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root/OpenMD/trunk/src/math/ConvexHull.cpp

Comparing trunk/src/math/ConvexHull.cpp (file contents):
Revision 1137 by chuckv, Tue May 29 22:50:14 2007 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 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 1.2 2007-05-29 22:50:14 chuckv Exp $
47	>	*  @version $Id$
48		*
49		*/
50
51	<	#include "math/ConvexHull.hpp"
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	<	char options[] = "qhull Qt FA";
62	<	int dim_ = 3;
61	>	#ifdef IS_MPI
62	>	#include <mpi.h>
63	>	#endif
64
65	<	using namespace oopse;
65	>	#include "math/qhull.hpp"
66
67	<	ConvexHull::ConvexHull(){}
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	<	{
75	<	FILE *outfile = stdout;
66	<	FILE *errfile = stderr;
67	<	facetT *facet;
68	<	int exitcode;
69	<	boolT ismalloc = False;
70	<	int curlong,totlong;
71	<
72	<	int numpoints = pos.size();
73	<
74	<	coordT points[numpoints][dim_];
75	<
76	<	for (int i=0; i<numpoints; i++)
77	<	{
78	<	points[i][0] = pos[i][0];
79	<	points[i][1] = pos[i][1];
80	<	points[i][2] = pos[i][2];
81	<	}
82	<
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	+	setT *vertices;
82	+	int curlong, totlong;
83	+	pointT *intPoint;
84	+
85	+	std::vector<double> ptArray(numpoints*dim_);
86
87	<	qh_initflags (options);
88	<	qh_init_B (points[0], numpoints, dim_, ismalloc);
89	<	qh_qhull();
90	<	qh_check_output();
91	<
92	<
93	<
94	<	qh_getarea(qh facet_list);
95	<	volume_ = qh totvol;
96	<	area_ = qh totarea;
97	<
98	<
99	<
100	<	qh_freeqhull(!qh_ALL);
101	<	qh_memfreeshort (&curlong, &totlong);
102	<	if (curlong || totlong)
103	<	fprintf (errfile, "qhull internal warning (main): did not free %d bytes of long memory (%d pieces)\n",
104	<	totlong, curlong);
105	<
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	>	/* 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
105	–	return true;
106	–	}
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	<	RealType ConvexHull::getVolume()
121	<	{
122	<	return volume_;
123	<	}
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	<	void ConvexHull::geomviewHull(const std::string& geomFileName)
126	<	{
125	>	std::vector<double> coords;
126	>	std::vector<double> vels;
127	>	std::vector<int> indexMap;
128	>	std::vector<double> masses;
129
130	<	std::ofstream newGeomFile;
130	>	FORALLvertices{
131	>	localHullSites++;
132	>
133	>	int idx = qh_pointid(vertex->point);
134
135	<	//create new .md file based on old .md file
120	<	newGeomFile.open(geomFileName.c_str());
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	<	newGeomFile.close();
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	+	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	+	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	+	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	+	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::printHull(const std::string& geomFileName) {
299	+
300	+	#ifdef IS_MPI
301	+	if (worldRank == 0)  {
302	+	#endif
303	+	FILE *newGeomFile;
304	+
305	+	//create new .md file based on old .md file
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	+	fclose(newGeomFile);
312	+	#ifdef IS_MPI
313	+	}
314	+	#endif
315	+	}
316	+	#endif //QHULL

Comparing trunk/src/math/ConvexHull.cpp (property svn:keywords):
Revision 1137 by chuckv, Tue May 29 22:50:14 2007 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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