--- trunk/src/math/Triangle.hpp	2008/10/20 19:36:32	1307
+++ trunk/src/math/Triangle.hpp	2013/06/16 15:15:42	1879
@@ -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, 234107 (2008).          
+ * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
  *
  *  Triangle.hpp
  *
- *  Purpose: Provide facets from hull to oopse
+ *  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 1.2 2008-10-20 19:36:32 chuckv Exp $
+ *  @version $Id$
  *
  */
 
@@ -53,57 +53,91 @@
 #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.
    */
   class Triangle {
 
   public:
-    Triangle(){};
+    Triangle();
     virtual ~Triangle() { };
 
     void setNormal(Vector3d normal) {
       normal_ = normal;
+      HaveNormal_ = true;
     }
+    void setUnitNormal(Vector3d normal) {
+      unitnormal_ = normal;
+      HaveUnitNormal_ = true;
+    }
 
-    void addVertex(StuntDouble* thisSD){
+    void addVertices(Vector3d P1, Vector3d P2, Vector3d P3);
+
+    void addVertexSD(StuntDouble* thisSD){
       vertexSD_.push_back(thisSD);
     }
-    
+
     std::vector<StuntDouble*> getVertices(){return vertexSD_;}
 
     void setArea(RealType area) {
       area_ = area;
+      HaveArea_ = true;
     }
     
-    Vector3d getNormal() { 
-      return normal_;
+    Vector3d getNormal() {
+      if (HaveNormal_) {
+	return normal_;
+      } else {
+	return computeNormal();
+      }
     }
+   Vector3d getUnitNormal() {
+      if (HaveUnitNormal_) {
+	return unitnormal_;
+      } else {
+	return computeUnitNormal();
+      }
+    }
     
     RealType getArea() { 
-      return area_;
+      if(HaveArea_){
+	return area_;
+      }else{
+	return computeArea();
+      }
     }
 
+    RealType computeArea();
+    Vector3d computeNormal();
+    Vector3d computeCentroid();
+    Vector3d computeUnitNormal();
+
     void setCentroid(Vector3d centroid) { 
       centroid_ = centroid;
+      HaveCentroid_ = true;
     }
 
-    Vector3d getCentroid() { 
-      return centroid_;
+    Vector3d getCentroid() {
+      if (HaveCentroid_) {
+	return centroid_;
+      } else {
+	return computeCentroid();
+      }
     }
-
+    
     Vector3d getFacetVelocity(){
       return facetVelocity_;
     }
@@ -112,20 +146,80 @@ namespace oopse {
       facetVelocity_ = facetVelocity;
     }
 
+    void setFacetMass(RealType mass){
+      mass_ = mass;
+    }
 
+    RealType getFacetMass(){
+      return mass_;
+    }
+
+    RealType a(){
+      return a_.length();
+    }
+
+    RealType b(){
+      return b_.length();
+    }
+
+    RealType c(){
+      return c_.length();
+    }
+
+    RealType getHydroLength() {
+      RealType a1 = a();
+      RealType b1 = b();
+      RealType c1 = c();
+      RealType t1 =  a1 + b1 + c1;
+      RealType t4 =  a1 + b1 - c1;
+
+      return 32.0 * c1 / log(t1*t1/t4/t4);
+    }
+
+
+    RealType getIncircleRadius() {
+      return 2.0 * getArea() / (a() + b() + c());
+    }
+
+    RealType getCircumcircleRadius() {
+      RealType a1 = a();
+      RealType b1 = b();
+      RealType c1 = c();
+      RealType t1 =  a1 + b1 + c1;
+      RealType t2 = -a1 + b1 + c1;
+      RealType t3 =  a1 - b1 + c1;
+      RealType t4 =  a1 + b1 - c1;
+      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_;
-    RealType area_;
+    Vector3d vertices_[3];
+    RealType area_;    
+    RealType mass_;
     Vector3d facetVelocity_;
+    //Length of triangle sides
+    Vector3d a_,b_,c_;
+    RealType alpha_,beta_,gamma_;
+    bool HaveArea_;
+    bool HaveNormal_;
+    bool HaveUnitNormal_;
+    bool HaveCentroid_;
     
   }; // End class Triangle
     
     
 
-} //End Namespace oopse
+} //end namespace OpenMD