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root/OpenMD/trunk/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.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 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	+	#ifdef IS_MPI
47	+	#include <mpi.h>
48	+	#endif
49	+
50	+	/* Standard includes independent of library */
51	+
52		#include <iostream>
53		#include <fstream>
54	+	#include <list>
55	+	#include <algorithm>
56	+	#include <iterator>
57		#include "math/ConvexHull.hpp"
58	+	#include "utils/simError.h"
59
60	<	using namespace oopse;
60	>	#include "math/qhull.hpp"
61
62	<	ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt FA") {
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	>	vector<double> ptArray(numpoints*dim_);
81	>
82	>	// Copy the positon vector into a points vector for qhull.
83	>	vector<StuntDouble*>::iterator SD;
84	>	int i = 0;
85	>
86	>	for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){
87	>	Vector3d pos = (*SD)->getPos();
88	>	ptArray[dim_ * i] = pos.x();
89	>	ptArray[dim_ * i + 1] = pos.y();
90	>	ptArray[dim_ * i + 2] = pos.z();
91	>	i++;
92		}
93
94	+	/* Clean up memory from previous convex hull calculations */
95	+	boolT ismalloc = False;
96
97	+	/* compute the hull for our local points (or all the points for single
98	+	processor versions) */
99	+	if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc,
100	+	const_cast<char *>(options_.c_str()), NULL, stderr)) {
101	+
102	+	sprintf(painCave.errMsg, "ConvexHull: Qhull failed to compute convex hull");
103	+	painCave.isFatal = 1;
104	+	simError();
105	+
106	+	} //qh_new_qhull
107	+
108	+
109	+	#ifdef IS_MPI
110	+	//If we are doing the mpi version, set up some vectors for data communication
111
112	<	qh_initflags (const_cast<char *>(options_.c_str()));
113	<	qh_init_B (points[0], numpoints, dim_, ismalloc);
82	<	qh_qhull();
83	<	qh_check_output();
112	>	int nproc;
113	>	int myrank;
114
115	+	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
116	+	MPI_Comm_rank( MPI_COMM_WORLD, &myrank);
117	+
118	+	int localHullSites = 0;
119	+
120	+	vector<int> hullSitesOnProc(nproc, 0);
121	+	vector<int> coordsOnProc(nproc, 0);
122	+	vector<int> displacements(nproc, 0);
123	+	vector<int> vectorDisplacements(nproc, 0);
124	+
125	+	vector<double> coords;
126	+	vector<double> vels;
127	+	vector<int> indexMap;
128	+	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_Allgather(&localHullSites, 1, MPI_INT, &hullSitesOnProc[0],
152	+	1, MPI_INT, MPI_COMM_WORLD);
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	+	vector<double> globalCoords(dim_ * globalHullSites);
169	+	vector<double> globalVels(dim_ * globalHullSites);
170	+	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;
174	>	MPI_Allgatherv(&coords[0], count, MPI_DOUBLE, &globalCoords[0],
175	>	&coordsOnProc[0], &vectorDisplacements[0],
176	>	MPI_DOUBLE, MPI_COMM_WORLD);
177
178	+	MPI_Allgatherv(&vels[0], count, MPI_DOUBLE, &globalVels[0],
179	+	&coordsOnProc[0], &vectorDisplacements[0],
180	+	MPI_DOUBLE, MPI_COMM_WORLD);
181
182	+	MPI_Allgatherv(&masses[0], localHullSites, MPI_DOUBLE,
183	+	&globalMasses[0], &hullSitesOnProc[0],
184	+	&displacements[0], MPI_DOUBLE, MPI_COMM_WORLD);
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	+	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
198	+	const_cast<char *>(options_.c_str()), NULL, stderr)){
199	+
200	+	sprintf(painCave.errMsg,
201	+	"ConvexHull: Qhull failed to compute global convex hull");
202	+	painCave.isFatal = 1;
203	+	simError();
204	+
205	+	} //qh_new_qhull
206	+
207	+	#endif
208	+	// commented out below, so comment out here also.
209	+	// intPoint = qh interior_point;
210	+	// RealType calcvol = 0.0;
211
212	<	return true;
101	<	}
212	>	qh_triangulate ();
213
214	+	FORALLfacets {
215	+	Triangle face;
216	+	//Qhull sets the unit normal in facet->normal
217	+	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
218	+	face.setUnitNormal(V3dNormal);
219	+
220	+	RealType faceArea = qh_facetarea(facet);
221	+	face.setArea(faceArea);
222	+
223	+	vertices = qh_facet3vertex(facet);
224	+
225	+	coordT *center = qh_getcenter(vertices);
226	+	Vector3d V3dCentroid(center[0], center[1], center[2]);
227	+	face.setCentroid(V3dCentroid);
228
229	<	RealType ConvexHull::getVolume() {
230	<	return volume_;
229	>	Vector3d faceVel = V3Zero;
230	>	Vector3d p[3];
231	>	RealType faceMass = 0.0;
232	>
233	>	int ver = 0;
234	>
235	>	FOREACHvertex_(vertices){
236	>	int id = qh_pointid(vertex->point);
237	>	p[ver][0] = vertex->point[0];
238	>	p[ver][1] = vertex->point[1];
239	>	p[ver][2] = vertex->point[2];
240	>	Vector3d vel;
241	>	RealType mass;
242	>
243	>	#ifdef IS_MPI
244	>	vel = Vector3d(globalVels[dim_ * id],
245	>	globalVels[dim_ * id + 1],
246	>	globalVels[dim_ * id + 2]);
247	>	mass = globalMasses[id];
248	>
249	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
250	>	// own this guy.
251	>
252	>	int localID = id - displacements[myrank];
253	>
254	>
255	>	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
256	>	face.addVertexSD(bodydoubles[indexMap[localID]]);
257	>	}else{
258	>	face.addVertexSD(NULL);
259	>	}
260	>	#else
261	>	vel = bodydoubles[id]->getVel();
262	>	mass = bodydoubles[id]->getMass();
263	>	face.addVertexSD(bodydoubles[id]);
264	>	#endif
265	>	faceVel = faceVel + vel;
266	>	faceMass = faceMass + mass;
267	>	ver++;
268	>	} //Foreachvertex
269	>
270	>	face.addVertices(p[0], p[1], p[2]);
271	>	face.setFacetMass(faceMass);
272	>	face.setFacetVelocity(faceVel / RealType(3.0));
273	>	/*
274	>	RealType comparea = face.computeArea();
275	>	realT calcarea = qh_facetarea (facet);
276	>	Vector3d V3dCompNorm = -face.computeUnitNormal();
277	>	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
278	>	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
279	>	cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  endl;
280	>	calcvol +=  -dist*comparea/qh hull_dim;
281	>	*/
282	>	Triangles_.push_back(face);
283	>	qh_settempfree(&vertices);
284	>
285	>	} //FORALLfacets
286	>
287	>	qh_getarea(qh facet_list);
288	>	volume_ = qh totvol;
289	>	area_ = qh totarea;
290	>
291	>	qh_freeqhull(!qh_ALL);
292	>	qh_memfreeshort(&curlong, &totlong);
293	>	if (curlong || totlong) {
294	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
295	>	"\tdid not free %d bytes of long memory (%d pieces)",
296	>	totlong, curlong);
297	>	painCave.isFatal = 1;
298	>	simError();
299	>	}
300		}
301
302	<	void ConvexHull::geomviewHull(const std::string& geomFileName) {
302	>	void ConvexHull::printHull(const string& geomFileName) {
303
304	<	std::ofstream newGeomFile;
305	<
306	<	//create new .md file based on old .md file
307	<	newGeomFile.open(geomFileName.c_str());
308	<
309	<
310	<	newGeomFile.close();
304	>	#ifdef IS_MPI
305	>	if (worldRank == 0)  {
306	>	#endif
307	>	FILE *newGeomFile;
308	>
309	>	//create new .md file based on old .md file
310	>	newGeomFile = fopen(geomFileName.c_str(), "w");
311	>	qh_findgood_all(qh facet_list);
312	>	for (int i = 0; i < qh_PRINTEND; i++)
313	>	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
314	>
315	>	fclose(newGeomFile);
316	>	#ifdef IS_MPI
317	>	}
318	>	#endif
319		}
320	+	#endif //QHULL

Comparing trunk/src/math/ConvexHull.cpp (property svn:keywords):
Revision 1141 by chuckv, Wed May 30 18:47:04 2007 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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