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root/OpenMD/trunk/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.
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 1.5 2007-11-22 16:39:45 chuckv Exp $
47	>	*  @version $Id$
48		*
49		*/
50
51	+	/* Standard includes independent of library */
52	+
53		#include <iostream>
54		#include <fstream>
55		#include <list>
#	Line 55 | Line 57
57		#include <iterator>
58		#include "math/ConvexHull.hpp"
59		#include "utils/simError.h"
58	–	using namespace oopse;
60
61	<	/* Old options Qt Qu Qg QG0 FA */
62	<	ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
63	<	//ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
63	<	{}
61	>	#ifdef IS_MPI
62	>	#include <mpi.h>
63	>	#endif
64
65	<	bool ConvexHull::genHull(std::vector<Vector3d> pos)
66	<	{
65	>	#include "math/qhull.hpp"
66
67	+	#ifdef HAVE_QHULL
68	+	using namespace OpenMD;
69
70	<	int numpoints = pos.size();
71	<	coordT* pt_array;
71	<	coordT* surfpt_array;
72	<	std::list<int> surface_atoms;
73	<	FILE *outdummy = NULL;
74	<	FILE *errdummy = NULL;
70	>	ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") {
71	>	}
72
73	<	pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));
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	<	for (int i = 0; i < numpoints; i++) {
88	<	pt_array[dim_ * i] = pos[i][0];
89	<	pt_array[dim_ * i + 1] = pos[i][1];
90	<	pt_array[dim_ * i + 2] = pos[i][2];
91	<	}
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
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	<	/*
126	<	qh_initflags(const_cast<char *>(options_.c_str()));
127	<	qh_init_B(pospoints, numpoints, dim_, ismalloc);
128	<	qh_qhull();
92	<	qh_check_output();
125	>	std::vector<double> coords;
126	>	std::vector<double> vels;
127	>	std::vector<int> indexMap;
128	>	std::vector<double> masses;
129
130	<	qh_produce_output();
131	<	*/
132	<	boolT ismalloc = False;
130	>	FORALLvertices{
131	>	localHullSites++;
132	>
133	>	int idx = qh_pointid(vertex->point);
134
135	<	if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
99	<	const_cast<char *>(options_.c_str()), NULL, stderr)) {
135	>	indexMap.push_back(idx);
136
137	<	vertexT *vertex, **vertexp;
138	<	facetT *facet;
139	<	setT *vertices;
104	<	unsigned int nf = qh num_facets;
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	<	//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	<	}
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	<	qh_getarea(qh facet_list);
155	<	volume_ = qh totvol;
156	<	area_ = qh totarea;
157	<	//      FILE *newGeomFile;
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	<	/*
169	<	FORALLfacets {
170	<	for (int k=0; k < qh hull_dim; k++)
161	<	printf ("%6.2g ", facet->normal[k]);
162	<	printf ("\n");
163	<	}
164	<	*/
168	>	std::vector<double> globalCoords(dim_ * globalHullSites);
169	>	std::vector<double> globalVels(dim_ * globalHullSites);
170	>	std::vector<double> globalMasses(globalHullSites);
171
172	<	int curlong,totlong;
173	<	//      geomviewHull("junk.off");
174	<	qh_freeqhull(!qh_ALL);
175	<	qh_memfreeshort(&curlong, &totlong);
176	<	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;
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	<	if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
179	<	const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
178	>	MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0],
179	>	&coordsOnProc[0], &vectorDisplacements[0],
180	>	MPI::DOUBLE);
181
182	<	qh visit_id++;
183	<	FORALLfacets {
184	<	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	<	}
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	<	}
225	>	Vector3d faceVel = V3Zero;
226	>	Vector3d p[3];
227	>	RealType faceMass = 0.0;
228
229	<	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	<	}
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	<	RealType ConvexHull::getVolume()
246	<	{
234	<	return volume_;
235	<	}
245	>	// localID will be between 0 and hullSitesOnProc[myrank] if we
246	>	// own this guy.
247
248	<	void ConvexHull::geomviewHull(const std::string& geomFileName)
238	<	{
248	>	int localID = id - displacements[myrank];
249
240	–	FILE *newGeomFile;
250
251	<	//create new .md file based on old .md file
252	<	newGeomFile = fopen(geomFileName.c_str(), "w");
253	<	qh_findgood_all(qh facet_list);
254	<	for (int i = 0; i < qh_PRINTEND; i++)
255	<	qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
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	<	fclose(newGeomFile);
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	<
301	<
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 1188 by chuckv, Thu Nov 22 16:39:45 2007 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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