--- trunk/src/math/SquareMatrix3.hpp	2009/09/07 16:31:51	1360
+++ trunk/src/math/SquareMatrix3.hpp	2014/05/31 22:35:05	2000
@@ -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, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 /**
@@ -47,12 +48,14 @@
  */
 #ifndef MATH_SQUAREMATRIX3_HPP
 #define  MATH_SQUAREMATRIX3_HPP
+#include "config.h"
+#include <cmath>
 #include <vector>
 #include "Quaternion.hpp"
 #include "SquareMatrix.hpp"
 #include "Vector3.hpp"
 #include "utils/NumericConstant.hpp"
-namespace oopse {
+namespace OpenMD {
 
   template<typename Real>
   class SquareMatrix3 : public SquareMatrix<Real, 3> {
@@ -109,6 +112,7 @@ namespace oopse {
       return *this;
     }
 
+    
     /**
      * Sets this matrix to a rotation matrix by three euler angles
      * @ param euler
@@ -121,7 +125,7 @@ namespace oopse {
      * Sets this matrix to a rotation matrix by three euler angles
      * @param phi
      * @param theta
-     * @psi theta
+     * @param psi
      */
     void setupRotMat(Real phi, Real theta, Real psi) {
       Real sphi, stheta, spsi;
@@ -187,7 +191,6 @@ namespace oopse {
     }
 
 
-
     /**
      * Returns the quaternion from this rotation matrix
      * @return the quaternion from this rotation matrix
@@ -321,12 +324,12 @@ namespace oopse {
     SquareMatrix3<Real>  inverse() const {
       SquareMatrix3<Real> m;
       RealType det = determinant();
-      if (fabs(det) <= oopse::epsilon) {
+      if (fabs(det) <= OpenMD::epsilon) {
 	//"The method was called on a matrix with |determinant| <= 1e-6.",
 	//"This is a runtime or a programming error in your application.");
         std::vector<int> zeroDiagElementIndex;
         for (int i =0; i < 3; ++i) {
-            if (fabs(this->data_[i][i]) <= oopse::epsilon) {
+            if (fabs(this->data_[i][i]) <= OpenMD::epsilon) {
                 zeroDiagElementIndex.push_back(i);
             }
         }
@@ -349,8 +352,8 @@ namespace oopse {
       
 /*
         for(std::vector<int>::iterator iter = zeroDiagElementIndex.begin(); iter != zeroDiagElementIndex.end() ++iter) {
-            if (this->data_[*iter][0] > oopse::epsilon || this->data_[*iter][1] ||this->data_[*iter][2] ||
-                this->data_[0][*iter] > oopse::epsilon || this->data_[1][*iter] ||this->data_[2][*iter] ) {
+            if (this->data_[*iter][0] > OpenMD::epsilon || this->data_[*iter][1] ||this->data_[*iter][2] ||
+                this->data_[0][*iter] > OpenMD::epsilon || this->data_[1][*iter] ||this->data_[2][*iter] ) {
                 std::cout << "can not inverse matrix" << std::endl;
             }
         }
@@ -417,7 +420,7 @@ namespace oopse {
     Vector3<Real> v_maxI, v_k, v_j;
 
     // diagonalize using Jacobi
-    jacobi(a, w, v);
+    SquareMatrix3<Real>::jacobi(a, w, v);
     // if all the eigenvalues are the same, return identity matrix
     if (w[0] == w[1] && w[0] == w[2] ) {
       v = SquareMatrix3<Real>::identity();
@@ -566,6 +569,9 @@ namespace oopse {
   typedef SquareMatrix3<RealType> Mat3x3d;
   typedef SquareMatrix3<RealType> RotMat3x3d;
 
-} //namespace oopse
+  const Mat3x3d M3Zero(0.0);
+
+
+} //namespace OpenMD
 #endif // MATH_SQUAREMATRIX_HPP