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/* Copyright (c) 2008, 2009, 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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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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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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gezelter |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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gezelter |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
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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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gezelter |
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* @version $Id$ |
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* |
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*/ |
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/* Standard includes independent of library */ |
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#include <iostream> |
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#include <fstream> |
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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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using namespace OpenMD; |
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#ifdef HAVE_QHULL |
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double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim); |
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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) { |
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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; |
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// vertexT **vertexp; |
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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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std::vector<double> ptArray(numpoints*dim_); |
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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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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] = pos.x(); |
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ptArray[dim_ * i + 1] = pos.y(); |
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ptArray[dim_ * i + 2] = pos.z(); |
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i++; |
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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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int ridgesCount=0; |
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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 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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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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FORALLvertices{ |
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localHullSites++; |
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int idx = qh_pointid(vertex->point); |
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indexMap.push_back(idx); |
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coords.push_back(ptArray[dim_ * idx]); |
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coords.push_back(ptArray[dim_ * idx + 1]); |
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coords.push_back(ptArray[dim_ * idx + 2]); |
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StuntDouble* sd = bodydoubles[idx]; |
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Vector3d vel = sd->getVel(); |
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vels.push_back(vel.x()); |
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vels.push_back(vel.y()); |
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vels.push_back(vel.z()); |
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masses.push_back(sd->getMass()); |
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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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int globalHullSites = 0; |
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for (int iproc = 0; iproc < nproc; iproc++){ |
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globalHullSites += hullSitesOnProc[iproc]; |
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coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc]; |
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} |
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displacements[0] = 0; |
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vectorDisplacements[0] = 0; |
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for (int iproc = 1; iproc < nproc; iproc++){ |
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displacements[iproc] = displacements[iproc-1] + hullSitesOnProc[iproc-1]; |
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vectorDisplacements[iproc] = vectorDisplacements[iproc-1] + coordsOnProc[iproc-1]; |
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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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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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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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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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// 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 (qh_new_qhull(dim_, globalHullSites, &globalCoords[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 global 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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#endif |
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//Set facet->center as the Voronoi center |
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qh_setvoronoi_all(); |
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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 |
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//contain them. |
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// tri::Allocator<CMeshO>::AddVertices(pm.cm,convexNumVert); |
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/*ivp length is 'qh num_vertices' because each vertex is accessed through its ID whose range is |
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0<=qh_pointid(vertex->point)<qh num_vertices*/ |
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// vector<tri::Allocator<CMeshO>::VertexPointer> ivp(qh num_vertices); |
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/*i=0; |
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FORALLvertices{ |
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if ((*vertex).point){ |
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// pm.cm.vert[i].P()[0] = (*vertex).point[0]; |
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// pm.cm.vert[i].P()[1] = (*vertex).point[1]; |
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//pm.cm.vert[i].P()[2] = (*vertex).point[2]; |
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// ivp[qh_pointid(vertex->point)] = &pm.cm.vert[i]; |
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i++; |
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} |
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} |
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*/ |
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//Set of alpha complex triangles for alphashape filtering |
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setT* set= qh_settemp(4* qh num_facets); |
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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) { |
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//For all facets (that are tetrahedrons)calculate the radius of the empty circumsphere considering |
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//the distance between the circumcenter and a vertex of the facet |
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vertexT* vertex = (vertexT *)(facet->vertices->e[0].p); |
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double* center = facet->center; |
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double radius = qh_pointdist(vertex->point,center,dim_); |
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if (radius>alpha_) // if the facet is not good consider the ridges |
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{ |
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//if calculating the alphashape, unmark the facet ('good' is used as 'marked'). |
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facet->good=false; |
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//Compute each ridge (triangle) once and test the cironference radius with alpha |
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facet->visitid= qh visit_id; |
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qh_makeridges(facet); |
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ridgeT *ridge, **ridgep; |
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int goodTriangles=0; |
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FOREACHridge_(facet->ridges) { |
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neighbor= otherfacet_(ridge, facet); |
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if (( neighbor->visitid != qh visit_id)){ |
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//Calculate the radius of the circumference |
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pointT* p0 = ((vertexT*) (ridge->vertices->e[0].p))->point; |
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pointT* p1 = ((vertexT*) (ridge->vertices->e[1].p))->point; |
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pointT* p2 = ((vertexT*) (ridge->vertices->e[2].p))->point; |
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radius = calculate_circumradius(p0,p1,p2, dim_); |
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if(radius <=alpha_){ |
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goodTriangles++; |
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//save the triangle (ridge) for subsequent filtering |
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qh_setappend(&set, ridge); |
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} |
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} |
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} |
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//If calculating the alphashape, mark the facet('good' is used as 'marked'). |
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//This facet will have some triangles hidden by the facet's neighbor. |
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if(goodTriangles==4) |
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facet->good=true; |
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} |
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else //the facet is good. Put all the triangles of the tetrahedron in the mesh |
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{ |
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//Compute each ridge (triangle) once |
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facet->visitid= qh visit_id; |
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//If calculating the alphashape, mark the facet('good' is used as 'marked'). |
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//This facet will have some triangles hidden by the facet's neighbor. |
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facet->good=true; |
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qh_makeridges(facet); |
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ridgeT *ridge, **ridgep; |
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FOREACHridge_(facet->ridges) { |
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neighbor= otherfacet_(ridge, facet); |
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if ((neighbor->visitid != qh visit_id)){ |
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qh_setappend(&set, ridge); |
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} |
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} |
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} |
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} |
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} |
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//assert(numFacets== qh num_facets); |
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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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ridgeT *ridge, **ridgep; |
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FOREACHridge_(set) { |
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if ((!ridge->top->good || !ridge->bottom->good || ridge->top->upperdelaunay || ridge->bottom->upperdelaunay)){ |
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// tri::Allocator<CMeshO>::FaceIterator fi=tri::Allocator<CMeshO>::AddFaces(pm.cm,1); |
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ridgesCount++; |
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int vertex_n, vertex_i; |
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Triangle face; |
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// Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]); |
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//face.setNormal(V3dNormal); |
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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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//Vector3d V3dCentroid(center[0], center[1], center[2]); |
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//face.setCentroid(V3dCentroid); |
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Vector3d faceVel = V3Zero; |
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Vector3d p[3]; |
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RealType faceMass = 0.0; |
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int ver = 0; |
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std::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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p[ver][1] = vertex->point[1]; |
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p[ver][2] = vertex->point[2]; |
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Vector3d vel; |
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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; |
| 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 |
chuckv |
1402 |
facetlist.push_back(virtexlist); |
| 349 |
chuckv |
1404 |
face.addVertices(p[0],p[1],p[2]); |
| 350 |
|
|
face.setFacetMass(faceMass); |
| 351 |
gezelter |
1668 |
face.setFacetVelocity(faceVel / RealType(3.0)); |
| 352 |
chuckv |
1404 |
|
| 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 |
chuckv |
1402 |
} |
| 363 |
|
|
} |
| 364 |
|
|
|
| 365 |
chuckv |
1404 |
std::cout << "Volume is: " << volume_ << std::endl; |
| 366 |
|
|
|
| 367 |
chuckv |
1402 |
//assert(pm.cm.fn == ridgesCount); |
| 368 |
chuckv |
1404 |
/* |
| 369 |
chuckv |
1402 |
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){ |
| 372 |
|
|
Vector3d pos = (*SD)->getPos(); |
| 373 |
|
|
std::cout << pos.x() << " " << pos.y() << " " << pos.z() << std::endl; |
| 374 |
|
|
} |
| 375 |
|
|
|
| 376 |
|
|
|
| 377 |
|
|
std::vector<std::vector<int> >::iterator thisfacet; |
| 378 |
|
|
std::vector<int>::iterator thisvertex; |
| 379 |
|
|
|
| 380 |
|
|
for (thisfacet = facetlist.begin(); thisfacet != facetlist.end(); thisfacet++){ |
| 381 |
|
|
std::cout << (*thisfacet).size(); |
| 382 |
|
|
for (thisvertex = (*thisfacet).begin(); thisvertex != (*thisfacet).end(); thisvertex++){ |
| 383 |
|
|
std::cout << " " << *thisvertex; |
| 384 |
|
|
} |
| 385 |
|
|
std::cout << std::endl; |
| 386 |
|
|
} |
| 387 |
chuckv |
1404 |
*/ |
| 388 |
chuckv |
1402 |
|
| 389 |
|
|
|
| 390 |
|
|
|
| 391 |
|
|
/* |
| 392 |
|
|
FORALLfacets { |
| 393 |
|
|
Triangle face; |
| 394 |
|
|
|
| 395 |
|
|
Vector3d V3dNormal(facet->normal[0], facet->normal[1], facet->normal[2]); |
| 396 |
|
|
face.setNormal(V3dNormal); |
| 397 |
|
|
|
| 398 |
|
|
RealType faceArea = qh_facetarea(facet); |
| 399 |
|
|
face.setArea(faceArea); |
| 400 |
|
|
|
| 401 |
|
|
vertices = qh_facet3vertex(facet); |
| 402 |
|
|
|
| 403 |
|
|
coordT *center = qh_getcenter(vertices); |
| 404 |
|
|
Vector3d V3dCentroid(center[0], center[1], center[2]); |
| 405 |
|
|
face.setCentroid(V3dCentroid); |
| 406 |
|
|
|
| 407 |
|
|
Vector3d faceVel = V3Zero; |
| 408 |
|
|
Vector3d p[3]; |
| 409 |
|
|
RealType faceMass = 0.0; |
| 410 |
|
|
|
| 411 |
|
|
int ver = 0; |
| 412 |
|
|
|
| 413 |
|
|
FOREACHvertex_(vertices){ |
| 414 |
|
|
int id = qh_pointid(vertex->point); |
| 415 |
|
|
p[ver][0] = vertex->point[0]; |
| 416 |
|
|
p[ver][1] = vertex->point[1]; |
| 417 |
|
|
p[ver][2] = vertex->point[2]; |
| 418 |
|
|
|
| 419 |
|
|
Vector3d vel; |
| 420 |
|
|
RealType mass; |
| 421 |
|
|
|
| 422 |
|
|
#ifdef IS_MPI |
| 423 |
|
|
vel = Vector3d(globalVels[dim_ * id], |
| 424 |
|
|
globalVels[dim_ * id + 1], |
| 425 |
|
|
globalVels[dim_ * id + 2]); |
| 426 |
|
|
mass = globalMasses[id]; |
| 427 |
|
|
|
| 428 |
|
|
// localID will be between 0 and hullSitesOnProc[myrank] if we |
| 429 |
|
|
// own this guy. |
| 430 |
|
|
|
| 431 |
|
|
int localID = id - displacements[myrank]; |
| 432 |
|
|
|
| 433 |
|
|
if (localID >= 0 && localID < hullSitesOnProc[myrank]) |
| 434 |
|
|
face.addVertexSD(bodydoubles[indexMap[localID]]); |
| 435 |
|
|
|
| 436 |
|
|
#else |
| 437 |
|
|
vel = bodydoubles[id]->getVel(); |
| 438 |
|
|
mass = bodydoubles[id]->getMass(); |
| 439 |
|
|
face.addVertexSD(bodydoubles[id]); |
| 440 |
|
|
#endif |
| 441 |
|
|
|
| 442 |
|
|
faceVel = faceVel + vel; |
| 443 |
|
|
faceMass = faceMass + mass; |
| 444 |
|
|
ver++; |
| 445 |
|
|
} //Foreachvertex |
| 446 |
|
|
|
| 447 |
|
|
face.addVertices(p[0], p[1], p[2]); |
| 448 |
|
|
face.setFacetMass(faceMass); |
| 449 |
|
|
face.setFacetVelocity(faceVel/3.0); |
| 450 |
|
|
Triangles_.push_back(face); |
| 451 |
|
|
qh_settempfree(&vertices); |
| 452 |
|
|
|
| 453 |
|
|
} //FORALLfacets |
| 454 |
|
|
*/ |
| 455 |
chuckv |
1404 |
// qh_getarea(qh facet_list); |
| 456 |
|
|
//volume_ = qh totvol; |
| 457 |
|
|
// area_ = qh totarea; |
| 458 |
chuckv |
1402 |
|
| 459 |
|
|
qh_freeqhull(!qh_ALL); |
| 460 |
|
|
qh_memfreeshort(&curlong, &totlong); |
| 461 |
|
|
if (curlong || totlong) |
| 462 |
|
|
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 463 |
|
|
<< totlong << curlong << std::endl; |
| 464 |
|
|
} |
| 465 |
|
|
|
| 466 |
|
|
void AlphaHull::printHull(const std::string& geomFileName) { |
| 467 |
|
|
|
| 468 |
|
|
#ifdef IS_MPI |
| 469 |
|
|
if (worldRank == 0) { |
| 470 |
|
|
#endif |
| 471 |
|
|
FILE *newGeomFile; |
| 472 |
|
|
|
| 473 |
|
|
//create new .md file based on old .md file |
| 474 |
|
|
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 475 |
|
|
qh_findgood_all(qh facet_list); |
| 476 |
|
|
for (int i = 0; i < qh_PRINTEND; i++) |
| 477 |
|
|
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 478 |
|
|
|
| 479 |
|
|
fclose(newGeomFile); |
| 480 |
|
|
#ifdef IS_MPI |
| 481 |
|
|
} |
| 482 |
|
|
#endif |
| 483 |
|
|
} |
| 484 |
|
|
|
| 485 |
|
|
double calculate_circumradius(pointT* p0,pointT* p1,pointT* p2, int dim){ |
| 486 |
|
|
coordT a = qh_pointdist(p0,p1,dim); |
| 487 |
|
|
coordT b = qh_pointdist(p1,p2,dim); |
| 488 |
|
|
coordT c = qh_pointdist(p2,p0,dim); |
| 489 |
|
|
|
| 490 |
|
|
coordT sum =(a + b + c)*0.5; |
| 491 |
|
|
coordT area = sum*(a+b-sum)*(a+c-sum)*(b+c-sum); |
| 492 |
|
|
return (double) (a*b*c)/(4*sqrt(area)); |
| 493 |
|
|
} |
| 494 |
|
|
|
| 495 |
|
|
#endif //QHULL |
