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

Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1097 by chuckv, Thu Dec 14 19:32:32 2006 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 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 and radius
44	<	*  using the CGAL library.
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 1.1 2006-12-14 19:32:32 chuckv Exp $
47	>	*  @version $Id$
48		*
49		*/
50
51	<	#include "math/ConvexHull.hpp"
51	>	/* Standard includes independent of library */
52	>
53		#include <iostream>
54		#include <fstream>
55	+	#include <list>
56	+	#include <algorithm>
57	+	#include <iterator>
58	+	#include "math/ConvexHull.hpp"
59	+	#include "utils/simError.h"
60
61	+	#ifdef IS_MPI
62	+	#include <mpi.h>
63	+	#endif
64
65	<	using namespace oopse;
65	>	using namespace OpenMD;
66
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	+	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	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
88	<	{
87	>	Triangles_.clear();
88	>
89	>	vertexT *vertex, **vertexp;
90	>	facetT *facet;
91	>	setT *vertices;
92	>	int curlong, totlong;
93	>	pointT *intPoint;
94	>
95	>	std::vector<double> ptArray(numpoints*dim_);
96
97	<	std::vector<Point_3> points;
98	<	points.reserve(pos.size());
99	<	// Copy the positon vector into a points vector for cgal.
100	<	for (int i = 0; i < pos.size(); ++i)
101	<	{
102	<	Point_3 pt(pos[i][0],pos[i][1],pos[i][2]);
103	<	points.push_back(pt);
104	<	}
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	>	/* 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
74	–	// compute convex hull
75	–	CGAL::convex_hull_3(points.begin(), points.end(), ch_object);
76	–	// Make sure hull is a polyhedron
77	–	if ( CGAL::assign(ch_polyhedron, ch_object) )
78	–	{
79	–	return true;
80	–	}
81	–	else
82	–	{
83	–	return false;
84	–	}
85	–	}
122
123	<	RealType ConvexHull::getVolume()
124	<	{
125	<	/*
126	<	std::list<Point> L;
127	<	L.push_front(Point(0,0,0));
128	<	L.push_front(Point(1,0,0));
93	<	L.push_front(Point(0,1,0));
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	<	Triangulation T(L.begin(), L.end());
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	<	int n = T.number_of_vertices();
135	>	std::vector<double> coords;
136	>	std::vector<double> vels;
137	>	std::vector<int> indexMap;
138	>	std::vector<double> masses;
139
140	<	// insertion from a vector :
141	<	std::vector<Point> V(3);
142	<	V[0] = Point(0,0,1);
143	<	V[1] = Point(1,1,1);
103	<	V[2] = Point(2,2,2);
140	>	FORALLvertices{
141	>	localHullSites++;
142	>
143	>	int idx = qh_pointid(vertex->point);
144
145	<	n = n + T.insert(V.begin(), V.end());
145	>	indexMap.push_back(idx);
146
147	<	assert( n == 6 );       // 6 points have been inserted
148	<	assert( T.is_valid() ); // checking validity of T
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	<	double sum_v = 0;
111	<	for(Triangulation::Cell_iterator c_it = T.cells_begin(); c_it != T.cells_end(); ++c_it)
112	<	{
113	<	sum_v += T.tetrahedron(c_it).volume();
114	<	}
115	<	std::cout << "sum_v " << sum_v << std::endl;
116	<	*/
117	<	return 0.0;
118	<	}
151	>	StuntDouble* sd = bodydoubles[idx];
152
153	<	void ConvexHull::geomviewHull(const std::string& geomFileName)
154	<	{
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	<	std::ofstream newGeomFile;
158	>	masses.push_back(sd->getMass());
159	>	}
160
161	<	//create new .md file based on old .md file
162	<	newGeomFile.open(geomFileName.c_str());
161	>	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
162	>	1, MPI::INT);
163
164	<	// Write polyhedron in Object File Format (OFF).
165	<	CGAL::set_ascii_mode( std::cout);
166	<	newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' '
167	<	<< ch_polyhedron.size_of_facets() << " 0" << std::endl;
168	<	std::copy( ch_polyhedron.points_begin(), ch_polyhedron.points_end(),
133	<	std::ostream_iterator<Point_3>( newGeomFile, "\n"));
134	<	for (  Facet_iterator i = ch_polyhedron.facets_begin(); i != ch_polyhedron.facets_end(); ++i)
135	<	{
136	<	Halfedge_facet_circulator j = i->facet_begin();
137	<	// Facets in polyhedral surfaces are at least triangles.
138	<	CGAL_assertion( CGAL::circulator_size(j) >= 3);
139	<	newGeomFile << CGAL::circulator_size(j) << ' ';
140	<	do
141	<	{
142	<	newGeomFile << ' ' << std::distance(ch_polyhedron.vertices_begin(), j->vertex());
143	<	}
144	<	while ( ++j != i->facet_begin());
145	<	newGeomFile << std::endl;
146	<	}
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	<	newGeomFile.close();
170	>	displacements[0] = 0;
171	>	vectorDisplacements[0] = 0;
172	>
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	+	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
185	+	&coordsOnProc[0], &vectorDisplacements[0],
186	+	MPI::DOUBLE);
187	+
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_, globalHullSites, &globalCoords[0], ismalloc,
208	+	const_cast<char *>(options_.c_str()), NULL, stderr)){
209	+
210	+	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
211	+	painCave.isFatal = 1;
212	+	simError();
213	+
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	+	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	+	#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	+	int localID = id - displacements[myrank];
258	+
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	+	} //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::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
315	+	newGeomFile = fopen(geomFileName.c_str(), "w");
316	+	qh_findgood_all(qh facet_list);
317	+	for (int i = 0; i < qh_PRINTEND; i++)
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

Comparing trunk/src/math/ConvexHull.cpp (property svn:keywords):
Revision 1097 by chuckv, Thu Dec 14 19:32:32 2006 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

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