--- trunk/src/math/RectMatrix.hpp	2005/04/15 22:04:00	507
+++ trunk/src/math/RectMatrix.hpp	2009/11/25 20:02:06	1390
@@ -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 +28,15 @@
  * 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]  Vardeman & Gezelter, in progress (2009).                        
  */
  
 /**
@@ -52,7 +52,7 @@
 #include <cmath>
 #include "Vector.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   /**
    * @class RectMatrix RectMatrix.hpp "math/RectMatrix.hpp"
@@ -151,7 +151,7 @@ namespace oopse {
     Vector<Real, Row> getRow(unsigned int row) {
       Vector<Real, Row> v;
 
-      for (unsigned int i = 0; i < Row; i++)
+      for (unsigned int i = 0; i < Col; i++)
 	v[i] = this->data_[row][i];
 
       return v;
@@ -164,7 +164,7 @@ namespace oopse {
      */                
     void setRow(unsigned int row, const Vector<Real, Row>& v) {
 
-      for (unsigned int i = 0; i < Row; i++)
+      for (unsigned int i = 0; i < Col; i++)
 	this->data_[row][i] = v[i];
     }
 
@@ -176,7 +176,7 @@ namespace oopse {
     Vector<Real, Col> getColumn(unsigned int col) {
       Vector<Real, Col> v;
 
-      for (unsigned int j = 0; j < Col; j++)
+      for (unsigned int j = 0; j < Row; j++)
 	v[j] = this->data_[j][col];
 
       return v;
@@ -189,7 +189,7 @@ namespace oopse {
      */                
     void setColumn(unsigned int col, const Vector<Real, Col>& v){
 
-      for (unsigned int j = 0; j < Col; j++)
+      for (unsigned int j = 0; j < Row; j++)
 	this->data_[j][col] = v[j];
     }         
 
@@ -389,7 +389,30 @@ namespace oopse {
 
       return result;
     }
-        
+
+    template<class MatrixType>
+    void setSubMatrix(unsigned int beginRow, unsigned int beginCol, const MatrixType& m) {
+        assert(beginRow + m.getNRow() -1 <= getNRow());
+        assert(beginCol + m.getNCol() -1 <= getNCol());
+
+        for (unsigned int i = 0; i < m.getNRow(); ++i)
+            for (unsigned int j = 0; j < m.getNCol(); ++j)
+                this->data_[beginRow+i][beginCol+j] = m(i, j);
+    }
+
+    template<class MatrixType>
+    void getSubMatrix(unsigned int beginRow, unsigned int beginCol, MatrixType& m) {
+        assert(beginRow + m.getNRow() -1 <= getNRow());
+        assert(beginCol + m.getNCol() - 1 <= getNCol());
+
+        for (unsigned int i = 0; i < m.getNRow(); ++i)
+            for (unsigned int j = 0; j < m.getNCol(); ++j)
+                m(i, j) = this->data_[beginRow+i][beginCol+j];
+    }
+    
+    unsigned int getNRow() const {return Row;}
+    unsigned int getNCol() const {return Col;}        
+
   protected:
     Real data_[Row][Col];
   };