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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 $Id$ |
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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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#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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#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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#ifdef HAVE_QHULL |
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using namespace std; |
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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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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 Pp") { |
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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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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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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, *verticestop, *verticesbottom; |
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int curlong, totlong; |
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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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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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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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} //qh_new_qhull |
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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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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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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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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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int count = coordsOnProc[myrank]; |
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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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#endif |
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//Set facet->center as the Voronoi center |
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|
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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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vector<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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|
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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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int ridgesCount=0; |
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|
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ridgeT *ridge, **ridgep; |
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FOREACHridge_(set) { |
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|
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|
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//coordT *center = qh_getcenter(ridge->vertices); |
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//std::cout << "Centers are " << center[0] << " " <<center[1] << " " << center[2] << std::endl; |
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> |
//cout << "Centers are " << center[0] << " " <<center[1] << " " << center[2] << endl; |
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//Vector3d V3dCentroid(center[0], center[1], center[2]); |
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//face.setCentroid(V3dCentroid); |
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|
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RealType faceMass = 0.0; |
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|
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int ver = 0; |
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std::vector<int> virtexlist; |
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vector<int> virtexlist; |
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FOREACHvertex_i_(ridge->vertices){ |
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int id = qh_pointid(vertex->point); |
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p[ver][0] = vertex->point[0]; |
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RealType mass; |
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ver++; |
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virtexlist.push_back(id); |
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// std::cout << "Ridge: " << ridgesCount << " Vertex " << id << std::endl; |
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> |
// cout << "Ridge: " << ridgesCount << " Vertex " << id << endl; |
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|
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vel = bodydoubles[id]->getVel(); |
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mass = bodydoubles[id]->getMass(); |
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facetlist.push_back(virtexlist); |
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face.addVertices(p[0],p[1],p[2]); |
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face.setFacetMass(faceMass); |
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face.setFacetVelocity(faceVel/3.0); |
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face.setFacetVelocity(faceVel / RealType(3.0)); |
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|
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RealType area = face.getArea(); |
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area_ += area; |
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Vector3d normal = face.getUnitNormal(); |
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RealType offset = ((0.0-p[0][0])*normal[0] + (0.0-p[0][1])*normal[1] + (0.0-p[0][2])*normal[2]); |
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RealType dist = normal[0] * interiorPoint[0] + normal[1]*interiorPoint[1] + normal[2]*interiorPoint[2]; |
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std::cout << "Dist and normal and area are: " << normal << std::endl; |
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> |
cout << "Dist and normal and area are: " << normal << endl; |
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volume_ += dist *area/qh hull_dim; |
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|
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Triangles_.push_back(face); |
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} |
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} |
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|
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std::cout << "Volume is: " << volume_ << std::endl; |
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> |
cout << "Volume is: " << volume_ << endl; |
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|
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//assert(pm.cm.fn == ridgesCount); |
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/* |
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|
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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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|
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void AlphaHull::printHull(const std::string& geomFileName) { |
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|
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> |
void AlphaHull::printHull(const string& geomFileName) { |
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> |
|
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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< |
FILE *newGeomFile; |
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< |
|
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< |
//create new .md file based on old .md file |
| 482 |
< |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
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< |
qh_findgood_all(qh facet_list); |
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for (int i = 0; i < qh_PRINTEND; i++) |
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< |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 486 |
< |
|
| 487 |
< |
fclose(newGeomFile); |
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> |
FILE *newGeomFile; |
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> |
|
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> |
//create new .md file based on old .md file |
| 482 |
> |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
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> |
qh_findgood_all(qh facet_list); |
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> |
for (int i = 0; i < qh_PRINTEND; i++) |
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> |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 486 |
> |
|
| 487 |
> |
fclose(newGeomFile); |
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#ifdef IS_MPI |
| 489 |
|
} |
| 490 |
|
#endif |
