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root/OpenMD/trunk/src/math/ConvexHull.hpp

Comparing trunk/src/math/ConvexHull.hpp (file contents):
Revision 1316 by chuckv, Fri Nov 14 15:44:34 2008 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 1 | Line 1
1	<	/* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved.
1	>	/* Copyright (c) 2008, 2009 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	+	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40		*
41		*  ConvexHull.hpp
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.hpp,v 1.16 2008-11-14 15:44:34 chuckv Exp $
47	>	*  @version $Id$
48		*
49		*/
50
#	Line 59 | Line 59
59		#include <cassert>
60		#include <vector>
61		#include <string>
62	–	extern "C"
63	–	{
64	–	#if defined(HAVE_QHULL)
65	–	#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	–	#endif
74	–	}
75	–	#ifdef IS_MPI
76	–	#include <mpi.h>
77	–	#endif
62
63
64	<	namespace oopse {
64	>	namespace OpenMD {
65		class ConvexHull : public Hull {
66		public:
83	–	ConvexHull();
67
68	+	ConvexHull();
69		virtual ~ConvexHull(){};
70	<	void computeHull(std::vector<StuntDouble*> bodydoubles);
71	<	RealType getArea(){return area_;} //Total area of Hull
72	<	int getNs(){return Ns_;}  //Number of Surface Atoms
73	<	RealType getVolume(){return volume_;} //Total Volume inclosed by Hull
74	<	std::vector< StuntDouble* > getSurfaceAtoms(){return surfaceSDs_;} //Returns a list of surface atoms
70	>
71	>	void computeHull( std::vector<StuntDouble*> bodydoubles );
72	>
73	>	/* Total area of Hull*/
74	>	RealType getArea(){return area_;}
75	>
76	>	/* Total Volume enclosed by Hull */
77	>	RealType getVolume(){ return volume_; }
78	>
79	>	/* Bounding Box for Hull sites */
80	>	Mat3x3d getBoundingBox(){ return boundingBox_; }
81	>
82		std::vector<Triangle> getMesh(){return Triangles_;}
92	–	int getNMeshElements() {return nTriangles_;}
83		void printHull(const std::string& geomFileName);
84	+
85		protected:
86	<	double volume_;
87	<	double area_;
86	>	RealType volume_;
87	>	RealType area_;
88	>	Mat3x3d boundingBox_;
89		int dim_;
98	–	int Ns_;
99	–	int nTriangles_;
100	–	std::vector<StuntDouble*> surfaceSDs_;
90		const std::string options_;
91	<
92	<	private:
91	>
92	>	private:
93		std::vector<Triangle> Triangles_;
105	–
106	–	#ifdef IS_MPI
107	–	int* NstoProc_;
108	–	int* displs_;
109	–	int* vecdispls_;
110	–	int Nsglobal_;
111	–	int nproc_;
112	–	int myrank_;
113	–	struct surfacePt_{
114	–	double x,y,z;
115	–	};
116	–
117	–	MPI::Datatype surfacePtType;
118	–	std::vector<surfacePt_> surfacePtsLocal_;
119	–	std::vector<surfacePt_> surfacePtsGlobal_;
120	–	#endif
121	–
94		};
95		}
124	–
96		#endif /*MATH_CONVEXHULL_HPP_*/

Comparing trunk/src/math/ConvexHull.hpp (property svn:keywords):
Revision 1316 by chuckv, Fri Nov 14 15:44:34 2008 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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