ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1261 by chuckv, Wed Jun 18 17:03:30 2008 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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 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 1.7 2008-06-18 17:03:30 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 56 | Line 56
56		#include <iterator>
57		#include "math/ConvexHull.hpp"
58		#include "utils/simError.h"
59	–	using namespace oopse;
59
60	<	/* CGAL version of convex hull first then QHULL */
62	<	#ifdef HAVE_CGAL
60	>	#include "math/qhull.hpp"
61
62	<	#include <CGAL/basic.h>
63	<	#include <CGAL/Simple_cartesian.h>
64	<	#include <CGAL/Convex_hull_traits_3.h>
67	<	#include <CGAL/convex_hull_3.h>
68	<	#include <CGAL/double.h>
62	>	#ifdef HAVE_QHULL
63	>	using namespace OpenMD;
64	>	using namespace std;
65
66	<	#include <CGAL/Quotient.h>
67	<	#include <CGAL/MP_Float.h>
72	<	#include <CGAL/Lazy_exact_nt.h>
66	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") {
67	>	}
68
69	<	typedef double RT;
70	<	typedef CGAL::Simple_cartesian<RT>                K;
71	<	typedef CGAL::Convex_hull_traits_3<K>             Traits;
72	<	typedef Traits::Polyhedron_3                      Polyhedron_3;
73	<	typedef K::Point_3                                Point_3;
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	<	ConvexHull::ConvexHull(){}
83	<
84	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
85	<	{
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	<	std::vector<Point_3> points;
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	+	#ifdef IS_MPI
110	+	//If we are doing the mpi version, set up some vectors for data communication
111
112	<	// Copy the positon vector into a points vector for cgal.
113	<	for (int i = 0; i < pos.size(); ++i)
91	<	{
92	<	Point_3 pt(pos[i][0],pos[i][1],pos[i][2]);
93	<	points.push_back(pt);
94	<	}
112	>	int nproc;
113	>	int myrank;
114
115	<	// define object to hold convex hull
116	<	CGAL::Object ch_object_;
98	<	Polyhedron_3 polyhedron;
115	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
116	>	MPI_Comm_rank( MPI_COMM_WORLD, &myrank);
117
118	<	// compute convex hull
101	<	std::cerr << "Creating hull" << std::endl;
102	<	CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
103	<	std::cerr << "Done Creating hull" << std::endl;
104	<	std::vector<Point_3>::const_iterator p_it;
118	>	int localHullSites = 0;
119
120	<	for (p_it = points.begin(); p_it != points.end(); p_it++)
121	<	{
122	<	std::cerr << (*p_it).x() << std::endl;
123	<	}
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	<	/*
126	<	for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin();
127	<	ch_object_.vertices_end(); ++v){
128	<	std::cout<< v.point()<<std::endl;
125	>	vector<double> coords;
126	>	vector<double> vels;
127	>	vector<int> indexMap;
128	>	vector<double> masses;
129	>
130	>	FORALLvertices{
131	>	localHullSites++;
132	>
133	>	int idx = qh_pointid(vertex->point);
134	>
135	>	indexMap.push_back(idx);
136	>
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	>	StuntDouble* sd = bodydoubles[idx];
142	>
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	>	masses.push_back(sd->getMass());
149		}
116	–	*/
117	–	}
150
151	+	MPI_Allgather(&localHullSites, 1, MPI_INT, &hullSitesOnProc[0],
152	+	1, MPI_INT, MPI_COMM_WORLD);
153
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	<	#else
161	<	#ifdef HAVE_QHULL
162	<	/* Old options Qt Qu Qg QG0 FA */
163	<	ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
164	<	//ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
165	<	{}
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	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
169	<	{
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	<	int numpoints = pos.size();
179	<	coordT* pt_array;
180	<	coordT* surfpt_array;
135	<	std::list<int> surface_atoms;
136	<	FILE *outdummy = NULL;
137	<	FILE *errdummy = NULL;
178	>	MPI_Allgatherv(&vels[0], count, MPI_DOUBLE, &globalVels[0],
179	>	&coordsOnProc[0], &vectorDisplacements[0],
180	>	MPI_DOUBLE, MPI_COMM_WORLD);
181
182	<	pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
182	>	MPI_Allgatherv(&masses[0], localHullSites, MPI_DOUBLE,
183	>	&globalMasses[0], &hullSitesOnProc[0],
184	>	&displacements[0], MPI_DOUBLE, MPI_COMM_WORLD);
185
186	<
187	<	for (int i = 0; i < numpoints; i++) {
188	<	pt_array[dim_ * i] = pos[i][0];
189	<	pt_array[dim_ * i + 1] = pos[i][1];
190	<	pt_array[dim_ * i + 2] = pos[i][2];
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	<
198	<
150	<
151	<	/*
152	<	qh_initflags(const_cast<char *>(options_.c_str()));
153	<	qh_init_B(pospoints, numpoints, dim_, ismalloc);
154	<	qh_qhull();
155	<	qh_check_output();
156	<
157	<	qh_produce_output();
158	<	*/
159	<	boolT ismalloc = False;
160	<
161	<	if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
162	<	const_cast<char *>(options_.c_str()), NULL, stderr)) {
197	>	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
198	>	const_cast<char *>(options_.c_str()), NULL, stderr)){
199
200	<	vertexT *vertex, **vertexp;
201	<	facetT *facet;
202	<	setT *vertices;
203	<	unsigned int nf = qh num_facets;
200	>	sprintf(painCave.errMsg,
201	>	"ConvexHull: Qhull failed to compute global convex hull");
202	>	painCave.isFatal = 1;
203	>	simError();
204
205	<	//Matrix idx(nf, dim);
206	<	/*
207	<	int j, i = 0, id = 0;
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	<	int id2 = 0;
226	<	coordT *point,**pointp;
227	<	realT dist;
176	<	FORALLfacets {
177	<	j = 0;
178	<
179	<	if (!facet->simplicial){
180	<	// should never happen with Qt
181	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
182	<	painCave.isFatal = 0;
183	<	simError();
184	<	}
185	<
186	<	vertices = qh_facet3vertex(facet);
187	<	FOREACHvertex_(vertices){
188	<	id = qh_pointid(vertex->point);
189	<	surface_atoms.push_back(id);
190	<	//std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
191	<	}
192	<	qh_settempfree(&vertices);
193	<
194	<	FOREACHpoint_(facet->coplanarset){
195	<	vertex= qh_nearvertex (facet, point, &dist);
196	<	//id= qh_pointid (vertex->point);
197	<	id2= qh_pointid (point);
198	<	surface_atoms.push_back(id2);
199	<	//std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
200	<	//printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
201	<	//std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
202	<
203	<	}
204	<
205	<	}
206	<
207	<	*/
208	<
209	<
210	<	}
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	<	qh_getarea(qh facet_list);
244	<	volume_ = qh totvol;
245	<	area_ = qh totarea;
246	<	//    FILE *newGeomFile;
247	<
220	<
221	<	/*
222	<	FORALLfacets {
223	<	for (int k=0; k < qh hull_dim; k++)
224	<	printf ("%6.2g ", facet->normal[k]);
225	<	printf ("\n");
226	<	}
227	<	*/
228	<
229	<	int curlong,totlong;
230	<	//    geomviewHull("junk.off");
231	<	qh_freeqhull(!qh_ALL);
232	<	qh_memfreeshort(&curlong, &totlong);
233	<	if (curlong || totlong)
234	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
235	<	<< totlong << curlong << std::endl;
236	<	free(pt_array);
237	<	/*
238	<	int j = 0;
239	<	surface_atoms.sort();
240	<	surface_atoms.unique();
241	<	surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
242	<	for(std::list<int>::iterator list_iter = surface_atoms.begin();
243	<	list_iter != surface_atoms.end(); list_iter++)
244	<	{
245	<	int i = *list_iter;
246	<	//surfpt_array[dim_ * j] = pos[i][0];
247	<	//surfpt_array[dim_ * j + 1] = pos[i][1];
248	<	//surfpt_array[dim_ * j + 2] = pos[i][2];
249	<	std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
250	<	j++;
251	<	}
252	<	*/
253	<
254	<	/*
255	<	std::string deloptions_ = "qhull d Qt";
256	<	facetT *facet, *neighbor;
257	<	ridgeT *ridge, **ridgep;
258	<
259	<	if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
260	<	const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
261	<
262	<	qh visit_id++;
263	<	FORALLfacets {
264	<	if (!facet->upperdelaunay) {
265	<	facet->visitid= qh visit_id;
266	<	qh_makeridges(facet);
267	<	FOREACHridge_(facet->ridges) {
268	<	neighbor= otherfacet_(ridge, facet);
269	<	if (neighbor->visitid != qh visit_id) {
270	<
271	<	FOREACHvertex_(ridge->vertices)
272	<	int id2 = qh_pointid (vertex->point);
273	<	std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
274	<	}
275	<	}
276	<	}
277	<
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	<
281	<	}
252	>	int localID = id - displacements[myrank];
253
283	–	qh_freeqhull(!qh_ALL);
284	–	qh_memfreeshort(&curlong, &totlong);
285	–	if (curlong || totlong)
286	–	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
287	–	<< totlong << curlong << std::endl;
288	–	free(surfpt_array);
289	–	*/
290	–	return true;
291	–	}
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	<	RealType ConvexHull::getVolume()
286	<	{
287	<	return volume_;
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::geomviewHull(const std::string& geomFileName)
301	<	{
302	<
303	<	FILE *newGeomFile;
302	>	void ConvexHull::printHull(const string& geomFileName) {
303
304	<	//create new .md file based on old .md file
305	<	newGeomFile = fopen(geomFileName.c_str(), "w");
306	<	qh_findgood_all(qh facet_list);
307	<	for (int i = 0; i < qh_PRINTEND; i++)
308	<	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
309	<
310	<	fclose(newGeomFile);
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
314	–	#endif //CGAL
315	–
316	–
317	–

Comparing trunk/src/math/ConvexHull.cpp (property svn:keywords):
Revision 1261 by chuckv, Wed Jun 18 17:03:30 2008 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines