--- trunk/src/math/RectMatrix.hpp 2004/10/25 22:46:19 151 +++ trunk/src/math/RectMatrix.hpp 2005/03/01 20:10:14 385 @@ -1,29 +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 RectMatrix.hpp * @author Teng Lin @@ -33,7 +48,7 @@ #ifndef MATH_RECTMATRIX_HPP #define MATH_RECTMATRIX_HPP - +#include #include #include "Vector.hpp" @@ -53,20 +68,20 @@ namespace oopse { RectMatrix() { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] = 0.0; + this->data_[i][j] = 0.0; } /** Constructs and initializes every element of this matrix to a scalar */ RectMatrix(Real s) { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] = s; + this->data_[i][j] = s; } RectMatrix(Real* array) { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] = array[i * Row + j]; + this->data_[i][j] = array[i * Row + j]; } /** copy constructor */ @@ -84,7 +99,7 @@ namespace oopse { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] = m.data_[i][j]; + this->data_[i][j] = m.data_[i][j]; return *this; } @@ -92,22 +107,22 @@ namespace oopse { * Return the reference of a single element of this matrix. * @return the reference of a single element of this matrix * @param i row index - * @param j colum index + * @param j Column index */ Real& operator()(unsigned int i, unsigned int j) { //assert( i < Row && j < Col); - return data_[i][j]; + return this->data_[i][j]; } /** * Return the value of a single element of this matrix. * @return the value of a single element of this matrix * @param i row index - * @param j colum index + * @param j Column index */ Real operator()(unsigned int i, unsigned int j) const { - return data_[i][j]; + return this->data_[i][j]; } /** @@ -117,7 +132,7 @@ namespace oopse { void getArray(Real* array) { for (unsigned int i = 0; i < Row; i++) { for (unsigned int j = 0; j < Col; j++) { - array[i * Row + j] = data_[i][j]; + array[i * Row + j] = this->data_[i][j]; } } } @@ -125,7 +140,7 @@ namespace oopse { /** Returns the pointer of internal array */ Real* getArrayPointer() { - return &data_[0][0]; + return &this->data_[0][0]; } /** @@ -137,7 +152,7 @@ namespace oopse { Vector v; for (unsigned int i = 0; i < Row; i++) - v[i] = data_[row][i]; + v[i] = this->data_[row][i]; return v; } @@ -150,7 +165,7 @@ namespace oopse { void setRow(unsigned int row, const Vector& v) { for (unsigned int i = 0; i < Row; i++) - data_[row][i] = v[i]; + this->data_[row][i] = v[i]; } /** @@ -158,11 +173,11 @@ namespace oopse { * @return a column of this matrix as a vector * @param col the column index */ - Vector getColum(unsigned int col) { + Vector getColumn(unsigned int col) { Vector v; for (unsigned int j = 0; j < Col; j++) - v[j] = data_[j][col]; + v[j] = this->data_[j][col]; return v; } @@ -172,10 +187,10 @@ namespace oopse { * @param col the column index * @param v the vector to be set */ - void setColum(unsigned int col, const Vector& v){ + void setColumn(unsigned int col, const Vector& v){ for (unsigned int j = 0; j < Col; j++) - data_[j][col] = v[j]; + this->data_[j][col] = v[j]; } /** @@ -187,19 +202,19 @@ namespace oopse { assert(i < Row && j < Row); for (unsigned int k = 0; k < Col; k++) - std::swap(data_[i][k], data_[j][k]); + std::swap(this->data_[i][k], this->data_[j][k]); } /** - * swap two colums of this matrix - * @param i the first colum - * @param j the second colum + * swap two Columns of this matrix + * @param i the first Column + * @param j the second Column */ - void swapColum(unsigned int i, unsigned int j){ + void swapColumn(unsigned int i, unsigned int j){ assert(i < Col && j < Col); for (unsigned int k = 0; k < Row; k++) - std::swap(data_[k][i], data_[k][j]); + std::swap(this->data_[k][i], this->data_[k][j]); } /** @@ -212,7 +227,7 @@ namespace oopse { bool operator ==(const RectMatrix& m) { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - if (!equal(data_[i][j], m.data_[i][j])) + if (!equal(this->data_[i][j], m.data_[i][j])) return false; return true; @@ -231,7 +246,7 @@ namespace oopse { inline void negate() { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] = -data_[i][j]; + this->data_[i][j] = -this->data_[i][j]; } /** @@ -241,7 +256,7 @@ namespace oopse { inline void negate(const RectMatrix& m) { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] = -m.data_[i][j]; + this->data_[i][j] = -m.data_[i][j]; } /** @@ -251,7 +266,7 @@ namespace oopse { inline void add( const RectMatrix& m ) { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] += m.data_[i][j]; + this->data_[i][j] += m.data_[i][j]; } /** @@ -262,7 +277,7 @@ namespace oopse { inline void add( const RectMatrix& m1, const RectMatrix& m2 ) { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] = m1.data_[i][j] + m2.data_[i][j]; + this->data_[i][j] = m1.data_[i][j] + m2.data_[i][j]; } /** @@ -272,7 +287,7 @@ namespace oopse { inline void sub( const RectMatrix& m ) { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] -= m.data_[i][j]; + this->data_[i][j] -= m.data_[i][j]; } /** @@ -283,7 +298,7 @@ namespace oopse { inline void sub( const RectMatrix& m1, const RectMatrix& m2){ for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] = m1.data_[i][j] - m2.data_[i][j]; + this->data_[i][j] = m1.data_[i][j] - m2.data_[i][j]; } /** @@ -293,7 +308,7 @@ namespace oopse { inline void mul( Real s ) { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] *= s; + this->data_[i][j] *= s; } /** @@ -304,7 +319,7 @@ namespace oopse { inline void mul( Real s, const RectMatrix& m ) { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] = s * m.data_[i][j]; + this->data_[i][j] = s * m.data_[i][j]; } /** @@ -314,7 +329,7 @@ namespace oopse { inline void div( Real s) { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] /= s; + this->data_[i][j] /= s; } /** @@ -325,7 +340,7 @@ namespace oopse { inline void div( Real s, const RectMatrix& m ) { for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - data_[i][j] = m.data_[i][j] / s; + this->data_[i][j] = m.data_[i][j] / s; } /** @@ -365,12 +380,12 @@ namespace oopse { } /** Return the transpose of this matrix */ - RectMatrix transpose(){ + RectMatrix transpose() const{ RectMatrix result; for (unsigned int i = 0; i < Row; i++) for (unsigned int j = 0; j < Col; j++) - result(j, i) = data_[i][j]; + result(j, i) = this->data_[i][j]; return result; }