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

Comparing:
trunk/src/math/ConvexHull.cpp (file contents), Revision 1143 by chuckv, Wed May 30 19:51:07 2007 UTC vs.
branches/development/src/math/ConvexHull.cpp (file contents), Revision 1708 by gezelter, Tue May 15 13:02:10 2012 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] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
39	+	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40		*
41		*  ConvexHull.cpp
42		*
#	Line 44 | Line 44
44		*
45		*  Created by Charles F. Vardeman II on 11 Dec 2006.
46		*  @author  Charles F. Vardeman II
47	<	*  @version $Id: ConvexHull.cpp,v 1.4 2007-05-30 19:51:07 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	>	#include "math/qhull.hpp"
66	>
67	>	#ifdef HAVE_QHULL
68	>	using namespace OpenMD;
69	>
70	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
71		}
72
73	<	bool ConvexHull::genHull(std::vector<Vector3d> pos) {
74	<	FILE *outfile = stdout;
75	<	FILE *errfile = stderr;
73	>	void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) {
74	>
75	>	int numpoints = bodydoubles.size();
76	>
77	>	Triangles_.clear();
78	>
79	>	vertexT *vertex, **vertexp;
80		facetT *facet;
81	<	int exitcode;
82	<	boolT ismalloc = False;
83	<	int curlong,totlong;
81	>	setT *vertices;
82	>	int curlong, totlong;
83	>	pointT *intPoint;
84
85	<	int numpoints = pos.size();
69	<
70	<	coordT* points;
71	<	points = (coordT*) malloc(sizeof(coordT) * (numpoints*dim_));
85	>	std::vector<double> ptArray(numpoints*dim_);
86
87	<	for (int i=0; i<numpoints; i++) {
88	<	points[dim_ * i] = pos[i][0];
89	<	points[dim_ * i + 1] = pos[i][1];
90	<	points[dim_ * i + 2] = pos[i][2];
87	>	// Copy the positon vector into a points vector for qhull.
88	>	std::vector<StuntDouble*>::iterator SD;
89	>	int i = 0;
90	>	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
91	>	Vector3d pos = (*SD)->getPos();
92	>	ptArray[dim_ * i] = pos.x();
93	>	ptArray[dim_ * i + 1] = pos.y();
94	>	ptArray[dim_ * i + 2] = pos.z();
95	>	i++;
96		}
97
98	+	/* Clean up memory from previous convex hull calculations */
99	+	boolT ismalloc = False;
100
101	<	qh_initflags (const_cast<char *>(options_.c_str()));
102	<	qh_init_B (points, numpoints, dim_, ismalloc);
103	<	qh_qhull();
104	<	qh_check_output();
101	>	/* compute the hull for our local points (or all the points for single
102	>	processor versions) */
103	>	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
104	>	const_cast<char *>(options_.c_str()), NULL, stderr)) {
105	>
106	>	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
107	>	painCave.isFatal = 1;
108	>	simError();
109	>
110	>	} //qh_new_qhull
111	>
112	>
113	>	#ifdef IS_MPI
114	>	//If we are doing the mpi version, set up some vectors for data communication
115
116	+	int nproc = MPI::COMM_WORLD.Get_size();
117	+	int myrank = MPI::COMM_WORLD.Get_rank();
118	+	int localHullSites = 0;
119	+
120	+	std::vector<int> hullSitesOnProc(nproc, 0);
121	+	std::vector<int> coordsOnProc(nproc, 0);
122	+	std::vector<int> displacements(nproc, 0);
123	+	std::vector<int> vectorDisplacements(nproc, 0);
124	+
125	+	std::vector<double> coords;
126	+	std::vector<double> vels;
127	+	std::vector<int> indexMap;
128	+	std::vector<double> masses;
129	+
130	+	FORALLvertices{
131	+	localHullSites++;
132	+
133	+	int idx = qh_pointid(vertex->point);
134	+
135	+	indexMap.push_back(idx);
136	+
137	+	coords.push_back(ptArray[dim_  * idx]);
138	+	coords.push_back(ptArray[dim_  * idx + 1]);
139	+	coords.push_back(ptArray[dim_  * idx + 2]);
140	+
141	+	StuntDouble* sd = bodydoubles[idx];
142	+
143	+	Vector3d vel = sd->getVel();
144	+	vels.push_back(vel.x());
145	+	vels.push_back(vel.y());
146	+	vels.push_back(vel.z());
147	+
148	+	masses.push_back(sd->getMass());
149	+	}
150	+
151	+	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
152	+	1, MPI::INT);
153	+
154	+	int globalHullSites = 0;
155	+	for (int iproc = 0; iproc < nproc; iproc++){
156	+	globalHullSites += hullSitesOnProc[iproc];
157	+	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
158	+	}
159	+
160	+	displacements[0] = 0;
161	+	vectorDisplacements[0] = 0;
162
163	+	for (int iproc = 1; iproc < nproc; iproc++){
164	+	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
165	+	vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
166	+	}
167	+
168	+	std::vector<double> globalCoords(dim_ * globalHullSites);
169	+	std::vector<double> globalVels(dim_ * globalHullSites);
170	+	std::vector<double> globalMasses(globalHullSites);
171	+
172	+	int count = coordsOnProc[myrank];
173
174	<	qh_getarea(qh facet_list);
175	<	volume_ = qh totvol;
176	<	area_ = qh totarea;
177	<
178	<
179	<
174	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
175	>	&coordsOnProc[0], &vectorDisplacements[0],
176	>	MPI::DOUBLE);
177	>
178	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
179	>	&coordsOnProc[0], &vectorDisplacements[0],
180	>	MPI::DOUBLE);
181	>
182	>	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
183	>	&globalMasses[0], &hullSitesOnProc[0],
184	>	&displacements[0], MPI::DOUBLE);
185	>
186	>	// Free previous hull
187		qh_freeqhull(!qh_ALL);
188	<	qh_memfreeshort (&curlong, &totlong);
189	<	if (curlong || totlong)
190	<	fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
191	<	totlong, curlong);
188	>	qh_memfreeshort(&curlong, &totlong);
189	>	if (curlong || totlong) {
190	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
191	>	"\tdid not free %d bytes of long memory (%d pieces)",
192	>	totlong, curlong);
193	>	painCave.isFatal = 1;
194	>	simError();
195	>	}
196
197	<
198	<	return true;
199	<	}
197	>	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
198	>	const_cast<char *>(options_.c_str()), NULL, stderr)){
199	>
200	>	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute global convex hull");
201	>	painCave.isFatal = 1;
202	>	simError();
203	>
204	>	} //qh_new_qhull
205
206	+	#endif
207
208	<	RealType ConvexHull::getVolume() {
209	<	return volume_;
208	>	intPoint = qh interior_point;
209	>	RealType calcvol = 0.0;
210	>	FORALLfacets {
211	>	Triangle face;
212	>	//Qhull sets the unit normal in facet->normal
213	>	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
214	>	face.setUnitNormal(V3dNormal);
215	>
216	>	RealType faceArea = qh_facetarea(facet);
217	>	face.setArea(faceArea);
218	>
219	>	vertices = qh_facet3vertex(facet);
220	>
221	>	coordT *center = qh_getcenter(vertices);
222	>	Vector3d V3dCentroid(center[0], center[1], center[2]);
223	>	face.setCentroid(V3dCentroid);
224	>
225	>	Vector3d faceVel = V3Zero;
226	>	Vector3d p[3];
227	>	RealType faceMass = 0.0;
228	>
229	>	int ver = 0;
230	>
231	>	FOREACHvertex_(vertices){
232	>	int id = qh_pointid(vertex->point);
233	>	p[ver][0] = vertex->point[0];
234	>	p[ver][1] = vertex->point[1];
235	>	p[ver][2] = vertex->point[2];
236	>	Vector3d vel;
237	>	RealType mass;
238	>
239	>	#ifdef IS_MPI
240	>	vel = Vector3d(globalVels[dim_ * id],
241	>	globalVels[dim_ * id + 1],
242	>	globalVels[dim_ * id + 2]);
243	>	mass = globalMasses[id];
244	>
245	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
246	>	// own this guy.
247	>
248	>	int localID = id - displacements[myrank];
249	>
250	>
251	>	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
252	>	face.addVertexSD(bodydoubles[indexMap[localID]]);
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
261	>	faceVel = faceVel + vel;
262	>	faceMass = faceMass + mass;
263	>	ver++;
264	>	} //Foreachvertex
265	>
266	>	face.addVertices(p[0], p[1], p[2]);
267	>	face.setFacetMass(faceMass);
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	>	std::cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  std::endl;
276	>	calcvol +=  -dist*comparea/qh hull_dim;
277	>	*/
278	>	Triangles_.push_back(face);
279	>	qh_settempfree(&vertices);
280	>
281	>	} //FORALLfacets
282	>
283	>	qh_getarea(qh facet_list);
284	>	volume_ = qh totvol;
285	>	area_ = qh totarea;
286	>	//  std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl;
287	>	qh_freeqhull(!qh_ALL);
288	>	qh_memfreeshort(&curlong, &totlong);
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::geomviewHull(const std::string& geomFileName) {
298	>	void ConvexHull::printHull(const std::string& geomFileName) {
299	>
300	>	#ifdef IS_MPI
301	>	if (worldRank == 0)  {
302	>	#endif
303	>	FILE *newGeomFile;
304
110	–	std::ofstream newGeomFile;
111	–
305		//create new .md file based on old .md file
306	<	newGeomFile.open(geomFileName.c_str());
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	<
312	<	newGeomFile.close();
311	>	fclose(newGeomFile);
312	>	#ifdef IS_MPI
313	>	}
314	>	#endif
315		}
316	+	#endif //QHULL

Comparing:
trunk/src/math/ConvexHull.cpp (property svn:keywords), Revision 1143 by chuckv, Wed May 30 19:51:07 2007 UTC vs.
branches/development/src/math/ConvexHull.cpp (property svn:keywords), Revision 1708 by gezelter, Tue May 15 13:02:10 2012 UTC

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