--- trunk/src/math/Triangle.cpp	2008/12/05 16:20:39	1325
+++ branches/development/src/math/Triangle.cpp	2010/07/09 23:08:25	1465
@@ -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.
@@ -37,25 +28,35 @@
  * 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]  Vardeman & Gezelter, in progress (2009).                        
  *
+ *
  *  Triangle.cpp
  *
- *  Purpose: Provide basic triangle object for OOPSE
+ *  Purpose: Provide basic triangle object for OpenMD
  *
  *  Created by Charles F. Vardeman II on 29 July 2008.
  *  @author  Charles F. Vardeman II
- *  @version $Id: Triangle.cpp,v 1.2 2008-12-05 16:20:38 chuckv Exp $
+ *  @version $Id$
  *
  */
 
 #include "math/Triangle.hpp"
 
-using namespace oopse;
+using namespace OpenMD;
 
 
-Triangle::Triangle() : HaveNormal_(false), HaveCentroid_(false),HaveArea_(false), area_(0.0), normal_(V3Zero), 
-		       centroid_(V3Zero),facetVelocity_(V3Zero), mass_(0.0),
-		       a_(V3Zero),b_(V3Zero),c_(V3Zero){
+Triangle::Triangle() : HaveNormal_(false), HaveUnitNormal_(false), HaveCentroid_(false),
+                       HaveArea_(false), area_(0.0), normal_(V3Zero), 
+		       centroid_(V3Zero), facetVelocity_(V3Zero), mass_(0.0),
+		       a_(V3Zero), b_(V3Zero), c_(V3Zero){
 }
 
 void Triangle::addVertices(Vector3d P1, Vector3d P2, Vector3d P3){
@@ -75,15 +76,64 @@ RealType Triangle::computeArea(){
   area_ = getNormal().length() * 0.5;
   return area_;
 }
-
+// This should return the normal for our calculations.
 Vector3d Triangle::computeNormal(){
   HaveNormal_ = true;
   normal_ = cross(a_,b_);
   return normal_;
 }
+// This should return the normal for our calculations.
+Vector3d Triangle::computeUnitNormal(){
+  HaveUnitNormal_ = true;
+  unitnormal_ = cross(a_,b_);
+  unitnormal_.normalize();
+  return unitnormal_;
+}
 
 Vector3d Triangle::computeCentroid(){
   HaveCentroid_ = true;
   centroid_ = (vertices_[0] + vertices_[1] + vertices_[2])/3.0;
   return centroid_;
 }
+
+
+Mat3x3d Triangle::computeHydrodynamicTensor(RealType viscosity) {
+  
+  Vector3d u0 = -a_;
+  Vector3d v0 = centroid_ - vertices_[0];
+  RealType s0 = 0.5*cross(u0,v0).length();
+  
+  Vector3d u1 = -c_;
+  Vector3d v1 = centroid_ - vertices_[1];
+  RealType s1 = 0.5*cross(u1,v1).length();
+  
+  Vector3d u2 = b_;
+  Vector3d v2 = centroid_ - vertices_[2];
+  RealType s2 = 0.5*cross(u2,v2).length();
+  
+  Mat3x3d H;
+  H = hydro_tensor(centroid_,centroid_,vertices_[1],vertices_[0],s0,viscosity)+
+    hydro_tensor(centroid_,centroid_,vertices_[1],vertices_[2],s1,viscosity)+
+    hydro_tensor(centroid_,centroid_,vertices_[2],vertices_[0],s2,viscosity);
+
+  return H.inverse();
+}
+
+Mat3x3d Triangle::hydro_tensor(
+                               const Vector3d& ri,
+                               const Vector3d& rj0,
+                               const Vector3d& rj1,
+                               const Vector3d& rj2,
+                               RealType s, RealType viscosity){
+  
+  Vector3d v2 = (rj0 + rj1 + rj2)/3.0;  // sub-centroid
+  Vector3d dr = ri - v2;                // real centroid to sub-centroid
+  RealType l2 = 1.0/dr.lengthSquare();  
+ 
+  Mat3x3d G;
+  G = (SquareMatrix3<RealType>::identity() + outProduct(dr,dr)*l2)*sqrt(l2);
+
+  G *= 0.125/3.14159285358979;
+  G *= s/viscosity;
+  return G;
+}