--- trunk/src/math/Triangle.cpp	2009/05/13 22:27:29	1344
+++ trunk/src/math/Triangle.cpp	2015/03/07 21:41:51	2071
@@ -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.
@@ -37,27 +28,36 @@
  * 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.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 1.3 2009-05-13 22:27:29 gezelter 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() :  normal_(V3Zero), centroid_(V3Zero), area_(0.0), 
+			mass_(0.0), facetVelocity_(V3Zero), 
+			a_(V3Zero), b_(V3Zero), c_(V3Zero),
+			HaveArea_(false), HaveNormal_(false), 
+			HaveUnitNormal_(false), HaveCentroid_(false) {}
 
 void Triangle::addVertices(Vector3d P1, Vector3d P2, Vector3d P3){
   vertices_[0] = P1;
@@ -76,16 +76,23 @@ 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;
+  centroid_ = (vertices_[0] + vertices_[1] + vertices_[2])/RealType(3.0);
   return centroid_;
 }
 
@@ -119,12 +126,12 @@ Mat3x3d Triangle::hydro_tensor(
                                const Vector3d& rj2,
                                RealType s, RealType viscosity){
   
-  Vector3d v2 = (rj0 + rj1 + rj2)/3.0;  // sub-centroid
+  Vector3d v2 = (rj0 + rj1 + rj2) / RealType(3.0);  // sub-centroid
   Vector3d dr = ri - v2;                // real centroid to sub-centroid
-  RealType l2 = 1.0/dr.lengthSquare();  
+  RealType l2 = RealType(1.0)/dr.lengthSquare();  
  
   Mat3x3d G;
-  G = (SquareMatrix3<RealType>::identity() + outProduct(dr,dr)*l2)*sqrt(l2);
+  G = (SquareMatrix3<RealType>::identity() + outProduct(dr,dr)*l2)*RealType(sqrt(l2));
 
   G *= 0.125/3.14159285358979;
   G *= s/viscosity;