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

Comparing:
trunk/src/math/ConvexHull.cpp (file contents), Revision 1374 by chuckv, Tue Oct 20 20:05:28 2009 UTC vs.
branches/development/src/math/ConvexHull.cpp (file contents), Revision 1867 by gezelter, Mon Apr 29 17:53:48 2013 UTC

#	Line 1 | Line 1
1	<	/* Copyright (c) 2008, 2009 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 1.16 2009-10-20 20:05:28 chuckv Exp $
48	<	*
43	>	*  Purpose: To calculate a convex hull.
44		*/
45
46		/* Standard includes independent of library */
#	Line 62 | Line 57
57		#include <mpi.h>
58		#endif
59
60	<	using namespace oopse;
60	>	#include "math/qhull.hpp"
61
62		#ifdef HAVE_QHULL
63	<	extern "C"
64	<	{
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	<	}
63	>	using namespace OpenMD;
64	>	using namespace std;
65
66	<	/* Old options Qt Qu Qg QG0 FA */
81	<	/* More old opts Qc Qi Pp*/
82	<
83	<	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
66	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") {
67		}
68
69	<	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
70	<
69	>	void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) {
70	>
71		int numpoints = bodydoubles.size();
72	<
72	>
73		Triangles_.clear();
74
75		vertexT *vertex, **vertexp;
76		facetT *facet;
77		setT *vertices;
78		int curlong, totlong;
96	–
97	–	std::vector<double> ptArray(numpoints*3);
98	–	std::vector<bool> isSurfaceID(numpoints);
79
80	+	vector<double> ptArray(numpoints*dim_);
81	+
82		// Copy the positon vector into a points vector for qhull.
83	<	std::vector<StuntDouble*>::iterator SD;
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();
#	Line 108 | Line 91 | void ConvexHull::computeHull(std::vector<StuntDouble*>
91		i++;
92		}
93
94	+	/* Clean up memory from previous convex hull calculations */
95		boolT ismalloc = False;
112	–	/* Clean up memory from previous convex hull calculations*/
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	<
101	>
102		sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
103		painCave.isFatal = 1;
104		simError();
#	Line 127 | Line 112 | void ConvexHull::computeHull(std::vector<StuntDouble*>
112		int nproc = MPI::COMM_WORLD.Get_size();
113		int myrank = MPI::COMM_WORLD.Get_rank();
114		int localHullSites = 0;
130	–	int* hullSitesOnProc = new int[nproc];
131	–	int* coordsOnProc = new int[nproc];
132	–	int* displacements = new int[nproc];
133	–	int* vectorDisplacements = new int[nproc];
115
116	<	std::vector<double> coords;
117	<	std::vector<double> vels;
118	<	std::vector<int> objectIDs;
119	<	std::vector<double> masses;
116	>	vector<int> hullSitesOnProc(nproc, 0);
117	>	vector<int> coordsOnProc(nproc, 0);
118	>	vector<int> displacements(nproc, 0);
119	>	vector<int> vectorDisplacements(nproc, 0);
120
121	+	vector<double> coords;
122	+	vector<double> vels;
123	+	vector<int> indexMap;
124	+	vector<double> masses;
125	+
126		FORALLvertices{
127		localHullSites++;
128
129		int idx = qh_pointid(vertex->point);
130	+
131	+	indexMap.push_back(idx);
132	+
133		coords.push_back(ptArray[dim_  * idx]);
134		coords.push_back(ptArray[dim_  * idx + 1]);
135		coords.push_back(ptArray[dim_  * idx + 2]);
#	Line 159 | Line 148 | void ConvexHull::computeHull(std::vector<StuntDouble*>
148		1, MPI::INT);
149
150		int globalHullSites = 0;
151	<	for (int iproc = 0; i < nproc; iproc++){
151	>	for (int iproc = 0; iproc < nproc; iproc++){
152		globalHullSites += hullSitesOnProc[iproc];
153		coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
154		}
#	Line 167 | Line 156 | void ConvexHull::computeHull(std::vector<StuntDouble*>
156		displacements[0] = 0;
157		vectorDisplacements[0] = 0;
158
159	<	for (int iproc = 1; i < nproc; iproc++){
159	>	for (int iproc = 1; iproc < nproc; iproc++){
160		displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
161		vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
162		}
163
164	<	std::vector<double> globalCoords(dim_*globalHullSites);
165	<	std::vector<double> globalVels(dim_*globalHullSites);
166	<	std::vector<double> globalMasses(globalHullSites);
164	>	vector<double> globalCoords(dim_ * globalHullSites);
165	>	vector<double> globalVels(dim_ * globalHullSites);
166	>	vector<double> globalMasses(globalHullSites);
167	>
168		int count = coordsOnProc[myrank];
169
170	<	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE,
171	<	&globalCoords[0], &coordsOnProc[0], &vectorDisplacements[0],
170	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
171	>	&coordsOnProc[0], &vectorDisplacements[0],
172		MPI::DOUBLE);
173
174	<	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE,
175	<	&globalVels[0], &coordsOnProc[0], &vectorDisplacements[0],
174	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
175	>	&coordsOnProc[0], &vectorDisplacements[0],
176		MPI::DOUBLE);
177
178		MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
179	<	&globalMasses[0], &hullSitesOnProc[0], &displacements[0],
180	<	MPI::DOUBLE);
179	>	&globalMasses[0], &hullSitesOnProc[0],
180	>	&displacements[0], MPI::DOUBLE);
181
182		// Free previous hull
183		qh_freeqhull(!qh_ALL);
184		qh_memfreeshort(&curlong, &totlong);
185	<	if (curlong || totlong)
186	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
187	<	<< totlong << curlong << std::endl;
185	>	if (curlong || totlong) {
186	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
187	>	"\tdid not free %d bytes of long memory (%d pieces)",
188	>	totlong, curlong);
189	>	painCave.isFatal = 1;
190	>	simError();
191	>	}
192
193		if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
194		const_cast<char *>(options_.c_str()), NULL, stderr)){
195
196	<	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
196	>	sprintf(painCave.errMsg,
197	>	"ConvexHull: Qhull failed to compute global convex hull");
198		painCave.isFatal = 1;
199		simError();
200
201		} //qh_new_qhull
202
203		#endif
204	+	// commented out below, so comment out here also.
205	+	// intPoint = qh interior_point;
206	+	// RealType calcvol = 0.0;
207	+
208	+	qh_triangulate ();
209	+	int num_facets = qh num_facets;
210	+	int num_vertices = qh num_vertices;
211
212		FORALLfacets {
213		Triangle face;
214	<
214	>	//Qhull sets the unit normal in facet->normal
215		Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
216	<	face.setNormal(V3dNormal);
216	>	face.setUnitNormal(V3dNormal);
217
218		RealType faceArea = qh_facetarea(facet);
219		face.setArea(faceArea);
#	Line 225 | Line 227 | void ConvexHull::computeHull(std::vector<StuntDouble*>
227		Vector3d faceVel = V3Zero;
228		Vector3d p[3];
229		RealType faceMass = 0.0;
230	+
231		int ver = 0;
232
233		FOREACHvertex_(vertices){
#	Line 232 | Line 235 | void ConvexHull::computeHull(std::vector<StuntDouble*>
235		p[ver][0] = vertex->point[0];
236		p[ver][1] = vertex->point[1];
237		p[ver][2] = vertex->point[2];
235	–
238		Vector3d vel;
239		RealType mass;
240
#	Line 242 | Line 244 | void ConvexHull::computeHull(std::vector<StuntDouble*>
244		globalVels[dim_ * id + 2]);
245		mass = globalMasses[id];
246
247	<	// localID will be between 0 and hullSitesOnProc[myrank] if we own this guy.
247	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
248	>	// own this guy.
249	>
250		int localID = id - displacements[myrank];
251	<	if (id >= 0 && id < hullSitesOnProc[myrank])
252	<	face.addVertexSD(bodydoubles[localID]);
253	<	else
251	>
252	>
253	>	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
254	>	face.addVertexSD(bodydoubles[indexMap[localID]]);
255	>	}else{
256		face.addVertexSD(NULL);
257	+	}
258		#else
259		vel = bodydoubles[id]->getVel();
260		mass = bodydoubles[id]->getMass();
261		face.addVertexSD(bodydoubles[id]);
262	<	#endif
256	<
262	>	#endif
263		faceVel = faceVel + vel;
264		faceMass = faceMass + mass;
265		ver++;
#	Line 261 | Line 267 | void ConvexHull::computeHull(std::vector<StuntDouble*>
267
268		face.addVertices(p[0], p[1], p[2]);
269		face.setFacetMass(faceMass);
270	<	face.setFacetVelocity(faceVel/3.0);
270	>	face.setFacetVelocity(faceVel / RealType(3.0));
271	>	/*
272	>	RealType comparea = face.computeArea();
273	>	realT calcarea = qh_facetarea (facet);
274	>	Vector3d V3dCompNorm = -face.computeUnitNormal();
275	>	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
276	>	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
277	>	cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  endl;
278	>	calcvol +=  -dist*comparea/qh hull_dim;
279	>	*/
280		Triangles_.push_back(face);
281		qh_settempfree(&vertices);
282
#	Line 270 | Line 285 | void ConvexHull::computeHull(std::vector<StuntDouble*>
285		qh_getarea(qh facet_list);
286		volume_ = qh totvol;
287		area_ = qh totarea;
288	<
274	<	#ifdef IS_MPI
275	<	delete [] hullSitesOnProc;
276	<	delete [] coordsOnProc;
277	<	delete [] displacements;
278	<	delete [] vectorDisplacements;
279	<	#endif
280	<
288	>
289		qh_freeqhull(!qh_ALL);
290		qh_memfreeshort(&curlong, &totlong);
291	<	if (curlong || totlong)
292	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
293	<	<< totlong << curlong << std::endl;
291	>	if (curlong || totlong) {
292	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
293	>	"\tdid not free %d bytes of long memory (%d pieces)",
294	>	totlong, curlong);
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298		}
299
300	<
289	<
290	<	void ConvexHull::printHull(const std::string& geomFileName) {
291	<	FILE *newGeomFile;
300	>	void ConvexHull::printHull(const string& geomFileName) {
301
302	<	//create new .md file based on old .md file
303	<	newGeomFile = fopen(geomFileName.c_str(), "w");
304	<	qh_findgood_all(qh facet_list);
305	<	for (int i = 0; i < qh_PRINTEND; i++)
306	<	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
307	<
308	<	fclose(newGeomFile);
302	>	#ifdef IS_MPI
303	>	if (worldRank == 0)  {
304	>	#endif
305	>	FILE *newGeomFile;
306	>
307	>	//create new .md file based on old .md file
308	>	newGeomFile = fopen(geomFileName.c_str(), "w");
309	>	qh_findgood_all(qh facet_list);
310	>	for (int i = 0; i < qh_PRINTEND; i++)
311	>	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
312	>
313	>	fclose(newGeomFile);
314	>	#ifdef IS_MPI
315	>	}
316	>	#endif
317		}
318		#endif //QHULL

Comparing:
trunk/src/math/ConvexHull.cpp (property svn:keywords), Revision 1374 by chuckv, Tue Oct 20 20:05:28 2009 UTC vs.
branches/development/src/math/ConvexHull.cpp (property svn:keywords), Revision 1867 by gezelter, Mon Apr 29 17:53:48 2013 UTC

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