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

Comparing:
trunk/src/math/ConvexHull.cpp (file contents), Revision 1188 by chuckv, Thu Nov 22 16:39:45 2007 UTC vs.
branches/development/src/math/ConvexHull.cpp (file contents), Revision 1867 by gezelter, Mon Apr 29 17:53:48 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 1.5 2007-11-22 16:39:45 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>
#	Line 55 | Line 52
52		#include <iterator>
53		#include "math/ConvexHull.hpp"
54		#include "utils/simError.h"
58	–	using namespace oopse;
55
56	<	/* Old options Qt Qu Qg QG0 FA */
57	<	ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
58	<	//ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
63	<	{}
56	>	#ifdef IS_MPI
57	>	#include <mpi.h>
58	>	#endif
59
60	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
66	<	{
60	>	#include "math/qhull.hpp"
61
62	+	#ifdef HAVE_QHULL
63	+	using namespace OpenMD;
64	+	using namespace std;
65
66	<	int numpoints = pos.size();
67	<	coordT* pt_array;
71	<	coordT* surfpt_array;
72	<	std::list<int> surface_atoms;
73	<	FILE *outdummy = NULL;
74	<	FILE *errdummy = NULL;
66	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") {
67	>	}
68
69	<	pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
69	>	void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) {
70	>
71	>	int numpoints = bodydoubles.size();
72	>
73	>	Triangles_.clear();
74	>
75	>	vertexT *vertex, **vertexp;
76	>	facetT *facet;
77	>	setT *vertices;
78	>	int curlong, totlong;
79
80	+	vector<double> ptArray(numpoints*dim_);
81
82	<	for (int i = 0; i < numpoints; i++) {
83	<	pt_array[dim_ * i] = pos[i][0];
84	<	pt_array[dim_ * i + 1] = pos[i][1];
85	<	pt_array[dim_ * i + 2] = pos[i][2];
86	<	}
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	+	int nproc = MPI::COMM_WORLD.Get_size();
113	+	int myrank = MPI::COMM_WORLD.Get_rank();
114	+	int localHullSites = 0;
115
116	+	vector<int> hullSitesOnProc(nproc, 0);
117	+	vector<int> coordsOnProc(nproc, 0);
118	+	vector<int> displacements(nproc, 0);
119	+	vector<int> vectorDisplacements(nproc, 0);
120
121	<	/*
122	<	qh_initflags(const_cast<char *>(options_.c_str()));
123	<	qh_init_B(pospoints, numpoints, dim_, ismalloc);
124	<	qh_qhull();
92	<	qh_check_output();
121	>	vector<double> coords;
122	>	vector<double> vels;
123	>	vector<int> indexMap;
124	>	vector<double> masses;
125
126	<	qh_produce_output();
127	<	*/
128	<	boolT ismalloc = False;
126	>	FORALLvertices{
127	>	localHullSites++;
128	>
129	>	int idx = qh_pointid(vertex->point);
130
131	<	if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
99	<	const_cast<char *>(options_.c_str()), NULL, stderr)) {
131	>	indexMap.push_back(idx);
132
133	<	vertexT *vertex, **vertexp;
134	<	facetT *facet;
135	<	setT *vertices;
104	<	unsigned int nf = qh num_facets;
133	>	coords.push_back(ptArray[dim_  * idx]);
134	>	coords.push_back(ptArray[dim_  * idx + 1]);
135	>	coords.push_back(ptArray[dim_  * idx + 2]);
136
137	<	//Matrix idx(nf, dim);
107	<	/*
108	<	int j, i = 0, id = 0;
109	<
110	<	int id2 = 0;
111	<	coordT *point,**pointp;
112	<	realT dist;
113	<	FORALLfacets {
114	<	j = 0;
115	<
116	<	if (!facet->simplicial){
117	<	// should never happen with Qt
118	<	sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
119	<	painCave.isFatal = 0;
120	<	simError();
121	<	}
122	<
123	<	vertices = qh_facet3vertex(facet);
124	<	FOREACHvertex_(vertices){
125	<	id = qh_pointid(vertex->point);
126	<	surface_atoms.push_back(id);
127	<	//std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
128	<	}
129	<	qh_settempfree(&vertices);
130	<
131	<	FOREACHpoint_(facet->coplanarset){
132	<	vertex= qh_nearvertex (facet, point, &dist);
133	<	//id= qh_pointid (vertex->point);
134	<	id2= qh_pointid (point);
135	<	surface_atoms.push_back(id2);
136	<	//std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
137	<	//printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
138	<	//std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
139	<
140	<	}
141	<
142	<	}
143	<
144	<	*/
145	<
146	<
147	<	}
137	>	StuntDouble* sd = bodydoubles[idx];
138
139	+	Vector3d vel = sd->getVel();
140	+	vels.push_back(vel.x());
141	+	vels.push_back(vel.y());
142	+	vels.push_back(vel.z());
143
144	+	masses.push_back(sd->getMass());
145	+	}
146
147	+	MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0],
148	+	1, MPI::INT);
149
150	<	qh_getarea(qh facet_list);
151	<	volume_ = qh totvol;
152	<	area_ = qh totarea;
153	<	//      FILE *newGeomFile;
150	>	int globalHullSites = 0;
151	>	for (int iproc = 0; iproc < nproc; iproc++){
152	>	globalHullSites += hullSitesOnProc[iproc];
153	>	coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc];
154	>	}
155
156	+	displacements[0] = 0;
157	+	vectorDisplacements[0] = 0;
158	+
159	+	for (int iproc = 1; iproc < nproc; iproc++){
160	+	displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1];
161	+	vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1];
162	+	}
163
164	<	/*
165	<	FORALLfacets {
166	<	for (int k=0; k < qh hull_dim; k++)
161	<	printf ("%6.2g ", facet->normal[k]);
162	<	printf ("\n");
163	<	}
164	<	*/
164	>	vector<double> globalCoords(dim_ * globalHullSites);
165	>	vector<double> globalVels(dim_ * globalHullSites);
166	>	vector<double> globalMasses(globalHullSites);
167
168	<	int curlong,totlong;
169	<	//      geomviewHull("junk.off");
170	<	qh_freeqhull(!qh_ALL);
171	<	qh_memfreeshort(&curlong, &totlong);
172	<	if (curlong || totlong)
171	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
172	<	<< totlong << curlong << std::endl;
173	<	free(pt_array);
174	<	/*
175	<	int j = 0;
176	<	surface_atoms.sort();
177	<	surface_atoms.unique();
178	<	surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
179	<	for(std::list<int>::iterator list_iter = surface_atoms.begin();
180	<	list_iter != surface_atoms.end(); list_iter++)
181	<	{
182	<	int i = *list_iter;
183	<	//surfpt_array[dim_ * j] = pos[i][0];
184	<	//surfpt_array[dim_ * j + 1] = pos[i][1];
185	<	//surfpt_array[dim_ * j + 2] = pos[i][2];
186	<	std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
187	<	j++;
188	<	}
189	<	*/
190	<
191	<	/*
192	<	std::string deloptions_ = "qhull d Qt";
193	<	facetT *facet, *neighbor;
194	<	ridgeT *ridge, **ridgep;
168	>	int count = coordsOnProc[myrank];
169	>
170	>	MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0],
171	>	&coordsOnProc[0], &vectorDisplacements[0],
172	>	MPI::DOUBLE);
173
174	<	if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
175	<	const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
174	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
175	>	&coordsOnProc[0], &vectorDisplacements[0],
176	>	MPI::DOUBLE);
177
178	<	qh visit_id++;
179	<	FORALLfacets {
180	<	if (!facet->upperdelaunay) {
202	<	facet->visitid= qh visit_id;
203	<	qh_makeridges(facet);
204	<	FOREACHridge_(facet->ridges) {
205	<	neighbor= otherfacet_(ridge, facet);
206	<	if (neighbor->visitid != qh visit_id) {
207	<
208	<	FOREACHvertex_(ridge->vertices)
209	<	int id2 = qh_pointid (vertex->point);
210	<	std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
211	<	}
212	<	}
213	<	}
178	>	MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE,
179	>	&globalMasses[0], &hullSitesOnProc[0],
180	>	&displacements[0], MPI::DOUBLE);
181
182	+	// Free previous hull
183	+	qh_freeqhull(!qh_ALL);
184	+	qh_memfreeshort(&curlong, &totlong);
185	+	if (curlong || totlong) {
186	+	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
187	+	"\tdid not free %d bytes of long memory (%d pieces)",
188	+	totlong, curlong);
189	+	painCave.isFatal = 1;
190	+	simError();
191	+	}
192	+
193	+	if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc,
194	+	const_cast<char *>(options_.c_str()), NULL, stderr)){
195	+
196	+	sprintf(painCave.errMsg,
197	+	"ConvexHull: Qhull failed to compute global convex hull");
198	+	painCave.isFatal = 1;
199	+	simError();
200	+
201	+	} //qh_new_qhull
202
203	+	#endif
204	+	// commented out below, so comment out here also.
205	+	// intPoint = qh interior_point;
206	+	// RealType calcvol = 0.0;
207	+
208	+	qh_triangulate ();
209	+	int num_facets = qh num_facets;
210	+	int num_vertices = qh num_vertices;
211
212	+	FORALLfacets {
213	+	Triangle face;
214	+	//Qhull sets the unit normal in facet->normal
215	+	Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]);
216	+	face.setUnitNormal(V3dNormal);
217	+
218	+	RealType faceArea = qh_facetarea(facet);
219	+	face.setArea(faceArea);
220	+
221	+	vertices = qh_facet3vertex(facet);
222	+
223	+	coordT *center = qh_getcenter(vertices);
224	+	Vector3d V3dCentroid(center[0], center[1], center[2]);
225	+	face.setCentroid(V3dCentroid);
226
227	<	}
227	>	Vector3d faceVel = V3Zero;
228	>	Vector3d p[3];
229	>	RealType faceMass = 0.0;
230
231	<	qh_freeqhull(!qh_ALL);
221	<	qh_memfreeshort(&curlong, &totlong);
222	<	if (curlong || totlong)
223	<	std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
224	<	<< totlong << curlong << std::endl;
225	<	free(surfpt_array);
226	<	*/
227	<	return true;
228	<	}
231	>	int ver = 0;
232
233	+	FOREACHvertex_(vertices){
234	+	int id = qh_pointid(vertex->point);
235	+	p[ver][0] = vertex->point[0];
236	+	p[ver][1] = vertex->point[1];
237	+	p[ver][2] = vertex->point[2];
238	+	Vector3d vel;
239	+	RealType mass;
240
241	+	#ifdef IS_MPI
242	+	vel = Vector3d(globalVels[dim_ * id],
243	+	globalVels[dim_ * id + 1],
244	+	globalVels[dim_ * id + 2]);
245	+	mass = globalMasses[id];
246
247	<	RealType ConvexHull::getVolume()
248	<	{
234	<	return volume_;
235	<	}
247	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
248	>	// own this guy.
249
250	<	void ConvexHull::geomviewHull(const std::string& geomFileName)
238	<	{
250	>	int localID = id - displacements[myrank];
251
240	–	FILE *newGeomFile;
252
253	<	//create new .md file based on old .md file
254	<	newGeomFile = fopen(geomFileName.c_str(), "w");
255	<	qh_findgood_all(qh facet_list);
256	<	for (int i = 0; i < qh_PRINTEND; i++)
257	<	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
253	>	if (localID >= 0 && localID < hullSitesOnProc[myrank]){
254	>	face.addVertexSD(bodydoubles[indexMap[localID]]);
255	>	}else{
256	>	face.addVertexSD(NULL);
257	>	}
258	>	#else
259	>	vel = bodydoubles[id]->getVel();
260	>	mass = bodydoubles[id]->getMass();
261	>	face.addVertexSD(bodydoubles[id]);
262	>	#endif
263	>	faceVel = faceVel + vel;
264	>	faceMass = faceMass + mass;
265	>	ver++;
266	>	} //Foreachvertex
267
268	<	fclose(newGeomFile);
268	>	face.addVertices(p[0], p[1], p[2]);
269	>	face.setFacetMass(faceMass);
270	>	face.setFacetVelocity(faceVel / RealType(3.0));
271	>	/*
272	>	RealType comparea = face.computeArea();
273	>	realT calcarea = qh_facetarea (facet);
274	>	Vector3d V3dCompNorm = -face.computeUnitNormal();
275	>	RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]);
276	>	RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2];
277	>	cout << "facet offset and computed offset: " << facet->offset << "  " << thisOffset <<  endl;
278	>	calcvol +=  -dist*comparea/qh hull_dim;
279	>	*/
280	>	Triangles_.push_back(face);
281	>	qh_settempfree(&vertices);
282	>
283	>	} //FORALLfacets
284	>
285	>	qh_getarea(qh facet_list);
286	>	volume_ = qh totvol;
287	>	area_ = qh totarea;
288	>
289	>	qh_freeqhull(!qh_ALL);
290	>	qh_memfreeshort(&curlong, &totlong);
291	>	if (curlong || totlong) {
292	>	sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n"
293	>	"\tdid not free %d bytes of long memory (%d pieces)",
294	>	totlong, curlong);
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298		}
299
300	<
301	<
302	<
300	>	void ConvexHull::printHull(const string& geomFileName) {
301	>
302	>	#ifdef IS_MPI
303	>	if (worldRank == 0)  {
304	>	#endif
305	>	FILE *newGeomFile;
306	>
307	>	//create new .md file based on old .md file
308	>	newGeomFile = fopen(geomFileName.c_str(), "w");
309	>	qh_findgood_all(qh facet_list);
310	>	for (int i = 0; i < qh_PRINTEND; i++)
311	>	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
312	>
313	>	fclose(newGeomFile);
314	>	#ifdef IS_MPI
315	>	}
316	>	#endif
317	>	}
318	>	#endif //QHULL

Comparing:
trunk/src/math/ConvexHull.cpp (property svn:keywords), Revision 1188 by chuckv, Thu Nov 22 16:39:45 2007 UTC vs.
branches/development/src/math/ConvexHull.cpp (property svn:keywords), Revision 1867 by gezelter, Mon Apr 29 17:53:48 2013 UTC

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