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Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1374 by chuckv, Tue Oct 20 20:05:28 2009 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 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, 24107 (2008).
38	+	* [4]  Vardeman & Gezelter, in progress (2009).
39		*
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 $
47	>	*  @version $Id$
48		*
49		*/
50
#	Line 62 | Line 62
62		#include <mpi.h>
63		#endif
64
65	<	using namespace oopse;
65	>	using namespace OpenMD;
66
67		#ifdef HAVE_QHULL
68		extern "C"
#	Line 77 | Line 77 | extern "C"
77		#include <qhull/stat.h>
78		}
79
80	–	/* Old options Qt Qu Qg QG0 FA */
81	–	/* More old opts Qc Qi Pp*/
82	–
80		ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81		}
82
#	Line 93 | Line 90 | void ConvexHull::computeHull(std::vector<StuntDouble*>
90		facetT *facet;
91		setT *vertices;
92		int curlong, totlong;
93	+	pointT *intPoint;
94
95	<	std::vector<double> ptArray(numpoints*3);
98	<	std::vector<bool> isSurfaceID(numpoints);
95	>	std::vector<double> ptArray(numpoints*dim_);
96
97		// Copy the positon vector into a points vector for qhull.
98		std::vector<StuntDouble*>::iterator SD;
#	Line 108 | Line 105 | void ConvexHull::computeHull(std::vector<StuntDouble*>
105		i++;
106		}
107
108	+	/* Clean up memory from previous convex hull calculations */
109		boolT ismalloc = False;
112	–	/* Clean up memory from previous convex hull calculations*/
110
111	+	/* compute the hull for our local points (or all the points for single
112	+	processor versions) */
113		if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
114		const_cast<char *>(options_.c_str()), NULL, stderr)) {
115	<
115	>
116		sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
117		painCave.isFatal = 1;
118		simError();
#	Line 127 | Line 126 | void ConvexHull::computeHull(std::vector<StuntDouble*>
126		int nproc = MPI::COMM_WORLD.Get_size();
127		int myrank = MPI::COMM_WORLD.Get_rank();
128		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];
129
130	+	std::vector<int> hullSitesOnProc(nproc, 0);
131	+	std::vector<int> coordsOnProc(nproc, 0);
132	+	std::vector<int> displacements(nproc, 0);
133	+	std::vector<int> vectorDisplacements(nproc, 0);
134	+
135		std::vector<double> coords;
136		std::vector<double> vels;
137	<	std::vector<int> objectIDs;
137	>	std::vector<int> indexMap;
138		std::vector<double> masses;
139
140		FORALLvertices{
141		localHullSites++;
142
143		int idx = qh_pointid(vertex->point);
144	+
145	+	indexMap.push_back(idx);
146	+
147		coords.push_back(ptArray[dim_  * idx]);
148		coords.push_back(ptArray[dim_  * idx + 1]);
149		coords.push_back(ptArray[dim_  * idx + 2]);
#	Line 159 | Line 162 | void ConvexHull::computeHull(std::vector<StuntDouble*>
162		1, MPI::INT);
163
164		int globalHullSites = 0;
165	<	for (int iproc = 0; i < nproc; iproc++){
165	>	for (int iproc = 0; iproc < nproc; iproc++){
166		globalHullSites += hullSitesOnProc[iproc];
167		coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
168		}
#	Line 167 | Line 170 | void ConvexHull::computeHull(std::vector<StuntDouble*>
170		displacements[0] = 0;
171		vectorDisplacements[0] = 0;
172
173	<	for (int iproc = 1; i < nproc; iproc++){
173	>	for (int iproc = 1; iproc < nproc; iproc++){
174		displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
175		vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
176		}
177
178	<	std::vector<double> globalCoords(dim_*globalHullSites);
179	<	std::vector<double> globalVels(dim_*globalHullSites);
178	>	std::vector<double> globalCoords(dim_ * globalHullSites);
179	>	std::vector<double> globalVels(dim_ * globalHullSites);
180		std::vector<double> globalMasses(globalHullSites);
181	+
182		int count = coordsOnProc[myrank];
183
184	<	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE,
185	<	&globalCoords[0], &coordsOnProc[0], &vectorDisplacements[0],
184	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
185	>	&coordsOnProc[0], &vectorDisplacements[0],
186		MPI::DOUBLE);
187
188	<	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE,
189	<	&globalVels[0], &coordsOnProc[0], &vectorDisplacements[0],
188	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
189	>	&coordsOnProc[0], &vectorDisplacements[0],
190		MPI::DOUBLE);
191
192		MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
193	<	&globalMasses[0], &hullSitesOnProc[0], &displacements[0],
194	<	MPI::DOUBLE);
193	>	&globalMasses[0], &hullSitesOnProc[0],
194	>	&displacements[0], MPI::DOUBLE);
195
196		// Free previous hull
197		qh_freeqhull(!qh_ALL);
198		qh_memfreeshort(&curlong, &totlong);
199	<	if (curlong || totlong)
200	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
201	<	<< totlong << curlong << std::endl;
199	>	if (curlong || totlong) {
200	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
201	>	"\tdid not free %d bytes of long memory (%d pieces)",
202	>	totlong, curlong);
203	>	painCave.isFatal = 1;
204	>	simError();
205	>	}
206
207		if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
208		const_cast<char *>(options_.c_str()), NULL, stderr)){
#	Line 206 | Line 214 | void ConvexHull::computeHull(std::vector<StuntDouble*>
214		} //qh_new_qhull
215
216		#endif
217	<
217	>	intPoint = qh interior_point;
218	>	RealType calcvol = 0.0;
219		FORALLfacets {
220		Triangle face;
221	<
221	>	//Qhull sets the unit normal in facet->normal
222		Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
223	<	face.setNormal(V3dNormal);
223	>	face.setUnitNormal(V3dNormal);
224
225		RealType faceArea = qh_facetarea(facet);
226		face.setArea(faceArea);
#	Line 225 | Line 234 | void ConvexHull::computeHull(std::vector<StuntDouble*>
234		Vector3d faceVel = V3Zero;
235		Vector3d p[3];
236		RealType faceMass = 0.0;
237	+
238		int ver = 0;
239
240		FOREACHvertex_(vertices){
#	Line 232 | Line 242 | void ConvexHull::computeHull(std::vector<StuntDouble*>
242		p[ver][0] = vertex->point[0];
243		p[ver][1] = vertex->point[1];
244		p[ver][2] = vertex->point[2];
235	–
245		Vector3d vel;
246		RealType mass;
247
#	Line 242 | Line 251 | void ConvexHull::computeHull(std::vector<StuntDouble*>
251		globalVels[dim_ * id + 2]);
252		mass = globalMasses[id];
253
254	<	// localID will be between 0 and hullSitesOnProc[myrank] if we own this guy.
254	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
255	>	// own this guy.
256	>
257		int localID = id - displacements[myrank];
258	<	if (id >= 0 && id < hullSitesOnProc[myrank])
259	<	face.addVertexSD(bodydoubles[localID]);
260	<	else
258	>
259	>
260	>	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
261	>	face.addVertexSD(bodydoubles[indexMap[localID]]);
262	>	}else{
263		face.addVertexSD(NULL);
264	+	}
265		#else
266		vel = bodydoubles[id]->getVel();
267		mass = bodydoubles[id]->getMass();
268		face.addVertexSD(bodydoubles[id]);
269	<	#endif
256	<
269	>	#endif
270		faceVel = faceVel + vel;
271		faceMass = faceMass + mass;
272		ver++;
#	Line 262 | Line 275 | void ConvexHull::computeHull(std::vector<StuntDouble*>
275		face.addVertices(p[0], p[1], p[2]);
276		face.setFacetMass(faceMass);
277		face.setFacetVelocity(faceVel/3.0);
278	+	/*
279	+	RealType comparea = face.computeArea();
280	+	realT calcarea = qh_facetarea (facet);
281	+	Vector3d V3dCompNorm = -face.computeUnitNormal();
282	+	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
283	+	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
284	+	std::cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  std::endl;
285	+	calcvol +=  -dist*comparea/qh hull_dim;
286	+	*/
287		Triangles_.push_back(face);
288		qh_settempfree(&vertices);
289
#	Line 270 | Line 292 | void ConvexHull::computeHull(std::vector<StuntDouble*>
292		qh_getarea(qh facet_list);
293		volume_ = qh totvol;
294		area_ = qh totarea;
295	<
274	<	#ifdef IS_MPI
275	<	delete [] hullSitesOnProc;
276	<	delete [] coordsOnProc;
277	<	delete [] displacements;
278	<	delete [] vectorDisplacements;
279	<	#endif
280	<
295	>	//  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl;
296		qh_freeqhull(!qh_ALL);
297		qh_memfreeshort(&curlong, &totlong);
298	<	if (curlong || totlong)
299	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
300	<	<< totlong << curlong << std::endl;
298	>	if (curlong || totlong) {
299	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
300	>	"\tdid not free %d bytes of long memory (%d pieces)",
301	>	totlong, curlong);
302	>	painCave.isFatal = 1;
303	>	simError();
304	>	}
305		}
306
288	–
289	–
307		void ConvexHull::printHull(const std::string& geomFileName) {
308	+
309	+	#ifdef IS_MPI
310	+	if (worldRank == 0)  {
311	+	#endif
312		FILE *newGeomFile;
313
314		//create new .md file based on old .md file
#	Line 297 | Line 318 | void ConvexHull::printHull(const std::string& geomFile
318		qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
319
320		fclose(newGeomFile);
321	+	#ifdef IS_MPI
322	+	}
323	+	#endif
324		}
325		#endif //QHULL

Comparing trunk/src/math/ConvexHull.cpp (property svn:keywords):
Revision 1374 by chuckv, Tue Oct 20 20:05:28 2009 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 0 | Line 1
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