| 34 |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 36 |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 37 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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|
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 39 |
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* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 40 |
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* |
| 62 |
|
#include <mpi.h> |
| 63 |
|
#endif |
| 64 |
|
|
| 65 |
< |
using namespace OpenMD; |
| 65 |
> |
#include "math/qhull.hpp" |
| 66 |
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|
| 67 |
|
#ifdef HAVE_QHULL |
| 68 |
< |
extern "C" |
| 69 |
< |
{ |
| 70 |
< |
#include <qhull/libqhull.h> |
| 71 |
< |
#include <qhull/mem.h> |
| 72 |
< |
#include <qhull/qset.h> |
| 73 |
< |
#include <qhull/geom.h> |
| 74 |
< |
#include <qhull/merge.h> |
| 75 |
< |
#include <qhull/poly.h> |
| 76 |
< |
#include <qhull/io.h> |
| 77 |
< |
#include <qhull/stat.h> |
| 78 |
< |
} |
| 68 |
> |
using namespace OpenMD; |
| 69 |
|
|
| 70 |
|
ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") { |
| 71 |
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} |
| 80 |
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facetT *facet; |
| 81 |
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setT *vertices; |
| 82 |
|
int curlong, totlong; |
| 83 |
< |
pointT *intPoint; |
| 83 |
> |
// pointT *intPoint; |
| 84 |
|
|
| 85 |
|
std::vector<double> ptArray(numpoints*dim_); |
| 86 |
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|
| 87 |
|
// Copy the positon vector into a points vector for qhull. |
| 88 |
|
std::vector<StuntDouble*>::iterator SD; |
| 89 |
|
int i = 0; |
| 90 |
+ |
|
| 91 |
|
for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){ |
| 92 |
|
Vector3d pos = (*SD)->getPos(); |
| 93 |
|
ptArray[dim_ * i] = pos.x(); |
| 205 |
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} //qh_new_qhull |
| 206 |
|
|
| 207 |
|
#endif |
| 208 |
< |
intPoint = qh interior_point; |
| 209 |
< |
RealType calcvol = 0.0; |
| 208 |
> |
// commented out below, so comment out here also. |
| 209 |
> |
// intPoint = qh interior_point; |
| 210 |
> |
// RealType calcvol = 0.0; |
| 211 |
|
FORALLfacets { |
| 212 |
|
Triangle face; |
| 213 |
|
//Qhull sets the unit normal in facet->normal |
| 266 |
|
|
| 267 |
|
face.addVertices(p[0], p[1], p[2]); |
| 268 |
|
face.setFacetMass(faceMass); |
| 269 |
< |
face.setFacetVelocity(faceVel/3.0); |
| 269 |
> |
face.setFacetVelocity(faceVel / RealType(3.0)); |
| 270 |
|
/* |
| 271 |
|
RealType comparea = face.computeArea(); |
| 272 |
|
realT calcarea = qh_facetarea (facet); |
| 284 |
|
qh_getarea(qh facet_list); |
| 285 |
|
volume_ = qh totvol; |
| 286 |
|
area_ = qh totarea; |
| 287 |
< |
// std::cout << "My volume is: " << calcvol << " qhull volume is:" << volume_ << std::endl; |
| 287 |
> |
// std::cout << " qhull volume is:" << volume_ << std::endl; |
| 288 |
|
qh_freeqhull(!qh_ALL); |
| 289 |
|
qh_memfreeshort(&curlong, &totlong); |
| 290 |
|
if (curlong || totlong) { |
