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/* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved. |
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/* Copyright (c) 2008, 2009 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, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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* |
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* |
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* ConvexHull.hpp |
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* |
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* Purpose: To calculate convexhull, hull volume using the QuickHull algorithm provided by QHull. |
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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.hpp,v 1.17 2008-11-14 21:54:54 chuckv Exp $ |
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* @version $Id: ConvexHull.hpp,v 1.19 2009-11-25 20:02:01 gezelter Exp $ |
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* |
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*/ |
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#include <cassert> |
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#include <vector> |
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#include <string> |
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extern "C" |
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{ |
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#if defined(HAVE_QHULL) |
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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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#endif |
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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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namespace oopse { |
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namespace OpenMD { |
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class ConvexHull : public Hull { |
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public: |
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ConvexHull(); |
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ConvexHull(); |
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virtual ~ConvexHull(){}; |
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void computeHull(std::vector<StuntDouble*> bodydoubles); |
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RealType getArea(){return area_;} //Total area of Hull |
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int getNs(){return Ns_;} //Number of Surface Atoms |
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RealType getVolume(){return volume_;} //Total Volume inclosed by Hull |
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std::vector< StuntDouble* > getSurfaceAtoms(){return surfaceSDs_;} //Returns a list of surface atoms |
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|
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void computeHull( std::vector<StuntDouble*> bodydoubles ); |
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|
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/* Total area of Hull*/ |
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RealType getArea(){return area_;} |
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|
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/* Total Volume enclosed by Hull */ |
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RealType getVolume(){ return volume_; } |
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|
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std::vector<Triangle> getMesh(){return Triangles_;} |
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int getNMeshElements() {return nTriangles_;} |
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void printHull(const std::string& geomFileName); |
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protected: |
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double volume_; |
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double area_; |
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RealType volume_; |
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RealType area_; |
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int dim_; |
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int Ns_; |
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int nTriangles_; |
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std::vector<StuntDouble*> surfaceSDs_; |
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const std::string options_; |
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private: |
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private: |
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std::vector<Triangle> Triangles_; |
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#ifdef IS_MPI |
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int* NstoProc_; |
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int* vecNstoProc_; |
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int* displs_; |
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int* vecdispls_; |
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int Nsglobal_; |
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int nproc_; |
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int myrank_; |
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struct surfacePt_{ |
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double x,y,z; |
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}; |
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MPI::Datatype surfacePtType; |
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std::vector<surfacePt_> surfacePtsLocal_; |
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std::vector<surfacePt_> surfacePtsGlobal_; |
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#endif |
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}; |
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} |
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#endif /*MATH_CONVEXHULL_HPP_*/ |
