--- trunk/src/math/Polynomial.hpp	2009/09/08 15:48:33	1362
+++ trunk/src/math/Polynomial.hpp	2013/06/16 15:15:42	1879
@@ -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).
  */
  
 /**
@@ -57,7 +58,7 @@
 #include "config.h"
 #include "math/Eigenvalue.hpp"
 
-namespace oopse {
+namespace OpenMD {
   
   template<typename Real> Real fastpow(Real x, int N) {
     Real result(1); //or 1.0?
@@ -158,7 +159,7 @@ namespace oopse {
      * this Polynomial.
      * @return the coefficient associated with the given power for
      * this Polynomial
-     * @exponent exponent of any term in this Polynomial
+     * @param exponent exponent of any term in this Polynomial
      */
     Real getCoefficient(ExponentType exponent) {
       iterator i = polyPairMap_.find(exponent);
@@ -272,8 +273,8 @@ namespace oopse {
      * Returns the first derivative of this polynomial.
      * @return the first derivative of this polynomial
      */
-    PolynomialType & getDerivative() {
-      Polynomial<Real> p();
+    PolynomialType* getDerivative() {
+      Polynomial<Real>* p = new Polynomial<Real>();
       
       typename Polynomial<Real>::const_iterator i;
       ExponentType exponent;
@@ -282,7 +283,7 @@ namespace oopse {
       for (i =  this->begin(); i  != this->end(); ++i) {
         exponent = i->first;
         coefficient = i->second;
-        p.setCoefficient(exponent-1, coefficient * exponent);
+        p->setCoefficient(exponent-1, coefficient * exponent);
       }
     
       return p;
@@ -337,7 +338,6 @@ namespace oopse {
         roots.push_back( -fC0 / fC1);
         return roots;
       }
-        break;      
       case 2: {
         Real fC2 = getCoefficient(2);
         Real fC1 = getCoefficient(1);
@@ -346,13 +346,13 @@ namespace oopse {
         if (abs(fDiscr) <= fEpsilon) {
           fDiscr = (Real)0.0;
         }
-      
+        
         if (fDiscr < (Real)0.0) {  // complex roots only
           return roots;
         }
-      
+        
         Real fTmp = ((Real)0.5)/fC2;
-      
+        
         if (fDiscr > (Real)0.0) { // 2 real roots
           fDiscr = sqrt(fDiscr);
           roots.push_back(fTmp*(-fC1 - fDiscr));
@@ -361,9 +361,7 @@ namespace oopse {
           roots.push_back(-fTmp * fC1);  // 1 real root
         }
       }
-        return roots;
-        break;
-      
+        return roots;      
       case 3: {
         Real fC3 = getCoefficient(3);
         Real fC2 = getCoefficient(2);
@@ -430,7 +428,6 @@ namespace oopse {
         }
       }
         return roots;
-        break;
       case 4: {
         Real fC4 = getCoefficient(4);
         Real fC3 = getCoefficient(3);
@@ -516,7 +513,6 @@ namespace oopse {
         }
       }
         return roots;
-        break;
       default: {
         DynamicRectMatrix<Real> companion = CreateCompanion();
         JAMA::Eigenvalue<Real> eig(companion);
@@ -530,12 +526,9 @@ namespace oopse {
         }      
       }
         return roots;
-        break;
       }
-
-      return roots; // should be empty if you got here
     }
-   
+    
   private:
         
     PolynomialPairMap polyPairMap_;
@@ -629,8 +622,8 @@ namespace oopse {
    * @return the first derivative of this polynomial
    */
   template<typename Real>
-  Polynomial<Real> getDerivative(const Polynomial<Real>& p1) {
-    Polynomial<Real> p();
+  Polynomial<Real> * getDerivative(const Polynomial<Real>& p1) {
+    Polynomial<Real> * p = new Polynomial<Real>();
     
     typename Polynomial<Real>::const_iterator i;
     int exponent;
@@ -639,7 +632,7 @@ namespace oopse {
     for (i =  p1.begin(); i  != p1.end(); ++i) {
       exponent = i->first;
       coefficient = i->second;
-      p.setCoefficient(exponent-1, coefficient * exponent);
+      p->setCoefficient(exponent-1, coefficient * exponent);
     }
     
     return p;
@@ -675,5 +668,5 @@ namespace oopse {
 
   typedef Polynomial<RealType> DoublePolynomial;
 
-} //end namespace oopse
+} //end namespace OpenMD
 #endif //MATH_POLYNOMIAL_HPP