| 35 |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 36 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 37 |
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* [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 |
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* Purpose: To calculate Alpha hull, hull volume libqhull. |
| 44 |
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* |
| 45 |
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* Created by Charles F. Vardeman II on 11 Dec 2006. |
| 46 |
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* @author Charles F. Vardeman II |
| 47 |
< |
* @version $Id: ConvexHull.cpp,v 1.21 2009-11-25 20:02:01 gezelter Exp $ |
| 47 |
> |
* @version $Id$ |
| 48 |
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* |
| 49 |
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*/ |
| 50 |
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|
| 68 |
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#ifdef HAVE_QHULL |
| 69 |
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extern "C" |
| 70 |
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{ |
| 71 |
< |
#include <qhull/qhull.h> |
| 71 |
> |
#include <qhull/libqhull.h> |
| 72 |
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#include <qhull/mem.h> |
| 73 |
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#include <qhull/qset.h> |
| 74 |
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#include <qhull/geom.h> |
| 79 |
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} |
| 80 |
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double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim); |
| 81 |
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|
| 82 |
< |
AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha), options_("qhull d QJ Tcv ") { |
| 82 |
> |
AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha), options_("qhull d QJ Tcv Pp") { |
| 83 |
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} |
| 84 |
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|
| 85 |
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void AlphaHull::computeHull(std::vector<StuntDouble*> bodydoubles) { |
| 91 |
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|
| 92 |
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vertexT *vertex, **vertexp; |
| 93 |
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facetT *facet, *neighbor; |
| 94 |
< |
setT *vertices; |
| 94 |
> |
setT *vertices, *verticestop, *verticesbottom; |
| 95 |
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int curlong, totlong; |
| 96 |
+ |
pointT *interiorPoint; |
| 97 |
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|
| 98 |
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std::vector<double> ptArray(numpoints*dim_); |
| 99 |
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|
| 244 |
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qh visit_id++; |
| 245 |
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int numFacets=0; |
| 246 |
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std::vector<std::vector <int> > facetlist; |
| 247 |
+ |
interiorPoint = qh interior_point; |
| 248 |
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FORALLfacet_(qh facet_list) { |
| 249 |
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numFacets++; |
| 250 |
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if (!facet->upperdelaunay) { |
| 309 |
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//assert(numFacets== qh num_facets); |
| 310 |
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|
| 311 |
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//Filter the triangles (only the ones on the boundary of the alpha complex) and build the mesh |
| 312 |
+ |
|
| 313 |
+ |
|
| 314 |
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|
| 315 |
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ridgeT *ridge, **ridgep; |
| 316 |
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FOREACHridge_(set) { |
| 323 |
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// Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]); |
| 324 |
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//face.setNormal(V3dNormal); |
| 325 |
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|
| 322 |
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// RealType faceArea = qh_facetarea(facet); |
| 323 |
– |
//face.setArea(faceArea); |
| 326 |
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|
| 327 |
< |
//vertices = qh_facet3vertex(facet); |
| 328 |
< |
|
| 327 |
< |
//coordT *center = qh_getcenter(vertices); |
| 327 |
> |
//coordT *center = qh_getcenter(ridge->vertices); |
| 328 |
> |
//std::cout << "Centers are " << center[0] << " " <<center[1] << " " << center[2] << std::endl; |
| 329 |
|
//Vector3d V3dCentroid(center[0], center[1], center[2]); |
| 330 |
|
//face.setCentroid(V3dCentroid); |
| 331 |
+ |
|
| 332 |
|
|
| 333 |
< |
//Vector3d faceVel = V3Zero; |
| 333 |
> |
Vector3d faceVel = V3Zero; |
| 334 |
|
Vector3d p[3]; |
| 335 |
< |
//RealType faceMass = 0.0; |
| 335 |
> |
RealType faceMass = 0.0; |
| 336 |
|
|
| 337 |
|
int ver = 0; |
| 338 |
|
std::vector<int> virtexlist; |
| 345 |
|
RealType mass; |
| 346 |
|
ver++; |
| 347 |
|
virtexlist.push_back(id); |
| 348 |
< |
} |
| 349 |
< |
facetlist.push_back(virtexlist); |
| 348 |
> |
// std::cout << "Ridge: " << ridgesCount << " Vertex " << id << std::endl; |
| 349 |
> |
|
| 350 |
> |
vel = bodydoubles[id]->getVel(); |
| 351 |
> |
mass = bodydoubles[id]->getMass(); |
| 352 |
> |
face.addVertexSD(bodydoubles[id]); |
| 353 |
|
|
| 354 |
+ |
|
| 355 |
+ |
faceVel = faceVel + vel; |
| 356 |
+ |
faceMass = faceMass + mass; |
| 357 |
+ |
} //FOREACH Vertex |
| 358 |
+ |
facetlist.push_back(virtexlist); |
| 359 |
+ |
face.addVertices(p[0],p[1],p[2]); |
| 360 |
+ |
face.setFacetMass(faceMass); |
| 361 |
+ |
face.setFacetVelocity(faceVel / RealType(3.0)); |
| 362 |
+ |
|
| 363 |
+ |
RealType area = face.getArea(); |
| 364 |
+ |
area_ += area; |
| 365 |
+ |
Vector3d normal = face.getUnitNormal(); |
| 366 |
+ |
RealType offset = ((0.0-p[0][0])*normal[0] + (0.0-p[0][1])*normal[1] + (0.0-p[0][2])*normal[2]); |
| 367 |
+ |
RealType dist = normal[0] * interiorPoint[0] + normal[1]*interiorPoint[1] + normal[2]*interiorPoint[2]; |
| 368 |
+ |
std::cout << "Dist and normal and area are: " << normal << std::endl; |
| 369 |
+ |
volume_ += dist *area/qh hull_dim; |
| 370 |
+ |
|
| 371 |
+ |
Triangles_.push_back(face); |
| 372 |
|
} |
| 373 |
|
} |
| 351 |
– |
|
| 374 |
|
|
| 375 |
< |
//assert(pm.cm.fn == ridgesCount); |
| 375 |
> |
std::cout << "Volume is: " << volume_ << std::endl; |
| 376 |
|
|
| 377 |
+ |
//assert(pm.cm.fn == ridgesCount); |
| 378 |
+ |
/* |
| 379 |
|
std::cout <<"OFF"<<std::endl; |
| 380 |
|
std::cout << bodydoubles.size() << " " << facetlist.size() << " " << 3*facetlist.size() << std::endl; |
| 381 |
|
for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){ |
| 394 |
|
} |
| 395 |
|
std::cout << std::endl; |
| 396 |
|
} |
| 397 |
+ |
*/ |
| 398 |
|
|
| 399 |
|
|
| 400 |
|
|
| 376 |
– |
|
| 401 |
|
/* |
| 402 |
|
FORALLfacets { |
| 403 |
|
Triangle face; |
| 462 |
|
|
| 463 |
|
} //FORALLfacets |
| 464 |
|
*/ |
| 465 |
< |
qh_getarea(qh facet_list); |
| 466 |
< |
volume_ = qh totvol; |
| 467 |
< |
area_ = qh totarea; |
| 465 |
> |
// qh_getarea(qh facet_list); |
| 466 |
> |
//volume_ = qh totvol; |
| 467 |
> |
// area_ = qh totarea; |
| 468 |
|
|
| 469 |
|
qh_freeqhull(!qh_ALL); |
| 470 |
|
qh_memfreeshort(&curlong, &totlong); |
