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

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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 1858 by gezelter, Wed Apr 3 21:32:13 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 1.6 2008-05-14 14:31:48 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;
66	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
67	>	}
68
69	<
81	<	ConvexHull::ConvexHull(){}
82	<
83	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
84	<	{
69	>	void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) {
70
71	<	std::vector<Point> points;
71	>	int numpoints = bodydoubles.size();
72
73	+	Triangles_.clear();
74
75	<	// Copy the positon vector into a points vector for cgal.
76	<	for (int i = 0; i < pos.size(); ++i)
77	<	{
78	<	Point pt(pos[i][0],pos[i][1],pos[i][2]);
79	<	points.push_back(pt);
80	<	}
75	>	vertexT *vertex, **vertexp;
76	>	facetT *facet;
77	>	setT *vertices;
78	>	int curlong, totlong;
79	>
80	>	Vector3d boxMax;
81	>	Vector3d boxMin;
82
83	<	// define object to hold convex hull
84	<	Polyhedron_3 ch_object_;
85	<	// compute convex hull
86	<	CGAL::convex_hull_3(points.begin(), points.end(), ch_object_);
83	>	vector<double> ptArray(numpoints*dim_);
84	>
85	>	// Copy the positon vector into a points vector for qhull.
86	>	vector<StuntDouble*>::iterator SD;
87	>	int i = 0;
88
89	<	for (Polyhedron_3::Vertex_iterator v = ch_object_.vertices_begin(); ch_object_.vertices_end(); ++v){
90	<	std::cout<< v.point()<<std::endl;
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	+	/* Clean up memory from previous convex hull calculations */
98	+	boolT ismalloc = False;
99
100	<	}
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	+	int nproc = MPI::COMM_WORLD.Get_size();
116	+	int myrank = MPI::COMM_WORLD.Get_rank();
117	+	int localHullSites = 0;
118
119	<	#else
120	<	#ifdef HAVE_QHULL
121	<	/* Old options Qt Qu Qg QG0 FA */
122	<	ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
114	<	//ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
115	<	{}
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	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
125	<	{
124	>	vector<double> coords;
125	>	vector<double> vels;
126	>	vector<int> indexMap;
127	>	vector<double> masses;
128	>
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	>	StuntDouble* sd = bodydoubles[idx];
141	>
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;
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];
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	<
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();
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	>	FORALLfacets {
211	>	Triangle face;
212	>	//Qhull sets the unit normal in facet->normal
213	>	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
214	>	face.setUnitNormal(V3dNormal);
215	>
216	>	RealType faceArea = qh_facetarea(facet);
217	>	face.setArea(faceArea);
218	>
219	>	vertices = qh_facet3vertex(facet);
220
221	<	if (!facet->simplicial){
222	<	// should never happen with Qt
223	<	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	<	}
221	>	coordT *center = qh_getcenter(vertices);
222	>	Vector3d V3dCentroid(center[0], center[1], center[2]);
223	>	face.setCentroid(V3dCentroid);
224
225	+	Vector3d faceVel = V3Zero;
226	+	Vector3d p[3];
227	+	RealType faceMass = 0.0;
228
229	+	int ver = 0;
230
231	+	FOREACHvertex_(vertices){
232	+	int id = qh_pointid(vertex->point);
233	+	p[ver][0] = vertex->point[0];
234	+	p[ver][1] = vertex->point[1];
235	+	p[ver][2] = vertex->point[2];
236	+	Vector3d vel;
237	+	RealType mass;
238
239	+	#ifdef IS_MPI
240	+	vel = Vector3d(globalVels[dim_ * id],
241	+	globalVels[dim_ * id + 1],
242	+	globalVels[dim_ * id + 2]);
243	+	mass = globalMasses[id];
244	+
245	+	// localID will be between 0 and hullSitesOnProc[myrank] if we
246	+	// own this guy.
247	+
248	+	int localID = id - displacements[myrank];
249	+
250	+
251	+	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
252	+	face.addVertexSD(bodydoubles[indexMap[localID]]);
253	+	}else{
254	+	face.addVertexSD(NULL);
255	+	}
256	+	#else
257	+	vel = bodydoubles[id]->getVel();
258	+	mass = bodydoubles[id]->getMass();
259	+	face.addVertexSD(bodydoubles[id]);
260	+	#endif
261	+	faceVel = faceVel + vel;
262	+	faceMass = faceMass + mass;
263	+	ver++;
264	+	} //Foreachvertex
265	+
266	+	face.addVertices(p[0], p[1], p[2]);
267	+	face.setFacetMass(faceMass);
268	+	face.setFacetVelocity(faceVel / RealType(3.0));
269	+	/*
270	+	RealType comparea = face.computeArea();
271	+	realT calcarea = qh_facetarea (facet);
272	+	Vector3d V3dCompNorm = -face.computeUnitNormal();
273	+	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
274	+	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
275	+	cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  endl;
276	+	calcvol +=  -dist*comparea/qh hull_dim;
277	+	*/
278	+	Triangles_.push_back(face);
279	+	qh_settempfree(&vertices);
280	+
281	+	} //FORALLfacets
282	+
283		qh_getarea(qh facet_list);
284		volume_ = qh totvol;
285		area_ = qh totarea;
286	<	//    FILE *newGeomFile;
287	<
288	<
289	<	/*
290	<	FORALLfacets {
291	<	for (int k=0; k < qh hull_dim; k++)
292	<	printf ("%6.2g ", facet->normal[k]);
293	<	printf ("\n");
286	>
287	>	int index = 0;
288	>	FORALLvertices {
289	>	Vector3d point(vertex->point[0], vertex->point[1], vertex->point[2]);
290	>	if (index == 0) {
291	>	boxMax = point;
292	>	boxMin = point;
293	>	} else {
294	>	for (int i = 0; i < 3; i++) {
295	>	boxMax[i] = max(boxMax[i], point[i]);
296	>	boxMin[i] = min(boxMin[i], point[i]);
297	>	}
298		}
299	<	*/
300	<
301	<	int curlong,totlong;
302	<	//    geomviewHull("junk.off");
299	>	index++;
300	>	}
301	>	boundingBox_ = Mat3x3d(0.0);
302	>	boundingBox_(0,0) = boxMax[0] - boxMin[0];
303	>	boundingBox_(1,1) = boxMax[1] - boxMin[1];
304	>	boundingBox_(2,2) = boxMax[2] - boxMin[2];
305	>
306		qh_freeqhull(!qh_ALL);
307		qh_memfreeshort(&curlong, &totlong);
308	<	if (curlong || totlong)
309	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
310	<	<< totlong << curlong << std::endl;
311	<	free(pt_array);
312	<	/*
313	<	int j = 0;
314	<	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	<
267	<
268	<
269	<
270	<	}
271	<
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;
308	>	if (curlong || totlong) {
309	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
310	>	"\tdid not free %d bytes of long memory (%d pieces)",
311	>	totlong, curlong);
312	>	painCave.isFatal = 1;
313	>	simError();
314	>	}
315		}
316
317	<
283	<
284	<	RealType ConvexHull::getVolume()
285	<	{
286	<	return volume_;
287	<	}
288	<
289	<	void ConvexHull::geomviewHull(const std::string& geomFileName)
290	<	{
291	<
292	<	FILE *newGeomFile;
317	>	void ConvexHull::printHull(const string& geomFileName) {
318
319	<	//create new .md file based on old .md file
320	<	newGeomFile = fopen(geomFileName.c_str(), "w");
321	<	qh_findgood_all(qh facet_list);
322	<	for (int i = 0; i < qh_PRINTEND; i++)
323	<	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
324	<
325	<	fclose(newGeomFile);
319	>	#ifdef IS_MPI
320	>	if (worldRank == 0)  {
321	>	#endif
322	>	FILE *newGeomFile;
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);
331	>	#ifdef IS_MPI
332	>	}
333	>	#endif
334		}
335		#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 1858 by gezelter, Wed Apr 3 21:32:13 2013 UTC

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