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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 1866 by gezelter, Thu Apr 25 14:32:56 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;
79	+
80	+	Vector3d boxMax;
81	+	Vector3d boxMin;
82
83	<	std::vector<double> ptArray(numpoints*3);
98	<	std::vector<bool> isSurfaceID(numpoints);
83	>	vector<double> ptArray(numpoints*dim_);
84
85		// Copy the positon vector into a points vector for qhull.
86	<	std::vector<StuntDouble*>::iterator SD;
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();
#	Line 108 | Line 94 | void ConvexHull::computeHull(std::vector<StuntDouble*>
94		i++;
95		}
96
97	+	/* Clean up memory from previous convex hull calculations */
98		boolT ismalloc = False;
112	–	/* Clean up memory from previous convex hull calculations*/
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	<
104	>
105		sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
106		painCave.isFatal = 1;
107		simError();
#	Line 127 | Line 115 | void ConvexHull::computeHull(std::vector<StuntDouble*>
115		int nproc = MPI::COMM_WORLD.Get_size();
116		int myrank = MPI::COMM_WORLD.Get_rank();
117		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];
118
119	<	std::vector<double> coords;
120	<	std::vector<double> vels;
121	<	std::vector<int> objectIDs;
122	<	std::vector<double> masses;
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	+	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]);
#	Line 159 | Line 151 | void ConvexHull::computeHull(std::vector<StuntDouble*>
151		1, MPI::INT);
152
153		int globalHullSites = 0;
154	<	for (int iproc = 0; i < nproc; iproc++){
154	>	for (int iproc = 0; iproc < nproc; iproc++){
155		globalHullSites += hullSitesOnProc[iproc];
156		coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
157		}
#	Line 167 | Line 159 | void ConvexHull::computeHull(std::vector<StuntDouble*>
159		displacements[0] = 0;
160		vectorDisplacements[0] = 0;
161
162	<	for (int iproc = 1; i < nproc; iproc++){
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	<	std::vector<double> globalCoords(dim_*globalHullSites);
168	<	std::vector<double> globalVels(dim_*globalHullSites);
169	<	std::vector<double> globalMasses(globalHullSites);
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	<	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE,
174	<	&globalCoords[0], &coordsOnProc[0], &vectorDisplacements[0],
173	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
174	>	&coordsOnProc[0], &vectorDisplacements[0],
175		MPI::DOUBLE);
176
177	<	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE,
178	<	&globalVels[0], &coordsOnProc[0], &vectorDisplacements[0],
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], &displacements[0],
183	<	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	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
190	<	<< totlong << curlong << std::endl;
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_, globalHullSites, &globalCoords[0], ismalloc,
197		const_cast<char *>(options_.c_str()), NULL, stderr)){
198
199	<	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
199	>	sprintf(painCave.errMsg,
200	>	"ConvexHull: Qhull failed to compute global convex hull");
201		painCave.isFatal = 1;
202		simError();
203
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	<
217	>	//Qhull sets the unit normal in facet->normal
218		Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
219	<	face.setNormal(V3dNormal);
219	>	face.setUnitNormal(V3dNormal);
220
221		RealType faceArea = qh_facetarea(facet);
222		face.setArea(faceArea);
#	Line 225 | Line 230 | void ConvexHull::computeHull(std::vector<StuntDouble*>
230		Vector3d faceVel = V3Zero;
231		Vector3d p[3];
232		RealType faceMass = 0.0;
233	+
234		int ver = 0;
235
236		FOREACHvertex_(vertices){
#	Line 232 | Line 238 | void ConvexHull::computeHull(std::vector<StuntDouble*>
238		p[ver][0] = vertex->point[0];
239		p[ver][1] = vertex->point[1];
240		p[ver][2] = vertex->point[2];
235	–
241		Vector3d vel;
242		RealType mass;
243
#	Line 242 | Line 247 | void ConvexHull::computeHull(std::vector<StuntDouble*>
247		globalVels[dim_ * id + 2]);
248		mass = globalMasses[id];
249
250	<	// localID will be between 0 and hullSitesOnProc[myrank] if we own this guy.
250	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
251	>	// own this guy.
252	>
253		int localID = id - displacements[myrank];
254	<	if (id >= 0 && id < hullSitesOnProc[myrank])
255	<	face.addVertexSD(bodydoubles[localID]);
256	<	else
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
256	<
265	>	#endif
266		faceVel = faceVel + vel;
267		faceMass = faceMass + mass;
268		ver++;
#	Line 261 | Line 270 | void ConvexHull::computeHull(std::vector<StuntDouble*>
270
271		face.addVertices(p[0], p[1], p[2]);
272		face.setFacetMass(faceMass);
273	<	face.setFacetVelocity(faceVel/3.0);
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
#	Line 271 | Line 289 | void ConvexHull::computeHull(std::vector<StuntDouble*>
289		volume_ = qh totvol;
290		area_ = qh totarea;
291
292	<	#ifdef IS_MPI
293	<	delete [] hullSitesOnProc;
294	<	delete [] coordsOnProc;
295	<	delete [] displacements;
296	<	delete [] vectorDisplacements;
297	<	#endif
298	<
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	>	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;
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	<
289	<
290	<	void ConvexHull::printHull(const std::string& geomFileName) {
291	<	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

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 1866 by gezelter, Thu Apr 25 14:32:56 2013 UTC

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