| 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). |
| 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.cpp |
| 42 |
|
* |
| 43 |
|
* Purpose: To calculate Alpha hull, hull volume libqhull. |
| 58 |
|
#include <utility> |
| 59 |
|
#include "math/AlphaHull.hpp" |
| 60 |
|
#include "utils/simError.h" |
| 61 |
– |
|
| 61 |
|
#ifdef IS_MPI |
| 62 |
|
#include <mpi.h> |
| 63 |
|
#endif |
| 64 |
+ |
#include "math/qhull.hpp" |
| 65 |
|
|
| 66 |
|
using namespace OpenMD; |
| 67 |
|
|
| 68 |
|
#ifdef HAVE_QHULL |
| 69 |
– |
extern "C" |
| 70 |
– |
{ |
| 71 |
– |
#include <qhull/libqhull.h> |
| 72 |
– |
#include <qhull/mem.h> |
| 73 |
– |
#include <qhull/qset.h> |
| 74 |
– |
#include <qhull/geom.h> |
| 75 |
– |
#include <qhull/merge.h> |
| 76 |
– |
#include <qhull/poly.h> |
| 77 |
– |
#include <qhull/io.h> |
| 78 |
– |
#include <qhull/stat.h> |
| 79 |
– |
} |
| 69 |
|
double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim); |
| 70 |
|
|
| 71 |
|
AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha), options_("qhull d QJ Tcv Pp") { |
| 74 |
|
void AlphaHull::computeHull(std::vector<StuntDouble*> bodydoubles) { |
| 75 |
|
|
| 76 |
|
int numpoints = bodydoubles.size(); |
| 77 |
< |
bool alphashape=true; |
| 77 |
> |
// bool alphashape=true; |
| 78 |
|
|
| 79 |
|
Triangles_.clear(); |
| 80 |
|
|
| 81 |
< |
vertexT *vertex, **vertexp; |
| 81 |
> |
vertexT *vertex; |
| 82 |
> |
// vertexT **vertexp; |
| 83 |
|
facetT *facet, *neighbor; |
| 84 |
< |
setT *vertices, *verticestop, *verticesbottom; |
| 84 |
> |
// setT *vertices, *verticestop, *verticesbottom; |
| 85 |
|
int curlong, totlong; |
| 86 |
|
pointT *interiorPoint; |
| 87 |
|
|
| 348 |
|
facetlist.push_back(virtexlist); |
| 349 |
|
face.addVertices(p[0],p[1],p[2]); |
| 350 |
|
face.setFacetMass(faceMass); |
| 351 |
< |
face.setFacetVelocity(faceVel/3.0); |
| 351 |
> |
face.setFacetVelocity(faceVel / RealType(3.0)); |
| 352 |
|
|
| 353 |
|
RealType area = face.getArea(); |
| 354 |
|
area_ += area; |
