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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, 24107 (2008). |
38 | + | * [4] Vardeman & Gezelter, in progress (2009). |
39 | * | |
40 | + | * |
41 | * ConvexHull.hpp | |
42 | * | |
43 | * Purpose: To calculate convexhull, hull volume using the QuickHull algorithm provided by QHull. | |
44 | * | |
45 | * Created by Charles F. Vardeman II on 11 Dec 2006. | |
46 | * @author Charles F. Vardeman II | |
47 | < | * @version $Id: ConvexHull.hpp,v 1.17 2008-11-14 21:54:54 chuckv Exp $ |
47 | > | * @version $Id: ConvexHull.hpp,v 1.19 2009-11-25 20:02:01 gezelter Exp $ |
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 | std::vector<Triangle> getMesh(){return Triangles_;} | |
92 | – | int getNMeshElements() {return nTriangles_;} |
80 | void printHull(const std::string& geomFileName); | |
81 | + | |
82 | protected: | |
83 | < | double volume_; |
84 | < | double area_; |
83 | > | RealType volume_; |
84 | > | RealType area_; |
85 | int dim_; | |
98 | – | int Ns_; |
99 | – | int nTriangles_; |
100 | – | std::vector<StuntDouble*> surfaceSDs_; |
86 | const std::string options_; | |
87 | < | |
88 | < | private: |
87 | > | |
88 | > | private: |
89 | std::vector<Triangle> Triangles_; | |
105 | – | |
106 | – | #ifdef IS_MPI |
107 | – | int* NstoProc_; |
108 | – | int* vecNstoProc_; |
109 | – | int* displs_; |
110 | – | int* vecdispls_; |
111 | – | int Nsglobal_; |
112 | – | int nproc_; |
113 | – | int myrank_; |
114 | – | struct surfacePt_{ |
115 | – | double x,y,z; |
116 | – | }; |
117 | – | |
118 | – | MPI::Datatype surfacePtType; |
119 | – | std::vector<surfacePt_> surfacePtsLocal_; |
120 | – | std::vector<surfacePt_> surfacePtsGlobal_; |
121 | – | #endif |
122 | – | |
90 | }; | |
91 | } | |
125 | – | |
92 | #endif /*MATH_CONVEXHULL_HPP_*/ |
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