| 35 |
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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). |
| 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). * |
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* |
| 40 |
– |
* |
| 41 |
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* AlphaHull.cpp |
| 42 |
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* |
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* Purpose: To calculate Alpha hull, hull volume libqhull. |
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* |
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* Created by Charles F. Vardeman II on 11 Dec 2006. |
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* @author Charles F. Vardeman II |
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< |
* @version $Id: ConvexHull.cpp,v 1.21 2009-11-25 20:02:01 gezelter Exp $ |
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> |
* @version $Id$ |
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* |
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*/ |
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|
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#include <utility> |
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#include "math/AlphaHull.hpp" |
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#include "utils/simError.h" |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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#include "math/qhull.hpp" |
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using namespace OpenMD; |
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#ifdef HAVE_QHULL |
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extern "C" |
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{ |
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#include <qhull/qhull.h> |
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#include <qhull/mem.h> |
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#include <qhull/qset.h> |
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#include <qhull/geom.h> |
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#include <qhull/merge.h> |
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#include <qhull/poly.h> |
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#include <qhull/io.h> |
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#include <qhull/stat.h> |
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} |
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double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim); |
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|
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AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha), options_("qhull d QJ Tcv ") { |
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> |
AlphaHull::AlphaHull(double alpha) : Hull(), dim_(3), alpha_(alpha), options_("qhull d QJ Tcv Pp") { |
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} |
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void AlphaHull::computeHull(std::vector<StuntDouble*> bodydoubles) { |
| 75 |
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int numpoints = bodydoubles.size(); |
| 77 |
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bool alphashape=true; |
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// bool alphashape=true; |
| 78 |
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Triangles_.clear(); |
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|
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vertexT *vertex, **vertexp; |
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vertexT *vertex; |
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> |
// vertexT **vertexp; |
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facetT *facet, *neighbor; |
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setT *vertices; |
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> |
// setT *vertices, *verticestop, *verticesbottom; |
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int curlong, totlong; |
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pointT *interiorPoint; |
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|
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std::vector<double> ptArray(numpoints*dim_); |
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|
| 234 |
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qh visit_id++; |
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int numFacets=0; |
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std::vector<std::vector <int> > facetlist; |
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+ |
interiorPoint = qh interior_point; |
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FORALLfacet_(qh facet_list) { |
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numFacets++; |
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if (!facet->upperdelaunay) { |
| 299 |
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//assert(numFacets== qh num_facets); |
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|
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//Filter the triangles (only the ones on the boundary of the alpha complex) and build the mesh |
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|
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+ |
|
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|
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ridgeT *ridge, **ridgep; |
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FOREACHridge_(set) { |
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// Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]); |
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//face.setNormal(V3dNormal); |
| 315 |
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|
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// RealType faceArea = qh_facetarea(facet); |
| 323 |
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//face.setArea(faceArea); |
| 316 |
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|
| 317 |
< |
//vertices = qh_facet3vertex(facet); |
| 318 |
< |
|
| 327 |
< |
//coordT *center = qh_getcenter(vertices); |
| 317 |
> |
//coordT *center = qh_getcenter(ridge->vertices); |
| 318 |
> |
//std::cout << "Centers are " << center[0] << " " <<center[1] << " " << center[2] << std::endl; |
| 319 |
|
//Vector3d V3dCentroid(center[0], center[1], center[2]); |
| 320 |
|
//face.setCentroid(V3dCentroid); |
| 321 |
+ |
|
| 322 |
|
|
| 323 |
< |
//Vector3d faceVel = V3Zero; |
| 323 |
> |
Vector3d faceVel = V3Zero; |
| 324 |
|
Vector3d p[3]; |
| 325 |
< |
//RealType faceMass = 0.0; |
| 325 |
> |
RealType faceMass = 0.0; |
| 326 |
|
|
| 327 |
|
int ver = 0; |
| 328 |
|
std::vector<int> virtexlist; |
| 335 |
|
RealType mass; |
| 336 |
|
ver++; |
| 337 |
|
virtexlist.push_back(id); |
| 338 |
< |
} |
| 347 |
< |
facetlist.push_back(virtexlist); |
| 338 |
> |
// std::cout << "Ridge: " << ridgesCount << " Vertex " << id << std::endl; |
| 339 |
|
|
| 340 |
+ |
vel = bodydoubles[id]->getVel(); |
| 341 |
+ |
mass = bodydoubles[id]->getMass(); |
| 342 |
+ |
face.addVertexSD(bodydoubles[id]); |
| 343 |
+ |
|
| 344 |
+ |
|
| 345 |
+ |
faceVel = faceVel + vel; |
| 346 |
+ |
faceMass = faceMass + mass; |
| 347 |
+ |
} //FOREACH Vertex |
| 348 |
+ |
facetlist.push_back(virtexlist); |
| 349 |
+ |
face.addVertices(p[0],p[1],p[2]); |
| 350 |
+ |
face.setFacetMass(faceMass); |
| 351 |
+ |
face.setFacetVelocity(faceVel / RealType(3.0)); |
| 352 |
+ |
|
| 353 |
+ |
RealType area = face.getArea(); |
| 354 |
+ |
area_ += area; |
| 355 |
+ |
Vector3d normal = face.getUnitNormal(); |
| 356 |
+ |
RealType offset = ((0.0-p[0][0])*normal[0] + (0.0-p[0][1])*normal[1] + (0.0-p[0][2])*normal[2]); |
| 357 |
+ |
RealType dist = normal[0] * interiorPoint[0] + normal[1]*interiorPoint[1] + normal[2]*interiorPoint[2]; |
| 358 |
+ |
std::cout << "Dist and normal and area are: " << normal << std::endl; |
| 359 |
+ |
volume_ += dist *area/qh hull_dim; |
| 360 |
+ |
|
| 361 |
+ |
Triangles_.push_back(face); |
| 362 |
|
} |
| 363 |
|
} |
| 351 |
– |
|
| 364 |
|
|
| 365 |
< |
//assert(pm.cm.fn == ridgesCount); |
| 365 |
> |
std::cout << "Volume is: " << volume_ << std::endl; |
| 366 |
|
|
| 367 |
+ |
//assert(pm.cm.fn == ridgesCount); |
| 368 |
+ |
/* |
| 369 |
|
std::cout <<"OFF"<<std::endl; |
| 370 |
|
std::cout << bodydoubles.size() << " " << facetlist.size() << " " << 3*facetlist.size() << std::endl; |
| 371 |
|
for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){ |
| 384 |
|
} |
| 385 |
|
std::cout << std::endl; |
| 386 |
|
} |
| 387 |
+ |
*/ |
| 388 |
|
|
| 389 |
|
|
| 390 |
|
|
| 376 |
– |
|
| 391 |
|
/* |
| 392 |
|
FORALLfacets { |
| 393 |
|
Triangle face; |
| 452 |
|
|
| 453 |
|
} //FORALLfacets |
| 454 |
|
*/ |
| 455 |
< |
qh_getarea(qh facet_list); |
| 456 |
< |
volume_ = qh totvol; |
| 457 |
< |
area_ = qh totarea; |
| 455 |
> |
// qh_getarea(qh facet_list); |
| 456 |
> |
//volume_ = qh totvol; |
| 457 |
> |
// area_ = qh totarea; |
| 458 |
|
|
| 459 |
|
qh_freeqhull(!qh_ALL); |
| 460 |
|
qh_memfreeshort(&curlong, &totlong); |
