| 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. |
| 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 1.15 2008-10-21 16:44:00 chuckv Exp $ |
| 47 |
> |
* @version $Id: ConvexHull.hpp,v 1.19 2009-11-25 20:02:01 gezelter Exp $ |
| 48 |
|
* |
| 49 |
|
*/ |
| 50 |
|
|
| 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* 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 |
– |
|
| 90 |
|
}; |
| 91 |
|
} |
| 123 |
– |
|
| 92 |
|
#endif /*MATH_CONVEXHULL_HPP_*/ |
