src/math/ConvexHull.hpp

/* Copyright (c) 2008 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.hpp
 *
 *  Purpose: To calculate convexhull, hull volume using the QuickHull algorithm provided by QHull.
 *
 *  Created by Charles F. Vardeman II on 11 Dec 2006.
 *  @author  Charles F. Vardeman II
 *  @version $Id: ConvexHull.hpp,v 1.15 2008-10-21 16:44:00 chuckv Exp $
 *
 */

#ifndef MATH_CONVEXHULL_HPP_
#define MATH_CONVEXHULL_HPP_

#include "math/Vector3.hpp"
#include "config.h"
#include "math/Hull.hpp"
#include "math/Triangle.hpp"

#include <cassert>
#include <vector>
#include <string>
extern "C"
{
#if defined(HAVE_QHULL)
#include <qhull/qhull.h>
#include <qhull/mem.h>
#include <qhull/qset.h>
#include <qhull/geom.h>
#include <qhull/merge.h>
#include <qhull/poly.h>
#include <qhull/io.h>
#include <qhull/stat.h>
#endif
}
#ifdef IS_MPI
#include <mpi.h>
#endif


namespace oopse {
  class ConvexHull : public Hull {
  public:
    ConvexHull();

    virtual ~ConvexHull(){};
    void computeHull(std::vector<StuntDouble*> bodydoubles);
    RealType getArea(){return area_;} //Total area of Hull
    int getNs(){return Ns_;}  //Number of Surface Atoms
    RealType getVolume(){return volume_;} //Total Volume inclosed by Hull
    std::vector< StuntDouble* > getSurfaceAtoms(){return surfaceSDs_;} //Returns a list of surface atoms
    std::vector<Triangle> getMesh(){return Triangles_;}
    int getNMeshElements() {return nTriangles_;}
    void printHull(const std::string& geomFileName);
  protected:
    double volume_;
    double area_;
    int dim_;
    int Ns_;
    int nTriangles_;
    std::vector<StuntDouble*> surfaceSDs_;
    const std::string options_;

    private:
    std::vector<Triangle> Triangles_;

#ifdef IS_MPI
    int* NstoProc_;
    int* displs_;
    int Nsglobal_;
    int nproc_;
    int myrank_;
    struct surfacePt_{
        double x,y,z;
    };

    MPI::Datatype surfacePtType;
    std::vector<surfacePt_> surfacePtsLocal_;
    std::vector<surfacePt_> surfacePtsGlobal_;
#endif 

  };
}

#endif /*MATH_CONVEXHULL_HPP_*/
Revision:	1308
Committed:	Tue Oct 21 16:44:00 2008 UTC (17 years ago) by chuckv
File size:	4038 byte(s)
Log Message:	Fixed Memory Leak in ConvexHull.
#	User	Rev	Content
1	chuckv	1293	/* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved.
2	chuckv	1097	*
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.hpp
42			*
43	chuckv	1188	* Purpose: To calculate convexhull, hull volume using the QuickHull algorithm provided by QHull.
44	chuckv	1097	*
45			* Created by Charles F. Vardeman II on 11 Dec 2006.
46			* @author Charles F. Vardeman II
47	chuckv	1308	* @version $Id: ConvexHull.hpp,v 1.15 2008-10-21 16:44:00 chuckv Exp $
48	chuckv	1097	*
49			*/
50
51			#ifndef MATH_CONVEXHULL_HPP_
52			#define MATH_CONVEXHULL_HPP_
53
54			#include "math/Vector3.hpp"
55	chuckv	1188	#include "config.h"
56	chuckv	1295	#include "math/Hull.hpp"
57	chuckv	1293	#include "math/Triangle.hpp"
58	chuckv	1097
59			#include <cassert>
60			#include <vector>
61	chuckv	1137	#include <string>
62			extern "C"
63			{
64	chuckv	1209	#if defined(HAVE_QHULL)
65	chuckv	1304	#include <qhull/qhull.h>
66			#include <qhull/mem.h>
67			#include <qhull/qset.h>
68			#include <qhull/geom.h>
69			#include <qhull/merge.h>
70			#include <qhull/poly.h>
71			#include <qhull/io.h>
72			#include <qhull/stat.h>
73	chuckv	1209	#endif
74	chuckv	1137	}
75	chuckv	1293	#ifdef IS_MPI
76			#include <mpi.h>
77			#endif
78	chuckv	1097
79
80	chuckv	1141	namespace oopse {
81	chuckv	1293	class ConvexHull : public Hull {
82	chuckv	1141	public:
83			ConvexHull();
84	chuckv	1293
85			virtual ~ConvexHull(){};
86			void computeHull(std::vector<StuntDouble*> bodydoubles);
87			RealType getArea(){return area_;} //Total area of Hull
88			int getNs(){return Ns_;} //Number of Surface Atoms
89			RealType getVolume(){return volume_;} //Total Volume inclosed by Hull
90			std::vector< StuntDouble* > getSurfaceAtoms(){return surfaceSDs_;} //Returns a list of surface atoms
91	chuckv	1308	std::vector<Triangle> getMesh(){return Triangles_;}
92	chuckv	1307	int getNMeshElements() {return nTriangles_;}
93	chuckv	1293	void printHull(const std::string& geomFileName);
94	chuckv	1141	protected:
95			double volume_;
96			double area_;
97			int dim_;
98	chuckv	1293	int Ns_;
99	chuckv	1307	int nTriangles_;
100	chuckv	1302	std::vector<StuntDouble*> surfaceSDs_;
101	chuckv	1141	const std::string options_;
102	chuckv	1302
103	chuckv	1293	private:
104	chuckv	1308	std::vector<Triangle> Triangles_;
105	chuckv	1293
106			#ifdef IS_MPI
107			int* NstoProc_;
108			int* displs_;
109			int Nsglobal_;
110			int nproc_;
111			int myrank_;
112			struct surfacePt_{
113			double x,y,z;
114			};
115
116			MPI::Datatype surfacePtType;
117			std::vector<surfacePt_> surfacePtsLocal_;
118			std::vector<surfacePt_> surfacePtsGlobal_;
119			#endif
120
121	chuckv	1141	};
122	chuckv	1097	}
123
124			#endif /MATH_CONVEXHULL_HPP_/