| 1 |
/* Copyright (c) 2008 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.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 1.16 2008-11-14 15:44:34 chuckv Exp $ |
| 48 |
* |
| 49 |
*/ |
| 50 |
|
| 51 |
#ifndef MATH_CONVEXHULL_HPP_ |
| 52 |
#define MATH_CONVEXHULL_HPP_ |
| 53 |
|
| 54 |
#include "math/Vector3.hpp" |
| 55 |
#include "config.h" |
| 56 |
#include "math/Hull.hpp" |
| 57 |
#include "math/Triangle.hpp" |
| 58 |
|
| 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 |
| 78 |
|
| 79 |
|
| 80 |
namespace oopse { |
| 81 |
class ConvexHull : public Hull { |
| 82 |
public: |
| 83 |
ConvexHull(); |
| 84 |
|
| 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 |
std::vector<Triangle> getMesh(){return Triangles_;} |
| 92 |
int getNMeshElements() {return nTriangles_;} |
| 93 |
void printHull(const std::string& geomFileName); |
| 94 |
protected: |
| 95 |
double volume_; |
| 96 |
double area_; |
| 97 |
int dim_; |
| 98 |
int Ns_; |
| 99 |
int nTriangles_; |
| 100 |
std::vector<StuntDouble*> surfaceSDs_; |
| 101 |
const std::string options_; |
| 102 |
|
| 103 |
private: |
| 104 |
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 |
|
| 122 |
}; |
| 123 |
} |
| 124 |
|
| 125 |
#endif /*MATH_CONVEXHULL_HPP_*/ |
