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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 1866 by gezelter, Thu Apr 25 14:32:56 2013 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, 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 1.3 2007-05-30 18:47:03 chuckv Exp $
48	<	*
43	>	*  Purpose: To calculate a convex hull.
44		*/
45
46	+	/* Standard includes independent of library */
47	+
48		#include <iostream>
49		#include <fstream>
50	+	#include <list>
51	+	#include <algorithm>
52	+	#include <iterator>
53		#include "math/ConvexHull.hpp"
54	+	#include "utils/simError.h"
55
56	<	using namespace oopse;
56	>	#ifdef IS_MPI
57	>	#include <mpi.h>
58	>	#endif
59
60	<	ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt FA") {
60	>	#include "math/qhull.hpp"
61	>
62	>	#ifdef HAVE_QHULL
63	>	using namespace OpenMD;
64	>	using namespace std;
65	>
66	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") {
67		}
68
69	<	bool ConvexHull::genHull(std::vector<Vector3d> pos) {
61	<	FILE *outfile = stdout;
62	<	FILE *errfile = stderr;
63	<	facetT *facet;
64	<	int exitcode;
65	<	boolT ismalloc = False;
66	<	int curlong,totlong;
69	>	void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) {
70
71	<	int numpoints = pos.size();
71	>	int numpoints = bodydoubles.size();
72
73	<	coordT points[numpoints][dim_];
73	>	Triangles_.clear();
74
75	<	for (int i=0; i<numpoints; i++) {
76	<	points[i][0] = pos[i][0];
77	<	points[i][1] = pos[i][1];
78	<	points[i][2] = pos[i][2];
75	>	vertexT *vertex, **vertexp;
76	>	facetT *facet;
77	>	setT *vertices;
78	>	int curlong, totlong;
79	>
80	>	Vector3d boxMax;
81	>	Vector3d boxMin;
82	>
83	>	vector<double> ptArray(numpoints*dim_);
84	>
85	>	// Copy the positon vector into a points vector for qhull.
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();
92	>	ptArray[dim_ * i + 1] = pos.y();
93	>	ptArray[dim_ * i + 2] = pos.z();
94	>	i++;
95		}
96
97	+	/* Clean up memory from previous convex hull calculations */
98	+	boolT ismalloc = False;
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	+
105	+	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
106	+	painCave.isFatal = 1;
107	+	simError();
108	+
109	+	} //qh_new_qhull
110	+
111	+
112	+	#ifdef IS_MPI
113	+	//If we are doing the mpi version, set up some vectors for data communication
114
115	<	qh_initflags (const_cast<char *>(options_.c_str()));
116	<	qh_init_B (points[0], numpoints, dim_, ismalloc);
117	<	qh_qhull();
118	<	qh_check_output();
115	>	int nproc = MPI::COMM_WORLD.Get_size();
116	>	int myrank = MPI::COMM_WORLD.Get_rank();
117	>	int localHullSites = 0;
118	>
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]);
139	>
140	>	StuntDouble* sd = bodydoubles[idx];
141	>
142	>	Vector3d vel = sd->getVel();
143	>	vels.push_back(vel.x());
144	>	vels.push_back(vel.y());
145	>	vels.push_back(vel.z());
146	>
147	>	masses.push_back(sd->getMass());
148	>	}
149	>
150	>	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
151	>	1, MPI::INT);
152	>
153	>	int globalHullSites = 0;
154	>	for (int iproc = 0; iproc < nproc; iproc++){
155	>	globalHullSites += hullSitesOnProc[iproc];
156	>	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
157	>	}
158	>
159	>	displacements[0] = 0;
160	>	vectorDisplacements[0] = 0;
161
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	+	vector<double> globalCoords(dim_ * globalHullSites);
168	+	vector<double> globalVels(dim_ * globalHullSites);
169	+	vector<double> globalMasses(globalHullSites);
170	+
171	+	int count = coordsOnProc[myrank];
172
173	<
174	<	qh_getarea(qh facet_list);
175	<	volume_ = qh totvol;
176	<	area_ = qh totarea;
177	<
178	<
179	<
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, &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],
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	<	fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
190	<	totlong, curlong);
187	>	qh_memfreeshort(&curlong, &totlong);
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,
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	<	return true;
212	<	}
211	>	qh_triangulate ();
212	>	int num_facets = qh num_facets;
213	>	int num_vertices = qh num_vertices;
214
215	+	FORALLfacets {
216	+	Triangle face;
217	+	//Qhull sets the unit normal in facet->normal
218	+	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
219	+	face.setUnitNormal(V3dNormal);
220	+
221	+	RealType faceArea = qh_facetarea(facet);
222	+	face.setArea(faceArea);
223	+
224	+	vertices = qh_facet3vertex(facet);
225	+
226	+	coordT *center = qh_getcenter(vertices);
227	+	Vector3d V3dCentroid(center[0], center[1], center[2]);
228	+	face.setCentroid(V3dCentroid);
229
230	<	RealType ConvexHull::getVolume() {
231	<	return volume_;
230	>	Vector3d faceVel = V3Zero;
231	>	Vector3d p[3];
232	>	RealType faceMass = 0.0;
233	>
234	>	int ver = 0;
235	>
236	>	FOREACHvertex_(vertices){
237	>	int id = qh_pointid(vertex->point);
238	>	p[ver][0] = vertex->point[0];
239	>	p[ver][1] = vertex->point[1];
240	>	p[ver][2] = vertex->point[2];
241	>	Vector3d vel;
242	>	RealType mass;
243	>
244	>	#ifdef IS_MPI
245	>	vel = Vector3d(globalVels[dim_ * id],
246	>	globalVels[dim_ * id + 1],
247	>	globalVels[dim_ * id + 2]);
248	>	mass = globalMasses[id];
249	>
250	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
251	>	// own this guy.
252	>
253	>	int localID = id - displacements[myrank];
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
266	>	faceVel = faceVel + vel;
267	>	faceMass = faceMass + mass;
268	>	ver++;
269	>	} //Foreachvertex
270	>
271	>	face.addVertices(p[0], p[1], p[2]);
272	>	face.setFacetMass(faceMass);
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	>
286	>	} //FORALLfacets
287	>
288	>	qh_getarea(qh facet_list);
289	>	volume_ = qh totvol;
290	>	area_ = qh totarea;
291	>
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	>	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	<	void ConvexHull::geomviewHull(const std::string& geomFileName) {
322	>	void ConvexHull::printHull(const string& geomFileName) {
323
324	<	std::ofstream newGeomFile;
325	<
326	<	//create new .md file based on old .md file
327	<	newGeomFile.open(geomFileName.c_str());
328	<
329	<
330	<	newGeomFile.close();
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 1141 by chuckv, Wed May 30 18:47:04 2007 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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