--- trunk/OOPSE-3.0/src/math/Vector.hpp 2004/10/19 21:28:55 1603 +++ trunk/OOPSE-3.0/src/math/Vector.hpp 2005/04/15 22:04:00 2204 @@ -1,28 +1,44 @@ /* - * Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project - * - * Contact: oopse@oopse.org - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. - * All we ask is that proper credit is given for our work, which includes - * - but is not limited to - adding the above copyright notice to the beginning - * of your source code files, and to any copyright notice that you may distribute - * with programs based on this work. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. + * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * + * The University of Notre Dame grants you ("Licensee") a + * non-exclusive, royalty free, license to use, modify and + * redistribute this software in source and binary code form, provided + * that the following conditions are met: + * + * 1. Acknowledgement of the program authors must be made in any + * publication of scientific results based in part on use of the + * program. An acceptable form of acknowledgement is citation of + * the article in which the program was described (Matthew + * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher + * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented + * Parallel Simulation Engine for Molecular Dynamics," + * J. Comput. Chem. 26, pp. 252-271 (2005)) + * + * 2. Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * + * 3. Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the + * distribution. + * + * This software is provided "AS IS," without a warranty of any + * kind. All express or implied conditions, representations and + * warranties, including any implied warranty of merchantability, + * fitness for a particular purpose or non-infringement, are hereby + * excluded. The University of Notre Dame and its licensors shall not + * be liable for any damages suffered by licensee as a result of + * using, modifying or distributing the software or its + * derivatives. In no event will the University of Notre Dame or its + * licensors be liable for any lost revenue, profit or data, or for + * direct, indirect, special, consequential, incidental or punitive + * damages, however caused and regardless of the theory of liability, + * arising out of the use of or inability to use software, even if the + * University of Notre Dame has been advised of the possibility of + * such damages. */ - + /** * @file Vector.hpp * @author Teng Lin @@ -36,426 +52,441 @@ #include #include #include - +#include namespace oopse { - const double epsilon = 0.000001; + static const double epsilon = 0.000001; - template - inline bool equal(T e1, T e2) { - return e1 == e2; - } + template + inline bool equal(T e1, T e2) { + return e1 == e2; + } - template<> - inline bool equal(float e1, float e2) { - return fabs(e1 - e2) < epsilon; - } + template<> + inline bool equal(float e1, float e2) { + return fabs(e1 - e2) < epsilon; + } - template<> - inline bool equal(double e1, double e2) { - return fabs(e1 - e2) < epsilon; - } + template<> + inline bool equal(double e1, double e2) { + return fabs(e1 - e2) < epsilon; + } - /** - * @class Vector Vector.hpp "math/Vector.hpp" - * @brief Fix length vector class - */ - template - class Vector{ - public: + /** + * @class Vector Vector.hpp "math/Vector.hpp" + * @brief Fix length vector class + */ + template + class Vector{ + public: - /** default constructor */ - inline Vector(){ - for (unsigned int i = 0; i < Dim; i++) - data_[i] = 0.0; - } + typedef Real ElemType; + typedef Real* ElemPoinerType; - /** Constructs and initializes a Vector from a vector */ - inline Vector(const Vector& v) { - *this = v; - } + /** default constructor */ + inline Vector(){ + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] = 0; + } - /** copy assignment operator */ - inline Vector& operator=(const Vector& v) { - if (this == &v) - return *this; + /** Constructs and initializes a Vector from a vector */ + inline Vector(const Vector& v) { + *this = v; + } + + /** copy assignment operator */ + inline Vector& operator=(const Vector& v) { + if (this == &v) + return *this; - for (unsigned int i = 0; i < Dim; i++) - data_[i] = v[i]; + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] = v[i]; - return *this; - } + return *this; + } - template - inline Vector(const T& s){ - for (unsigned int i = 0; i < Dim; i++) - data_[i] = s; - } + template + inline Vector(const T& s){ + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] = s; + } - /** Constructs and initializes a Vector from an array */ - inline Vector( Real* v) { - for (unsigned int i = 0; i < Dim; i++) - data_[i] = v[i]; - } + /** Constructs and initializes a Vector from an array */ + inline Vector( Real* v) { + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] = v[i]; + } - /** - * Returns reference of ith element. - * @return reference of ith element - * @param i index - */ - inline Real& operator[](unsigned int i) { - assert( i < Dim); - return data_[i]; - } + /** + * Returns reference of ith element. + * @return reference of ith element + * @param i index + */ + inline Real& operator[](unsigned int i) { + assert( i < Dim); + return this->data_[i]; + } - /** - * Returns reference of ith element. - * @return reference of ith element - * @param i index - */ - inline Real& operator()(unsigned int i) { - assert( i < Dim); - return data_[i]; - } + /** + * Returns reference of ith element. + * @return reference of ith element + * @param i index + */ + inline Real& operator()(unsigned int i) { + assert( i < Dim); + return this->data_[i]; + } - /** - * Returns constant reference of ith element. - * @return reference of ith element - * @param i index - */ - inline const Real& operator[](unsigned int i) const { - assert( i < Dim); - return data_[i]; - } + /** + * Returns constant reference of ith element. + * @return reference of ith element + * @param i index + */ + inline const Real& operator[](unsigned int i) const { + assert( i < Dim); + return this->data_[i]; + } - /** - * Returns constant reference of ith element. - * @return reference of ith element - * @param i index - */ - inline const Real& operator()(unsigned int i) const { - assert( i < Dim); - return data_[i]; - } + /** + * Returns constant reference of ith element. + * @return reference of ith element + * @param i index + */ + inline const Real& operator()(unsigned int i) const { + assert( i < Dim); + return this->data_[i]; + } - /** - * Tests if this vetor is equal to other vector - * @return true if equal, otherwise return false - * @param v vector to be compared - */ - inline bool operator ==(const Vector& v) { + /** Copy the internal data to an array*/ + void getArray(Real* array) { + for (unsigned int i = 0; i < Dim; i ++) { + array[i] = this->data_[i]; + } + } - for (unsigned int i = 0; i < Dim; i ++) { - if (!equal(data_[i], v[i])) { - return false; - } - } + /** Returns the pointer of internal array */ + Real* getArrayPointer() { + return this->data_; + } + + /** + * Tests if this vetor is equal to other vector + * @return true if equal, otherwise return false + * @param v vector to be compared + */ + inline bool operator ==(const Vector& v) { + + for (unsigned int i = 0; i < Dim; i ++) { + if (!equal(this->data_[i], v[i])) { + return false; + } + } - return true; - } + return true; + } - /** - * Tests if this vetor is not equal to other vector - * @return true if equal, otherwise return false - * @param v vector to be compared - */ - inline bool operator !=(const Vector& v) { - return !(*this == v); - } + /** + * Tests if this vetor is not equal to other vector + * @return true if equal, otherwise return false + * @param v vector to be compared + */ + inline bool operator !=(const Vector& v) { + return !(*this == v); + } - /** Negates the value of this vector in place. */ - inline void negate() { - for (unsigned int i = 0; i < Dim; i++) - data_[i] = -data_[i]; - } + /** Negates the value of this vector in place. */ + inline void negate() { + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] = -this->data_[i]; + } - /** - * Sets the value of this vector to the negation of vector v1. - * @param v1 the source vector - */ - inline void negate(const Vector& v1) { - for (unsigned int i = 0; i < Dim; i++) - data_[i] = -v1.data_[i]; + /** + * Sets the value of this vector to the negation of vector v1. + * @param v1 the source vector + */ + inline void negate(const Vector& v1) { + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] = -v1.data_[i]; - } + } - /** - * Sets the value of this vector to the sum of itself and v1 (*this += v1). - * @param v1 the other vector - */ - inline void add( const Vector& v1 ) { - for (unsigned int i = 0; i < Dim; i++) - data_[i] += v1.data_[i]; - } + /** + * Sets the value of this vector to the sum of itself and v1 (*this += v1). + * @param v1 the other vector + */ + inline void add( const Vector& v1 ) { + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] += v1.data_[i]; + } - /** - * Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2). - * @param v1 the first vector - * @param v2 the second vector - */ - inline void add( const Vector& v1, const Vector& v2 ) { - for (unsigned int i = 0; i < Dim; i++) - data_[i] = v1.data_[i] + v2.data_[i]; - } + /** + * Sets the value of this vector to the sum of v1 and v2 (*this = v1 + v2). + * @param v1 the first vector + * @param v2 the second vector + */ + inline void add( const Vector& v1, const Vector& v2 ) { + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] = v1.data_[i] + v2.data_[i]; + } - /** - * Sets the value of this vector to the difference of itself and v1 (*this -= v1). - * @param v1 the other vector - */ - inline void sub( const Vector& v1 ) { - for (unsigned int i = 0; i < Dim; i++) - data_[i] -= v1.data_[i]; - } + /** + * Sets the value of this vector to the difference of itself and v1 (*this -= v1). + * @param v1 the other vector + */ + inline void sub( const Vector& v1 ) { + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] -= v1.data_[i]; + } - /** - * Sets the value of this vector to the difference of vector v1 and v2 (*this = v1 - v2). - * @param v1 the first vector - * @param v2 the second vector - */ - inline void sub( const Vector& v1, const Vector &v2 ){ - for (unsigned int i = 0; i < Dim; i++) - data_[i] = v1.data_[i] - v2.data_[i]; - } + /** + * Sets the value of this vector to the difference of vector v1 and v2 (*this = v1 - v2). + * @param v1 the first vector + * @param v2 the second vector + */ + inline void sub( const Vector& v1, const Vector &v2 ){ + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] = v1.data_[i] - v2.data_[i]; + } - /** - * Sets the value of this vector to the scalar multiplication of itself (*this *= s). - * @param s the scalar value - */ - inline void mul( Real s ) { - for (unsigned int i = 0; i < Dim; i++) - data_[i] *= s; - } + /** + * Sets the value of this vector to the scalar multiplication of itself (*this *= s). + * @param s the scalar value + */ + inline void mul( Real s ) { + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] *= s; + } - /** - * Sets the value of this vector to the scalar multiplication of vector v1 - * (*this = s * v1). - * @param v1 the vector - * @param s the scalar value - */ - inline void mul( const Vector& v1, Real s) { - for (unsigned int i = 0; i < Dim; i++) - data_[i] = s * v1.data_[i]; - } - - /** - * Sets the value of this vector to the scalar division of itself (*this /= s ). - * @param s the scalar value - */ - inline void div( Real s) { - for (unsigned int i = 0; i < Dim; i++) - data_[i] /= s; - } + /** + * Sets the value of this vector to the scalar multiplication of vector v1 + * (*this = s * v1). + * @param v1 the vector + * @param s the scalar value + */ + inline void mul( const Vector& v1, Real s) { + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] = s * v1.data_[i]; + } - /** - * Sets the value of this vector to the scalar division of vector v1 (*this = v1 / s ). - * @param v1 the source vector - * @param s the scalar value - */ - inline void div( const Vector& v1, Real s ) { - for (unsigned int i = 0; i < Dim; i++) - data_[i] = v1.data_[i] / s; - } + /** + * Sets the value of this vector to the scalar division of itself (*this /= s ). + * @param s the scalar value + */ + inline void div( Real s) { + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] /= s; + } - /** @see #add */ - inline Vector& operator +=( const Vector& v1 ) { - add(v1); - return *this; - } + /** + * Sets the value of this vector to the scalar division of vector v1 (*this = v1 / s ). + * @param v1 the source vector + * @param s the scalar value + */ + inline void div( const Vector& v1, Real s ) { + for (unsigned int i = 0; i < Dim; i++) + this->data_[i] = v1.data_[i] / s; + } - /** @see #sub */ - inline Vector& operator -=( const Vector& v1 ) { - sub(v1); - return *this; - } + /** @see #add */ + inline Vector& operator +=( const Vector& v1 ) { + add(v1); + return *this; + } - /** @see #mul */ - inline Vector& operator *=( Real s) { - mul(s); - return *this; - } + /** @see #sub */ + inline Vector& operator -=( const Vector& v1 ) { + sub(v1); + return *this; + } - /** @see #div */ - inline Vector& operator /=( Real s ) { - div(s); - return *this; - } + /** @see #mul */ + inline Vector& operator *=( Real s) { + mul(s); + return *this; + } - /** - * Returns the length of this vector. - * @return the length of this vector - */ - inline Real length() { - return sqrt(lengthSquare()); - } + /** @see #div */ + inline Vector& operator /=( Real s ) { + div(s); + return *this; + } + + /** + * Returns the length of this vector. + * @return the length of this vector + */ + inline Real length() { + return sqrt(lengthSquare()); + } - /** - * Returns the squared length of this vector. - * @return the squared length of this vector - */ - inline Real lengthSquare() { - return dot(*this, *this); - } + /** + * Returns the squared length of this vector. + * @return the squared length of this vector + */ + inline Real lengthSquare() { + return dot(*this, *this); + } - /** Normalizes this vector in place */ - inline void normalize() { - Real len; + /** Normalizes this vector in place */ + inline void normalize() { + Real len; - len = length(); + len = length(); - //if (len < oopse:epsilon) - // throw(); + //if (len < oopse:epsilon) + // throw(); - *this /= len; - } + *this /= len; + } - /** - * Tests if this vector is normalized - * @return true if this vector is normalized, otherwise return false - */ - inline bool isNormalized() { - return equal(lengthSquare(), 1.0); - } + /** + * Tests if this vector is normalized + * @return true if this vector is normalized, otherwise return false + */ + inline bool isNormalized() { + return equal(lengthSquare(), 1.0); + } - protected: - Real data_[Dim]; + protected: + Real data_[Dim]; - }; + }; - /** unary minus*/ - template - inline Vector operator -(const Vector& v1){ - Vector tmp(v1); - tmp.negate(); - return tmp; - } + /** unary minus*/ + template + inline Vector operator -(const Vector& v1){ + Vector tmp(v1); + tmp.negate(); + return tmp; + } - /** - * Return the sum of two vectors (v1 - v2). - * @return the sum of two vectors - * @param v1 the first vector - * @param v2 the second vector - */ - template - inline Vector operator +(const Vector& v1, const Vector& v2) { - Vector result; + /** + * Return the sum of two vectors (v1 - v2). + * @return the sum of two vectors + * @param v1 the first vector + * @param v2 the second vector + */ + template + inline Vector operator +(const Vector& v1, const Vector& v2) { + Vector result; - result.add(v1, v2); - return result; - } + result.add(v1, v2); + return result; + } - /** - * Return the difference of two vectors (v1 - v2). - * @return the difference of two vectors - * @param v1 the first vector - * @param v2 the second vector - */ - template - Vector operator -(const Vector& v1, const Vector& v2) { - Vector result; - result.sub(v1, v2); - return result; - } + /** + * Return the difference of two vectors (v1 - v2). + * @return the difference of two vectors + * @param v1 the first vector + * @param v2 the second vector + */ + template + Vector operator -(const Vector& v1, const Vector& v2) { + Vector result; + result.sub(v1, v2); + return result; + } - /** - * Returns the vaule of scalar multiplication of this vector v1 (v1 * r). - * @return the vaule of scalar multiplication of this vector - * @param v1 the source vector - * @param s the scalar value - */ - template - Vector operator * ( const Vector& v1, Real s) { - Vector result; - result.mul(v1,s); - return result; - } + /** + * Returns the vaule of scalar multiplication of this vector v1 (v1 * r). + * @return the vaule of scalar multiplication of this vector + * @param v1 the source vector + * @param s the scalar value + */ + template + Vector operator * ( const Vector& v1, Real s) { + Vector result; + result.mul(v1,s); + return result; + } - /** - * Returns the vaule of scalar multiplication of this vector v1 (v1 * r). - * @return the vaule of scalar multiplication of this vector - * @param s the scalar value - * @param v1 the source vector - */ - template - Vector operator * ( Real s, const Vector& v1 ) { - Vector result; - result.mul(v1, s); - return result; - } + /** + * Returns the vaule of scalar multiplication of this vector v1 (v1 * r). + * @return the vaule of scalar multiplication of this vector + * @param s the scalar value + * @param v1 the source vector + */ + template + Vector operator * ( Real s, const Vector& v1 ) { + Vector result; + result.mul(v1, s); + return result; + } - /** - * Returns the value of division of a vector by a scalar. - * @return the vaule of scalar division of this vector - * @param v1 the source vector - * @param s the scalar value - */ - template - Vector operator / ( const Vector& v1, Real s) { - Vector result; - result.div( v1,s); - return result; - } + /** + * Returns the value of division of a vector by a scalar. + * @return the vaule of scalar division of this vector + * @param v1 the source vector + * @param s the scalar value + */ + template + Vector operator / ( const Vector& v1, Real s) { + Vector result; + result.div( v1,s); + return result; + } - /** - * Returns the dot product of two Vectors - * @param v1 first vector - * @param v2 second vector - * @return the dot product of v1 and v2 - */ - template - inline Real dot( const Vector& v1, const Vector& v2 ) { - Real tmp; - tmp = 0; + /** + * Returns the dot product of two Vectors + * @param v1 first vector + * @param v2 second vector + * @return the dot product of v1 and v2 + */ + template + inline Real dot( const Vector& v1, const Vector& v2 ) { + Real tmp; + tmp = 0; - for (unsigned int i = 0; i < Dim; i++) - tmp += v1[i] * v2[i]; + for (unsigned int i = 0; i < Dim; i++) + tmp += v1[i] * v2[i]; - return tmp; - } + return tmp; + } - /** - * Returns the distance between two Vectors - * @param v1 first vector - * @param v2 second vector - * @return the distance between v1 and v2 - */ - template - inline Real distance( const Vector& v1, const Vector& v2 ) { - Vector tempVector = v1 - v2; - return tempVector.length(); - } + /** + * Returns the distance between two Vectors + * @param v1 first vector + * @param v2 second vector + * @return the distance between v1 and v2 + */ + template + inline Real distance( const Vector& v1, const Vector& v2 ) { + Vector tempVector = v1 - v2; + return tempVector.length(); + } - /** - * Returns the squared distance between two Vectors - * @param v1 first vector - * @param v2 second vector - * @return the squared distance between v1 and v2 - */ - template - inline Real distanceSquare( const Vector& v1, const Vector& v2 ) { - Vector tempVector = v1 - v2; - return tempVector.lengthSquare(); - } + /** + * Returns the squared distance between two Vectors + * @param v1 first vector + * @param v2 second vector + * @return the squared distance between v1 and v2 + */ + template + inline Real distanceSquare( const Vector& v1, const Vector& v2 ) { + Vector tempVector = v1 - v2; + return tempVector.lengthSquare(); + } - /** - * Write to an output stream - */ - template - std::ostream &operator<< ( std::ostream& o, const Vector& v) { + /** + * Write to an output stream + */ + template + std::ostream &operator<< ( std::ostream& o, const Vector& v) { - o << "[ "; + o << "[ "; - for (unsigned int i = 0 ; i< Dim; i++) { - o << v[i]; + for (unsigned int i = 0 ; i< Dim; i++) { + o << v[i]; - if (i != Dim -1) { - o<< ", "; - } - } - - o << " ]"; - return o; + if (i != Dim -1) { + o<< ", "; + } } + + o << " ]"; + return o; + } } #endif