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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 2071 by gezelter, Sat Mar 7 21:41:51 2015 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	+	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
40		*
41		*  ConvexHull.cpp
42		*
43	<	*  Purpose: To calculate convexhull, hull volume and radius
44	<	*  using the CGAL library.
45	<	*
46	<	*  Created by Charles F. Vardeman II on 11 Dec 2006.
47	<	*  @author  Charles F. Vardeman II
48	<	*  @version $Id: ConvexHull.cpp,v 1.1 2006-12-14 19:32:32 chuckv Exp $
49	<	*
43	>	*  Purpose: To calculate a convex hull.
44		*/
45
46	<	#include "math/ConvexHull.hpp"
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>
55	+	#include <algorithm>
56	+	#include <iterator>
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	+	ConvexHull::ConvexHull() : Hull(), options_("qhull FA Qt Pp"), dim_(3) {
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	+	vector<double> ptArray(numpoints*dim_);
81
82	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
83	<	{
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
65	–	std::vector<Point_3> points;
66	–	points.reserve(pos.size());
67	–	// Copy the positon vector into a points vector for cgal.
68	–	for (int i = 0; i < pos.size(); ++i)
69	–	{
70	–	Point_3 pt(pos[i][0],pos[i][1],pos[i][2]);
71	–	points.push_back(pt);
72	–	}
108
109	<	// compute convex hull
110	<	CGAL::convex_hull_3(points.begin(), points.end(), ch_object);
111	<	// Make sure hull is a polyhedron
112	<	if ( CGAL::assign(ch_polyhedron, ch_object) )
113	<	{
114	<	return true;
115	<	}
116	<	else
82	<	{
83	<	return false;
84	<	}
85	<	}
109	>	#ifdef IS_MPI
110	>	//If we are doing the mpi version, set up some vectors for data communication
111	>
112	>	int nproc;
113	>	int myrank;
114	>
115	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
116	>	MPI_Comm_rank( MPI_COMM_WORLD, &myrank);
117
118	<	RealType ConvexHull::getVolume()
88	<	{
89	<	/*
90	<	std::list<Point> L;
91	<	L.push_front(Point(0,0,0));
92	<	L.push_front(Point(1,0,0));
93	<	L.push_front(Point(0,1,0));
118	>	int localHullSites = 0;
119
120	<	Triangulation T(L.begin(), L.end());
120	>	vector<int> hullSitesOnProc(nproc, 0);
121	>	vector<int> coordsOnProc(nproc, 0);
122	>	vector<int> displacements(nproc, 0);
123	>	vector<int> vectorDisplacements(nproc, 0);
124
125	<	int n = T.number_of_vertices();
125	>	vector<double> coords;
126	>	vector<double> vels;
127	>	vector<int> indexMap;
128	>	vector<double> masses;
129
130	<	// insertion from a vector :
131	<	std::vector<Point> V(3);
132	<	V[0] = Point(0,0,1);
133	<	V[1] = Point(1,1,1);
103	<	V[2] = Point(2,2,2);
130	>	FORALLvertices{
131	>	localHullSites++;
132	>
133	>	int idx = qh_pointid(vertex->point);
134
135	<	n = n + T.insert(V.begin(), V.end());
135	>	indexMap.push_back(idx);
136
137	<	assert( n == 6 );       // 6 points have been inserted
138	<	assert( T.is_valid() ); // checking validity of T
137	>	coords.push_back(ptArray[dim_  * idx]);
138	>	coords.push_back(ptArray[dim_  * idx + 1]);
139	>	coords.push_back(ptArray[dim_  * idx + 2]);
140
141	<	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	<	}
141	>	StuntDouble* sd = bodydoubles[idx];
142
143	<	void ConvexHull::geomviewHull(const std::string& geomFileName)
144	<	{
143	>	Vector3d vel = sd->getVel();
144	>	vels.push_back(vel.x());
145	>	vels.push_back(vel.y());
146	>	vels.push_back(vel.z());
147
148	<	std::ofstream newGeomFile;
148	>	masses.push_back(sd->getMass());
149	>	}
150
151	<	//create new .md file based on old .md file
152	<	newGeomFile.open(geomFileName.c_str());
151	>	MPI_Allgather(&localHullSites, 1, MPI_INT, &hullSitesOnProc[0],
152	>	1, MPI_INT, MPI_COMM_WORLD);
153
154	<	// Write polyhedron in Object File Format (OFF).
155	<	CGAL::set_ascii_mode( std::cout);
156	<	newGeomFile << "OFF" << std::endl << ch_polyhedron.size_of_vertices() << ' '
157	<	<< ch_polyhedron.size_of_facets() << " 0" << std::endl;
158	<	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	<	}
154	>	int globalHullSites = 0;
155	>	for (int iproc = 0; iproc < nproc; iproc++){
156	>	globalHullSites += hullSitesOnProc[iproc];
157	>	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
158	>	}
159
160	<	newGeomFile.close();
160	>	displacements[0] = 0;
161	>	vectorDisplacements[0] = 0;
162	>
163	>	for (int iproc = 1; iproc < nproc; iproc++){
164	>	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
165	>	vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
166	>	}
167
168	+	vector<double> globalCoords(dim_ * globalHullSites);
169	+	vector<double> globalVels(dim_ * globalHullSites);
170	+	vector<double> globalMasses(globalHullSites);
171
172	+	int count = coordsOnProc[myrank];
173	+
174	+	MPI_Allgatherv(&coords[0], count, MPI_DOUBLE, &globalCoords[0],
175	+	&coordsOnProc[0], &vectorDisplacements[0],
176	+	MPI_DOUBLE, MPI_COMM_WORLD);
177	+
178	+	MPI_Allgatherv(&vels[0], count, MPI_DOUBLE, &globalVels[0],
179	+	&coordsOnProc[0], &vectorDisplacements[0],
180	+	MPI_DOUBLE, MPI_COMM_WORLD);
181	+
182	+	MPI_Allgatherv(&masses[0], localHullSites, MPI_DOUBLE,
183	+	&globalMasses[0], &hullSitesOnProc[0],
184	+	&displacements[0], MPI_DOUBLE, MPI_COMM_WORLD);
185	+
186	+	// Free previous hull
187	+	qh_freeqhull(!qh_ALL);
188	+	qh_memfreeshort(&curlong, &totlong);
189	+	if (curlong || totlong) {
190	+	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
191	+	"\tdid not free %d bytes of long memory (%d pieces)",
192	+	totlong, curlong);
193	+	painCave.isFatal = 1;
194	+	simError();
195	+	}
196	+
197	+	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
198	+	const_cast<char *>(options_.c_str()), NULL, stderr)){
199	+
200	+	sprintf(painCave.errMsg,
201	+	"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	+
212	+	qh_triangulate ();
213	+
214	+	FORALLfacets {
215	+	Triangle face;
216	+	//Qhull sets the unit normal in facet->normal
217	+	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
218	+	face.setUnitNormal(V3dNormal);
219	+
220	+	RealType faceArea = qh_facetarea(facet);
221	+	face.setArea(faceArea);
222	+
223	+	vertices = qh_facet3vertex(facet);
224	+
225	+	coordT *center = qh_getcenter(vertices);
226	+	Vector3d V3dCentroid(center[0], center[1], center[2]);
227	+	face.setCentroid(V3dCentroid);
228	+
229	+	Vector3d faceVel = V3Zero;
230	+	Vector3d p[3];
231	+	RealType faceMass = 0.0;
232	+
233	+	int ver = 0;
234	+
235	+	FOREACHvertex_(vertices){
236	+	int id = qh_pointid(vertex->point);
237	+	p[ver][0] = vertex->point[0];
238	+	p[ver][1] = vertex->point[1];
239	+	p[ver][2] = vertex->point[2];
240	+	Vector3d vel;
241	+	RealType mass;
242	+
243	+	#ifdef IS_MPI
244	+	vel = Vector3d(globalVels[dim_ * id],
245	+	globalVels[dim_ * id + 1],
246	+	globalVels[dim_ * id + 2]);
247	+	mass = globalMasses[id];
248	+
249	+	// localID will be between 0 and hullSitesOnProc[myrank] if we
250	+	// own this guy.
251	+
252	+	int localID = id - displacements[myrank];
253	+
254	+
255	+	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
256	+	face.addVertexSD(bodydoubles[indexMap[localID]]);
257	+	}else{
258	+	face.addVertexSD(NULL);
259	+	}
260	+	#else
261	+	vel = bodydoubles[id]->getVel();
262	+	mass = bodydoubles[id]->getMass();
263	+	face.addVertexSD(bodydoubles[id]);
264	+	#endif
265	+	faceVel = faceVel + vel;
266	+	faceMass = faceMass + mass;
267	+	ver++;
268	+	} //Foreachvertex
269	+
270	+	face.addVertices(p[0], p[1], p[2]);
271	+	face.setFacetMass(faceMass);
272	+	face.setFacetVelocity(faceVel / RealType(3.0));
273	+	/*
274	+	RealType comparea = face.computeArea();
275	+	realT calcarea = qh_facetarea (facet);
276	+	Vector3d V3dCompNorm = -face.computeUnitNormal();
277	+	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
278	+	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
279	+	cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  endl;
280	+	calcvol +=  -dist*comparea/qh hull_dim;
281	+	*/
282	+	Triangles_.push_back(face);
283	+	qh_settempfree(&vertices);
284	+
285	+	} //FORALLfacets
286	+
287	+	qh_getarea(qh facet_list);
288	+	volume_ = qh totvol;
289	+	area_ = qh totarea;
290	+
291	+	qh_freeqhull(!qh_ALL);
292	+	qh_memfreeshort(&curlong, &totlong);
293	+	if (curlong || totlong) {
294	+	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
295	+	"\tdid not free %d bytes of long memory (%d pieces)",
296	+	totlong, curlong);
297	+	painCave.isFatal = 1;
298	+	simError();
299	+	}
300		}
301	+
302	+	void ConvexHull::printHull(const string& geomFileName) {
303	+
304	+	#ifdef IS_MPI
305	+	if (worldRank == 0)  {
306	+	#endif
307	+	FILE *newGeomFile;
308	+
309	+	//create new .md file based on old .md file
310	+	newGeomFile = fopen(geomFileName.c_str(), "w");
311	+	qh_findgood_all(qh facet_list);
312	+	for (int i = 0; i < qh_PRINTEND; i++)
313	+	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
314	+
315	+	fclose(newGeomFile);
316	+	#ifdef IS_MPI
317	+	}
318	+	#endif
319	+	}
320	+	#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 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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