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

Comparing:
trunk/src/math/ConvexHull.cpp (file contents), Revision 1141 by chuckv, Wed May 30 18:47:04 2007 UTC vs.
branches/development/src/math/ConvexHull.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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, 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 1.3 2007-05-30 18:47:03 chuckv Exp $
47	>	*  @version $Id$
48		*
49		*/
50
51	+	/* Standard includes independent of library */
52	+
53		#include <iostream>
54		#include <fstream>
55	+	#include <list>
56	+	#include <algorithm>
57	+	#include <iterator>
58		#include "math/ConvexHull.hpp"
59	+	#include "utils/simError.h"
60
61	<	using namespace oopse;
61	>	#ifdef IS_MPI
62	>	#include <mpi.h>
63	>	#endif
64
65	<	ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt FA") {
65	>	using namespace OpenMD;
66	>
67	>	#ifdef HAVE_QHULL
68	>	extern "C"
69	>	{
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		}
79
80	<	bool ConvexHull::genHull(std::vector<Vector3d> pos) {
81	<	FILE *outfile = stdout;
82	<	FILE *errfile = stderr;
80	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
81	>	}
82	>
83	>	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
84	>
85	>	int numpoints = bodydoubles.size();
86	>
87	>	Triangles_.clear();
88	>
89	>	vertexT *vertex, **vertexp;
90		facetT *facet;
91	<	int exitcode;
92	<	boolT ismalloc = False;
93	<	int curlong,totlong;
91	>	setT *vertices;
92	>	int curlong, totlong;
93	>	pointT *intPoint;
94
95	<	int numpoints = pos.size();
96	<
97	<	coordT points[numpoints][dim_];
98	<
99	<	for (int i=0; i<numpoints; i++) {
100	<	points[i][0] = pos[i][0];
101	<	points[i][1] = pos[i][1];
102	<	points[i][2] = pos[i][2];
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;
99	>	int i = 0;
100	>	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
101	>	Vector3d pos = (*SD)->getPos();
102	>	ptArray[dim_ * i] = pos.x();
103	>	ptArray[dim_ * i + 1] = pos.y();
104	>	ptArray[dim_ * i + 2] = pos.z();
105	>	i++;
106		}
107
108	+	/* Clean up memory from previous convex hull calculations */
109	+	boolT ismalloc = False;
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	+
116	+	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
117	+	painCave.isFatal = 1;
118	+	simError();
119	+
120	+	} //qh_new_qhull
121	+
122	+
123	+	#ifdef IS_MPI
124	+	//If we are doing the mpi version, set up some vectors for data communication
125
126	<	qh_initflags (const_cast<char *>(options_.c_str()));
127	<	qh_init_B (points[0], numpoints, dim_, ismalloc);
128	<	qh_qhull();
129	<	qh_check_output();
126	>	int nproc = MPI::COMM_WORLD.Get_size();
127	>	int myrank = MPI::COMM_WORLD.Get_rank();
128	>	int localHullSites = 0;
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> 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]);
150	>
151	>	StuntDouble* sd = bodydoubles[idx];
152	>
153	>	Vector3d vel = sd->getVel();
154	>	vels.push_back(vel.x());
155	>	vels.push_back(vel.y());
156	>	vels.push_back(vel.z());
157	>
158	>	masses.push_back(sd->getMass());
159	>	}
160	>
161	>	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
162	>	1, MPI::INT);
163	>
164	>	int globalHullSites = 0;
165	>	for (int iproc = 0; iproc < nproc; iproc++){
166	>	globalHullSites += hullSitesOnProc[iproc];
167	>	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
168	>	}
169	>
170	>	displacements[0] = 0;
171	>	vectorDisplacements[0] = 0;
172
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);
180	+	std::vector<double> globalMasses(globalHullSites);
181	+
182	+	int count = coordsOnProc[myrank];
183
184	<
185	<	qh_getarea(qh facet_list);
186	<	volume_ = qh totvol;
187	<	area_ = qh totarea;
188	<
189	<
190	<
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, &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],
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	<	fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
201	<	totlong, curlong);
198	>	qh_memfreeshort(&curlong, &totlong);
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	<
208	<	return true;
209	<	}
207	>	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
208	>	const_cast<char *>(options_.c_str()), NULL, stderr)){
209	>
210	>	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
211	>	painCave.isFatal = 1;
212	>	simError();
213	>
214	>	} //qh_new_qhull
215
216	+	#endif
217	+	intPoint = qh interior_point;
218	+	RealType calcvol = 0.0;
219	+	FORALLfacets {
220	+	Triangle face;
221	+	//Qhull sets the unit normal in facet->normal
222	+	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
223	+	face.setUnitNormal(V3dNormal);
224	+
225	+	RealType faceArea = qh_facetarea(facet);
226	+	face.setArea(faceArea);
227	+
228	+	vertices = qh_facet3vertex(facet);
229	+
230	+	coordT *center = qh_getcenter(vertices);
231	+	Vector3d V3dCentroid(center[0], center[1], center[2]);
232	+	face.setCentroid(V3dCentroid);
233
234	<	RealType ConvexHull::getVolume() {
235	<	return volume_;
234	>	Vector3d faceVel = V3Zero;
235	>	Vector3d p[3];
236	>	RealType faceMass = 0.0;
237	>
238	>	int ver = 0;
239	>
240	>	FOREACHvertex_(vertices){
241	>	int id = qh_pointid(vertex->point);
242	>	p[ver][0] = vertex->point[0];
243	>	p[ver][1] = vertex->point[1];
244	>	p[ver][2] = vertex->point[2];
245	>	Vector3d vel;
246	>	RealType mass;
247	>
248	>	#ifdef IS_MPI
249	>	vel = Vector3d(globalVels[dim_ * id],
250	>	globalVels[dim_ * id + 1],
251	>	globalVels[dim_ * id + 2]);
252	>	mass = globalMasses[id];
253	>
254	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
255	>	// own this guy.
256	>
257	>	int localID = id - displacements[myrank];
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
270	>	faceVel = faceVel + vel;
271	>	faceMass = faceMass + mass;
272	>	ver++;
273	>	} //Foreachvertex
274	>
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	>
290	>	} //FORALLfacets
291	>
292	>	qh_getarea(qh facet_list);
293	>	volume_ = qh totvol;
294	>	area_ = qh totarea;
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	>	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
307	<	void ConvexHull::geomviewHull(const std::string& geomFileName) {
307	>	void ConvexHull::printHull(const std::string& geomFileName) {
308	>
309	>	#ifdef IS_MPI
310	>	if (worldRank == 0)  {
311	>	#endif
312	>	FILE *newGeomFile;
313
110	–	std::ofstream newGeomFile;
111	–
314		//create new .md file based on old .md file
315	<	newGeomFile.open(geomFileName.c_str());
315	>	newGeomFile = fopen(geomFileName.c_str(), "w");
316	>	qh_findgood_all(qh facet_list);
317	>	for (int i = 0; i < qh_PRINTEND; i++)
318	>	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
319
320	<
321	<	newGeomFile.close();
320	>	fclose(newGeomFile);
321	>	#ifdef IS_MPI
322	>	}
323	>	#endif
324		}
325	+	#endif //QHULL

Comparing:
trunk/src/math/ConvexHull.cpp (property svn:keywords), Revision 1141 by chuckv, Wed May 30 18:47:04 2007 UTC vs.
branches/development/src/math/ConvexHull.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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