| 1 | < | /* Copyright (c) 2008 The University of Notre Dame. All Rights Reserved. | 
| 1 | > | /* Copyright (c) 2008, 2010 The University of Notre Dame. All Rights Reserved. | 
| 2 |  | * | 
| 3 |  | * The University of Notre Dame grants you ("Licensee") a | 
| 4 |  | * non-exclusive, royalty free, license to use, modify and | 
| 35 |  | * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). | 
| 36 |  | * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). | 
| 37 |  | * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). | 
| 38 | < | * [4]  Vardeman & Gezelter, in progress (2009). | 
| 38 | > | * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010). | 
| 39 | > | * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * | 
| 40 |  | * | 
| 40 | – | * | 
| 41 |  | *  Triangle.cpp | 
| 42 |  | * | 
| 43 |  | *  Purpose: Provide basic triangle object for OpenMD | 
| 44 |  | * | 
| 45 |  | *  Created by Charles F. Vardeman II on 29 July 2008. | 
| 46 |  | *  @author  Charles F. Vardeman II | 
| 47 | < | *  @version $Id: Triangle.cpp,v 1.4 2009-11-25 20:02:01 gezelter Exp $ | 
| 47 | > | *  @version $Id$ | 
| 48 |  | * | 
| 49 |  | */ | 
| 50 |  |  | 
| 53 |  | using namespace OpenMD; | 
| 54 |  |  | 
| 55 |  |  | 
| 56 | < | Triangle::Triangle() : HaveNormal_(false), HaveCentroid_(false), | 
| 56 | > | Triangle::Triangle() : HaveNormal_(false), HaveUnitNormal_(false), HaveCentroid_(false), | 
| 57 |  | HaveArea_(false), area_(0.0), normal_(V3Zero), | 
| 58 |  | centroid_(V3Zero), facetVelocity_(V3Zero), mass_(0.0), | 
| 59 |  | a_(V3Zero), b_(V3Zero), c_(V3Zero){ | 
| 76 |  | area_ = getNormal().length() * 0.5; | 
| 77 |  | return area_; | 
| 78 |  | } | 
| 79 | < |  | 
| 79 | > | // This should return the normal for our calculations. | 
| 80 |  | Vector3d Triangle::computeNormal(){ | 
| 81 |  | HaveNormal_ = true; | 
| 82 |  | normal_ = cross(a_,b_); | 
| 83 |  | return normal_; | 
| 84 |  | } | 
| 85 | + | // This should return the normal for our calculations. | 
| 86 | + | Vector3d Triangle::computeUnitNormal(){ | 
| 87 | + | HaveUnitNormal_ = true; | 
| 88 | + | unitnormal_ = cross(a_,b_); | 
| 89 | + | unitnormal_.normalize(); | 
| 90 | + | return unitnormal_; | 
| 91 | + | } | 
| 92 |  |  | 
| 93 |  | Vector3d Triangle::computeCentroid(){ | 
| 94 |  | HaveCentroid_ = true; | 
| 95 | < | centroid_ = (vertices_[0] + vertices_[1] + vertices_[2])/3.0; | 
| 95 | > | centroid_ = (vertices_[0] + vertices_[1] + vertices_[2])/RealType(3.0); | 
| 96 |  | return centroid_; | 
| 97 |  | } | 
| 98 |  |  | 
| 126 |  | const Vector3d& rj2, | 
| 127 |  | RealType s, RealType viscosity){ | 
| 128 |  |  | 
| 129 | < | Vector3d v2 = (rj0 + rj1 + rj2)/3.0;  // sub-centroid | 
| 129 | > | Vector3d v2 = (rj0 + rj1 + rj2) / RealType(3.0);  // sub-centroid | 
| 130 |  | Vector3d dr = ri - v2;                // real centroid to sub-centroid | 
| 131 | < | RealType l2 = 1.0/dr.lengthSquare(); | 
| 131 | > | RealType l2 = RealType(1.0)/dr.lengthSquare(); | 
| 132 |  |  | 
| 133 |  | Mat3x3d G; | 
| 134 | < | G = (SquareMatrix3<RealType>::identity() + outProduct(dr,dr)*l2)*sqrt(l2); | 
| 134 | > | G = (SquareMatrix3<RealType>::identity() + outProduct(dr,dr)*l2)*RealType(sqrt(l2)); | 
| 135 |  |  | 
| 136 |  | G *= 0.125/3.14159285358979; | 
| 137 |  | G *= s/viscosity; |