--- trunk/src/math/DynamicRectMatrix.hpp	2006/02/22 20:35:16	891
+++ branches/development/src/math/DynamicRectMatrix.hpp	2012/10/22 20:42:10	1808
@@ -6,19 +6,10 @@
  * 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
+ * 1. 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
+ * 2. 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.
@@ -37,6 +28,16 @@
  * 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.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 /**
@@ -52,7 +53,7 @@
 #include <cmath>
 #include "math/DynamicVector.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   /**
    * @class DynamicRectMatrix DynamicRectMatrix.hpp "math/DynamicRectMatrix.hpp"
@@ -66,6 +67,12 @@ namespace oopse {
     typedef DynamicRectMatrix<Real> SelfType;
             
     /** default constructor */
+    DynamicRectMatrix(){
+      nrow_ = 0;
+      ncol_ = 0;
+      data_ = NULL;
+    }
+
     DynamicRectMatrix(int nrow, int ncol) {
       allocate(nrow, ncol);
 
@@ -226,7 +233,7 @@ namespace oopse {
     /**
      * 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
      */
@@ -243,7 +250,7 @@ namespace oopse {
     /**
      * 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) {
       return !(*this == m);
@@ -433,19 +440,19 @@ namespace oopse {
     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;