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

Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1365 by chuckv, Mon Oct 12 20:11:29 2009 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

#	Line 1 | Line 1
1	<	/* Copyright (c) 2008, 2009 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 1.14 2009-10-12 20:11:29 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	+	// Copy the positon vector into a points vector for qhull.
83	+	vector<StuntDouble*>::iterator SD;
84	+	int i = 0;
85	+
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	+
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
108
109	<	typedef CGAL::MP_Float RT;
110	<	//typedef double RT;
111	<	//typedef CGAL::Homogeneous<RT>                     K;
112	<	typedef CGAL::Exact_predicates_exact_constructions_kernel K;
113	<	typedef K::Vector_3                               Vector_3;
114	<	//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;
109	>	#ifdef IS_MPI
110	>	//If we are doing the mpi version, set up some vectors for data communication
111	>
112	>	int nproc = MPI::COMM_WORLD.Get_size();
113	>	int myrank = MPI::COMM_WORLD.Get_rank();
114	>	int localHullSites = 0;
115
116	+	vector<int> hullSitesOnProc(nproc, 0);
117	+	vector<int> coordsOnProc(nproc, 0);
118	+	vector<int> displacements(nproc, 0);
119	+	vector<int> vectorDisplacements(nproc, 0);
120
121	<	typedef Polyhedron_3::HalfedgeDS             HalfedgeDS;
122	<	typedef Polyhedron_3::Facet_iterator                   Facet_iterator;
123	<	typedef Polyhedron_3::Halfedge_around_facet_circulator Halfedge_facet_circulator;
124	<	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	<
121	>	vector<double> coords;
122	>	vector<double> vels;
123	>	vector<int> indexMap;
124	>	vector<double> masses;
125
126	+	FORALLvertices{
127	+	localHullSites++;
128	+
129	+	int idx = qh_pointid(vertex->point);
130
131	<	class Enriched_Point_3 : public K::Point_3{
110	<	public:
111	<	Enriched_Point_3(double x,double y,double z) : K::Point_3(x,y,z), yupMyPoint(false), mySD(NULL) {}
131	>	indexMap.push_back(idx);
132
133	<	bool isMyPoint() const{ return yupMyPoint; }
134	<	void myPoint(){ yupMyPoint = true; }
135	<	void setSD(StuntDouble* SD){mySD = SD;}
116	<	StuntDouble* getStuntDouble(){return mySD;}
117	<	private:
118	<	bool yupMyPoint;
119	<	StuntDouble* mySD;
133	>	coords.push_back(ptArray[dim_  * idx]);
134	>	coords.push_back(ptArray[dim_  * idx + 1]);
135	>	coords.push_back(ptArray[dim_  * idx + 2]);
136
137	<	};
137	>	StuntDouble* sd = bodydoubles[idx];
138
139	+	Vector3d vel = sd->getVel();
140	+	vels.push_back(vel.x());
141	+	vels.push_back(vel.y());
142	+	vels.push_back(vel.z());
143
144	+	masses.push_back(sd->getMass());
145	+	}
146
147	+	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
148	+	1, MPI::INT);
149
150	+	int globalHullSites = 0;
151	+	for (int iproc = 0; iproc < nproc; iproc++){
152	+	globalHullSites += hullSitesOnProc[iproc];
153	+	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
154	+	}
155
156	<	// compare Point_3's... used in setting up the STL map from points to indices
157	<	template <typename Pt3>
158	<	struct Point_3_comp {
159	<	bool operator() (const Pt3 & p, const Pt3 & q) const {
160	<	return CGAL::lexicographically_xyz_smaller(p,q); // this is defined inline & hence we had to create fn object & not ptrfun
156	>	displacements[0] = 0;
157	>	vectorDisplacements[0] = 0;
158	>
159	>	for (int iproc = 1; iproc < nproc; iproc++){
160	>	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
161	>	vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
162		}
133	–	};
163
164	<	// coordinate-based hashing inefficient but can we do better if pts are copied?
165	<	typedef std::map<Point_3, StuntDouble* ,Point_3_comp<Point_3> > ptMapType;
164	>	vector<double> globalCoords(dim_ * globalHullSites);
165	>	vector<double> globalVels(dim_ * globalHullSites);
166	>	vector<double> globalMasses(globalHullSites);
167
168	<	#ifdef IS_MPI
169	<	struct {
170	<	double x,y,z;
171	<	} surfacePt;
172	<	#endif
168	>	int count = coordsOnProc[myrank];
169	>
170	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
171	>	&coordsOnProc[0], &vectorDisplacements[0],
172	>	MPI::DOUBLE);
173
174	<	ConvexHull::ConvexHull() : Hull(){
175	<	//If we are doing the mpi version, set up some vectors for data communication
176	<	#ifdef IS_MPI
174	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[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	<	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	<
158	<
159	<	#endif
160	<	}
161	<
162	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
163	<	{
164	<
165	<	std::vector<Enriched_Point_3> points;
166	<	ptMapType myMap;
167	<	Point_iterator   hc;
168	<
169	<	// Copy the positon vector into a points vector for cgal.
170	<	std::vector<StuntDouble*>::iterator SD;
178	>	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
179	>	&globalMasses[0], &hullSitesOnProc[0],
180	>	&displacements[0], MPI::DOUBLE);
181
182	<	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
183	<	{
184	<	Vector3d pos = (*SD)->getPos();
185	<	Enriched_Point_3* pt = new Enriched_Point_3(pos.x(),pos.y(),pos.z());
186	<	pt->setSD(*SD);
187	<	points.push_back(*pt);
188	<	// myMap[pt]=(*SD);
189	<	}
190	<
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];
182	>	// Free previous hull
183	>	qh_freeqhull(!qh_ALL);
184	>	qh_memfreeshort(&curlong, &totlong);
185	>	if (curlong || totlong) {
186	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
187	>	"\tdid not free %d bytes of long memory (%d pieces)",
188	>	totlong, curlong);
189	>	painCave.isFatal = 1;
190	>	simError();
191		}
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	–	}
192
193	<	int noffset = vecdispls_[myrank_];
194	<	/* gather the potential hull */
195	<
196	<
197	<	for (hc =polyhedron.points_begin();hc != polyhedron.points_end(); ++hc){
198	<	Point_3 mypoint = *hc;
199	<	surfacePt_ mpiSurfacePt;
200	<	mpiSurfacePt.x = CGAL::to_double(mypoint.x());
201	<	mpiSurfacePt.y = CGAL::to_double(mypoint.y());
228	<	mpiSurfacePt.z = CGAL::to_double(mypoint.z());
229	<	surfacePtsLocal_.push_back(mpiSurfacePt);
230	<	}
193	>	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
194	>	const_cast<char *>(options_.c_str()), NULL, stderr)){
195	>
196	>	sprintf(painCave.errMsg,
197	>	"ConvexHull: Qhull failed to compute global convex hull");
198	>	painCave.isFatal = 1;
199	>	simError();
200	>
201	>	} //qh_new_qhull
202
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	–
203		#endif
204	<
205	<
204	>	// commented out below, so comment out here also.
205	>	// intPoint = qh interior_point;
206	>	// RealType calcvol = 0.0;
207
208	<	/* 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();
208	>	qh_triangulate ();
209
210	<	Point_3 r0=h->vertex()->point();
211	<	Point_3 r1=h->next()->vertex()->point();
212	<	Point_3 r2=h->next()->next()->vertex()->point();
213	<
214	<	Point_3* pr0 = &r0;
215	<	Point_3* pr1 = &r1;
216	<	Point_3* pr2 = &r2;
217	<
218	<	Enriched_Point_3* er0 = static_cast<Enriched_Point_3*>(pr0);
219	<	Enriched_Point_3* er1 = static_cast<Enriched_Point_3*>(pr1);
220	<	Enriched_Point_3* er2 = static_cast<Enriched_Point_3*>(pr2);
221	<
222	<	// StuntDouble* sd = er0->getStuntDouble();
223	<	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	<
301	<
302	<
303	<	}
304	<	void ConvexHull::printHull(const std::string& geomFileName)
305	<	{
306	<	/*
307	<	std::ofstream newGeomFile;
308	<
309	<	//create new .md file based on old .md file
310	<	newGeomFile.open("testhull.off");
311	<
312	<	// Write polyhedron in Object File Format (OFF).
313	<	CGAL::set_ascii_mode( std::cout);
314	<	newGeomFile << "OFF" << std::endl << polyhedron.size_of_vertices() << ' '
315	<	<< polyhedron.size_of_facets() << " 0" << std::endl;
316	<	std::copy( polyhedron.points_begin(), polyhedron.points_end(),
317	<	std::ostream_iterator<Point_3>( newGeomFile, "\n"));
318	<	for (  Facet_iterator i = polyhedron.facets_begin(); i != polyhedron.facets_end(); ++i) {
319	<	Halfedge_facet_circulator j = i->facet_begin();
320	<	// Facets in polyhedral surfaces are at least triangles.
321	<	CGAL_assertion( CGAL::circulator_size(j) >= 3);
322	<	newGeomFile << CGAL::circulator_size(j) << ' ';
323	<	do {
324	<	newGeomFile << ' ' << std::distance(polyhedron.vertices_begin(), j->vertex());
325	<	} while ( ++j != i->facet_begin());
326	<	newGeomFile << std::endl;
327	<	}
328	<
329	<	newGeomFile.close();
330	<	*/
331	<	/*
332	<	std::ofstream newGeomFile;
333	<
334	<	//create new .md file based on old .md file
335	<	newGeomFile.open(geomFileName.c_str());
336	<
337	<	// Write polyhedron in Object File Format (OFF).
338	<	CGAL::set_ascii_mode( std::cout);
339	<	newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' '
340	<	<< ch_polyhedron.size_of_facets() << " 0" << std::endl;
341	<	std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(),
342	<	std::ostream_iterator<Point_3>( newGeomFile, "\n"));
343	<	for (  Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i)
344	<	{
345	<	Halfedge_facet_circulator j = i->facet_begin();
346	<	// Facets in polyhedral surfaces are at least triangles.
347	<	CGAL_assertion( CGAL::circulator_size(j) >= 3);
348	<	newGeomFile << CGAL::circulator_size(j) << ' ';
349	<	do
350	<	{
351	<	newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex());
352	<	}
353	<	while ( ++j != i->facet_begin());
354	<	newGeomFile << std::endl;
355	<	}
356	<
357	<	newGeomFile.close();
358	<	*/
359	<
360	<	}
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	+	Vector3d faceVel = V3Zero;
226	+	Vector3d p[3];
227	+	RealType faceMass = 0.0;
228
229	+	int ver = 0;
230
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
365	–
366	–
367	–
368	–	#else
369	–	#ifdef HAVE_QHULL
370	–	/* Old options Qt Qu Qg QG0 FA */
371	–	/* More old opts Qc Qi Pp*/
372	–	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp"), Ns_(200), nTriangles_(0) {
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	<	vecdispls_   = new int[nproc_];
381	<	vecNstoProc_ = new int[nproc_];
382	<	displs_ = new int[nproc_];
248	>	int localID = id - displacements[myrank];
249
384	–	// Create a surface point type in MPI to send
385	–	//surfacePtType = MPI::DOUBLE.Create_contiguous(3);
386	–	// surfacePtType.Commit();
387	–
250
251	<	#endif
252	<	}
253	<
254	<
393	<
394	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles)
395	<	{
396	<
397	<	std::vector<int> surfaceIDs;
398	<	std::vector<int> surfaceIDsGlobal;
399	<	std::vector<int> localPtsMap;
400	<	int numpoints = bodydoubles.size();
401	<
402	<	//coordT* pt_array;
403	<	coordT* surfpt_array;
404	<	vertexT *vertex, **vertexp;
405	<	facetT *facet;
406	<	setT *vertices;
407	<	int curlong,totlong;
408	<	int id;
409	<
410	<	coordT *point,**pointp;
411	<
412	<
413	<	FILE *outdummy = NULL;
414	<	FILE *errdummy = NULL;
415	<
416	<	//pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
417	<
418	<	//  double* ptArray = new double[numpoints * 3];
419	<	std::vector<double> ptArray(numpoints*3);
420	<	std::vector<bool> isSurfaceID(numpoints);
421	<
422	<	// Copy the positon vector into a points vector for qhull.
423	<	std::vector<StuntDouble*>::iterator SD;
424	<	int i = 0;
425	<	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD)
426	<	{
427	<	Vector3d pos = (*SD)->getPos();
428	<
429	<	ptArray[dim_ * i] = pos.x();
430	<	ptArray[dim_ * i + 1] = pos.y();
431	<	ptArray[dim_ * i + 2] = pos.z();
432	<	i++;
433	<	}
434	<
435	<
436	<
437	<
438	<
439	<
440	<	boolT ismalloc = False;
441	<	/* Clean up memory from previous convex hull calculations*/
442	<
443	<	Triangles_.clear();
444	<	surfaceSDs_.clear();
445	<	surfaceSDs_.reserve(Ns_);
446	<
447	<	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
448	<	const_cast<char *>(options_.c_str()), NULL, stderr)) {
449	<
450	<	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
451	<	painCave.isFatal = 1;
452	<	simError();
453	<
454	<	} //qh_new_qhull
455	<
456	<
457	<	#ifdef IS_MPI
458	<	std::vector<double> localPts;
459	<	std::vector<double> localVel;
460	<	std::vector<double> localMass;
461	<	int localPtArraySize;
462	<
463	<
464	<	std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
465	<
466	<
467	<	FORALLfacets {
468	<
469	<	if (!facet->simplicial){
470	<	// should never happen with Qt
471	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
472	<	painCave.isFatal = 1;
473	<	simError();
474	<	}
475	<
476	<
477	<	vertices = qh_facet3vertex(facet);
478	<	FOREACHvertex_(vertices){
479	<	id = qh_pointid(vertex->point);
480	<
481	<	if( !isSurfaceID[id] ){
482	<	isSurfaceID[id] = true;
251	>	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
252	>	face.addVertexSD(bodydoubles[indexMap[localID]]);
253	>	}else{
254	>	face.addVertexSD(NULL);
255		}
256	<	}
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	>	face.addVertices(p[0], p[1], p[2]);
267	>	face.setFacetMass(faceMass);
268	>	face.setFacetVelocity(faceVel / RealType(3.0));
269	>	/*
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	>	cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  endl;
276	>	calcvol +=  -dist*comparea/qh hull_dim;
277	>	*/
278	>	Triangles_.push_back(face);
279		qh_settempfree(&vertices);
486	–
487	–	} //FORALLfacets
280
281	<
490	<
491	<
492	<	int idx = 0;
493	<	int nIsIts = 0;
494	<	FORALLvertices {
495	<	idx = qh_pointid(vertex->point);
496	<	localPts.push_back(ptArray[dim_ * idx]);
497	<	localPts.push_back(ptArray[dim_ * idx + 1]);
498	<	localPts.push_back(ptArray[dim_ * idx + 2]);
499	<
500	<	Vector3d vel = bodydoubles[idx]->getVel();
501	<	localVel.push_back(vel.x());
502	<	localVel.push_back(vel.y());
503	<	localVel.push_back(vel.z());
504	<
505	<
506	<	RealType bdmass = bodydoubles[idx]->getMass();
507	<	localMass.push_back(bdmass);
508	<
509	<	localPtsMap.push_back(idx);
510	<
511	<	}
512	<
513	<
514	<	localPtArraySize = int(localPts.size()/3.0);
515	<
516	<	MPI::COMM_WORLD.Allgather(&localPtArraySize,1,MPI::INT,&NstoProc_[0],1,MPI::INT);
281	>	} //FORALLfacets
282
283	<	Nsglobal_=0;
284	<	for (int i = 0; i < nproc_; i++){
285	<	Nsglobal_ += NstoProc_[i];
286	<	vecNstoProc_[i] = NstoProc_[i]*3;
522	<	}
523	<
524	<
525	<	int nglobalPts = Nsglobal_*3;
526	<
527	<
528	<	std::vector<double> globalPts(nglobalPts);
529	<	std::vector<double> globalVel(nglobalPts);
530	<	std::vector<double> globalMass(Nsglobal_);
531	<
532	<
533	<
534	<	isSurfaceID.resize(nglobalPts);
535	<
536	<
537	<	std::fill(globalPts.begin(),globalPts.end(),0.0);
538	<
539	<	vecdispls_[0] = 0;
540	<	/* Build a displacements array */
541	<	for (int i = 1; i < nproc_; i++){
542	<	vecdispls_[i] = vecdispls_[i-1] + vecNstoProc_[i-1];
543	<	}
544	<
545	<	displs_[0] = 0;
546	<	for (int i = 1; i < nproc_; i++){
547	<	displs_[i] = displs_[i-1] + NstoProc_[i-1];
548	<	}
549	<
550	<	int noffset = vecdispls_[myrank_];
551	<	/* gather the potential hull */
552	<
553	<	MPI::COMM_WORLD.Allgatherv(&localPts[0],localPtArraySize*3,MPI::DOUBLE,&globalPts[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
554	<	MPI::COMM_WORLD.Allgatherv(&localVel[0],localPtArraySize*3,MPI::DOUBLE,&globalVel[0],&vecNstoProc_[0],&vecdispls_[0],MPI::DOUBLE);
555	<	MPI::COMM_WORLD.Allgatherv(&localMass[0],localPtArraySize,MPI::DOUBLE,&globalMass[0],&NstoProc_[0],&displs_[0],MPI::DOUBLE);
556	<
557	<	/*
558	<	int tmpidx = 0;
559	<
560	<	if (myrank_ == 0){
561	<	for (i = 0; i < nglobalPts-3; i++){
562	<	std::cout << "Au   " << globalPts[tmpidx] << "  " << globalPts[tmpidx+1] << "  " << globalPts[tmpidx +2] << std::endl;
563	<	tmpidx = tmpidx + 3;
564	<	}
565	<	}
566	<	*/
567	<
568	<	// Free previous hull
283	>	qh_getarea(qh facet_list);
284	>	volume_ = qh totvol;
285	>	area_ = qh totarea;
286	>
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;
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	<	if (qh_new_qhull(dim_, Nsglobal_, &globalPts[0], ismalloc,
299	<	const_cast<char *>(options_.c_str()), NULL, stderr)){
577	<
578	<	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
579	<	painCave.isFatal = 1;
580	<	simError();
581	<
582	<	} //qh_new_qhull
583	<
584	<	#endif
585	<
586	<
587	<
588	<
589	<
590	<
591	<	unsigned int nf = qh num_facets;
592	<
593	<	/* Build Surface SD list first */
594	<
595	<	std::fill(isSurfaceID.begin(),isSurfaceID.end(),false);
596	<
597	<	FORALLfacets {
598	<
599	<	if (!facet->simplicial){
600	<	// should never happen with Qt
601	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
602	<	painCave.isFatal = 1;
603	<	simError();
604	<	} //simplicical
605	<
606	<	Triangle face;
607	<	Vector3d  V3dNormal(facet->normal[0],facet->normal[1],facet->normal[2]);
608	<	face.setNormal(V3dNormal);
609	<
610	<
611	<
612	<	//RealType faceArea = 0.5*V3dNormal.length();
613	<	RealType faceArea = qh_facetarea(facet);
614	<	face.setArea(faceArea);
615	<
616	<
617	<	vertices = qh_facet3vertex(facet);
618	<
619	<	coordT *center = qh_getcenter(vertices);
620	<	Vector3d V3dCentroid(center[0], center[1], center[2]);
621	<	face.setCentroid(V3dCentroid);
622	<	Vector3d faceVel = V3Zero;
623	<	Vector3d p[3];
624	<	RealType faceMass = 0.0;
625	<	int ver = 0;
626	<	FOREACHvertex_(vertices){
627	<	id = qh_pointid(vertex->point);
628	<	p[ver][0] = vertex->point[0];
629	<	p[ver][1] = vertex->point[1];
630	<	p[ver][2] = vertex->point[2];
631	<	int localindex = id;
298	>	void ConvexHull::printHull(const string& geomFileName) {
299	>
300		#ifdef IS_MPI
301	<	Vector3d velVector(globalVel[dim_ * id],globalVel[dim_ * id + 1], globalVel[dim_ * id + 1]);
634	<
635	<	faceVel = faceVel + velVector;
636	<	faceMass = faceMass + globalMass[id];
637	<	if (id >= noffset/3 && id < (noffset + localPtArraySize)/3 ){
638	<	localindex = localPtsMap[id-noffset/3];
639	<	#else
640	<	faceVel = faceVel + bodydoubles[localindex]->getVel();
641	<	faceMass = faceMass + bodydoubles[localindex]->getMass();
301	>	if (worldRank == 0)  {
302		#endif
303	<	face.addVertexSD(bodydoubles[localindex]);
644	<	if( !isSurfaceID[id] ){
645	<	isSurfaceID[id] = true;
646	<	#ifdef IS_MPI
647	<
648	<	#endif
649	<
650	<	surfaceSDs_.push_back(bodydoubles[localindex]);
651	<
652	<	} //IF isSurfaceID
653	<
654	<	#ifdef IS_MPI
655	<
656	<	}else{
657	<	face.addVertexSD(NULL);
658	<	}
659	<	#endif
660	<	ver++;
661	<	} //Foreachvertex
662	<	/*
663	<	if (!SETempty_(facet->coplanarset)){
664	<	FOREACHpoint_(facet->coplanarset){
665	<	id = qh_pointid(point);
666	<	surfaceSDs_.push_back(bodydoubles[id]);
667	<	}
668	<	}
669	<	*/
670	<	face.addVertices(p[0],p[1],p[2]);
671	<	face.setFacetMass(faceMass);
672	<	face.setFacetVelocity(faceVel/3.0);
673	<	Triangles_.push_back(face);
674	<	qh_settempfree(&vertices);
675	<
676	<	} //FORALLfacets
677	<
678	<	/*
679	<	std::cout << surfaceSDs_.size() << std::endl;
680	<	for (SD = surfaceSDs_.begin(); SD != surfaceSDs_.end(); ++SD){
681	<	Vector3d thisatom = (*SD)->getPos();
682	<	std::cout << "Au " << thisatom.x() << "  " << thisatom.y() << " " << thisatom.z() << std::endl;
683	<	}
684	<	*/
685	<
686	<
687	<
688	<	Ns_ = surfaceSDs_.size();
689	<	nTriangles_ = Triangles_.size();
303	>	FILE *newGeomFile;
304
305	<	qh_getarea(qh facet_list);
306	<	volume_ = qh totvol;
307	<	area_ = qh totarea;
305	>	//create new .md file based on old .md file
306	>	newGeomFile = fopen(geomFileName.c_str(), "w");
307	>	qh_findgood_all(qh facet_list);
308	>	for (int i = 0; i < qh_PRINTEND; i++)
309	>	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
310
311	<
312	<
313	<	qh_freeqhull(!qh_ALL);
314	<	qh_memfreeshort(&curlong, &totlong);
699	<	if (curlong || totlong)
700	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
701	<	<< totlong << curlong << std::endl;
702	<
703	<
704	<
311	>	fclose(newGeomFile);
312	>	#ifdef IS_MPI
313	>	}
314	>	#endif
315		}
706	–
707	–
708	–
709	–	void ConvexHull::printHull(const std::string& geomFileName)
710	–	{
711	–
712	–	FILE *newGeomFile;
713	–
714	–	//create new .md file based on old .md file
715	–	newGeomFile = fopen(geomFileName.c_str(), "w");
716	–	qh_findgood_all(qh facet_list);
717	–	for (int i = 0; i < qh_PRINTEND; i++)
718	–	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
719	–
720	–	fclose(newGeomFile);
721	–	}
316		#endif //QHULL
723	–	#endif //CGAL
724	–
725	–
726	–

Comparing trunk/src/math/ConvexHull.cpp (property svn:keywords):
Revision 1365 by chuckv, Mon Oct 12 20:11:29 2009 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

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