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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. 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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* 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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* |
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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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* 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] 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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|
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/** |
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* @file DynamicRectMatrix.hpp |
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* @author Teng Lin |
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* @date 10/11/2004 |
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* @version 1.0 |
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*/ |
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|
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#ifndef MATH_DYNAMICRECTMATRIX_HPP |
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#define MATH_DYNAMICRECTMATRIX_HPP |
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#include <math.h> |
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#include <cmath> |
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#include "math/DynamicVector.hpp" |
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|
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namespace OpenMD { |
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|
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/** |
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* @class DynamicRectMatrix DynamicRectMatrix.hpp "math/DynamicRectMatrix.hpp" |
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* @brief rectangular matrix class |
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*/ |
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template<typename Real> |
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class DynamicRectMatrix { |
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public: |
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typedef Real ElemType; |
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typedef Real* ElemPoinerType; |
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typedef DynamicRectMatrix<Real> SelfType; |
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|
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/** default constructor */ |
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DynamicRectMatrix(){ |
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nrow_ = 0; |
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ncol_ = 0; |
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data_ = NULL; |
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} |
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|
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DynamicRectMatrix(int nrow, int ncol) { |
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allocate(nrow, ncol); |
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|
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] = 0.0; |
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} |
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|
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/** Constructs and initializes every element of this matrix to a scalar */ |
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DynamicRectMatrix(int nrow, int ncol, Real s) { |
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allocate(nrow, ncol); |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] = s; |
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} |
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|
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DynamicRectMatrix(int nrow, int ncol, Real* array) { |
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allocate(nrow, ncol); |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] = array[i * nrow_ + j]; |
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} |
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|
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/** copy constructor */ |
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DynamicRectMatrix(const SelfType& m) { |
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allocate(m.getNRow(), m.getNCol()); |
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|
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] = m.data_[i][j]; |
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} |
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|
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/** destructor*/ |
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~DynamicRectMatrix() { deallocate();} |
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|
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/** copy assignment operator */ |
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DynamicRectMatrix<Real> operator =(const DynamicRectMatrix<Real> m) { |
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if (this == &m) |
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return *this; |
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if (nrow_ != m.getNRow() || ncol_ != m.getNCol()) { |
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deallocate(); |
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allocate(m.getNRow(), m.getNCol()); |
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} |
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|
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] = m.data_[i][j]; |
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return *this; |
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} |
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|
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/** |
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* Return the reference of a single element of this matrix. |
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* @return the reference of a single element of this matrix |
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* @param i row index |
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* @param j Column index |
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*/ |
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Real& operator()(unsigned int i, unsigned int j) { |
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return this->data_[i][j]; |
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} |
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|
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/** |
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* Return the value of a single element of this matrix. |
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* @return the value of a single element of this matrix |
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* @param i row index |
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* @param j Column index |
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*/ |
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Real operator()(unsigned int i, unsigned int j) const { |
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|
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return this->data_[i][j]; |
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} |
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|
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/** |
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* Copy the internal data to an array |
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* @param array the pointer of destination array |
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*/ |
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void getArray(Real* array) { |
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for (unsigned int i = 0; i < nrow_; i++) { |
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for (unsigned int j = 0; j < ncol_; j++) { |
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array[i * nrow_ + j] = this->data_[i][j]; |
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} |
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} |
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} |
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|
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/** |
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* Returns a row of this matrix as a vector. |
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* @return a row of this matrix as a vector |
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* @param row the row index |
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*/ |
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DynamicVector<Real> getRow(unsigned int row) { |
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DynamicVector<Real> v; |
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|
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for (unsigned int i = 0; i < ncol_; i++) |
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v[i] = this->data_[row][i]; |
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|
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return v; |
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} |
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|
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/** |
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* Sets a row of this matrix |
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* @param row the row index |
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* @param v the vector to be set |
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*/ |
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void setRow(unsigned int row, const DynamicVector<Real>& v) { |
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assert(v.size() == nrow_); |
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for (unsigned int i = 0; i < ncol_; i++) |
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this->data_[row][i] = v[i]; |
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} |
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|
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/** |
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* Returns a column of this matrix as a vector. |
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* @return a column of this matrix as a vector |
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* @param col the column index |
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*/ |
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DynamicVector<Real> getColumn(unsigned int col) { |
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DynamicVector<Real> v(ncol_); |
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|
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for (unsigned int j = 0; j < nrow_; j++) |
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v[j] = this->data_[j][col]; |
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|
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return v; |
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} |
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|
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/** |
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* Sets a column of this matrix |
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* @param col the column index |
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* @param v the vector to be set |
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*/ |
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void setColumn(unsigned int col, const DynamicVector<Real>& v){ |
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|
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for (unsigned int j = 0; j < nrow_; j++) |
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this->data_[j][col] = v[j]; |
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} |
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|
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/** |
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* swap two rows of this matrix |
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* @param i the first row |
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* @param j the second row |
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*/ |
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void swapRow(unsigned int i, unsigned int j){ |
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assert(i < nrow_ && j < nrow_); |
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|
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for (unsigned int k = 0; k < ncol_; k++) |
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std::swap(this->data_[i][k], this->data_[j][k]); |
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} |
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|
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/** |
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* swap two Columns of this matrix |
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* @param i the first Column |
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* @param j the second Column |
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*/ |
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void swapColumn(unsigned int i, unsigned int j){ |
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assert(i < ncol_ && j < ncol_); |
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|
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for (unsigned int k = 0; k < nrow_; k++) |
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std::swap(this->data_[k][i], this->data_[k][j]); |
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} |
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|
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/** |
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* Tests if this matrix is identical to matrix m |
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* @return true if this matrix is equal to the matrix m, return false otherwise |
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* @m matrix to be compared |
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* |
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* @todo replace operator == by template function equal |
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*/ |
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bool operator ==(const DynamicRectMatrix<Real> m) { |
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assert(nrow_ == m.getNRow() && ncol_ == m.getNCol()); |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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if (!equal(this->data_[i][j], m.data_[i][j])) |
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return false; |
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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 matrix is not equal to matrix m |
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* @return true if this matrix is not equal to the matrix m, return false otherwise |
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* @m matrix to be compared |
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*/ |
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bool operator !=(const DynamicRectMatrix<Real> m) { |
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return !(*this == m); |
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} |
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|
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/** Negates the value of this matrix in place. */ |
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inline void negate() { |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] = -this->data_[i][j]; |
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} |
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|
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/** |
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* Sets the value of this matrix to the negation of matrix m. |
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* @param m the source matrix |
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*/ |
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inline void negate(const DynamicRectMatrix<Real> m) { |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] = -m.data_[i][j]; |
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} |
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|
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/** |
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* Sets the value of this matrix to the sum of itself and m (*this += m). |
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* @param m the other matrix |
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*/ |
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inline void add( const DynamicRectMatrix<Real> m ) { |
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assert(nrow_ == m.getNRow() && ncol_ == m.getNCol()); |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] += m.data_[i][j]; |
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} |
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|
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/** |
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* Sets the value of this matrix to the sum of m1 and m2 (*this = m1 + m2). |
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* @param m1 the first matrix |
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* @param m2 the second matrix |
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*/ |
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inline void add( const DynamicRectMatrix<Real> m1, const DynamicRectMatrix<Real> m2 ) { |
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assert(m1.getNRow() == m2.getNRow() && m1.getNCol() == m2.getNCol()); |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] = m1.data_[i][j] + m2.data_[i][j]; |
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} |
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|
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/** |
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* Sets the value of this matrix to the difference of itself and m (*this -= m). |
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* @param m the other matrix |
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*/ |
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inline void sub( const DynamicRectMatrix<Real> m ) { |
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assert(nrow_ == m.getNRow() && ncol_ == m.getNCol()); |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] -= m.data_[i][j]; |
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} |
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|
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/** |
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* Sets the value of this matrix to the difference of matrix m1 and m2 (*this = m1 - m2). |
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* @param m1 the first matrix |
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* @param m2 the second matrix |
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*/ |
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inline void sub( const DynamicRectMatrix<Real> m1, const DynamicRectMatrix<Real> m2){ |
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assert(m1.getNRow() == m2.getNRow() && m1.getNCol() == m2.getNCol()); |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] = m1.data_[i][j] - m2.data_[i][j]; |
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} |
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|
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/** |
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* Sets the value of this matrix 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( Real s ) { |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] *= s; |
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} |
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|
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/** |
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* Sets the value of this matrix to the scalar multiplication of matrix m (*this = s * m). |
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* @param s the scalar value |
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* @param m the matrix |
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*/ |
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inline void mul( Real s, const DynamicRectMatrix<Real> m ) { |
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assert(nrow_ == m.getNRow() && ncol_ == m.getNCol()); |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] = s * m.data_[i][j]; |
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} |
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|
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/** |
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* Sets the value of this matrix 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( Real s) { |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] /= s; |
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} |
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|
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/** |
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* Sets the value of this matrix to the scalar division of matrix m (*this = m /s). |
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* @param s the scalar value |
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* @param m the matrix |
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*/ |
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inline void div( Real s, const DynamicRectMatrix<Real> m ) { |
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assert(nrow_ == m.getNRow() && ncol_ == m.getNCol()); |
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for (unsigned int i = 0; i < nrow_; i++) |
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for (unsigned int j = 0; j < ncol_; j++) |
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this->data_[i][j] = m.data_[i][j] / s; |
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} |
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|
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/** |
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* Multiples a scalar into every element of this matrix. |
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* @param s the scalar value |
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*/ |
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DynamicRectMatrix<Real> operator *=(const Real s) { |
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this->mul(s); |
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return *this; |
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} |
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|
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/** |
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* Divides every element of this matrix by a scalar. |
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* @param s the scalar value |
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*/ |
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DynamicRectMatrix<Real> operator /=(const Real s) { |
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this->div(s); |
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return *this; |
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} |
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|
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/** |
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* Sets the value of this matrix to the sum of the other matrix and itself (*this += m). |
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* @param m the other matrix |
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*/ |
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DynamicRectMatrix<Real> operator += (const DynamicRectMatrix<Real> m) { |
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assert(nrow_ == m.getNRow() && ncol_ == m.getNCol()); |
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add(m); |
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return *this; |
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} |
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|
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/** |
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* Sets the value of this matrix to the differerence of itself and the other matrix (*this -= m) |
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* @param m the other matrix |
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*/ |
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DynamicRectMatrix<Real> operator -= (const DynamicRectMatrix<Real> m){ |
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assert(nrow_ == m.getNRow() && ncol_ == m.getNCol()); |
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sub(m); |
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return *this; |
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} |
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|
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/** Return the transpose of this matrix */ |
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DynamicRectMatrix<Real> transpose() const{ |
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DynamicRectMatrix<Real> result(ncol_,nrow_); |
| 407 |
|
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for (unsigned int i = 0; i < nrow_; i++) |
| 409 |
for (unsigned int j = 0; j < ncol_; j++) |
| 410 |
result(j, i) = this->data_[i][j]; |
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|
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return result; |
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} |
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|
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unsigned int getNRow() const {return nrow_;} |
| 416 |
unsigned int getNCol() const {return ncol_;} |
| 417 |
|
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template<class MatrixType> |
| 419 |
void setSubMatrix(unsigned int beginRow, unsigned int beginCol, const MatrixType& m) { |
| 420 |
assert(beginRow + m.getNRow() -1 <= nrow_); |
| 421 |
assert(beginCol + m.getNCol() -1 <= ncol_); |
| 422 |
|
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for (unsigned int i = 0; i < m.getNRow(); ++i) |
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for (unsigned int j = 0; j < m.getNCol(); ++j) |
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this->data_[beginRow+i][beginCol+j] = m(i, j); |
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} |
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|
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template<class MatrixType> |
| 429 |
void getSubMatrix(unsigned int beginRow, unsigned int beginCol, MatrixType& m) { |
| 430 |
assert(beginRow + m.getNRow() -1 <= nrow_); |
| 431 |
assert(beginCol + m.getNCol() - 1 <= ncol_); |
| 432 |
|
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for (unsigned int i = 0; i < m.getNRow(); ++i) |
| 434 |
for (unsigned int j = 0; j < m.getNCol(); ++j) |
| 435 |
m(i, j) = this->data_[beginRow+i][beginCol+j]; |
| 436 |
} |
| 437 |
|
| 438 |
protected: |
| 439 |
Real** data_; |
| 440 |
unsigned int nrow_; |
| 441 |
unsigned int ncol_; |
| 442 |
private: |
| 443 |
void allocate( int nrow, int ncol ) { |
| 444 |
nrow_ = (unsigned int) nrow; |
| 445 |
ncol_ = (unsigned int) ncol; |
| 446 |
data_ = new Real*[nrow_]; |
| 447 |
for (unsigned int i = 0; i < nrow_; ++i) |
| 448 |
data_[i] = new Real[ncol_]; |
| 449 |
} |
| 450 |
|
| 451 |
void deallocate() { |
| 452 |
for (unsigned int i = 0; i < nrow_; ++i) |
| 453 |
delete data_[i]; |
| 454 |
delete []data_; |
| 455 |
|
| 456 |
nrow_ = 0; |
| 457 |
ncol_ = 0; |
| 458 |
data_ = NULL; |
| 459 |
} |
| 460 |
|
| 461 |
}; |
| 462 |
|
| 463 |
/** Negate the value of every element of this matrix. */ |
| 464 |
template<typename Real> |
| 465 |
inline DynamicRectMatrix<Real> operator -(const DynamicRectMatrix<Real> m) { |
| 466 |
DynamicRectMatrix<Real> result(m); |
| 467 |
|
| 468 |
result.negate(); |
| 469 |
|
| 470 |
return result; |
| 471 |
} |
| 472 |
|
| 473 |
/** |
| 474 |
* Return the sum of two matrixes (m1 + m2). |
| 475 |
* @return the sum of two matrixes |
| 476 |
* @param m1 the first matrix |
| 477 |
* @param m2 the second matrix |
| 478 |
*/ |
| 479 |
template<typename Real> |
| 480 |
inline DynamicRectMatrix<Real> operator + (const DynamicRectMatrix<Real> m1,const DynamicRectMatrix<Real> m2) { |
| 481 |
|
| 482 |
DynamicRectMatrix<Real> result(m1.getNRow(), m1.getNCol()); |
| 483 |
|
| 484 |
result.add(m1, m2); |
| 485 |
|
| 486 |
return result; |
| 487 |
} |
| 488 |
|
| 489 |
/** |
| 490 |
* Return the difference of two matrixes (m1 - m2). |
| 491 |
* @return the sum of two matrixes |
| 492 |
* @param m1 the first matrix |
| 493 |
* @param m2 the second matrix |
| 494 |
*/ |
| 495 |
template<typename Real> |
| 496 |
inline DynamicRectMatrix<Real> operator - (const DynamicRectMatrix<Real> m1, const DynamicRectMatrix<Real> m2) { |
| 497 |
DynamicRectMatrix<Real> result(m1.getNRow(), m1.getNCol()); |
| 498 |
|
| 499 |
result.sub(m1, m2); |
| 500 |
|
| 501 |
return result; |
| 502 |
} |
| 503 |
|
| 504 |
/** |
| 505 |
* Return the multiplication of scalra and matrix (m * s). |
| 506 |
* @return the multiplication of a scalra and a matrix |
| 507 |
* @param m the matrix |
| 508 |
* @param s the scalar |
| 509 |
*/ |
| 510 |
template<typename Real> |
| 511 |
inline DynamicRectMatrix<Real> operator *(const DynamicRectMatrix<Real> m, Real s) { |
| 512 |
DynamicRectMatrix<Real> result(m.getNRow(), m.getNCol()); |
| 513 |
|
| 514 |
result.mul(s, m); |
| 515 |
|
| 516 |
return result; |
| 517 |
} |
| 518 |
|
| 519 |
/** |
| 520 |
* Return the multiplication of a scalra and a matrix (s * m). |
| 521 |
* @return the multiplication of a scalra and a matrix |
| 522 |
* @param s the scalar |
| 523 |
* @param m the matrix |
| 524 |
*/ |
| 525 |
template<typename Real> |
| 526 |
inline DynamicRectMatrix<Real> operator *(Real s, const DynamicRectMatrix<Real> m) { |
| 527 |
DynamicRectMatrix<Real> result(m.getNRow(), m.getNCol()); |
| 528 |
|
| 529 |
result.mul(s, m); |
| 530 |
|
| 531 |
return result; |
| 532 |
} |
| 533 |
|
| 534 |
/** |
| 535 |
* Return the multiplication of two matrixes (m1 * m2). |
| 536 |
* @return the multiplication of two matrixes |
| 537 |
* @param m1 the first matrix |
| 538 |
* @param m2 the second matrix |
| 539 |
*/ |
| 540 |
template<typename Real> |
| 541 |
inline DynamicRectMatrix<Real> operator *(const DynamicRectMatrix<Real>& m1, const DynamicRectMatrix<Real>& m2) { |
| 542 |
assert(m1.getNCol() == m2.getNRow()); |
| 543 |
unsigned int sameDim = m1.getNCol(); |
| 544 |
int nrow = m1.getNRow(); |
| 545 |
int ncol = m2.getNCol(); |
| 546 |
DynamicRectMatrix<Real> result(nrow, ncol ); |
| 547 |
for (unsigned int i = 0; i < nrow; i++) |
| 548 |
for (unsigned int j = 0; j < ncol; j++) |
| 549 |
for (unsigned int k = 0; k < sameDim; k++) |
| 550 |
result(i, j) += m1(i, k) * m2(k, j); |
| 551 |
|
| 552 |
return result; |
| 553 |
} |
| 554 |
|
| 555 |
/** |
| 556 |
* Return the multiplication of a matrix and a vector (m * v). |
| 557 |
* @return the multiplication of a matrix and a vector |
| 558 |
* @param m the matrix |
| 559 |
* @param v the vector |
| 560 |
*/ |
| 561 |
template<typename Real> |
| 562 |
inline DynamicVector<Real> operator *(const DynamicRectMatrix<Real> m, const DynamicVector<Real>& v) { |
| 563 |
int nrow = m.getNRow(); |
| 564 |
int ncol = m.getNCol(); |
| 565 |
assert(ncol = v.size()); |
| 566 |
DynamicVector<Real> result(nrow); |
| 567 |
|
| 568 |
for (unsigned int i = 0; i < nrow ; i++) |
| 569 |
for (unsigned int j = 0; j < ncol ; j++) |
| 570 |
result[i] += m(i, j) * v[j]; |
| 571 |
|
| 572 |
return result; |
| 573 |
} |
| 574 |
|
| 575 |
/** |
| 576 |
* Return the scalar division of matrix (m / s). |
| 577 |
* @return the scalar division of matrix |
| 578 |
* @param m the matrix |
| 579 |
* @param s the scalar |
| 580 |
*/ |
| 581 |
template<typename Real> |
| 582 |
inline DynamicRectMatrix<Real> operator /(const DynamicRectMatrix<Real> m, Real s) { |
| 583 |
DynamicRectMatrix<Real> result(m.getNRow(), m.getNCol()); |
| 584 |
|
| 585 |
result.div(s, m); |
| 586 |
|
| 587 |
return result; |
| 588 |
} |
| 589 |
|
| 590 |
/** |
| 591 |
* Write to an output stream |
| 592 |
*/ |
| 593 |
template<typename Real> |
| 594 |
std::ostream &operator<< ( std::ostream& o, const DynamicRectMatrix<Real> m) { |
| 595 |
for (unsigned int i = 0; i < m.getNRow() ; i++) { |
| 596 |
o << "("; |
| 597 |
for (unsigned int j = 0; j < m.getNCol() ; j++) { |
| 598 |
o << m(i, j); |
| 599 |
if (j != m.getNCol() -1) |
| 600 |
o << "\t"; |
| 601 |
} |
| 602 |
o << ")" << std::endl; |
| 603 |
} |
| 604 |
return o; |
| 605 |
} |
| 606 |
} |
| 607 |
#endif //MATH_RECTMATRIX_HPP |
| 608 |
|
