI to send
155	<	surfacePtType = MPI::DOUBLE.Create_contiguous(3);
156	<	surfacePtType.Commit();
157	<
181	>	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
182	>	&globalMasses[0], &hullSitesOnProc[0],
183	>	&displacements[0], MPI::DOUBLE);
184
185	<	#endif
186	<	}
187	<
188	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
189	<	{
190	<
191	<	std::vector<Enriched_Point_3> points;
192	<	ptMapType myMap;
193	<	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];
185	>	// Free previous hull
186	>	qh_freeqhull(!qh_ALL);
187	>	qh_memfreeshort(&curlong, &totlong);
188	>	if (curlong || totlong) {
189	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
190	>	"\tdid not free %d bytes of long memory (%d pieces)",
191	>	totlong, curlong);
192	>	painCave.isFatal = 1;
193	>	simError();
194		}
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	–	vecdispls_[i] = vecdispls_[i-1] + NstoProc_[i-1];
217	–	}
195
196	<	int noffset = vecdispls_[myrank_];
197	<	/* gather the potential hull */
198	<
199	<
200	<	for (hc =polyhedron.points_begin();hc != polyhedron.points_end(); ++hc){
201	<	Point_3 mypoint = *hc;
202	<	surfacePt_ mpiSurfacePt;
203	<	mpiSurfacePt.x = CGAL::to_double(mypoint.x());
204	<	mpiSurfacePt.y = CGAL::to_double(mypoint.y());
228	<	mpiSurfacePt.z = CGAL::to_double(mypoint.z());
229	<	surfacePtsLocal_.push_back(mpiSurfacePt);
230	<	}
196	>	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
197	>	const_cast<char *>(options_.c_str()), NULL, stderr)){
198	>
199	>	sprintf(painCave.errMsg,
200	>	"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_,vecdispls_,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	<
207	>	// commented out below, so comment out here also.
208	>	// intPoint = qh interior_point;
209	>	// RealType calcvol = 0.0;
210
211	<	/* Loop over all of the surface triangles and build data structures for atoms and normals*/
212	<	Facet_iterator j;
213	<	area_ = 0;
264	<	for ( j = polyhedron.facets_begin(); j !=polyhedron.facets_end(); ++j) {
265	<	Halfedge_handle h = j->halfedge();
211	>	qh_triangulate ();
212	>	int num_facets = qh num_facets;
213	>	int num_vertices = qh num_vertices;
214
215	<	Point_3 r0=h->vertex()->point();
216	<	Point_3 r1=h->next()->vertex()->point();
217	<	Point_3 r2=h->next()->next()->vertex()->point();
215	>	FORALLfacets {
216	>	Triangle face;
217	>	//Qhull sets the unit normal in facet->normal
218	>	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
219	>	face.setUnitNormal(V3dNormal);
220	>
221	>	RealType faceArea = qh_facetarea(facet);
222	>	face.setArea(faceArea);
223	>
224	>	vertices = qh_facet3vertex(facet);
225	>
226	>	coordT *center = qh_getcenter(vertices);
227	>	Vector3d V3dCentroid(center[0], center[1], center[2]);
228	>	face.setCentroid(V3dCentroid);
229
230	<	Point_3* pr0 = &r0;
231	<	Point_3* pr1 = &r1;
232	<	Point_3* pr2 = &r2;
230	>	Vector3d faceVel = V3Zero;
231	>	Vector3d p[3];
232	>	RealType faceMass = 0.0;
233
234	<	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);
234	>	int ver = 0;
235
236	<	// StuntDouble* sd = er0->getStuntDouble();
237	<	std::cerr << "sd globalIndex = " << to_double(er0->x()) << "\n";
238	<
239	<	Point_3 thisCentroid = CGAL::centroid(r0,r1,r2);
240	<
241	<	Vector_3 normal = CGAL::cross_product(r1-r0,r2-r0);
242	<
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	<	}
236	>	FOREACHvertex_(vertices){
237	>	int id = qh_pointid(vertex->point);
238	>	p[ver][0] = vertex->point[0];
239	>	p[ver][1] = vertex->point[1];
240	>	p[ver][2] = vertex->point[2];
241	>	Vector3d vel;
242	>	RealType mass;
243
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
244		#ifdef IS_MPI
245	+	vel = Vector3d(globalVels[dim_ * id],
246	+	globalVels[dim_ * id + 1],
247	+	globalVels[dim_ * id + 2]);
248	+	mass = globalMasses[id];
249
250	+	// localID will be between 0 and hullSitesOnProc[myrank] if we
251	+	// own this guy.
252
253	<	nproc_ = MPI::COMM_WORLD.Get_size();
379	<	myrank_ = MPI::COMM_WORLD.Get_rank();
380	<	NstoProc_ = new int[nproc_];
381	<	vecdispls_   = new int[nproc_];
382	<	vecNstoProc_ = new int[nproc_];
383	<	displs_ = new int[nproc_];
253	>	int localID = id - displacements[myrank];
254
385	–	// Create a surface point type in MPI to send
386	–	//surfacePtType = MPI::DOUBLE.Create_contiguous(3);
387	–	// surfacePtType.Commit();
388	–
255
256	<	#endif
257	<	}
258	<
259	<
394	<
395	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
396	<	{
397	<
398	<	std::vector<int> surfaceIDs;
399	<	std::vector<int> surfaceIDsGlobal;
400	<	std::vector<int> localPtsMap;
401	<	int numpoints = bodydoubles.size();
402	<
403	<	//coordT* pt_array;
404	<	coordT* surfpt_array;
405	<	vertexT *vertex, **vertexp;
406	<	facetT *facet;
407	<	setT *vertices;
408	<	int curlong,totlong;
409	<	int id;
410	<
411	<	coordT *point,**pointp;
412	<
413	<
414	<	FILE *outdummy = NULL;
415	<	FILE *errdummy = NULL;
416	<
417	<	//pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
418	<
419	<	//  double* ptArray = new double[numpoints * 3];
420	<	std::vector<double> ptArray(numpoints*3);
421	<	std::vector<bool> isSurfaceID(numpoints);
422	<
423	<	// Copy the positon vector into a points vector for qhull.
424	<	std::vector<StuntDouble*>::iterator SD;
425	<	int i = 0;
426	<	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
427	<	{
428	<	Vector3d pos = (*SD)->getPos();
429	<
430	<	ptArray[dim_ * i] = pos.x();
431	<	ptArray[dim_ * i + 1] = pos.y();
432	<	ptArray[dim_ * i + 2] = pos.z();
433	<	i++;
434	<	}
435	<
436	<
437	<
438	<
439	<
440	<
441	<	boolT ismalloc = False;
442	<	/* Clean up memory from previous convex hull calculations*/
443	<
444	<	Triangles_.clear();
445	<	surfaceSDs_.clear();
446	<	surfaceSDs_.reserve(Ns_);
447	<
448	<	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
449	<	const_cast<char *>(options_.c_str()), NULL, stderr)) {
450	<
451	<	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
452	<	painCave.isFatal = 1;
453	<	simError();
454	<
455	<	} //qh_new_qhull
456	<
457	<
458	<	#ifdef IS_MPI
459	<	std::vector<double> localPts;
460	<	std::vector<double> localVel;
461	<	std::vector<double> localMass;
462	<	int localPtArraySize;
463	<
464	<
465	<	std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
466	<
467	<
468	<	FORALLfacets {
469	<
470	<	if (!facet->simplicial){
471	<	// should never happen with Qt
472	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
473	<	painCave.isFatal = 1;
474	<	simError();
475	<	}
476	<
477	<
478	<	vertices = qh_facet3vertex(facet);
479	<	FOREACHvertex_(vertices){
480	<	id = qh_pointid(vertex->point);
481	<
482	<	if( !isSurfaceID[id] ){
483	<	isSurfaceID[id] = true;
256	>	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
257	>	face.addVertexSD(bodydoubles[indexMap[localID]]);
258	>	}else{
259	>	face.addVertexSD(NULL);
260		}
261	<	}
261	>	#else
262	>	vel = bodydoubles[id]->getVel();
263	>	mass = bodydoubles[id]->getMass();
264	>	face.addVertexSD(bodydoubles[id]);
265	>	#endif
266	>	faceVel = faceVel + vel;
267	>	faceMass = faceMass + mass;
268	>	ver++;
269	>	} //Foreachvertex
270	>
271	>	face.addVertices(p[0], p[1], p[2]);
272	>	face.setFacetMass(faceMass);
273	>	face.setFacetVelocity(faceVel / RealType(3.0));
274	>	/*
275	>	RealType comparea = face.computeArea();
276	>	realT calcarea = qh_facetarea (facet);
277	>	Vector3d V3dCompNorm = -face.computeUnitNormal();
278	>	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
279	>	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
280	>	cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  endl;
281	>	calcvol +=  -dist*comparea/qh hull_dim;
282	>	*/
283	>	Triangles_.push_back(face);
284		qh_settempfree(&vertices);
487	–
488	–	} //FORALLfacets
285
286	<
491	<
492	<
493	<	int idx = 0;
494	<	int nIsIts = 0;
495	<	FORALLvertices {
496	<	idx = qh_pointid(vertex->point);
497	<	localPts.push_back(ptArray[dim_ * idx]);
498	<	localPts.push_back(ptArray[dim_ * idx + 1]);
499	<	localPts.push_back(ptArray[dim_ * idx + 2]);
500	<
501	<	Vector3d vel = bodydoubles[idx]->getVel();
502	<	localVel.push_back(vel.x());
503	<	localVel.push_back(vel.y());
504	<	localVel.push_back(vel.z());
505	<
506	<	RealType bdmass = bodydoubles[idx]->getMass();
507	<	localMass.push_back(bdmass);
508	<
509	<	localPtsMap.push_back(idx);
510	<
511	<
512	<	}
513	<
514	<
515	<
516	<	localPtArraySize = int(localPts.size()/3.0);
517	<
518	<
519	<	MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
286	>	} //FORALLfacets
287
288	<	Nsglobal_=0;
289	<	for (int i = 0; i < nproc_; i++){
290	<	Nsglobal_ += NstoProc_[i];
524	<	vecNstoProc_[i] = NstoProc_[i]*3;
525	<	}
526	<
527	<
528	<	int nglobalPts = Nsglobal_*3;
529	<
288	>	qh_getarea(qh facet_list);
289	>	volume_ = qh totvol;
290	>	area_ = qh totarea;
291
292	<	std::vector<double> globalPts(nglobalPts);
293	<	std::vector<double> globalVel(nglobalPts);
294	<	std::vector<double> globalMass(Nsglobal_);
295	<
296	<	isSurfaceID.resize(nglobalPts);
297	<
298	<
299	<	std::fill(globalPts.begin(),globalPts.end(),0.0);
300	<
301	<	vecdispls_[0] = 0;
302	<	/* Build a displacements array */
542	<	for (int i = 1; i < nproc_; i++){
543	<	vecdispls_[i] = vecdispls_[i-1] + vecNstoProc_[i-1];
544	<	}
545	<
546	<	displs_[0] = 0;
547	<	for (int i = 1; i < nproc_; i++){
548	<	displs_[i] = displs_[i-1] + NstoProc_[i-1];
549	<	}
550	<
551	<	int noffset = vecdispls_[myrank_];
552	<	/* gather the potential hull */
553	<
554	<	MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize,MPI::DOUBLE,&globalPts[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
555	<	MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize,MPI::DOUBLE,&globalVel[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
556	<	MPI::COMM_WORLD.Allgatherv(&localMass[0],localPtArraySize,MPI::DOUBLE,&globalMass[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
557	<	/*
558	<	if (myrank_ == 0){
559	<	for (i = 0; i < globalPts.size(); i++){
560	<	std::cout << globalPts[i] << std::endl;
292	>	int index = 0;
293	>	FORALLvertices {
294	>	Vector3d point(vertex->point[0], vertex->point[1], vertex->point[2]);
295	>	if (index == 0) {
296	>	boxMax = point;
297	>	boxMin = point;
298	>	} else {
299	>	for (int i = 0; i < 3; i++) {
300	>	boxMax[i] = max(boxMax[i], point[i]);
301	>	boxMin[i] = min(boxMin[i], point[i]);
302	>	}
303		}
304	+	index++;
305		}
306	<	*/
307	<	// Free previous hull
306	>	boundingBox_ = Mat3x3d(0.0);
307	>	boundingBox_(0,0) = boxMax[0] - boxMin[0];
308	>	boundingBox_(1,1) = boxMax[1] - boxMin[1];
309	>	boundingBox_(2,2) = boxMax[2] - boxMin[2];
310	>
311		qh_freeqhull(!qh_ALL);
312		qh_memfreeshort(&curlong, &totlong);
313	<	if (curlong || totlong)
314	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
315	<	<< totlong << curlong << std::endl;
313	>	if (curlong || totlong) {
314	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
315	>	"\tdid not free %d bytes of long memory (%d pieces)",
316	>	totlong, curlong);
317	>	painCave.isFatal = 1;
318	>	simError();
319	>	}
320	>	}
321
322	<	if (qh_new_qhull(dim_, nglobalPts, &globalPts[0], ismalloc,
323	<	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;
603	<	Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
604	<	face.setNormal(V3dNormal);
605	<
606	<
607	<
608	<	//RealType faceArea = 0.5*V3dNormal.length();
609	<	RealType faceArea = qh_facetarea(facet);
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	<	Vector3d faceVel = V3Zero;
619	<	Vector3d p[3];
620	<	RealType faceMass = 0.0;
621	<	int ver = 0;
622	<	FOREACHvertex_(vertices){
623	<	id = qh_pointid(vertex->point);
624	<	p[ver][0] = vertex->point[0];
625	<	p[ver][1] = vertex->point[1];
626	<	p[ver][2] = vertex->point[2];
627	<	int localindex = id;
322	>	void ConvexHull::printHull(const string& geomFileName) {
323	>
324		#ifdef IS_MPI
325	<	Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 1]);
630	<
631	<	faceVel = faceVel + velVector;
632	<	faceMass = faceMass + globalMass[id];
633	<	if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
634	<	localindex = localPtsMap[id-noffset/3];
635	<	#else
636	<	faceVel = faceVel + bodydoubles[localindex]->getVel();
637	<	faceMass = faceMass + bodydoubles[localindex]->getMass();
325	>	if (worldRank == 0)  {
326		#endif
327	<	face.addVertexSD(bodydoubles[localindex]);
640	<	if( !isSurfaceID[id] ){
641	<	isSurfaceID[id] = true;
642	<	#ifdef IS_MPI
643	<
644	<	#endif
645	<
646	<	surfaceSDs_.push_back(bodydoubles[localindex]);
647	<
648	<	} //IF isSurfaceID
649	<
650	<	#ifdef IS_MPI
651	<
652	<	}else{
653	<	face.addVertexSD(NULL);
654	<	}
655	<	#endif
656	<	ver++;
657	<	} //Foreachvertex
658	<	/*
659	<	if (!SETempty_(facet->coplanarset)){
660	<	FOREACHpoint_(facet->coplanarset){
661	<	id = qh_pointid(point);
662	<	surfaceSDs_.push_back(bodydoubles[id]);
663	<	}
664	<	}
665	<	*/
666	<	face.addVertices(p[0],p[1],p[2]);
667	<	face.setFacetMass(faceMass);
668	<	face.setFacetVelocity(faceVel/3.0);
669	<	Triangles_.push_back(face);
670	<	qh_settempfree(&vertices);
671	<
672	<	} //FORALLfacets
673	<
674	<	/*
675	<	std::cout << surfaceSDs_.size() << std::endl;
676	<	for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
677	<	Vector3d thisatom = (*SD)->getPos();
678	<	std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
679	<	}
680	<	*/
681	<
682	<
683	<
684	<	Ns_ = surfaceSDs_.size();
685	<	nTriangles_ = Triangles_.size();
327	>	FILE *newGeomFile;
328
329	<	qh_getarea(qh facet_list);
330	<	volume_ = qh totvol;
331	<	area_ = qh totarea;
329	>	//create new .md file based on old .md file
330	>	newGeomFile = fopen(geomFileName.c_str(), "w");
331	>	qh_findgood_all(qh facet_list);
332	>	for (int i = 0; i < qh_PRINTEND; i++)
333	>	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
334
335	<
336	<
337	<	qh_freeqhull(!qh_ALL);
338	<	qh_memfreeshort(&curlong, &totlong);
695	<	if (curlong || totlong)
696	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
697	<	<< totlong << curlong << std::endl;
698	<
699	<
700	<
335	>	fclose(newGeomFile);
336	>	#ifdef IS_MPI
337	>	}
338	>	#endif
339		}
702	–
703	–
704	–
705	–	void ConvexHull::printHull(const std::string& geomFileName)
706	–	{
707	–
708	–	FILE *newGeomFile;
709	–
710	–	//create new .md file based on old .md file
711	–	newGeomFile = fopen(geomFileName.c_str(), "w");
712	–	qh_findgood_all(qh facet_list);
713	–	for (int i = 0; i < qh_PRINTEND; i++)
714	–	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
715	–
716	–	fclose(newGeomFile);
717	–	}
340		#endif //QHULL
719	–	#endif //CGAL
720	–
721	–
722	–

Comparing:
trunk/src/math/ConvexHull.cpp (property svn:keywords), Revision 1316 by chuckv, Fri Nov 14 15:44:34 2008 UTC vs.
branches/development/src/math/ConvexHull.cpp (property svn:keywords), Revision 1866 by gezelter, Thu Apr 25 14:32:56 2013 UTC

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