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

Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 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
#	Line 32 | Line 32
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, 24107 (2008).
38	<	* [4]  Vardeman & Gezelter, in progress (2009).
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		*
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 1.21 2009-11-25 20:02:01 gezelter 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 OpenMD;
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	<	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;
93	–
94	–	std::vector<double> ptArray(numpoints*dim_);
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 104 | 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;
108	–	/* 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 124 | Line 113 | void ConvexHull::computeHull(std::vector<StuntDouble*>
113		int myrank = MPI::COMM_WORLD.Get_rank();
114		int localHullSites = 0;
115
116	<	std::vector<int> hullSitesOnProc(nproc, 0);
117	<	std::vector<int> coordsOnProc(nproc, 0);
118	<	std::vector<int> displacements(nproc, 0);
119	<	std::vector<int> vectorDisplacements(nproc, 0);
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	<	std::vector<double> coords;
122	<	std::vector<double> vels;
123	<	std::vector<int> indexMap;
124	<	std::vector<double> masses;
121	>	vector<double> coords;
122	>	vector<double> vels;
123	>	vector<int> indexMap;
124	>	vector<double> masses;
125
126		FORALLvertices{
127		localHullSites++;
#	Line 172 | Line 161 | void ConvexHull::computeHull(std::vector<StuntDouble*>
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
#	Line 193 | Line 182 | void ConvexHull::computeHull(std::vector<StuntDouble*>
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
210		FORALLfacets {
211		Triangle face;
212	<
212	>	//Qhull sets the unit normal in facet->normal
213		Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
214	<	face.setNormal(V3dNormal);
214	>	face.setUnitNormal(V3dNormal);
215
216		RealType faceArea = qh_facetarea(facet);
217		face.setArea(faceArea);
#	Line 234 | Line 233 | void ConvexHull::computeHull(std::vector<StuntDouble*>
233		p[ver][0] = vertex->point[0];
234		p[ver][1] = vertex->point[1];
235		p[ver][2] = vertex->point[2];
237	–
236		Vector3d vel;
237		RealType mass;
238
#	Line 249 | Line 247 | void ConvexHull::computeHull(std::vector<StuntDouble*>
247
248		int localID = id - displacements[myrank];
249
250	<	if (localID >= 0 && localID < hullSitesOnProc[myrank])
250	>
251	>	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
252		face.addVertexSD(bodydoubles[indexMap[localID]]);
253	<
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
260	<
260	>	#endif
261		faceVel = faceVel + vel;
262		faceMass = faceMass + mass;
263		ver++;
#	Line 265 | Line 265 | void ConvexHull::computeHull(std::vector<StuntDouble*>
265
266		face.addVertices(p[0], p[1], p[2]);
267		face.setFacetMass(faceMass);
268	<	face.setFacetVelocity(faceVel/3.0);
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
#	Line 274 | Line 283 | void ConvexHull::computeHull(std::vector<StuntDouble*>
283		qh_getarea(qh facet_list);
284		volume_ = qh totvol;
285		area_ = qh totarea;
286	<
286	>
287		qh_freeqhull(!qh_ALL);
288		qh_memfreeshort(&curlong, &totlong);
289	<	if (curlong || totlong)
290	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
291	<	<< totlong << curlong << std::endl;
289	>	if (curlong || totlong) {
290	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
291	>	"\tdid not free %d bytes of long memory (%d pieces)",
292	>	totlong, curlong);
293	>	painCave.isFatal = 1;
294	>	simError();
295	>	}
296		}
297
298	<	void ConvexHull::printHull(const std::string& geomFileName) {
299	<
298	>	void ConvexHull::printHull(const string& geomFileName) {
299	>
300		#ifdef IS_MPI
301		if (worldRank == 0)  {
302		#endif
303	<	FILE *newGeomFile;
304	<
305	<	//create new .md file based on old .md file
306	<	newGeomFile = fopen(geomFileName.c_str(), "w");
307	<	qh_findgood_all(qh facet_list);
308	<	for (int i = 0; i < qh_PRINTEND; i++)
309	<	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
310	<
311	<	fclose(newGeomFile);
303	>	FILE *newGeomFile;
304	>
305	>	//create new .md file based on old .md file
306	>	newGeomFile = fopen(geomFileName.c_str(), "w");
307	>	qh_findgood_all(qh facet_list);
308	>	for (int i = 0; i < qh_PRINTEND; i++)
309	>	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
310	>
311	>	fclose(newGeomFile);
312		#ifdef IS_MPI
313		}
314		#endif

Comparing trunk/src/math/ConvexHull.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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