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root/OpenMD/branches/development/src/math/ConvexHull.cpp

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trunk/src/math/ConvexHull.cpp (file contents), Revision 1261 by chuckv, Wed Jun 18 17:03:30 2008 UTC vs.
branches/development/src/math/ConvexHull.cpp (file contents), Revision 1866 by gezelter, Thu Apr 25 14:32:56 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	+	* [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		/* Standard includes independent of library */
47	+
48		#include <iostream>
49		#include <fstream>
50		#include <list>
#	Line 56 | Line 52
52		#include <iterator>
53		#include "math/ConvexHull.hpp"
54		#include "utils/simError.h"
59	–	using namespace oopse;
55
56	<	/* CGAL version of convex hull first then QHULL */
57	<	#ifdef HAVE_CGAL
56	>	#ifdef IS_MPI
57	>	#include <mpi.h>
58	>	#endif
59
60	<	#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>
60	>	#include "math/qhull.hpp"
61
62	<	#include <CGAL/Quotient.h>
63	<	#include <CGAL/MP_Float.h>
64	<	#include <CGAL/Lazy_exact_nt.h>
62	>	#ifdef HAVE_QHULL
63	>	using namespace OpenMD;
64	>	using namespace std;
65
66	<	typedef double RT;
67	<	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_3;
66	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") {
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	<	ConvexHull::ConvexHull(){}
80	>	Vector3d boxMax;
81	>	Vector3d boxMin;
82	>
83	>	vector<double> ptArray(numpoints*dim_);
84
85	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
86	<	{
85	>	// Copy the positon vector into a points vector for qhull.
86	>	vector<StuntDouble*>::iterator SD;
87	>	int i = 0;
88	>
89	>	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
90	>	Vector3d pos = (*SD)->getPos();
91	>	ptArray[dim_ * i] = pos.x();
92	>	ptArray[dim_ * i + 1] = pos.y();
93	>	ptArray[dim_ * i + 2] = pos.z();
94	>	i++;
95	>	}
96
97	<	std::vector<Point_3> points;
97	>	/* Clean up memory from previous convex hull calculations */
98	>	boolT ismalloc = False;
99
100	+	/* compute the hull for our local points (or all the points for single
101	+	processor versions) */
102	+	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
103	+	const_cast<char *>(options_.c_str()), NULL, stderr)) {
104	+
105	+	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
106	+	painCave.isFatal = 1;
107	+	simError();
108	+
109	+	} //qh_new_qhull
110	+
111	+
112	+	#ifdef IS_MPI
113	+	//If we are doing the mpi version, set up some vectors for data communication
114
115	<	// Copy the positon vector into a points vector for cgal.
116	<	for (int i = 0; i < pos.size(); ++i)
117	<	{
92	<	Point_3 pt(pos[i][0],pos[i][1],pos[i][2]);
93	<	points.push_back(pt);
94	<	}
95	<
96	<	// define object to hold convex hull
97	<	CGAL::Object ch_object_;
98	<	Polyhedron_3 polyhedron;
115	>	int nproc = MPI::COMM_WORLD.Get_size();
116	>	int myrank = MPI::COMM_WORLD.Get_rank();
117	>	int localHullSites = 0;
118
119	<	// compute convex hull
120	<	std::cerr << "Creating hull" << std::endl;
121	<	CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
122	<	std::cerr << "Done Creating hull" << std::endl;
104	<	std::vector<Point_3>::const_iterator p_it;
119	>	vector<int> hullSitesOnProc(nproc, 0);
120	>	vector<int> coordsOnProc(nproc, 0);
121	>	vector<int> displacements(nproc, 0);
122	>	vector<int> vectorDisplacements(nproc, 0);
123
124	<	for (p_it = points.begin(); p_it != points.end(); p_it++)
125	<	{
126	<	std::cerr << (*p_it).x() << std::endl;
127	<	}
124	>	vector<double> coords;
125	>	vector<double> vels;
126	>	vector<int> indexMap;
127	>	vector<double> masses;
128
129	<	/*
130	<	for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin();
131	<	ch_object_.vertices_end(); ++v){
132	<	std::cout<< v.point()<<std::endl;
115	<	}
116	<	*/
117	<	}
129	>	FORALLvertices{
130	>	localHullSites++;
131	>
132	>	int idx = qh_pointid(vertex->point);
133
134	+	indexMap.push_back(idx);
135
136	+	coords.push_back(ptArray[dim_  * idx]);
137	+	coords.push_back(ptArray[dim_  * idx + 1]);
138	+	coords.push_back(ptArray[dim_  * idx + 2]);
139
140	<	#else
122	<	#ifdef HAVE_QHULL
123	<	/* Old options Qt Qu Qg QG0 FA */
124	<	ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
125	<	//ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
126	<	{}
140	>	StuntDouble* sd = bodydoubles[idx];
141
142	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
143	<	{
142	>	Vector3d vel = sd->getVel();
143	>	vels.push_back(vel.x());
144	>	vels.push_back(vel.y());
145	>	vels.push_back(vel.z());
146	>
147	>	masses.push_back(sd->getMass());
148	>	}
149	>
150	>	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
151	>	1, MPI::INT);
152	>
153	>	int globalHullSites = 0;
154	>	for (int iproc = 0; iproc < nproc; iproc++){
155	>	globalHullSites += hullSitesOnProc[iproc];
156	>	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
157	>	}
158	>
159	>	displacements[0] = 0;
160	>	vectorDisplacements[0] = 0;
161
162	<
163	<	int numpoints = pos.size();
164	<	coordT* pt_array;
134	<	coordT* surfpt_array;
135	<	std::list<int> surface_atoms;
136	<	FILE *outdummy = NULL;
137	<	FILE *errdummy = NULL;
138	<
139	<	pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
140	<
141	<
142	<	for (int i = 0; i < numpoints; i++) {
143	<	pt_array[dim_ * i] = pos[i][0];
144	<	pt_array[dim_ * i + 1] = pos[i][1];
145	<	pt_array[dim_ * i + 2] = pos[i][2];
162	>	for (int iproc = 1; iproc < nproc; iproc++){
163	>	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
164	>	vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
165		}
166	+
167	+	vector<double> globalCoords(dim_ * globalHullSites);
168	+	vector<double> globalVels(dim_ * globalHullSites);
169	+	vector<double> globalMasses(globalHullSites);
170	+
171	+	int count = coordsOnProc[myrank];
172
173	<
174	<
175	<
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();
173	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
174	>	&coordsOnProc[0], &vectorDisplacements[0],
175	>	MPI::DOUBLE);
176
177	<	qh_produce_output();
178	<	*/
179	<	boolT ismalloc = False;
177	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
178	>	&coordsOnProc[0], &vectorDisplacements[0],
179	>	MPI::DOUBLE);
180	>
181	>	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
182	>	&globalMasses[0], &hullSitesOnProc[0],
183	>	&displacements[0], MPI::DOUBLE);
184	>
185	>	// Free previous hull
186	>	qh_freeqhull(!qh_ALL);
187	>	qh_memfreeshort(&curlong, &totlong);
188	>	if (curlong || totlong) {
189	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
190	>	"\tdid not free %d bytes of long memory (%d pieces)",
191	>	totlong, curlong);
192	>	painCave.isFatal = 1;
193	>	simError();
194	>	}
195
196	<	if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
197	<	const_cast<char *>(options_.c_str()), NULL, stderr)) {
196	>	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
197	>	const_cast<char *>(options_.c_str()), NULL, stderr)){
198
199	<	vertexT *vertex, **vertexp;
200	<	facetT *facet;
201	<	setT *vertices;
202	<	unsigned int nf = qh num_facets;
199	>	sprintf(painCave.errMsg,
200	>	"ConvexHull: Qhull failed to compute global convex hull");
201	>	painCave.isFatal = 1;
202	>	simError();
203
204	<	//Matrix idx(nf, dim);
205	<	/*
206	<	int j, i = 0, id = 0;
207	<
208	<	int id2 = 0;
209	<	coordT *point,**pointp;
210	<	realT dist;
211	<	FORALLfacets {
212	<	j = 0;
204	>	} //qh_new_qhull
205	>
206	>	#endif
207	>	// commented out below, so comment out here also.
208	>	// intPoint = qh interior_point;
209	>	// RealType calcvol = 0.0;
210	>
211	>	qh_triangulate ();
212	>	int num_facets = qh num_facets;
213	>	int num_vertices = qh num_vertices;
214	>
215	>	FORALLfacets {
216	>	Triangle face;
217	>	//Qhull sets the unit normal in facet->normal
218	>	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
219	>	face.setUnitNormal(V3dNormal);
220	>
221	>	RealType faceArea = qh_facetarea(facet);
222	>	face.setArea(faceArea);
223	>
224	>	vertices = qh_facet3vertex(facet);
225
226	<	if (!facet->simplicial){
227	<	// should never happen with Qt
228	<	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	<	}
226	>	coordT *center = qh_getcenter(vertices);
227	>	Vector3d V3dCentroid(center[0], center[1], center[2]);
228	>	face.setCentroid(V3dCentroid);
229
230	+	Vector3d faceVel = V3Zero;
231	+	Vector3d p[3];
232	+	RealType faceMass = 0.0;
233
234	+	int ver = 0;
235
236	+	FOREACHvertex_(vertices){
237	+	int id = qh_pointid(vertex->point);
238	+	p[ver][0] = vertex->point[0];
239	+	p[ver][1] = vertex->point[1];
240	+	p[ver][2] = vertex->point[2];
241	+	Vector3d vel;
242	+	RealType mass;
243
244	+	#ifdef IS_MPI
245	+	vel = Vector3d(globalVels[dim_ * id],
246	+	globalVels[dim_ * id + 1],
247	+	globalVels[dim_ * id + 2]);
248	+	mass = globalMasses[id];
249	+
250	+	// localID will be between 0 and hullSitesOnProc[myrank] if we
251	+	// own this guy.
252	+
253	+	int localID = id - displacements[myrank];
254	+
255	+
256	+	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
257	+	face.addVertexSD(bodydoubles[indexMap[localID]]);
258	+	}else{
259	+	face.addVertexSD(NULL);
260	+	}
261	+	#else
262	+	vel = bodydoubles[id]->getVel();
263	+	mass = bodydoubles[id]->getMass();
264	+	face.addVertexSD(bodydoubles[id]);
265	+	#endif
266	+	faceVel = faceVel + vel;
267	+	faceMass = faceMass + mass;
268	+	ver++;
269	+	} //Foreachvertex
270	+
271	+	face.addVertices(p[0], p[1], p[2]);
272	+	face.setFacetMass(faceMass);
273	+	face.setFacetVelocity(faceVel / RealType(3.0));
274	+	/*
275	+	RealType comparea = face.computeArea();
276	+	realT calcarea = qh_facetarea (facet);
277	+	Vector3d V3dCompNorm = -face.computeUnitNormal();
278	+	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
279	+	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
280	+	cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  endl;
281	+	calcvol +=  -dist*comparea/qh hull_dim;
282	+	*/
283	+	Triangles_.push_back(face);
284	+	qh_settempfree(&vertices);
285	+
286	+	} //FORALLfacets
287	+
288		qh_getarea(qh facet_list);
289		volume_ = qh totvol;
290		area_ = qh totarea;
291	<	//    FILE *newGeomFile;
292	<
293	<
294	<	/*
295	<	FORALLfacets {
296	<	for (int k=0; k < qh hull_dim; k++)
297	<	printf ("%6.2g ", facet->normal[k]);
298	<	printf ("\n");
291	>
292	>	int index = 0;
293	>	FORALLvertices {
294	>	Vector3d point(vertex->point[0], vertex->point[1], vertex->point[2]);
295	>	if (index == 0) {
296	>	boxMax = point;
297	>	boxMin = point;
298	>	} else {
299	>	for (int i = 0; i < 3; i++) {
300	>	boxMax[i] = max(boxMax[i], point[i]);
301	>	boxMin[i] = min(boxMin[i], point[i]);
302	>	}
303		}
304	<	*/
305	<
306	<	int curlong,totlong;
307	<	//    geomviewHull("junk.off");
304	>	index++;
305	>	}
306	>	boundingBox_ = Mat3x3d(0.0);
307	>	boundingBox_(0,0) = boxMax[0] - boxMin[0];
308	>	boundingBox_(1,1) = boxMax[1] - boxMin[1];
309	>	boundingBox_(2,2) = boxMax[2] - boxMin[2];
310	>
311		qh_freeqhull(!qh_ALL);
312		qh_memfreeshort(&curlong, &totlong);
313	<	if (curlong || totlong)
314	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
315	<	<< totlong << curlong << std::endl;
316	<	free(pt_array);
317	<	/*
318	<	int j = 0;
319	<	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	<
278	<
279	<
280	<
281	<	}
282	<
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;
313	>	if (curlong || totlong) {
314	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
315	>	"\tdid not free %d bytes of long memory (%d pieces)",
316	>	totlong, curlong);
317	>	painCave.isFatal = 1;
318	>	simError();
319	>	}
320		}
321
322	<
294	<
295	<	RealType ConvexHull::getVolume()
296	<	{
297	<	return volume_;
298	<	}
299	<
300	<	void ConvexHull::geomviewHull(const std::string& geomFileName)
301	<	{
302	<
303	<	FILE *newGeomFile;
322	>	void ConvexHull::printHull(const string& geomFileName) {
323
324	<	//create new .md file based on old .md file
325	<	newGeomFile = fopen(geomFileName.c_str(), "w");
326	<	qh_findgood_all(qh facet_list);
327	<	for (int i = 0; i < qh_PRINTEND; i++)
328	<	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
329	<
330	<	fclose(newGeomFile);
324	>	#ifdef IS_MPI
325	>	if (worldRank == 0)  {
326	>	#endif
327	>	FILE *newGeomFile;
328	>
329	>	//create new .md file based on old .md file
330	>	newGeomFile = fopen(geomFileName.c_str(), "w");
331	>	qh_findgood_all(qh facet_list);
332	>	for (int i = 0; i < qh_PRINTEND; i++)
333	>	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
334	>
335	>	fclose(newGeomFile);
336	>	#ifdef IS_MPI
337	>	}
338	>	#endif
339		}
340		#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.
branches/development/src/math/ConvexHull.cpp (property svn:keywords), Revision 1866 by gezelter, Thu Apr 25 14:32:56 2013 UTC

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