--- trunk/src/hydrodynamics/Ellipsoid.hpp	2006/06/05 18:24:45	981
+++ branches/development/src/hydrodynamics/Ellipsoid.hpp	2013/02/20 15:39:39	1850
@@ -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.
@@ -37,31 +28,58 @@
  * 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).
  */
 
 #ifndef HYDRODYNAMICS_ELLIPSOID_HPP
 #define HYDRODYNAMICS_ELLIPSOID_HPP
 #include "hydrodynamics/Shape.hpp"
 #include "math/SquareMatrix3.hpp"
-namespace oopse {
+namespace OpenMD {
   
-  /** @class Ellipsoid */
+  /** @class Ellipsoid 
+   *
+   * An ellipsoid in OpenMD is restricted to having two equal
+   * equatorial semi-axes.  OpenMD treats the "special" axis as the
+   * z-coordinate in the body fixed reference frame.  That is:
+   *
+   *   z^2 / a^2  +  (x^2 + y^2) / b^2   = 1
+   *
+   * If a >= b, the ellipsoid is a prolate spheroid, and if a < b, 
+   * the ellipsoid is oblate.  Ellipsoids are specified in the constructor 
+   * using an axial length (a), and a equatorial length (b).  A Vector3d 
+   * can be used to position the center of the ellipsoid, and a rotation 
+   * matrix can also be used to orient the ellipsoid to a preferred lab-fixed
+   * coordinate frame.
+   */
   class Ellipsoid : public Shape{
   public:
-    Ellipsoid(Vector3d origin, RealType rMajor, RealType rMinor, Mat3x3d rotMat);
+    Ellipsoid(Vector3d origin, RealType rAxial, RealType rEquatorial, Mat3x3d rotMat);
     virtual bool isInterior(Vector3d pos);
     virtual std::pair<Vector3d, Vector3d> getBoundingBox();
     virtual bool hasAnalyticalSolution() {return true;}
     
     virtual HydroProp* getHydroProp(RealType viscosity, RealType temperature);
     
-    
+    RealType getRAxial() {return rAxial_;}
+    RealType getREquatorial() {return rEquatorial_;}
     RealType getRMajor() {return rMajor_;}
     RealType getRMinor() {return rMinor_;}
     
   private:
     
     Vector3d origin_;
+    RealType rAxial_;
+    RealType rEquatorial_;
     RealType rMajor_;
     RealType rMinor_;
     Mat3x3d rotMat_;