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/* Copyright (c) 2008, 2009 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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* 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. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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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* [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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* ConvexHull.cpp |
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* |
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* Purpose: To calculate convexhull, 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 1.17 2009-10-20 20:36:56 gezelter Exp $ |
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* |
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* Purpose: To calculate a convex 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 "math/ConvexHull.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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using namespace oopse; |
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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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using namespace OpenMD; |
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using namespace std; |
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|
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/* Old options Qt Qu Qg QG0 FA */ |
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/* More old opts Qc Qi Pp*/ |
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|
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ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull Qt Pp") { |
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ConvexHull::ConvexHull() : Hull(), dim_(3), options_("qhull FA Qt Pp") { |
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} |
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|
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void ConvexHull::computeHull(std::vector<StuntDouble*> bodydoubles) { |
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|
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void ConvexHull::computeHull(vector<StuntDouble*> bodydoubles) { |
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|
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int numpoints = bodydoubles.size(); |
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|
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|
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Triangles_.clear(); |
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|
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vertexT *vertex, **vertexp; |
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facetT *facet; |
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setT *vertices; |
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int curlong, totlong; |
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|
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std::vector<double> ptArray(numpoints*3); |
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std::vector<bool> isSurfaceID(numpoints); |
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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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|
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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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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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boolT ismalloc = False; |
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/* Clean up memory from previous convex hull calculations*/ |
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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, "ConvexHull: Qhull failed to compute convex hull"); |
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painCave.isFatal = 1; |
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simError(); |
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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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|
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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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int* hullSitesOnProc = new int[nproc]; |
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int* coordsOnProc = new int[nproc]; |
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int* displacements = new int[nproc]; |
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int* vectorDisplacements = new int[nproc]; |
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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> objectIDs; |
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std::vector<double> masses; |
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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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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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indexMap.push_back(idx); |
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|
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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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masses.push_back(sd->getMass()); |
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} |
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|
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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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– |
|
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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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|
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int globalHullSites = 0; |
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for (int iproc = 0; iproc < nproc; iproc++){ |
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std::cerr << "iproc = " << iproc << " sites = " << hullSitesOnProc[iproc] << "\n"; |
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globalHullSites += hullSitesOnProc[iproc]; |
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coordsOnProc[iproc] = dim_ * hullSitesOnProc[iproc]; |
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} |
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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, |
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&globalCoords[0], &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, |
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&globalVels[0], &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], &displacements[0], |
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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, "ConvexHull: 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, "ConvexHull: Qhull failed to compute global convex hull"); |
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sprintf(painCave.errMsg, |
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"ConvexHull: 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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} //qh_new_qhull |
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|
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#endif |
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// commented out below, so comment out here also. |
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// intPoint = qh interior_point; |
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// RealType calcvol = 0.0; |
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|
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+ |
qh_triangulate (); |
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|
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|
FORALLfacets { |
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Triangle face; |
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|
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> |
//Qhull sets the unit normal in facet->normal |
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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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> |
face.setUnitNormal(V3dNormal); |
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|
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RealType faceArea = qh_facetarea(facet); |
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face.setArea(faceArea); |
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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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+ |
|
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|
int ver = 0; |
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|
|
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FOREACHvertex_(vertices){ |
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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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|
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|
Vector3d vel; |
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|
RealType mass; |
| 242 |
|
|
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|
globalVels[dim_ * id + 2]); |
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|
mass = globalMasses[id]; |
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|
|
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< |
// localID will be between 0 and hullSitesOnProc[myrank] if we own this guy. |
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> |
// localID will be between 0 and hullSitesOnProc[myrank] if we |
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> |
// own this guy. |
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> |
|
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|
int localID = id - displacements[myrank]; |
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< |
if (id >= 0 && id < hullSitesOnProc[myrank]) |
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< |
face.addVertexSD(bodydoubles[localID]); |
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< |
else |
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> |
|
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> |
|
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> |
if (localID >= 0 && localID < hullSitesOnProc[myrank]){ |
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> |
face.addVertexSD(bodydoubles[indexMap[localID]]); |
| 257 |
> |
}else{ |
| 258 |
|
face.addVertexSD(NULL); |
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+ |
} |
| 260 |
|
#else |
| 261 |
|
vel = bodydoubles[id]->getVel(); |
| 262 |
|
mass = bodydoubles[id]->getMass(); |
| 263 |
|
face.addVertexSD(bodydoubles[id]); |
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< |
#endif |
| 259 |
< |
|
| 264 |
> |
#endif |
| 265 |
|
faceVel = faceVel + vel; |
| 266 |
|
faceMass = faceMass + mass; |
| 267 |
|
ver++; |
| 269 |
|
|
| 270 |
|
face.addVertices(p[0], p[1], p[2]); |
| 271 |
|
face.setFacetMass(faceMass); |
| 272 |
< |
face.setFacetVelocity(faceVel/3.0); |
| 272 |
> |
face.setFacetVelocity(faceVel / RealType(3.0)); |
| 273 |
> |
/* |
| 274 |
> |
RealType comparea = face.computeArea(); |
| 275 |
> |
realT calcarea = qh_facetarea (facet); |
| 276 |
> |
Vector3d V3dCompNorm = -face.computeUnitNormal(); |
| 277 |
> |
RealType thisOffset = ((0.0-p[0][0])*V3dCompNorm[0] + (0.0-p[0][1])*V3dCompNorm[1] + (0.0-p[0][2])*V3dCompNorm[2]); |
| 278 |
> |
RealType dist = facet->offset + intPoint[0]*V3dNormal[0] + intPoint[1]*V3dNormal[1] + intPoint[2]*V3dNormal[2]; |
| 279 |
> |
cout << "facet offset and computed offset: " << facet->offset << " " << thisOffset << endl; |
| 280 |
> |
calcvol += -dist*comparea/qh hull_dim; |
| 281 |
> |
*/ |
| 282 |
|
Triangles_.push_back(face); |
| 283 |
|
qh_settempfree(&vertices); |
| 284 |
|
|
| 287 |
|
qh_getarea(qh facet_list); |
| 288 |
|
volume_ = qh totvol; |
| 289 |
|
area_ = qh totarea; |
| 290 |
< |
|
| 277 |
< |
#ifdef IS_MPI |
| 278 |
< |
delete [] hullSitesOnProc; |
| 279 |
< |
delete [] coordsOnProc; |
| 280 |
< |
delete [] displacements; |
| 281 |
< |
delete [] vectorDisplacements; |
| 282 |
< |
#endif |
| 283 |
< |
|
| 290 |
> |
|
| 291 |
|
qh_freeqhull(!qh_ALL); |
| 292 |
|
qh_memfreeshort(&curlong, &totlong); |
| 293 |
< |
if (curlong || totlong) |
| 294 |
< |
std::cerr << "qhull internal warning (main): did not free %d bytes of long memory (%d pieces) " |
| 295 |
< |
<< totlong << curlong << std::endl; |
| 293 |
> |
if (curlong || totlong) { |
| 294 |
> |
sprintf(painCave.errMsg, "ConvexHull: qhull internal warning:\n" |
| 295 |
> |
"\tdid not free %d bytes of long memory (%d pieces)", |
| 296 |
> |
totlong, curlong); |
| 297 |
> |
painCave.isFatal = 1; |
| 298 |
> |
simError(); |
| 299 |
> |
} |
| 300 |
|
} |
| 301 |
|
|
| 302 |
< |
|
| 292 |
< |
|
| 293 |
< |
void ConvexHull::printHull(const std::string& geomFileName) { |
| 294 |
< |
FILE *newGeomFile; |
| 302 |
> |
void ConvexHull::printHull(const string& geomFileName) { |
| 303 |
|
|
| 304 |
< |
//create new .md file based on old .md file |
| 305 |
< |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 306 |
< |
qh_findgood_all(qh facet_list); |
| 307 |
< |
for (int i = 0; i < qh_PRINTEND; i++) |
| 308 |
< |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 309 |
< |
|
| 310 |
< |
fclose(newGeomFile); |
| 304 |
> |
#ifdef IS_MPI |
| 305 |
> |
if (worldRank == 0) { |
| 306 |
> |
#endif |
| 307 |
> |
FILE *newGeomFile; |
| 308 |
> |
|
| 309 |
> |
//create new .md file based on old .md file |
| 310 |
> |
newGeomFile = fopen(geomFileName.c_str(), "w"); |
| 311 |
> |
qh_findgood_all(qh facet_list); |
| 312 |
> |
for (int i = 0; i < qh_PRINTEND; i++) |
| 313 |
> |
qh_printfacets(newGeomFile, qh PRINTout[i], qh facet_list, NULL, !qh_ALL); |
| 314 |
> |
|
| 315 |
> |
fclose(newGeomFile); |
| 316 |
> |
#ifdef IS_MPI |
| 317 |
> |
} |
| 318 |
> |
#endif |
| 319 |
|
} |
| 320 |
|
#endif //QHULL |
