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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 1850 by gezelter, Wed Feb 20 15:39:39 2013 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, 234107 (2008).
38	+	* [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
39	+	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40		*
41		*  ConvexHull.cpp
42		*
#	Line 44 | Line 44
44		*
45		*  Created by Charles F. Vardeman II on 11 Dec 2006.
46		*  @author  Charles F. Vardeman II
47	<	*  @version $Id: ConvexHull.cpp,v 1.6 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	>	#include "math/qhull.hpp"
66
67	<	#include <CGAL/Quotient.h>
68	<	#include <CGAL/MP_Float.h>
72	<	#include <CGAL/Lazy_exact_nt.h>
67	>	#ifdef HAVE_QHULL
68	>	using namespace OpenMD;
69
70	<	typedef double RT;
71	<	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;
70	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
71	>	}
72
73	+	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
74	+
75	+	int numpoints = bodydoubles.size();
76
77	<	ConvexHull::ConvexHull(){}
82	<
83	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
84	<	{
77	>	Triangles_.clear();
78
79	<	std::vector<Point> points;
79	>	vertexT *vertex, **vertexp;
80	>	facetT *facet;
81	>	setT *vertices;
82	>	int curlong, totlong;
83	>	// pointT *intPoint;
84
85	<
86	<	// Copy the positon vector into a points vector for cgal.
87	<	for (int i = 0; i < pos.size(); ++i)
88	<	{
89	<	Point pt(pos[i][0],pos[i][1],pos[i][2]);
90	<	points.push_back(pt);
91	<	}
92	<
93	<	// define object to hold convex hull
94	<	Polyhedron_3 ch_object_;
95	<	// compute convex hull
96	<	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;
85	>	std::vector<double> ptArray(numpoints*dim_);
86	>
87	>	// Copy the positon vector into a points vector for qhull.
88	>	std::vector<StuntDouble*>::iterator SD;
89	>	int i = 0;
90	>
91	>	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
92	>	Vector3d pos = (*SD)->getPos();
93	>	ptArray[dim_ * i] = pos.x();
94	>	ptArray[dim_ * i + 1] = pos.y();
95	>	ptArray[dim_ * i + 2] = pos.z();
96	>	i++;
97		}
98
99	+	/* Clean up memory from previous convex hull calculations */
100	+	boolT ismalloc = False;
101
102	<	}
102	>	/* compute the hull for our local points (or all the points for single
103	>	processor versions) */
104	>	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
105	>	const_cast<char *>(options_.c_str()), NULL, stderr)) {
106	>
107	>	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
108	>	painCave.isFatal = 1;
109	>	simError();
110	>
111	>	} //qh_new_qhull
112
113
114	+	#ifdef IS_MPI
115	+	//If we are doing the mpi version, set up some vectors for data communication
116	+
117	+	int nproc = MPI::COMM_WORLD.Get_size();
118	+	int myrank = MPI::COMM_WORLD.Get_rank();
119	+	int localHullSites = 0;
120
121	<	#else
122	<	#ifdef HAVE_QHULL
123	<	/* Old options Qt Qu Qg QG0 FA */
124	<	ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
114	<	//ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
115	<	{}
121	>	std::vector<int> hullSitesOnProc(nproc, 0);
122	>	std::vector<int> coordsOnProc(nproc, 0);
123	>	std::vector<int> displacements(nproc, 0);
124	>	std::vector<int> vectorDisplacements(nproc, 0);
125
126	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
127	<	{
126	>	std::vector<double> coords;
127	>	std::vector<double> vels;
128	>	std::vector<int> indexMap;
129	>	std::vector<double> masses;
130	>
131	>	FORALLvertices{
132	>	localHullSites++;
133	>
134	>	int idx = qh_pointid(vertex->point);
135	>
136	>	indexMap.push_back(idx);
137	>
138	>	coords.push_back(ptArray[dim_  * idx]);
139	>	coords.push_back(ptArray[dim_  * idx + 1]);
140	>	coords.push_back(ptArray[dim_  * idx + 2]);
141	>
142	>	StuntDouble* sd = bodydoubles[idx];
143	>
144	>	Vector3d vel = sd->getVel();
145	>	vels.push_back(vel.x());
146	>	vels.push_back(vel.y());
147	>	vels.push_back(vel.z());
148	>
149	>	masses.push_back(sd->getMass());
150	>	}
151	>
152	>	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
153	>	1, MPI::INT);
154	>
155	>	int globalHullSites = 0;
156	>	for (int iproc = 0; iproc < nproc; iproc++){
157	>	globalHullSites += hullSitesOnProc[iproc];
158	>	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
159	>	}
160	>
161	>	displacements[0] = 0;
162	>	vectorDisplacements[0] = 0;
163
164	<
165	<	int numpoints = pos.size();
166	<	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];
164	>	for (int iproc = 1; iproc < nproc; iproc++){
165	>	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
166	>	vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
167		}
168	+
169	+	std::vector<double> globalCoords(dim_ * globalHullSites);
170	+	std::vector<double> globalVels(dim_ * globalHullSites);
171	+	std::vector<double> globalMasses(globalHullSites);
172	+
173	+	int count = coordsOnProc[myrank];
174
175	<
176	<
177	<
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();
175	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
176	>	&coordsOnProc[0], &vectorDisplacements[0],
177	>	MPI::DOUBLE);
178
179	<	qh_produce_output();
180	<	*/
181	<	boolT ismalloc = False;
179	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
180	>	&coordsOnProc[0], &vectorDisplacements[0],
181	>	MPI::DOUBLE);
182	>
183	>	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
184	>	&globalMasses[0], &hullSitesOnProc[0],
185	>	&displacements[0], MPI::DOUBLE);
186	>
187	>	// Free previous hull
188	>	qh_freeqhull(!qh_ALL);
189	>	qh_memfreeshort(&curlong, &totlong);
190	>	if (curlong || totlong) {
191	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
192	>	"\tdid not free %d bytes of long memory (%d pieces)",
193	>	totlong, curlong);
194	>	painCave.isFatal = 1;
195	>	simError();
196	>	}
197
198	<	if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
199	<	const_cast<char *>(options_.c_str()), NULL, stderr)) {
152	<
153	<	vertexT *vertex, **vertexp;
154	<	facetT *facet;
155	<	setT *vertices;
156	<	unsigned int nf = qh num_facets;
198	>	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
199	>	const_cast<char *>(options_.c_str()), NULL, stderr)){
200
201	<	//Matrix idx(nf, dim);
202	<	/*
203	<	int j, i = 0, id = 0;
201	>	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
202	>	painCave.isFatal = 1;
203	>	simError();
204	>
205	>	} //qh_new_qhull
206	>
207	>	#endif
208	>	// commented out below, so comment out here also.
209	>	// intPoint = qh interior_point;
210	>	// RealType calcvol = 0.0;
211	>	FORALLfacets {
212	>	Triangle face;
213	>	//Qhull sets the unit normal in facet->normal
214	>	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
215	>	face.setUnitNormal(V3dNormal);
216	>
217	>	RealType faceArea = qh_facetarea(facet);
218	>	face.setArea(faceArea);
219	>
220	>	vertices = qh_facet3vertex(facet);
221
222	<	int id2 = 0;
223	<	coordT *point,**pointp;
224	<	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	<	}
222	>	coordT *center = qh_getcenter(vertices);
223	>	Vector3d V3dCentroid(center[0], center[1], center[2]);
224	>	face.setCentroid(V3dCentroid);
225
226	+	Vector3d faceVel = V3Zero;
227	+	Vector3d p[3];
228	+	RealType faceMass = 0.0;
229
230	+	int ver = 0;
231
232	+	FOREACHvertex_(vertices){
233	+	int id = qh_pointid(vertex->point);
234	+	p[ver][0] = vertex->point[0];
235	+	p[ver][1] = vertex->point[1];
236	+	p[ver][2] = vertex->point[2];
237	+	Vector3d vel;
238	+	RealType mass;
239
240	<	qh_getarea(qh facet_list);
241	<	volume_ = qh totvol;
242	<	area_ = qh totarea;
243	<	//    FILE *newGeomFile;
244	<
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	<
240	>	#ifdef IS_MPI
241	>	vel = Vector3d(globalVels[dim_ * id],
242	>	globalVels[dim_ * id + 1],
243	>	globalVels[dim_ * id + 2]);
244	>	mass = globalMasses[id];
245
246	+	// localID will be between 0 and hullSitesOnProc[myrank] if we
247	+	// own this guy.
248
249	<
270	<	}
249	>	int localID = id - displacements[myrank];
250
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	–	}
251
252	+	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
253	+	face.addVertexSD(bodydoubles[indexMap[localID]]);
254	+	}else{
255	+	face.addVertexSD(NULL);
256	+	}
257	+	#else
258	+	vel = bodydoubles[id]->getVel();
259	+	mass = bodydoubles[id]->getMass();
260	+	face.addVertexSD(bodydoubles[id]);
261	+	#endif
262	+	faceVel = faceVel + vel;
263	+	faceMass = faceMass + mass;
264	+	ver++;
265	+	} //Foreachvertex
266
267	+	face.addVertices(p[0], p[1], p[2]);
268	+	face.setFacetMass(faceMass);
269	+	face.setFacetVelocity(faceVel / RealType(3.0));
270	+	/*
271	+	RealType comparea = face.computeArea();
272	+	realT calcarea = qh_facetarea (facet);
273	+	Vector3d V3dCompNorm = -face.computeUnitNormal();
274	+	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
275	+	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
276	+	std::cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  std::endl;
277	+	calcvol +=  -dist*comparea/qh hull_dim;
278	+	*/
279	+	Triangles_.push_back(face);
280	+	qh_settempfree(&vertices);
281
282	<	RealType ConvexHull::getVolume()
283	<	{
284	<	return volume_;
282	>	} //FORALLfacets
283	>
284	>	qh_getarea(qh facet_list);
285	>	volume_ = qh totvol;
286	>	area_ = qh totarea;
287	>	//  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl;
288	>	qh_freeqhull(!qh_ALL);
289	>	qh_memfreeshort(&curlong, &totlong);
290	>	if (curlong || totlong) {
291	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
292	>	"\tdid not free %d bytes of long memory (%d pieces)",
293	>	totlong, curlong);
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297		}
298
299	<	void ConvexHull::geomviewHull(const std::string& geomFileName)
290	<	{
299	>	void ConvexHull::printHull(const std::string& geomFileName) {
300
301	+	#ifdef IS_MPI
302	+	if (worldRank == 0)  {
303	+	#endif
304		FILE *newGeomFile;
305
306		//create new .md file based on old .md file
#	Line 298 | Line 310 | void ConvexHull::geomviewHull(const std::string& geomF
310		qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
311
312		fclose(newGeomFile);
313	+	#ifdef IS_MPI
314	+	}
315	+	#endif
316		}
317		#endif //QHULL
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 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

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