| 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 | 
| 5 |  | * redistribute this software in source and binary code form, provided | 
| 6 |  | * that the following conditions are met: | 
| 7 |  | * | 
| 8 | < | * 1. Acknowledgement of the program authors must be made in any | 
| 9 | < | *    publication of scientific results based in part on use of the | 
| 10 | < | *    program.  An acceptable form of acknowledgement is citation of | 
| 11 | < | *    the article in which the program was described (Matthew | 
| 12 | < | *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher | 
| 13 | < | *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented | 
| 14 | < | *    Parallel Simulation Engine for Molecular Dynamics," | 
| 15 | < | *    J. Comput. Chem. 26, pp. 252-271 (2005)) | 
| 16 | < | * | 
| 17 | < | * 2. Redistributions of source code must retain the above copyright | 
| 8 | > | * 1. Redistributions of source code must retain the above copyright | 
| 9 |  | *    notice, this list of conditions and the following disclaimer. | 
| 10 |  | * | 
| 11 | < | * 3. Redistributions in binary form must reproduce the above copyright | 
| 11 | > | * 2. Redistributions in binary form must reproduce the above copyright | 
| 12 |  | *    notice, this list of conditions and the following disclaimer in the | 
| 13 |  | *    documentation and/or other materials provided with the | 
| 14 |  | *    distribution. | 
| 28 |  | * University of Notre Dame has been advised of the possibility of | 
| 29 |  | * such damages. | 
| 30 |  | * | 
| 31 | + | * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your | 
| 32 | + | * research, please cite the appropriate papers when you publish your | 
| 33 | + | * work.  Good starting points are: | 
| 34 | + | * | 
| 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). | 
| 39 |  | * | 
| 40 | + | * | 
| 41 |  | *  Triangle.cpp | 
| 42 |  | * | 
| 43 | < | *  Purpose: Provide basic triangle object for OOPSE | 
| 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 1.3 2009-05-13 22:27:29 gezelter Exp $ | 
| 47 | > | *  @version $Id: Triangle.cpp,v 1.4 2009-11-25 20:02:01 gezelter Exp $ | 
| 48 |  | * | 
| 49 |  | */ | 
| 50 |  |  | 
| 51 |  | #include "math/Triangle.hpp" | 
| 52 |  |  | 
| 53 | < | using namespace oopse; | 
| 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; |