--- branches/development/src/math/DynamicRectMatrix.hpp	2010/07/09 23:08:25	1465
+++ branches/development/src/math/DynamicRectMatrix.hpp	2013/05/15 15:09:35	1874
@@ -35,8 +35,9 @@
  *                                                                      
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
- * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 /**
@@ -108,7 +109,7 @@ namespace OpenMD {
     ~DynamicRectMatrix() { deallocate();}
 
     /** copy assignment operator */
-    DynamicRectMatrix<Real> operator =(const DynamicRectMatrix<Real> m) {
+    DynamicRectMatrix<Real> operator =(const DynamicRectMatrix<Real> &m) {
       if (this == &m)
 	  return *this;
       if (nrow_ != m.getNRow() || ncol_ != m.getNCol()) {
@@ -232,11 +233,11 @@ namespace OpenMD {
     /**
      * Tests if this matrix is identical to matrix m
      * @return true if this matrix is equal to the matrix m, return false otherwise
-     * @m matrix to be compared
+     * @param m matrix to be compared
      *
      * @todo replace operator == by template function equal
      */
-    bool operator ==(const DynamicRectMatrix<Real> m) {
+    bool operator ==(const DynamicRectMatrix<Real> &m) {
       assert(nrow_ == m.getNRow() && ncol_ == m.getNCol());
       for (unsigned int i = 0; i < nrow_; i++)
 	for (unsigned int j = 0; j < ncol_; j++)
@@ -249,9 +250,9 @@ namespace OpenMD {
     /**
      * Tests if this matrix is not equal to matrix m
      * @return true if this matrix is not equal to the matrix m, return false otherwise
-     * @m matrix to be compared
+     * @param m matrix to be compared
      */
-    bool operator !=(const DynamicRectMatrix<Real> m) {
+    bool operator !=(const DynamicRectMatrix<Real> &m) {
       return !(*this == m);
     }
 
@@ -266,7 +267,7 @@ namespace OpenMD {
      * Sets the value of this matrix to the negation of matrix m.
      * @param m the source matrix
      */
-    inline void negate(const DynamicRectMatrix<Real> m) {
+    inline void negate(const DynamicRectMatrix<Real> &m) {
       for (unsigned int i = 0; i < nrow_; i++)
 	for (unsigned int j = 0; j < ncol_; j++)
 	  this->data_[i][j] = -m.data_[i][j];        
@@ -276,7 +277,7 @@ namespace OpenMD {
      * Sets the value of this matrix to the sum of itself and m (*this += m).
      * @param m the other matrix
      */
-    inline void add( const DynamicRectMatrix<Real> m ) {
+    inline void add( const DynamicRectMatrix<Real> &m ) {
       assert(nrow_ == m.getNRow() && ncol_ == m.getNCol());
       for (unsigned int i = 0; i < nrow_; i++)
 	for (unsigned int j = 0; j < ncol_; j++)        
@@ -288,7 +289,7 @@ namespace OpenMD {
      * @param m1 the first matrix
      * @param m2 the second matrix
      */
-    inline void add( const DynamicRectMatrix<Real> m1, const DynamicRectMatrix<Real> m2 ) {
+    inline void add( const DynamicRectMatrix<Real> &m1, const DynamicRectMatrix<Real> &m2 ) {
       assert(m1.getNRow() == m2.getNRow() && m1.getNCol() == m2.getNCol());
       for (unsigned int i = 0; i < nrow_; i++)
 	for (unsigned int j = 0; j < ncol_; j++)        
@@ -299,7 +300,7 @@ namespace OpenMD {
      * Sets the value of this matrix to the difference  of itself and m (*this -= m).
      * @param m the other matrix
      */
-    inline void sub( const DynamicRectMatrix<Real> m ) {
+    inline void sub( const DynamicRectMatrix<Real> &m ) {
       assert(nrow_ == m.getNRow() && ncol_ == m.getNCol());
       for (unsigned int i = 0; i < nrow_; i++)
 	for (unsigned int j = 0; j < ncol_; j++)        
@@ -311,7 +312,7 @@ namespace OpenMD {
      * @param m1 the first matrix
      * @param m2 the second matrix
      */
-    inline void sub( const DynamicRectMatrix<Real> m1, const DynamicRectMatrix<Real> m2){
+    inline void sub( const DynamicRectMatrix<Real> &m1, const DynamicRectMatrix<Real> &m2){
       assert(m1.getNRow() == m2.getNRow() && m1.getNCol() == m2.getNCol());
       for (unsigned int i = 0; i < nrow_; i++)
 	for (unsigned int j = 0; j < ncol_; j++)        
@@ -333,7 +334,7 @@ namespace OpenMD {
      * @param s the scalar value
      * @param m the matrix
      */
-    inline void mul( Real s, const DynamicRectMatrix<Real> m ) {
+    inline void mul( Real s, const DynamicRectMatrix<Real> &m ) {
       assert(nrow_ == m.getNRow() && ncol_ == m.getNCol());    
       for (unsigned int i = 0; i < nrow_; i++)
 	for (unsigned int j = 0; j < ncol_; j++)  
@@ -355,7 +356,7 @@ namespace OpenMD {
      * @param s the scalar value
      * @param m the matrix
      */
-    inline void div( Real s, const DynamicRectMatrix<Real> m ) {
+    inline void div( Real s, const DynamicRectMatrix<Real> &m ) {
       assert(nrow_ == m.getNRow() && ncol_ == m.getNCol());
       for (unsigned int i = 0; i < nrow_; i++)
 	for (unsigned int j = 0; j < ncol_; j++)  
@@ -439,19 +440,19 @@ namespace OpenMD {
     unsigned int nrow_;
     unsigned int ncol_;
   private:
-    void allocate(int nrow, int ncol) {
-        nrow_ = nrow;
-        ncol_ = ncol;
-        data_ = new Real*[nrow_];
-        for (int i = 0; i < nrow_; ++i)
-            data_[i] = new Real[ncol_];
+    void allocate( int nrow,  int ncol ) {
+      nrow_ = (unsigned int) nrow;
+      ncol_ = (unsigned int) ncol;
+      data_ = new Real*[nrow_];
+      for (unsigned int i = 0; i < nrow_; ++i)
+        data_[i] = new Real[ncol_];
     }
-
+    
     void deallocate() {
-      for (int i = 0; i < nrow_; ++i)
+      for (unsigned int i = 0; i < nrow_; ++i)
         delete data_[i];
       delete []data_;
-
+      
       nrow_ = 0;
       ncol_ = 0;
       data_ = NULL;
@@ -461,7 +462,7 @@ namespace OpenMD {
 
   /** Negate the value of every element of this matrix. */
   template<typename Real> 
-  inline DynamicRectMatrix<Real> operator -(const DynamicRectMatrix<Real> m) {
+  inline DynamicRectMatrix<Real> operator -(const DynamicRectMatrix<Real> &m) {
     DynamicRectMatrix<Real> result(m);
 
     result.negate();
@@ -476,7 +477,7 @@ namespace OpenMD {
    * @param m2 the second matrix
    */ 
   template<typename Real> 
-  inline DynamicRectMatrix<Real> operator + (const DynamicRectMatrix<Real> m1,const DynamicRectMatrix<Real> m2) {
+  inline DynamicRectMatrix<Real> operator + (const DynamicRectMatrix<Real> &m1, const DynamicRectMatrix<Real> &m2) {
     
     DynamicRectMatrix<Real> result(m1.getNRow(), m1.getNCol());
 
@@ -492,7 +493,7 @@ namespace OpenMD {
    * @param m2 the second matrix
    */
   template<typename Real> 
-  inline DynamicRectMatrix<Real> operator - (const DynamicRectMatrix<Real> m1, const DynamicRectMatrix<Real> m2) {
+  inline DynamicRectMatrix<Real> operator - (const DynamicRectMatrix<Real> &m1, const DynamicRectMatrix<Real> &m2) {
     DynamicRectMatrix<Real> result(m1.getNRow(), m1.getNCol());
 
     result.sub(m1, m2);
@@ -507,7 +508,7 @@ namespace OpenMD {
    * @param s the scalar
    */
   template<typename Real> 
-  inline DynamicRectMatrix<Real> operator *(const DynamicRectMatrix<Real> m, Real s) {
+  inline DynamicRectMatrix<Real> operator *(const DynamicRectMatrix<Real> &m, Real s) {
     DynamicRectMatrix<Real> result(m.getNRow(), m.getNCol());
 
     result.mul(s, m);
@@ -522,7 +523,7 @@ namespace OpenMD {
    * @param m the matrix
    */
   template<typename Real> 
-  inline DynamicRectMatrix<Real> operator *(Real s, const DynamicRectMatrix<Real> m) {
+  inline DynamicRectMatrix<Real> operator *(Real s, const DynamicRectMatrix<Real> &m) {
     DynamicRectMatrix<Real> result(m.getNRow(), m.getNCol());
 
     result.mul(s, m);
@@ -558,10 +559,10 @@ namespace OpenMD {
    * @param v the vector
    */
   template<typename Real>
-  inline DynamicVector<Real> operator *(const DynamicRectMatrix<Real> m, const DynamicVector<Real>& v) {
+  inline DynamicVector<Real> operator *(const DynamicRectMatrix<Real> &m, const DynamicVector<Real> &v) {
     int nrow = m.getNRow();
     int ncol = m.getNCol();
-    assert(ncol = v.size());
+    assert(ncol == v.size());
     DynamicVector<Real> result(nrow);
     
     for (unsigned int i = 0; i < nrow ; i++)
@@ -578,7 +579,7 @@ namespace OpenMD {
    * @param s the scalar
    */
   template<typename Real> 
-  inline DynamicRectMatrix<Real> operator /(const DynamicRectMatrix<Real> m, Real s) {
+  inline DynamicRectMatrix<Real> operator /(const DynamicRectMatrix<Real> &m, Real s) {
     DynamicRectMatrix<Real> result(m.getNRow(), m.getNCol());
 
     result.div(s, m);
@@ -590,7 +591,7 @@ namespace OpenMD {
    * Write to an output stream
    */
   template<typename Real>
-  std::ostream &operator<< ( std::ostream& o, const DynamicRectMatrix<Real> m) {
+  std::ostream &operator<< ( std::ostream& o, const DynamicRectMatrix<Real> &m) {
     for (unsigned int i = 0; i < m.getNRow() ; i++) {
       o << "(";
       for (unsigned int j = 0; j < m.getNCol() ; j++) {