--- trunk/src/math/Triangle.hpp	2008/12/05 16:20:39	1325
+++ trunk/src/math/Triangle.hpp	2012/08/31 17:29:35	1792
@@ -1,23 +1,14 @@
-/* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved.
+/* Copyright (c) 2008, 2010 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
  * non-exclusive, royalty free, license to use, modify and
  * 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.
@@ -37,14 +28,23 @@
  * 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).
+ * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
  *
  *  Triangle.hpp
  *
- *  Purpose: Provide basic triangle class for oopse. Hates Particle class.
+ *  Purpose: Provide basic triangle class for OpenMD. Hates Particle class.
  *
  *  Created by Charles F. Vardeman II on 29 July 2008.
  *  @author  Charles F. Vardeman II
- *  @version $Id: Triangle.hpp,v 1.4 2008-12-05 16:20:39 chuckv Exp $
+ *  @version $Id$
  *
  */
 
@@ -53,18 +53,19 @@
 #define MATH_FACET_HPP
 
 #include "math/Vector3.hpp"
+#include "math/SquareMatrix3.hpp"
 #include "config.h"
 #include "primitives/StuntDouble.hpp"
 
 #include <vector>
 
 
-namespace oopse {
+namespace OpenMD {
 
 /**
    * @class Triangle
    *
-   * Triangle provides geometric data to oopse. Triangle includes
+   * Triangle provides geometric data to OpenMD. Triangle includes
    * information about the normal, centroid and the atoms
    * that belong to this triangle.
    */
@@ -78,6 +79,10 @@ namespace oopse {
       normal_ = normal;
       HaveNormal_ = true;
     }
+    void setUnitNormal(Vector3d normal) {
+      unitnormal_ = normal;
+      HaveUnitNormal_ = true;
+    }
 
     void addVertices(Vector3d P1, Vector3d P2, Vector3d P3);
 
@@ -99,6 +104,13 @@ namespace oopse {
 	return computeNormal();
       }
     }
+   Vector3d getUnitNormal() {
+      if (HaveUnitNormal_) {
+	return unitnormal_;
+      } else {
+	return computeUnitNormal();
+      }
+    }
     
     RealType getArea() { 
       if(HaveArea_){
@@ -111,6 +123,7 @@ namespace oopse {
     RealType computeArea();
     Vector3d computeNormal();
     Vector3d computeCentroid();
+    Vector3d computeUnitNormal();
 
     void setCentroid(Vector3d centroid) { 
       centroid_ = centroid;
@@ -176,19 +189,22 @@ namespace oopse {
       RealType t2 = -a1 + b1 + c1;
       RealType t3 =  a1 - b1 + c1;
       RealType t4 =  a1 + b1 - c1;
-      RealType junk = t1*t2*t3*t4;
       return a1 * b1 * c1 / sqrt(t1 * t2 * t3 * t4);
     }
       
+    Mat3x3d computeHydrodynamicTensor(RealType viscosity);
 
 
   private:
+    Mat3x3d hydro_tensor(const Vector3d& ri, const Vector3d& rj0, const Vector3d& rj1, const Vector3d& rj2,RealType s, RealType viscosity);
+    
     /* Local Indentity of vertex atoms in pos array*/
     std::vector <StuntDouble*> vertexSD_;
     Vector3d normal_;
+    Vector3d unitnormal_;
     Vector3d centroid_;
     Vector3d vertices_[3];
-    RealType area_;
+    RealType area_;    
     RealType mass_;
     Vector3d facetVelocity_;
     //Length of triangle sides
@@ -196,13 +212,14 @@ namespace oopse {
     RealType alpha_,beta_,gamma_;
     bool HaveArea_;
     bool HaveNormal_;
+    bool HaveUnitNormal_;
     bool HaveCentroid_;
     
   }; // End class Triangle
     
     
 
-} //End Namespace oopse
+} //end namespace OpenMD