| 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). |
| 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 |
|
* |
| 40 |
– |
* |
| 41 |
|
* AlphaHull.hpp |
| 42 |
|
* |
| 43 |
|
* Purpose: To calculate alphahull, hull volume using the QuickHull algorithm provided by QHull. |
| 60 |
|
#include <vector> |
| 61 |
|
#include <string> |
| 62 |
|
|
| 63 |
< |
|
| 63 |
> |
using namespace std; |
| 64 |
|
namespace OpenMD { |
| 65 |
|
class AlphaHull : public Hull { |
| 66 |
|
public: |
| 67 |
< |
|
| 68 |
< |
AlphaHull(double alpha); |
| 67 |
> |
|
| 68 |
> |
AlphaHull(RealType alpha); |
| 69 |
|
virtual ~AlphaHull(){}; |
| 70 |
< |
|
| 71 |
< |
void computeHull( std::vector<StuntDouble*> bodydoubles ); |
| 72 |
< |
|
| 70 |
> |
|
| 71 |
> |
void computeHull( vector<StuntDouble*> bodydoubles ); |
| 72 |
> |
|
| 73 |
|
/* Total area of Hull*/ |
| 74 |
< |
RealType getArea(){return area_;} |
| 75 |
< |
|
| 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_;} |
| 78 |
> |
|
| 79 |
> |
/* Bounding Box for Hull sites */ |
| 80 |
> |
Mat3x3d getBoundingBox(){ return boundingBox_; } |
| 81 |
> |
|
| 82 |
> |
vector<Triangle> getMesh(){ return Triangles_; } |
| 83 |
|
void printHull(const std::string& geomFileName); |
| 84 |
< |
|
| 84 |
> |
|
| 85 |
|
protected: |
| 86 |
|
RealType volume_; |
| 87 |
|
RealType area_; |
| 88 |
+ |
Mat3x3d boundingBox_; |
| 89 |
|
int dim_; |
| 90 |
< |
double alpha_; |
| 90 |
> |
RealType alpha_; |
| 91 |
|
const std::string options_; |
| 92 |
|
|
| 93 |
|
private: |
| 94 |
< |
std::vector<Triangle> Triangles_; |
| 94 |
> |
vector<Triangle> Triangles_; |
| 95 |
|
}; |
| 96 |
|
} |
| 97 |
< |
#endif /*MATH_CONVEXHULL_HPP_*/ |
| 97 |
> |
#endif |
