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Comparing:
trunk/src/math/ConvexHull.cpp (file contents), Revision 1242 by chuckv, Wed May 14 14:31:48 2008 UTC vs.
branches/development/src/math/ConvexHull.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 1 | Line 1
1	<	/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
1	>	/* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
2		*
3		* The University of Notre Dame grants you ("Licensee") a
4		* non-exclusive, royalty free, license to use, modify and
5		* redistribute this software in source and binary code form, provided
6		* that the following conditions are met:
7		*
8	<	* 1. Acknowledgement of the program authors must be made in any
9	<	*    publication of scientific results based in part on use of the
10	<	*    program.  An acceptable form of acknowledgement is citation of
11	<	*    the article in which the program was described (Matthew
12	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
13	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
14	<	*    Parallel Simulation Engine for Molecular Dynamics,"
15	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
16	<	*
17	<	* 2. Redistributions of source code must retain the above copyright
8	>	* 1. Redistributions of source code must retain the above copyright
9		*    notice, this list of conditions and the following disclaimer.
10		*
11	<	* 3. Redistributions in binary form must reproduce the above copyright
11	>	* 2. Redistributions in binary form must reproduce the above copyright
12		*    notice, this list of conditions and the following disclaimer in the
13		*    documentation and/or other materials provided with the
14		*    distribution.
#	Line 37 | Line 28
28		* University of Notre Dame has been advised of the possibility of
29		* such damages.
30		*
31	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
32	+	* research, please cite the appropriate papers when you publish your
33	+	* work.  Good starting points are:
34	+	*
35	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	+	* [4]  Vardeman & Gezelter, in progress (2009).
39		*
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 1.6 2008-05-14 14:31:48 chuckv Exp $
47	>	*  @version $Id$
48		*
49		*/
50
51		/* Standard includes independent of library */
52	+
53		#include <iostream>
54		#include <fstream>
55		#include <list>
#	Line 56 | Line 57
57		#include <iterator>
58		#include "math/ConvexHull.hpp"
59		#include "utils/simError.h"
59	–	using namespace oopse;
60
61	<	/* CGAL version of convex hull first then QHULL */
62	<	#ifdef HAVE_CGAL
61	>	#ifdef IS_MPI
62	>	#include <mpi.h>
63	>	#endif
64
65	<	#include <CGAL/basic.h>
65	<	#include <CGAL/Simple_cartesian.h>
66	<	#include <CGAL/Convex_hull_traits_3.h>
67	<	#include <CGAL/convex_hull_3.h>
68	<	#include <CGAL/double.h>
65	>	using namespace OpenMD;
66
67	<	#include <CGAL/Quotient.h>
68	<	#include <CGAL/MP_Float.h>
69	<	#include <CGAL/Lazy_exact_nt.h>
67	>	#ifdef HAVE_QHULL
68	>	extern "C"
69	>	{
70	>	#include <qhull/qhull.h>
71	>	#include <qhull/mem.h>
72	>	#include <qhull/qset.h>
73	>	#include <qhull/geom.h>
74	>	#include <qhull/merge.h>
75	>	#include <qhull/poly.h>
76	>	#include <qhull/io.h>
77	>	#include <qhull/stat.h>
78	>	}
79
80	<	typedef double RT;
81	<	typedef CGAL::Simple_cartesian<RT>                K;
76	<	typedef CGAL::Convex_hull_traits_3<K>             Traits;
77	<	typedef Traits::Polyhedron_3                      Polyhedron_3;
78	<	typedef K::Point_3                                Point;
80	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81	>	}
82
83	+	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
84	+
85	+	int numpoints = bodydoubles.size();
86
87	<	ConvexHull::ConvexHull(){}
82	<
83	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
84	<	{
87	>	Triangles_.clear();
88
89	<	std::vector<Point> points;
89	>	vertexT *vertex, **vertexp;
90	>	facetT *facet;
91	>	setT *vertices;
92	>	int curlong, totlong;
93	>	pointT *intPoint;
94
95	<
96	<	// Copy the positon vector into a points vector for cgal.
97	<	for (int i = 0; i < pos.size(); ++i)
98	<	{
99	<	Point pt(pos[i][0],pos[i][1],pos[i][2]);
100	<	points.push_back(pt);
101	<	}
102	<
103	<	// define object to hold convex hull
104	<	Polyhedron_3 ch_object_;
105	<	// compute convex hull
99	<	CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
100	<
101	<	for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin(); ch_object_.vertices_end(); ++v){
102	<	std::cout<< v.point()<<std::endl;
95	>	std::vector<double> ptArray(numpoints*dim_);
96	>
97	>	// Copy the positon vector into a points vector for qhull.
98	>	std::vector<StuntDouble*>::iterator SD;
99	>	int i = 0;
100	>	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
101	>	Vector3d pos = (*SD)->getPos();
102	>	ptArray[dim_ * i] = pos.x();
103	>	ptArray[dim_ * i + 1] = pos.y();
104	>	ptArray[dim_ * i + 2] = pos.z();
105	>	i++;
106		}
107
108	+	/* Clean up memory from previous convex hull calculations */
109	+	boolT ismalloc = False;
110
111	<	}
111	>	/* compute the hull for our local points (or all the points for single
112	>	processor versions) */
113	>	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
114	>	const_cast<char *>(options_.c_str()), NULL, stderr)) {
115	>
116	>	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
117	>	painCave.isFatal = 1;
118	>	simError();
119	>
120	>	} //qh_new_qhull
121
122
123	+	#ifdef IS_MPI
124	+	//If we are doing the mpi version, set up some vectors for data communication
125	+
126	+	int nproc = MPI::COMM_WORLD.Get_size();
127	+	int myrank = MPI::COMM_WORLD.Get_rank();
128	+	int localHullSites = 0;
129
130	<	#else
131	<	#ifdef HAVE_QHULL
132	<	/* Old options Qt Qu Qg QG0 FA */
133	<	ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
114	<	//ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
115	<	{}
130	>	std::vector<int> hullSitesOnProc(nproc, 0);
131	>	std::vector<int> coordsOnProc(nproc, 0);
132	>	std::vector<int> displacements(nproc, 0);
133	>	std::vector<int> vectorDisplacements(nproc, 0);
134
135	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
136	<	{
135	>	std::vector<double> coords;
136	>	std::vector<double> vels;
137	>	std::vector<int> indexMap;
138	>	std::vector<double> masses;
139	>
140	>	FORALLvertices{
141	>	localHullSites++;
142	>
143	>	int idx = qh_pointid(vertex->point);
144	>
145	>	indexMap.push_back(idx);
146	>
147	>	coords.push_back(ptArray[dim_  * idx]);
148	>	coords.push_back(ptArray[dim_  * idx + 1]);
149	>	coords.push_back(ptArray[dim_  * idx + 2]);
150	>
151	>	StuntDouble* sd = bodydoubles[idx];
152	>
153	>	Vector3d vel = sd->getVel();
154	>	vels.push_back(vel.x());
155	>	vels.push_back(vel.y());
156	>	vels.push_back(vel.z());
157	>
158	>	masses.push_back(sd->getMass());
159	>	}
160	>
161	>	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
162	>	1, MPI::INT);
163	>
164	>	int globalHullSites = 0;
165	>	for (int iproc = 0; iproc < nproc; iproc++){
166	>	globalHullSites += hullSitesOnProc[iproc];
167	>	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
168	>	}
169	>
170	>	displacements[0] = 0;
171	>	vectorDisplacements[0] = 0;
172
173	<
174	<	int numpoints = pos.size();
175	<	coordT* pt_array;
123	<	coordT* surfpt_array;
124	<	std::list<int> surface_atoms;
125	<	FILE *outdummy = NULL;
126	<	FILE *errdummy = NULL;
127	<
128	<	pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
129	<
130	<
131	<	for (int i = 0; i < numpoints; i++) {
132	<	pt_array[dim_ * i] = pos[i][0];
133	<	pt_array[dim_ * i + 1] = pos[i][1];
134	<	pt_array[dim_ * i + 2] = pos[i][2];
173	>	for (int iproc = 1; iproc < nproc; iproc++){
174	>	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
175	>	vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
176		}
177	+
178	+	std::vector<double> globalCoords(dim_ * globalHullSites);
179	+	std::vector<double> globalVels(dim_ * globalHullSites);
180	+	std::vector<double> globalMasses(globalHullSites);
181	+
182	+	int count = coordsOnProc[myrank];
183
184	<
185	<
186	<
140	<	/*
141	<	qh_initflags(const_cast<char *>(options_.c_str()));
142	<	qh_init_B(pospoints, numpoints, dim_, ismalloc);
143	<	qh_qhull();
144	<	qh_check_output();
184	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
185	>	&coordsOnProc[0], &vectorDisplacements[0],
186	>	MPI::DOUBLE);
187
188	<	qh_produce_output();
189	<	*/
190	<	boolT ismalloc = False;
188	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
189	>	&coordsOnProc[0], &vectorDisplacements[0],
190	>	MPI::DOUBLE);
191	>
192	>	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
193	>	&globalMasses[0], &hullSitesOnProc[0],
194	>	&displacements[0], MPI::DOUBLE);
195	>
196	>	// Free previous hull
197	>	qh_freeqhull(!qh_ALL);
198	>	qh_memfreeshort(&curlong, &totlong);
199	>	if (curlong || totlong) {
200	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
201	>	"\tdid not free %d bytes of long memory (%d pieces)",
202	>	totlong, curlong);
203	>	painCave.isFatal = 1;
204	>	simError();
205	>	}
206
207	<	if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
208	<	const_cast<char *>(options_.c_str()), NULL, stderr)) {
207	>	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
208	>	const_cast<char *>(options_.c_str()), NULL, stderr)){
209
210	<	vertexT *vertex, **vertexp;
211	<	facetT *facet;
212	<	setT *vertices;
156	<	unsigned int nf = qh num_facets;
210	>	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
211	>	painCave.isFatal = 1;
212	>	simError();
213
214	<	//Matrix idx(nf, dim);
215	<	/*
216	<	int j, i = 0, id = 0;
214	>	} //qh_new_qhull
215	>
216	>	#endif
217	>	intPoint = qh interior_point;
218	>	RealType calcvol = 0.0;
219	>	FORALLfacets {
220	>	Triangle face;
221	>	//Qhull sets the unit normal in facet->normal
222	>	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
223	>	face.setUnitNormal(V3dNormal);
224	>
225	>	RealType faceArea = qh_facetarea(facet);
226	>	face.setArea(faceArea);
227	>
228	>	vertices = qh_facet3vertex(facet);
229
230	<	int id2 = 0;
231	<	coordT *point,**pointp;
232	<	realT dist;
165	<	FORALLfacets {
166	<	j = 0;
167	<
168	<	if (!facet->simplicial){
169	<	// should never happen with Qt
170	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
171	<	painCave.isFatal = 0;
172	<	simError();
173	<	}
174	<
175	<	vertices = qh_facet3vertex(facet);
176	<	FOREACHvertex_(vertices){
177	<	id = qh_pointid(vertex->point);
178	<	surface_atoms.push_back(id);
179	<	//std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
180	<	}
181	<	qh_settempfree(&vertices);
182	<
183	<	FOREACHpoint_(facet->coplanarset){
184	<	vertex= qh_nearvertex (facet, point, &dist);
185	<	//id= qh_pointid (vertex->point);
186	<	id2= qh_pointid (point);
187	<	surface_atoms.push_back(id2);
188	<	//std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
189	<	//printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
190	<	//std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
191	<
192	<	}
193	<
194	<	}
195	<
196	<	*/
197	<
198	<
199	<	}
230	>	coordT *center = qh_getcenter(vertices);
231	>	Vector3d V3dCentroid(center[0], center[1], center[2]);
232	>	face.setCentroid(V3dCentroid);
233
234	+	Vector3d faceVel = V3Zero;
235	+	Vector3d p[3];
236	+	RealType faceMass = 0.0;
237
238	+	int ver = 0;
239
240	+	FOREACHvertex_(vertices){
241	+	int id = qh_pointid(vertex->point);
242	+	p[ver][0] = vertex->point[0];
243	+	p[ver][1] = vertex->point[1];
244	+	p[ver][2] = vertex->point[2];
245	+	Vector3d vel;
246	+	RealType mass;
247
248	<	qh_getarea(qh facet_list);
249	<	volume_ = qh totvol;
250	<	area_ = qh totarea;
251	<	//    FILE *newGeomFile;
252	<
209	<
210	<	/*
211	<	FORALLfacets {
212	<	for (int k=0; k < qh hull_dim; k++)
213	<	printf ("%6.2g ", facet->normal[k]);
214	<	printf ("\n");
215	<	}
216	<	*/
217	<
218	<	int curlong,totlong;
219	<	//    geomviewHull("junk.off");
220	<	qh_freeqhull(!qh_ALL);
221	<	qh_memfreeshort(&curlong, &totlong);
222	<	if (curlong || totlong)
223	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
224	<	<< totlong << curlong << std::endl;
225	<	free(pt_array);
226	<	/*
227	<	int j = 0;
228	<	surface_atoms.sort();
229	<	surface_atoms.unique();
230	<	surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
231	<	for(std::list<int>::iterator list_iter = surface_atoms.begin();
232	<	list_iter != surface_atoms.end(); list_iter++)
233	<	{
234	<	int i = *list_iter;
235	<	//surfpt_array[dim_ * j] = pos[i][0];
236	<	//surfpt_array[dim_ * j + 1] = pos[i][1];
237	<	//surfpt_array[dim_ * j + 2] = pos[i][2];
238	<	std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
239	<	j++;
240	<	}
241	<	*/
242	<
243	<	/*
244	<	std::string deloptions_ = "qhull d Qt";
245	<	facetT *facet, *neighbor;
246	<	ridgeT *ridge, **ridgep;
247	<
248	<	if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
249	<	const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
250	<
251	<	qh visit_id++;
252	<	FORALLfacets {
253	<	if (!facet->upperdelaunay) {
254	<	facet->visitid= qh visit_id;
255	<	qh_makeridges(facet);
256	<	FOREACHridge_(facet->ridges) {
257	<	neighbor= otherfacet_(ridge, facet);
258	<	if (neighbor->visitid != qh visit_id) {
259	<
260	<	FOREACHvertex_(ridge->vertices)
261	<	int id2 = qh_pointid (vertex->point);
262	<	std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
263	<	}
264	<	}
265	<	}
266	<
248	>	#ifdef IS_MPI
249	>	vel = Vector3d(globalVels[dim_ * id],
250	>	globalVels[dim_ * id + 1],
251	>	globalVels[dim_ * id + 2]);
252	>	mass = globalMasses[id];
253
254	+	// localID will be between 0 and hullSitesOnProc[myrank] if we
255	+	// own this guy.
256
257	<
270	<	}
257	>	int localID = id - displacements[myrank];
258
272	–	qh_freeqhull(!qh_ALL);
273	–	qh_memfreeshort(&curlong, &totlong);
274	–	if (curlong || totlong)
275	–	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
276	–	<< totlong << curlong << std::endl;
277	–	free(surfpt_array);
278	–	*/
279	–	return true;
280	–	}
259
260	+	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
261	+	face.addVertexSD(bodydoubles[indexMap[localID]]);
262	+	}else{
263	+	face.addVertexSD(NULL);
264	+	}
265	+	#else
266	+	vel = bodydoubles[id]->getVel();
267	+	mass = bodydoubles[id]->getMass();
268	+	face.addVertexSD(bodydoubles[id]);
269	+	#endif
270	+	faceVel = faceVel + vel;
271	+	faceMass = faceMass + mass;
272	+	ver++;
273	+	} //Foreachvertex
274
275	+	face.addVertices(p[0], p[1], p[2]);
276	+	face.setFacetMass(faceMass);
277	+	face.setFacetVelocity(faceVel/3.0);
278	+	/*
279	+	RealType comparea = face.computeArea();
280	+	realT calcarea = qh_facetarea (facet);
281	+	Vector3d V3dCompNorm = -face.computeUnitNormal();
282	+	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
283	+	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
284	+	std::cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  std::endl;
285	+	calcvol +=  -dist*comparea/qh hull_dim;
286	+	*/
287	+	Triangles_.push_back(face);
288	+	qh_settempfree(&vertices);
289
290	<	RealType ConvexHull::getVolume()
291	<	{
292	<	return volume_;
290	>	} //FORALLfacets
291	>
292	>	qh_getarea(qh facet_list);
293	>	volume_ = qh totvol;
294	>	area_ = qh totarea;
295	>	//  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl;
296	>	qh_freeqhull(!qh_ALL);
297	>	qh_memfreeshort(&curlong, &totlong);
298	>	if (curlong || totlong) {
299	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
300	>	"\tdid not free %d bytes of long memory (%d pieces)",
301	>	totlong, curlong);
302	>	painCave.isFatal = 1;
303	>	simError();
304	>	}
305		}
306
307	<	void ConvexHull::geomviewHull(const std::string& geomFileName)
290	<	{
307	>	void ConvexHull::printHull(const std::string& geomFileName) {
308
309	+	#ifdef IS_MPI
310	+	if (worldRank == 0)  {
311	+	#endif
312		FILE *newGeomFile;
313
314		//create new .md file based on old .md file
#	Line 298 | Line 318 | void ConvexHull::geomviewHull(const std::string& geomF
318		qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
319
320		fclose(newGeomFile);
321	+	#ifdef IS_MPI
322	+	}
323	+	#endif
324		}
325		#endif //QHULL
303	–	#endif //CGAL
304	–
305	–
306	–

Comparing:
trunk/src/math/ConvexHull.cpp (property svn:keywords), Revision 1242 by chuckv, Wed May 14 14:31:48 2008 UTC vs.
branches/development/src/math/ConvexHull.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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