src/math/ConvexHull.cpp

/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 *
 *  ConvexHull.cpp
 *
 *  Purpose: To calculate convexhull, hull volume libqhull.
 *
 *  Created by Charles F. Vardeman II on 11 Dec 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id: ConvexHull.cpp,v 1.5 2007-11-22 16:39:45 chuckv Exp $
 *
 */

#include <iostream>
#include <fstream>
#include <list>
#include <algorithm>
#include <iterator>
#include "math/ConvexHull.hpp"
#include "utils/simError.h"
using namespace oopse;

/* Old options Qt Qu Qg QG0 FA */
ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt  Qci Tcv Pp")
//ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
{}

bool ConvexHull::genHull(std::vector<Vector3d> pos)
{


        int numpoints = pos.size();
        coordT* pt_array;
        coordT* surfpt_array;
        std::list<int> surface_atoms;
  FILE *outdummy = NULL;
  FILE *errdummy = NULL;

        pt_array = (coordT*) malloc(sizeof(coordT) * (numpoints * dim_));


        for (int i = 0; i < numpoints; i++) {
                pt_array[dim_ * i] = pos[i][0];
                pt_array[dim_ * i + 1] = pos[i][1];
                pt_array[dim_ * i + 2] = pos[i][2];
        }


        /*
                qh_initflags(const_cast<char *>(options_.c_str()));
                qh_init_B(pospoints, numpoints, dim_, ismalloc);
                qh_qhull();
                qh_check_output();

                qh_produce_output();
        */
        boolT ismalloc = False;

        if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
                          const_cast<char *>(options_.c_str()), NULL, stderr)) {

                vertexT *vertex, **vertexp;
                facetT *facet;
                setT *vertices;
                unsigned int nf = qh num_facets;

                //Matrix idx(nf, dim);
/*
                int j, i = 0, id = 0;
                        
                        int id2 = 0;
                        coordT *point,**pointp;
                        realT dist;
                        FORALLfacets {
                            j = 0;
                        
                            if (!facet->simplicial){
                            // should never happen with Qt
                            sprintf(painCave.errMsg, "ConvexHull: non-simplicaial facet detected");
                                    painCave.isFatal = 0;
                                    simError();
                            }
                        
                            vertices = qh_facet3vertex(facet);
                            FOREACHvertex_(vertices){
                                                id = qh_pointid(vertex->point);
                                                surface_atoms.push_back(id);
                                                //std::cout << "Ag  " << pos[id][0] << "    " << pos[id][1] << "    " << pos[id][2]<< std::endl;
                                        }
                                        qh_settempfree(&vertices);
                                        
                            FOREACHpoint_(facet->coplanarset){
                            vertex= qh_nearvertex (facet, point, &dist);
                      //id= qh_pointid (vertex->point);
                      id2= qh_pointid (point);
                                        surface_atoms.push_back(id2);
                                        //std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
                      //printf ("%d %d %d " qh_REAL_1 "\n", id, id2, facet->id, dist);
                                        //std::cout << "Neighbors are: %d $d %d\n" << id << id2 << facet->id;
                                        
                                }
                                
                        }
                
*/
                
                
        }


        qh_getarea(qh facet_list);
        volume_ = qh totvol;
        area_ = qh totarea;
//      FILE *newGeomFile;


        /*
                FORALLfacets {
                    for (int k=0; k < qh hull_dim; k++)
                      printf ("%6.2g ", facet->normal[k]);
                    printf ("\n");
                  }
        */

        int curlong,totlong;
//      geomviewHull("junk.off");
        qh_freeqhull(!qh_ALL);
        qh_memfreeshort(&curlong, &totlong);
        if (curlong || totlong)
                std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
                << totlong << curlong << std::endl;
        free(pt_array);
/*
        int j = 0;
        surface_atoms.sort();
        surface_atoms.unique();
        surfpt_array = (coordT*) malloc(sizeof(coordT) * (surface_atoms.size() * dim_));
        for(std::list<int>::iterator list_iter = surface_atoms.begin(); 
            list_iter != surface_atoms.end(); list_iter++)
        {
                int i = *list_iter;
                        //surfpt_array[dim_ * j] = pos[i][0];
                        //surfpt_array[dim_ * j + 1] = pos[i][1];
                        //surfpt_array[dim_ * j + 2] = pos[i][2];
                        std::cout << "Ag  " << pos[i][0] << "  " << pos[i][1] << "  "<< pos[i][2] << std::endl;
                        j++;
        }
*/      
        
/*      
        std::string deloptions_ = "qhull d Qt";
        facetT *facet, *neighbor;
        ridgeT *ridge, **ridgep;

        if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
        const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {

                qh visit_id++;
                FORALLfacets {
                if (!facet->upperdelaunay) {
                        facet->visitid= qh visit_id;
                        qh_makeridges(facet);
                        FOREACHridge_(facet->ridges) {
                                neighbor= otherfacet_(ridge, facet);
                                if (neighbor->visitid != qh visit_id) {
                                                                                                                
                                        FOREACHvertex_(ridge->vertices)
                                                int id2 = qh_pointid (vertex->point); 
                                                std::cout << "Ag  " << pos[id2][0] << "    " << pos[id2][1] << "    " << pos[id2][2]<< std::endl;
                                }
                        }
                }


}

                qh_freeqhull(!qh_ALL);
                qh_memfreeshort(&curlong, &totlong);
                if (curlong || totlong)
                        std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) "
                        << totlong << curlong << std::endl;
                free(surfpt_array);
*/              
        return true;
}


RealType ConvexHull::getVolume()
{
        return volume_;
}

void ConvexHull::geomviewHull(const std::string& geomFileName)
{

        FILE *newGeomFile;

        //create new .md file based on old .md file
        newGeomFile = fopen(geomFileName.c_str(), "w");
        qh_findgood_all(qh facet_list);
        for (int i = 0; i < qh_PRINTEND; i++)
                qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);

        fclose(newGeomFile);
}


Revision:	1188
Committed:	Thu Nov 22 16:39:45 2007 UTC (17 years, 5 months ago) by chuckv
File size:	7136 byte(s)
Log Message:	Added volume calculation for hull.
#	User	Rev	Content
1	chuckv	1097	/* Copyright (c) 2006 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
18			* notice, this list of conditions and the following disclaimer.
19			*
20			* 3. Redistributions in binary form must reproduce the above copyright
21			* notice, this list of conditions and the following disclaimer in the
22			* documentation and/or other materials provided with the
23			* distribution.
24			*
25			* This software is provided "AS IS," without a warranty of any
26			* kind. All express or implied conditions, representations and
27			* warranties, including any implied warranty of merchantability,
28			* fitness for a particular purpose or non-infringement, are hereby
29			* excluded. The University of Notre Dame and its licensors shall not
30			* be liable for any damages suffered by licensee as a result of
31			* using, modifying or distributing the software or its
32			* derivatives. In no event will the University of Notre Dame or its
33			* licensors be liable for any lost revenue, profit or data, or for
34			* direct, indirect, special, consequential, incidental or punitive
35			* damages, however caused and regardless of the theory of liability,
36			* arising out of the use of or inability to use software, even if the
37			* University of Notre Dame has been advised of the possibility of
38			* such damages.
39			*
40			*
41			* ConvexHull.cpp
42			*
43	chuckv	1137	* Purpose: To calculate convexhull, hull volume libqhull.
44	chuckv	1097	*
45			* Created by Charles F. Vardeman II on 11 Dec 2006.
46			* @author Charles F. Vardeman II
47	chuckv	1188	* @version $Id: ConvexHull.cpp,v 1.5 2007-11-22 16:39:45 chuckv Exp $
48	chuckv	1097	*
49			*/
50
51			#include <iostream>
52			#include <fstream>
53	chuckv	1188	#include <list>
54			#include <algorithm>
55			#include <iterator>
56	chuckv	1141	#include "math/ConvexHull.hpp"
57	chuckv	1188	#include "utils/simError.h"
58	chuckv	1097	using namespace oopse;
59
60	chuckv	1188	/* Old options Qt Qu Qg QG0 FA */
61			ConvexHull::ConvexHull() : dim_(3), options_("qhull Qt Qci Tcv Pp")
62			//ConvexHull::ConvexHull() : dim_(3), options_("qhull d Qbb Qt i")
63			{}
64
65			bool ConvexHull::genHull(std::vector<Vector3d> pos)
66			{
67
68
69			int numpoints = pos.size();
70			coordT* pt_array;
71			coordT* surfpt_array;
72			std::list<int> surface_atoms;
73			FILE *outdummy = NULL;
74			FILE *errdummy = NULL;
75
76			pt_array = (coordT) malloc(sizeof(coordT) (numpoints * dim_));
77
78
79			for (int i = 0; i < numpoints; i++) {
80			pt_array[dim_ * i] = pos[i][0];
81			pt_array[dim_ * i + 1] = pos[i][1];
82			pt_array[dim_ * i + 2] = pos[i][2];
83			}
84
85
86
87
88			/*
89			qh_initflags(const_cast<char *>(options_.c_str()));
90			qh_init_B(pospoints, numpoints, dim_, ismalloc);
91			qh_qhull();
92			qh_check_output();
93
94			qh_produce_output();
95			*/
96			boolT ismalloc = False;
97
98			if (!qh_new_qhull(dim_, numpoints, pt_array, ismalloc,
99			const_cast<char *>(options_.c_str()), NULL, stderr)) {
100
101			vertexT vertex, *vertexp;
102			facetT *facet;
103			setT *vertices;
104			unsigned int nf = qh num_facets;
105
106			//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			}
148
149
150
151
152			qh_getarea(qh facet_list);
153			volume_ = qh totvol;
154			area_ = qh totarea;
155			// FILE *newGeomFile;
156
157
158			/*
159			FORALLfacets {
160			for (int k=0; k < qh hull_dim; k++)
161			printf ("%6.2g ", facet->normal[k]);
162			printf ("\n");
163			}
164			*/
165
166			int curlong,totlong;
167			// geomviewHull("junk.off");
168			qh_freeqhull(!qh_ALL);
169			qh_memfreeshort(&curlong, &totlong);
170			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;
195
196			if (!qh_new_qhull(dim_, surface_atoms.size(), surfpt_array, ismalloc,
197			const_cast<char *>(deloptions_.c_str()), NULL, stderr)) {
198
199			qh visit_id++;
200			FORALLfacets {
201			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			}
214
215
216
217
218	chuckv	1141	}
219	chuckv	1097
220	chuckv	1188	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	chuckv	1143
230	chuckv	1188
231
232			RealType ConvexHull::getVolume()
233			{
234			return volume_;
235	chuckv	1097	}
236
237	chuckv	1188	void ConvexHull::geomviewHull(const std::string& geomFileName)
238			{
239	chuckv	1137
240	chuckv	1188	FILE *newGeomFile;
241
242			//create new .md file based on old .md file
243			newGeomFile = fopen(geomFileName.c_str(), "w");
244			qh_findgood_all(qh facet_list);
245			for (int i = 0; i < qh_PRINTEND; i++)
246			qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL);
247
248			fclose(newGeomFile);
249	chuckv	1097	}
250
251	chuckv	1188
252
253