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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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/* |
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* Copyright (c) 2005 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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* 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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* 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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|
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/** |
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* @file Vector.hpp |
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* @author Teng Lin |
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|
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#include <cassert> |
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#include <cmath> |
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|
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#include <iostream> |
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#include <math.h> |
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namespace oopse { |
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|
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static const double epsilon = 0.000001; |
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|
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template<typename T> |
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inline bool equal(T e1, T e2) { |
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return e1 == e2; |
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} |
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|
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template<> |
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inline bool equal(float e1, float e2) { |
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return fabs(e1 - e2) < epsilon; |
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} |
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|
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template<> |
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inline bool equal(double e1, double e2) { |
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return fabs(e1 - e2) < epsilon; |
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} |
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|
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|
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/** |
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* @class Vector Vector.hpp "math/Vector.hpp" |
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* @brief Fix length vector class |
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*/ |
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template<typename Real, int Dim> |
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template<typename Real, unsigned int Dim> |
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class Vector{ |
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public: |
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|
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typedef Real ElemType; |
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typedef Real* ElemPoinerType; |
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|
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/** default constructor */ |
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inline Vector(){ |
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for (unsigned int i = 0; i < Dim; i++) |
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data_[i] = 0.0; |
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this->data_[i] = 0; |
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} |
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|
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/** Constructs and initializes a Vector from a vector */ |
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return *this; |
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|
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for (unsigned int i = 0; i < Dim; i++) |
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data_[i] = v[i]; |
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this->data_[i] = v[i]; |
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|
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return *this; |
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} |
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|
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template<typename T> |
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inline Vector(const T& s){ |
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for (unsigned int i = 0; i < Dim; i++) |
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this->data_[i] = s; |
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} |
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|
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/** Constructs and initializes a Vector from an array */ |
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inline Vector( double* v) { |
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for (unsigned int i = 0; i < Dim; i++) |
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data_[i] = v[i]; |
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inline Vector( Real* v) { |
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for (unsigned int i = 0; i < Dim; i++) |
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this->data_[i] = v[i]; |
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} |
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|
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/** |
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* @return reference of ith element |
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* @param i index |
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*/ |
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inline double& operator[](unsigned int i) { |
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inline Real& operator[](unsigned int i) { |
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assert( i < Dim); |
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return data_[i]; |
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return this->data_[i]; |
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} |
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|
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/** |
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* @return reference of ith element |
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* @param i index |
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*/ |
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inline double& operator()(unsigned int i) { |
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inline Real& operator()(unsigned int i) { |
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assert( i < Dim); |
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return data_[i]; |
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return this->data_[i]; |
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} |
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|
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/** |
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* @return reference of ith element |
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* @param i index |
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*/ |
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inline const double& operator[](unsigned int i) const { |
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inline const Real& operator[](unsigned int i) const { |
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assert( i < Dim); |
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return data_[i]; |
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return this->data_[i]; |
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} |
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|
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/** |
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* @return reference of ith element |
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* @param i index |
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*/ |
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inline const double& operator()(unsigned int i) const { |
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inline const Real& operator()(unsigned int i) const { |
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assert( i < Dim); |
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return data_[i]; |
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return this->data_[i]; |
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} |
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|
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/** Copy the internal data to an array*/ |
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void getArray(Real* array) { |
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for (unsigned int i = 0; i < Dim; i ++) { |
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array[i] = this->data_[i]; |
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} |
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} |
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|
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/** Returns the pointer of internal array */ |
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Real* getArrayPointer() { |
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return this->data_; |
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} |
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|
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/** |
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* Tests if this vetor is equal to other vector |
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* @return true if equal, otherwise return false |
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* @param v vector to be compared |
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*/ |
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inline bool operator ==(const Vector<Real, Dim>& v) { |
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|
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for (unsigned int i = 0; i < Dim; i ++) { |
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if (!equal(this->data_[i], v[i])) { |
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return false; |
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} |
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} |
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|
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return true; |
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} |
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|
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/** |
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* Tests if this vetor is not equal to other vector |
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* @return true if equal, otherwise return false |
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* @param v vector to be compared |
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*/ |
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inline bool operator !=(const Vector<Real, Dim>& v) { |
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return !(*this == v); |
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} |
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|
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/** Negates the value of this vector in place. */ |
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inline void negate() { |
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data_[0] = -data_[0]; |
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data_[1] = -data_[1]; |
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data_[2] = -data_[2]; |
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for (unsigned int i = 0; i < Dim; i++) |
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this->data_[i] = -this->data_[i]; |
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} |
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|
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/** |
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*/ |
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inline void negate(const Vector<Real, Dim>& v1) { |
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for (unsigned int i = 0; i < Dim; i++) |
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data_[i] = -v1.data_[i]; |
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this->data_[i] = -v1.data_[i]; |
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|
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} |
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|
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* @param v1 the other vector |
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*/ |
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inline void add( const Vector<Real, Dim>& v1 ) { |
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for (unsigned int i = 0; i < Dim; i++) |
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data_[i] += v1.data_[i]; |
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} |
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for (unsigned int i = 0; i < Dim; i++) |
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this->data_[i] += v1.data_[i]; |
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} |
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|
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/** |
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* Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2). |
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* @param v2 the second vector |
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*/ |
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inline void add( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) { |
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for (unsigned int i = 0; i < Dim; i++) |
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data_[i] = v1.data_[i] + v2.data_[i]; |
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for (unsigned int i = 0; i < Dim; i++) |
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this->data_[i] = v1.data_[i] + v2.data_[i]; |
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} |
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|
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/** |
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*/ |
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inline void sub( const Vector<Real, Dim>& v1 ) { |
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for (unsigned int i = 0; i < Dim; i++) |
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data_[i] -= v1.data_[i]; |
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this->data_[i] -= v1.data_[i]; |
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} |
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|
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/** |
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*/ |
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inline void sub( const Vector<Real, Dim>& v1, const Vector &v2 ){ |
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for (unsigned int i = 0; i < Dim; i++) |
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data_[i] = v1.data_[i] - v2.data_[i]; |
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this->data_[i] = v1.data_[i] - v2.data_[i]; |
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} |
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|
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/** |
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* Sets the value of this vector to the scalar multiplication of itself (*this *= s). |
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* @param s the scalar value |
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*/ |
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inline void mul( double s ) { |
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for (unsigned int i = 0; i < Dim; i++) |
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< |
data_[i] *= s; |
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> |
inline void mul( Real s ) { |
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> |
for (unsigned int i = 0; i < Dim; i++) |
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> |
this->data_[i] *= s; |
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} |
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|
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/** |
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* Sets the value of this vector to the scalar multiplication of vector v1 |
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* (*this = s * v1). |
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* @param v1 the vector |
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* @param s the scalar value |
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* @param v1 the vector |
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*/ |
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< |
inline void mul( double s, const Vector<Real, Dim>& v1 ) { |
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< |
for (unsigned int i = 0; i < Dim; i++) |
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< |
data_[i] = s * v1.data_[i]; |
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> |
inline void mul( const Vector<Real, Dim>& v1, Real s) { |
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> |
for (unsigned int i = 0; i < Dim; i++) |
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> |
this->data_[i] = s * v1.data_[i]; |
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} |
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|
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/** |
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* Sets the value of this vector to the scalar division of itself (*this /= s ). |
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* @param s the scalar value |
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*/ |
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< |
inline void div( double s) { |
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< |
for (unsigned int i = 0; i < Dim; i++) |
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< |
data_[i] /= s; |
276 |
> |
inline void div( Real s) { |
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> |
for (unsigned int i = 0; i < Dim; i++) |
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> |
this->data_[i] /= s; |
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} |
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|
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/** |
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* @param v1 the source vector |
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* @param s the scalar value |
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*/ |
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< |
inline void div( const Vector<Real, Dim>& v1, double s ) { |
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< |
for (unsigned int i = 0; i < Dim; i++) |
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< |
data_[i] = v1.data_[i] / s; |
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> |
inline void div( const Vector<Real, Dim>& v1, Real s ) { |
287 |
> |
for (unsigned int i = 0; i < Dim; i++) |
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> |
this->data_[i] = v1.data_[i] / s; |
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} |
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|
|
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/** @see #add */ |
292 |
< |
inline Vector<Real, Dim> operator +=( const Vector<Real, Dim>& v1 ) { |
292 |
> |
inline Vector<Real, Dim>& operator +=( const Vector<Real, Dim>& v1 ) { |
293 |
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add(v1); |
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return *this; |
295 |
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} |
296 |
|
|
297 |
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/** @see #sub */ |
298 |
< |
inline Vector<Real, Dim> operator -=( const Vector<Real, Dim>& v1 ) { |
298 |
> |
inline Vector<Real, Dim>& operator -=( const Vector<Real, Dim>& v1 ) { |
299 |
|
sub(v1); |
300 |
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return *this; |
301 |
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} |
302 |
|
|
303 |
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/** @see #mul */ |
304 |
< |
inline Vector<Real, Dim> operator *=( double s) { |
304 |
> |
inline Vector<Real, Dim>& operator *=( Real s) { |
305 |
|
mul(s); |
306 |
|
return *this; |
307 |
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} |
308 |
|
|
309 |
|
/** @see #div */ |
310 |
< |
inline Vector<Real, Dim> operator /=( double s ) { |
310 |
> |
inline Vector<Real, Dim>& operator /=( Real s ) { |
311 |
|
div(s); |
312 |
|
return *this; |
313 |
|
} |
316 |
|
* Returns the length of this vector. |
317 |
|
* @return the length of this vector |
318 |
|
*/ |
319 |
< |
inline double length() { |
320 |
< |
return sqrt(lengthSquared()); |
319 |
> |
inline Real length() { |
320 |
> |
return sqrt(lengthSquare()); |
321 |
|
} |
322 |
|
|
323 |
|
/** |
324 |
|
* Returns the squared length of this vector. |
325 |
|
* @return the squared length of this vector |
326 |
|
*/ |
327 |
< |
inline double lengthSquared() { |
327 |
> |
inline Real lengthSquare() { |
328 |
|
return dot(*this, *this); |
329 |
|
} |
330 |
|
|
331 |
|
/** Normalizes this vector in place */ |
332 |
|
inline void normalize() { |
333 |
< |
double len; |
333 |
> |
Real len; |
334 |
|
|
335 |
|
len = length(); |
336 |
+ |
|
337 |
+ |
//if (len < oopse:epsilon) |
338 |
+ |
// throw(); |
339 |
+ |
|
340 |
|
*this /= len; |
341 |
|
} |
342 |
+ |
|
343 |
+ |
/** |
344 |
+ |
* Tests if this vector is normalized |
345 |
+ |
* @return true if this vector is normalized, otherwise return false |
346 |
+ |
*/ |
347 |
+ |
inline bool isNormalized() { |
348 |
+ |
return equal(lengthSquare(), 1.0); |
349 |
+ |
} |
350 |
|
|
351 |
|
protected: |
352 |
< |
double data_[3]; |
352 |
> |
Real data_[Dim]; |
353 |
|
|
354 |
|
}; |
355 |
|
|
356 |
|
/** unary minus*/ |
357 |
< |
template<typename Real, int Dim> |
357 |
> |
template<typename Real, unsigned int Dim> |
358 |
|
inline Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1){ |
359 |
< |
Vector tmp(v1); |
360 |
< |
return tmp.negate(); |
359 |
> |
Vector<Real, Dim> tmp(v1); |
360 |
> |
tmp.negate(); |
361 |
> |
return tmp; |
362 |
|
} |
363 |
|
|
364 |
|
/** |
367 |
|
* @param v1 the first vector |
368 |
|
* @param v2 the second vector |
369 |
|
*/ |
370 |
< |
template<typename Real, int Dim> |
370 |
> |
template<typename Real, unsigned int Dim> |
371 |
|
inline Vector<Real, Dim> operator +(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) { |
372 |
|
Vector<Real, Dim> result; |
373 |
|
|
381 |
|
* @param v1 the first vector |
382 |
|
* @param v2 the second vector |
383 |
|
*/ |
384 |
< |
template<typename Real, int Dim> |
384 |
> |
template<typename Real, unsigned int Dim> |
385 |
|
Vector<Real, Dim> operator -(const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2) { |
386 |
|
Vector<Real, Dim> result; |
387 |
|
result.sub(v1, v2); |
394 |
|
* @param v1 the source vector |
395 |
|
* @param s the scalar value |
396 |
|
*/ |
397 |
< |
template<typename Real, int Dim> |
398 |
< |
Vector<Real, Dim> operator * ( const Vector<Real, Dim>& v1, double s) { |
397 |
> |
template<typename Real, unsigned int Dim> |
398 |
> |
Vector<Real, Dim> operator * ( const Vector<Real, Dim>& v1, Real s) { |
399 |
|
Vector<Real, Dim> result; |
400 |
< |
result.mul(s, v1); |
400 |
> |
result.mul(v1,s); |
401 |
|
return result; |
402 |
|
} |
403 |
|
|
407 |
|
* @param s the scalar value |
408 |
|
* @param v1 the source vector |
409 |
|
*/ |
410 |
< |
template<typename Real, int Dim> |
411 |
< |
Vector<Real, Dim> operator * ( double s, const Vector<Real, Dim>& v1 ) { |
410 |
> |
template<typename Real, unsigned int Dim> |
411 |
> |
Vector<Real, Dim> operator * ( Real s, const Vector<Real, Dim>& v1 ) { |
412 |
|
Vector<Real, Dim> result; |
413 |
< |
result.mul(s, v1); |
413 |
> |
result.mul(v1, s); |
414 |
|
return result; |
415 |
|
} |
416 |
|
|
420 |
|
* @param v1 the source vector |
421 |
|
* @param s the scalar value |
422 |
|
*/ |
423 |
< |
template<typename Real, int Dim> |
424 |
< |
Vector<Real, Dim> operator / ( const Vector<Real, Dim>& v1, double s) { |
423 |
> |
template<typename Real, unsigned int Dim> |
424 |
> |
Vector<Real, Dim> operator / ( const Vector<Real, Dim>& v1, Real s) { |
425 |
|
Vector<Real, Dim> result; |
426 |
|
result.div( v1,s); |
427 |
|
return result; |
428 |
|
} |
429 |
|
|
430 |
|
/** |
338 |
– |
* Returns the value of division of a vector by a scalar. |
339 |
– |
* @return the vaule of scalar division of this vector |
340 |
– |
* @param s the scalar value |
341 |
– |
* @param v1 the source vector |
342 |
– |
*/ |
343 |
– |
template<typename Real, int Dim> |
344 |
– |
inline Vector<Real, Dim> operator /( double s, const Vector<Real, Dim>& v1 ) { |
345 |
– |
Vector<Real, Dim> result; |
346 |
– |
result.div( v1,s); |
347 |
– |
return result; |
348 |
– |
} |
349 |
– |
|
350 |
– |
/** fuzzy comparson */ |
351 |
– |
template<typename Real, int Dim> |
352 |
– |
inline bool epsilonEqual( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) { |
353 |
– |
|
354 |
– |
} |
355 |
– |
|
356 |
– |
|
357 |
– |
/** |
431 |
|
* Returns the dot product of two Vectors |
432 |
|
* @param v1 first vector |
433 |
|
* @param v2 second vector |
434 |
|
* @return the dot product of v1 and v2 |
435 |
|
*/ |
436 |
< |
template<typename Real, int Dim> |
436 |
> |
template<typename Real, unsigned int Dim> |
437 |
|
inline Real dot( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) { |
438 |
< |
Real tmp; |
439 |
< |
tmp = 0; |
438 |
> |
Real tmp; |
439 |
> |
tmp = 0; |
440 |
|
|
441 |
< |
for (unsigned int i = 0; i < Dim; i++) |
442 |
< |
tmp += v1[i] + v2[i]; |
443 |
< |
|
444 |
< |
return tmp; |
441 |
> |
for (unsigned int i = 0; i < Dim; i++) |
442 |
> |
tmp += v1[i] * v2[i]; |
443 |
> |
|
444 |
> |
return tmp; |
445 |
|
} |
446 |
|
|
447 |
|
/** |
450 |
|
* @param v2 second vector |
451 |
|
* @return the distance between v1 and v2 |
452 |
|
*/ |
453 |
< |
template<typename Real, int Dim> |
453 |
> |
template<typename Real, unsigned int Dim> |
454 |
|
inline Real distance( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) { |
455 |
|
Vector<Real, Dim> tempVector = v1 - v2; |
456 |
|
return tempVector.length(); |
462 |
|
* @param v2 second vector |
463 |
|
* @return the squared distance between v1 and v2 |
464 |
|
*/ |
465 |
< |
template<typename Real, int Dim> |
465 |
> |
template<typename Real, unsigned int Dim> |
466 |
|
inline Real distanceSquare( const Vector<Real, Dim>& v1, const Vector<Real, Dim>& v2 ) { |
467 |
|
Vector<Real, Dim> tempVector = v1 - v2; |
468 |
|
return tempVector.lengthSquare(); |
471 |
|
/** |
472 |
|
* Write to an output stream |
473 |
|
*/ |
474 |
< |
template<typename Real, int Dim> |
475 |
< |
std::ostream &operator<< ( std::ostream& o, const Vector<Real, Dim>& v1 ) { |
474 |
> |
template<typename Real, unsigned int Dim> |
475 |
> |
std::ostream &operator<< ( std::ostream& o, const Vector<Real, Dim>& v) { |
476 |
> |
|
477 |
> |
o << "[ "; |
478 |
|
|
479 |
+ |
for (unsigned int i = 0 ; i< Dim; i++) { |
480 |
+ |
o << v[i]; |
481 |
+ |
|
482 |
+ |
if (i != Dim -1) { |
483 |
+ |
o<< ", "; |
484 |
+ |
} |
485 |
+ |
} |
486 |
+ |
|
487 |
+ |
o << " ]"; |
488 |
|
return o; |
489 |
|
} |
490 |
|
|