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/* Copyright (c) 2008, 2009, 2010 The University of Notre Dame. All Rights Reserved. |
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/* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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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). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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> |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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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, 234107 (2008). |
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> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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* |
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– |
* |
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* AlphaHull.cpp |
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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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* |
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* Purpose: To calculate an alpha-shape hull. |
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*/ |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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|
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/* Standard includes independent of library */ |
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|
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#include <iostream> |
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#include <list> |
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#include <algorithm> |
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#include <iterator> |
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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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|
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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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|
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#ifdef HAVE_QHULL |
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using namespace std; |
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using namespace OpenMD; |
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|
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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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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), |
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options_("qhull d QJ Tcv Pp") { |
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} |
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|
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void AlphaHull::computeHull(std::vector<StuntDouble*> bodydoubles) { |
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void AlphaHull::computeHull(vector<StuntDouble*> bodydoubles) { |
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int numpoints = bodydoubles.size(); |
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bool alphashape=true; |
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|
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Triangles_.clear(); |
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vertexT *vertex, **vertexp; |
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vertexT *vertex; |
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facetT *facet, *neighbor; |
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setT *vertices; |
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pointT *interiorPoint; |
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int curlong, totlong; |
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std::vector<double> ptArray(numpoints*dim_); |
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|
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vector<double> ptArray(numpoints*dim_); |
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|
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// Copy the positon vector into a points vector for qhull. |
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std::vector<StuntDouble*>::iterator SD; |
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vector<StuntDouble*>::iterator SD; |
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int i = 0; |
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for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){ |
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Vector3d pos = (*SD)->getPos(); |
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ptArray[dim_ * i + 2] = pos.z(); |
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i++; |
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} |
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|
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/* Clean up memory from previous convex hull calculations*/ |
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|
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/* Clean up memory from previous convex hull calculations*/ |
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boolT ismalloc = False; |
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|
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int ridgesCount=0; |
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|
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/* compute the hull for our local points (or all the points for single |
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processor versions) */ |
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if (qh_new_qhull(dim_, numpoints, &ptArray[0], ismalloc, |
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const_cast<char *>(options_.c_str()), NULL, stderr)) { |
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|
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|
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sprintf(painCave.errMsg, "AlphaHull: Qhull failed to compute convex hull"); |
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painCave.isFatal = 1; |
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simError(); |
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|
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} //qh_new_qhull |
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|
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#ifdef IS_MPI |
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//If we are doing the mpi version, set up some vectors for data communication |
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|
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int nproc = MPI::COMM_WORLD.Get_size(); |
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int myrank = MPI::COMM_WORLD.Get_rank(); |
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int nproc; |
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int myrank; |
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MPI_Comm_size( MPI_COMM_WORLD, &nproc); |
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MPI_Comm_rank( MPI_COMM_WORLD, &myrank); |
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|
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int localHullSites = 0; |
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|
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std::vector<int> hullSitesOnProc(nproc, 0); |
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std::vector<int> coordsOnProc(nproc, 0); |
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std::vector<int> displacements(nproc, 0); |
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std::vector<int> vectorDisplacements(nproc, 0); |
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vector<int> hullSitesOnProc(nproc, 0); |
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vector<int> coordsOnProc(nproc, 0); |
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vector<int> displacements(nproc, 0); |
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> |
vector<int> vectorDisplacements(nproc, 0); |
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|
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std::vector<double> coords; |
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std::vector<double> vels; |
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std::vector<int> indexMap; |
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std::vector<double> masses; |
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> |
vector<double> coords; |
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vector<double> vels; |
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> |
vector<int> indexMap; |
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> |
vector<double> masses; |
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|
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FORALLvertices{ |
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localHullSites++; |
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|
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int idx = qh_pointid(vertex->point); |
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|
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> |
|
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indexMap.push_back(idx); |
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|
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coords.push_back(ptArray[dim_ * idx]); |
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masses.push_back(sd->getMass()); |
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} |
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|
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< |
MPI::COMM_WORLD.Allgather(&localHullSites, 1, MPI::INT, &hullSitesOnProc[0], |
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1, MPI::INT); |
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> |
MPI_Allgather(&localHullSites, 1, MPI_INT, &hullSitesOnProc[0], |
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> |
1, MPI_INT, MPI_COMM_WORLD); |
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|
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int globalHullSites = 0; |
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for (int iproc = 0; iproc < nproc; iproc++){ |
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vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1]; |
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} |
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|
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std::vector<double> globalCoords(dim_ * globalHullSites); |
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std::vector<double> globalVels(dim_ * globalHullSites); |
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std::vector<double> globalMasses(globalHullSites); |
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> |
vector<double> globalCoords(dim_ * globalHullSites); |
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> |
vector<double> globalVels(dim_ * globalHullSites); |
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> |
vector<double> globalMasses(globalHullSites); |
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|
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int count = coordsOnProc[myrank]; |
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|
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MPI::COMM_WORLD.Allgatherv(&coords[0], count, MPI::DOUBLE, &globalCoords[0], |
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&coordsOnProc[0], &vectorDisplacements[0], |
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MPI::DOUBLE); |
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|
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MPI::COMM_WORLD.Allgatherv(&vels[0], count, MPI::DOUBLE, &globalVels[0], |
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&coordsOnProc[0], &vectorDisplacements[0], |
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MPI::DOUBLE); |
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|
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< |
MPI::COMM_WORLD.Allgatherv(&masses[0], localHullSites, MPI::DOUBLE, |
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&globalMasses[0], &hullSitesOnProc[0], |
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&displacements[0], MPI::DOUBLE); |
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|
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> |
MPI_Allgatherv(&coords[0], count, MPI_DOUBLE, &globalCoords[0], |
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&coordsOnProc[0], &vectorDisplacements[0], |
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MPI_DOUBLE, MPI_COMM_WORLD); |
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> |
|
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> |
MPI_Allgatherv(&vels[0], count, MPI_DOUBLE, &globalVels[0], |
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> |
&coordsOnProc[0], &vectorDisplacements[0], |
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> |
MPI_DOUBLE, MPI_COMM_WORLD); |
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> |
|
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> |
MPI_Allgatherv(&masses[0], localHullSites, MPI_DOUBLE, |
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> |
&globalMasses[0], &hullSitesOnProc[0], |
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&displacements[0], MPI_DOUBLE, MPI_COMM_WORLD); |
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|
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// Free previous hull |
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qh_freeqhull(!qh_ALL); |
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qh_memfreeshort(&curlong, &totlong); |
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if (curlong || totlong) |
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< |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
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< |
<< totlong << curlong << std::endl; |
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> |
if (curlong || totlong) { |
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> |
sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n" |
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> |
"\tdid not free %d bytes of long memory (%d pieces)", |
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totlong, curlong); |
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> |
painCave.isFatal = 1; |
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simError(); |
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> |
} |
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|
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|
if (qh_new_qhull(dim_, globalHullSites, &globalCoords[0], ismalloc, |
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|
const_cast<char *>(options_.c_str()), NULL, stderr)){ |
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|
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< |
sprintf(painCave.errMsg, "AlphaHull: Qhull failed to compute global convex hull"); |
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> |
sprintf(painCave.errMsg, |
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> |
"AlphaHull: Qhull failed to compute global convex hull"); |
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painCave.isFatal = 1; |
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simError(); |
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|
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> |
|
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|
} //qh_new_qhull |
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|
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– |
|
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|
#endif |
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|
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|
//Set facet->center as the Voronoi center |
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|
qh_setvoronoi_all(); |
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|
| 214 |
|
|
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< |
int convexNumVert = qh_setsize(qh_facetvertices (qh facet_list, NULL, false)); |
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< |
//Insert all the sample points, because, even with alpha=0, the alpha shape/alpha complex will |
| 217 |
< |
//contain them. |
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> |
// int convexNumVert = qh_setsize(qh_facetvertices (qh facet_list, NULL, false)); |
| 216 |
> |
//Insert all the sample points, because, even with alpha=0, the |
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> |
//alpha shape/alpha complex will contain them. |
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|
|
| 219 |
|
// tri::Allocator<CMeshO>::AddVertices(pm.cm,convexNumVert); |
| 220 |
|
|
| 237 |
|
|
| 238 |
|
qh visit_id++; |
| 239 |
|
int numFacets=0; |
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< |
std::vector<std::vector <int> > facetlist; |
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> |
vector<vector <int> > facetlist; |
| 241 |
> |
interiorPoint = qh interior_point; |
| 242 |
|
FORALLfacet_(qh facet_list) { |
| 243 |
|
numFacets++; |
| 244 |
|
if (!facet->upperdelaunay) { |
| 245 |
< |
//For all facets (that are tetrahedrons)calculate the radius of the empty circumsphere considering |
| 246 |
< |
//the distance between the circumcenter and a vertex of the facet |
| 245 |
> |
//For all facets (that are tetrahedrons)calculate the radius of |
| 246 |
> |
//the empty circumsphere considering the distance between the |
| 247 |
> |
//circumcenter and a vertex of the facet |
| 248 |
|
vertexT* vertex = (vertexT *)(facet->vertices->e[0].p); |
| 249 |
|
double* center = facet->center; |
| 250 |
|
double radius = qh_pointdist(vertex->point,center,dim_); |
| 251 |
|
|
| 252 |
|
if (radius>alpha_) // if the facet is not good consider the ridges |
| 253 |
|
{ |
| 254 |
< |
//if calculating the alphashape, unmark the facet ('good' is used as 'marked'). |
| 254 |
> |
//if calculating the alphashape, unmark the facet ('good' is |
| 255 |
> |
//used as 'marked'). |
| 256 |
|
facet->good=false; |
| 257 |
|
|
| 258 |
< |
//Compute each ridge (triangle) once and test the cironference radius with alpha |
| 258 |
> |
//Compute each ridge (triangle) once and test the |
| 259 |
> |
//cironference radius with alpha |
| 260 |
|
facet->visitid= qh visit_id; |
| 261 |
|
qh_makeridges(facet); |
| 262 |
|
ridgeT *ridge, **ridgep; |
| 279 |
|
} |
| 280 |
|
} |
| 281 |
|
|
| 282 |
< |
//If calculating the alphashape, mark the facet('good' is used as 'marked'). |
| 283 |
< |
//This facet will have some triangles hidden by the facet's neighbor. |
| 282 |
> |
//If calculating the alphashape, mark the facet('good' is |
| 283 |
> |
//used as 'marked'). This facet will have some triangles |
| 284 |
> |
//hidden by the facet's neighbor. |
| 285 |
|
if(goodTriangles==4) |
| 286 |
|
facet->good=true; |
| 287 |
|
|
| 288 |
|
} |
| 289 |
< |
else //the facet is good. Put all the triangles of the tetrahedron in the mesh |
| 289 |
> |
else //the facet is good. Put all the triangles of the |
| 290 |
> |
//tetrahedron in the mesh |
| 291 |
|
{ |
| 292 |
|
//Compute each ridge (triangle) once |
| 293 |
|
facet->visitid= qh visit_id; |
| 294 |
< |
//If calculating the alphashape, mark the facet('good' is used as 'marked'). |
| 295 |
< |
//This facet will have some triangles hidden by the facet's neighbor. |
| 294 |
> |
//If calculating the alphashape, mark the facet('good' is |
| 295 |
> |
//used as 'marked'). This facet will have some triangles |
| 296 |
> |
//hidden by the facet's neighbor. |
| 297 |
|
facet->good=true; |
| 298 |
|
qh_makeridges(facet); |
| 299 |
|
ridgeT *ridge, **ridgep; |
| 308 |
|
} |
| 309 |
|
//assert(numFacets== qh num_facets); |
| 310 |
|
|
| 311 |
< |
//Filter the triangles (only the ones on the boundary of the alpha complex) and build the mesh |
| 311 |
> |
//Filter the triangles (only the ones on the boundary of the alpha |
| 312 |
> |
//complex) and build the mesh |
| 313 |
> |
|
| 314 |
> |
int ridgesCount=0; |
| 315 |
|
|
| 316 |
|
ridgeT *ridge, **ridgep; |
| 317 |
|
FOREACHridge_(set) { |
| 324 |
|
// Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]); |
| 325 |
|
//face.setNormal(V3dNormal); |
| 326 |
|
|
| 322 |
– |
// RealType faceArea = qh_facetarea(facet); |
| 323 |
– |
//face.setArea(faceArea); |
| 327 |
|
|
| 328 |
< |
//vertices = qh_facet3vertex(facet); |
| 329 |
< |
|
| 327 |
< |
//coordT *center = qh_getcenter(vertices); |
| 328 |
> |
//coordT *center = qh_getcenter(ridge->vertices); |
| 329 |
> |
//cout << "Centers are " << center[0] << " " <<center[1] << " " << center[2] << endl; |
| 330 |
|
//Vector3d V3dCentroid(center[0], center[1], center[2]); |
| 331 |
|
//face.setCentroid(V3dCentroid); |
| 332 |
+ |
|
| 333 |
|
|
| 334 |
< |
//Vector3d faceVel = V3Zero; |
| 334 |
> |
Vector3d faceVel = V3Zero; |
| 335 |
|
Vector3d p[3]; |
| 336 |
< |
//RealType faceMass = 0.0; |
| 336 |
> |
RealType faceMass = 0.0; |
| 337 |
|
|
| 338 |
|
int ver = 0; |
| 339 |
< |
std::vector<int> virtexlist; |
| 339 |
> |
vector<int> virtexlist; |
| 340 |
|
FOREACHvertex_i_(ridge->vertices){ |
| 341 |
|
int id = qh_pointid(vertex->point); |
| 342 |
|
p[ver][0] = vertex->point[0]; |
| 346 |
|
RealType mass; |
| 347 |
|
ver++; |
| 348 |
|
virtexlist.push_back(id); |
| 349 |
< |
} |
| 347 |
< |
facetlist.push_back(virtexlist); |
| 349 |
> |
// cout << "Ridge: " << ridgesCount << " Vertex " << id << endl; |
| 350 |
|
|
| 351 |
+ |
vel = bodydoubles[id]->getVel(); |
| 352 |
+ |
mass = bodydoubles[id]->getMass(); |
| 353 |
+ |
face.addVertexSD(bodydoubles[id]); |
| 354 |
+ |
|
| 355 |
+ |
|
| 356 |
+ |
faceVel = faceVel + vel; |
| 357 |
+ |
faceMass = faceMass + mass; |
| 358 |
+ |
} //FOREACH Vertex |
| 359 |
+ |
facetlist.push_back(virtexlist); |
| 360 |
+ |
face.addVertices(p[0],p[1],p[2]); |
| 361 |
+ |
face.setFacetMass(faceMass); |
| 362 |
+ |
face.setFacetVelocity(faceVel / RealType(3.0)); |
| 363 |
+ |
|
| 364 |
+ |
RealType area = face.getArea(); |
| 365 |
+ |
area_ += area; |
| 366 |
+ |
Vector3d normal = face.getUnitNormal(); |
| 367 |
+ |
// RealType offset = ((0.0-p[0][0])*normal[0] + (0.0-p[0][1])*normal[1] + (0.0-p[0][2])*normal[2]); |
| 368 |
+ |
RealType dist = normal[0] * interiorPoint[0] + normal[1]*interiorPoint[1] + normal[2]*interiorPoint[2]; |
| 369 |
+ |
volume_ += dist *area/qh hull_dim; |
| 370 |
+ |
|
| 371 |
+ |
Triangles_.push_back(face); |
| 372 |
|
} |
| 373 |
|
} |
| 351 |
– |
|
| 374 |
|
|
| 353 |
– |
//assert(pm.cm.fn == ridgesCount); |
| 375 |
|
|
| 376 |
+ |
//assert(pm.cm.fn == ridgesCount); |
| 377 |
+ |
/* |
| 378 |
|
std::cout <<"OFF"<<std::endl; |
| 379 |
|
std::cout << bodydoubles.size() << " " << facetlist.size() << " " << 3*facetlist.size() << std::endl; |
| 380 |
|
for (SD =bodydoubles.begin(); SD != bodydoubles.end(); ++SD){ |
| 393 |
|
} |
| 394 |
|
std::cout << std::endl; |
| 395 |
|
} |
| 396 |
+ |
*/ |
| 397 |
|
|
| 398 |
|
|
| 399 |
|
|
| 376 |
– |
|
| 400 |
|
/* |
| 401 |
|
FORALLfacets { |
| 402 |
|
Triangle face; |
| 461 |
|
|
| 462 |
|
} //FORALLfacets |
| 463 |
|
*/ |
| 464 |
< |
qh_getarea(qh facet_list); |
| 465 |
< |
volume_ = qh totvol; |
| 466 |
< |
area_ = qh totarea; |
| 464 |
> |
// qh_getarea(qh facet_list); |
| 465 |
> |
//volume_ = qh totvol; |
| 466 |
> |
// area_ = qh totarea; |
| 467 |
|
|
| 468 |
|
qh_freeqhull(!qh_ALL); |
| 469 |
|
qh_memfreeshort(&curlong, &totlong); |
| 470 |
< |
if (curlong || totlong) |
| 471 |
< |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 472 |
< |
<< totlong << curlong << std::endl; |
| 470 |
> |
if (curlong || totlong) { |
| 471 |
> |
sprintf(painCave.errMsg, "AlphaHull: qhull internal warning:\n" |
| 472 |
> |
"\tdid not free %d bytes of long memory (%d pieces)", |
| 473 |
> |
totlong, curlong); |
| 474 |
> |
painCave.isFatal = 1; |
| 475 |
> |
simError(); |
| 476 |
> |
} |
| 477 |
|
} |
| 478 |
|
|
| 479 |
< |
void AlphaHull::printHull(const std::string& geomFileName) { |
| 480 |
< |
|
| 479 |
> |
void AlphaHull::printHull(const string& geomFileName) { |
| 480 |
> |
|
| 481 |
|
#ifdef IS_MPI |
| 482 |
|
if (worldRank == 0) { |
| 483 |
|
#endif |
| 484 |
< |
FILE *newGeomFile; |
| 485 |
< |
|
| 486 |
< |
//create new .md file based on old .md file |
| 487 |
< |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 488 |
< |
qh_findgood_all(qh facet_list); |
| 489 |
< |
for (int i = 0; i < qh_PRINTEND; i++) |
| 490 |
< |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 491 |
< |
|
| 492 |
< |
fclose(newGeomFile); |
| 484 |
> |
FILE *newGeomFile; |
| 485 |
> |
|
| 486 |
> |
//create new .md file based on old .md file |
| 487 |
> |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 488 |
> |
qh_findgood_all(qh facet_list); |
| 489 |
> |
for (int i = 0; i < qh_PRINTEND; i++) |
| 490 |
> |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 491 |
> |
|
| 492 |
> |
fclose(newGeomFile); |
| 493 |
|
#ifdef IS_MPI |
| 494 |
|
} |
| 495 |
|
#endif |
