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Comparing trunk/src/math/Triangle.hpp (file contents):
Revision 1325 by chuckv, Fri Dec 5 16:20:39 2008 UTC vs.
Revision 1404 by chuckv, Fri Jan 15 20:46:49 2010 UTC

# Line 1 | Line 1
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.
# Line 37 | Line 28
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.hpp
42   *
43 < *  Purpose: Provide basic triangle class for oopse. Hates Particle class.
43 > *  Purpose: Provide basic triangle class for OpenMD. Hates Particle class.
44   *
45   *  Created by Charles F. Vardeman II on 29 July 2008.
46   *  @author  Charles F. Vardeman II
47 < *  @version $Id: Triangle.hpp,v 1.4 2008-12-05 16:20:39 chuckv Exp $
47 > *  @version $Id: Triangle.hpp,v 1.6 2009-11-25 20:02:01 gezelter Exp $
48   *
49   */
50  
# Line 53 | Line 53
53   #define MATH_FACET_HPP
54  
55   #include "math/Vector3.hpp"
56 + #include "math/SquareMatrix3.hpp"
57   #include "config.h"
58   #include "primitives/StuntDouble.hpp"
59  
60   #include <vector>
61  
62  
63 < namespace oopse {
63 > namespace OpenMD {
64  
65   /**
66     * @class Triangle
67     *
68 <   * Triangle provides geometric data to oopse. Triangle includes
68 >   * Triangle provides geometric data to OpenMD. Triangle includes
69     * information about the normal, centroid and the atoms
70     * that belong to this triangle.
71     */
# Line 78 | Line 79 | namespace oopse {
79        normal_ = normal;
80        HaveNormal_ = true;
81      }
82 +    void setUnitNormal(Vector3d normal) {
83 +      unitnormal_ = normal;
84 +      HaveUnitNormal_ = true;
85 +    }
86  
87      void addVertices(Vector3d P1, Vector3d P2, Vector3d P3);
88  
# Line 99 | Line 104 | namespace oopse {
104          return computeNormal();
105        }
106      }
107 +   Vector3d getUnitNormal() {
108 +      if (HaveUnitNormal_) {
109 +        return unitnormal_;
110 +      } else {
111 +        return computeUnitNormal();
112 +      }
113 +    }
114      
115      RealType getArea() {
116        if(HaveArea_){
# Line 111 | Line 123 | namespace oopse {
123      RealType computeArea();
124      Vector3d computeNormal();
125      Vector3d computeCentroid();
126 +    Vector3d computeUnitNormal();
127  
128      void setCentroid(Vector3d centroid) {
129        centroid_ = centroid;
# Line 180 | Line 193 | namespace oopse {
193        return a1 * b1 * c1 / sqrt(t1 * t2 * t3 * t4);
194      }
195        
196 +    Mat3x3d computeHydrodynamicTensor(RealType viscosity);
197  
198  
199    private:
200 +    Mat3x3d hydro_tensor(const Vector3d& ri, const Vector3d& rj0, const Vector3d& rj1, const Vector3d& rj2,RealType s, RealType viscosity);
201 +    
202      /* Local Indentity of vertex atoms in pos array*/
203      std::vector <StuntDouble*> vertexSD_;
204      Vector3d normal_;
205 +    Vector3d unitnormal_;
206      Vector3d centroid_;
207      Vector3d vertices_[3];
208 <    RealType area_;
208 >    RealType area_;    
209      RealType mass_;
210      Vector3d facetVelocity_;
211      //Length of triangle sides
# Line 196 | Line 213 | namespace oopse {
213      RealType alpha_,beta_,gamma_;
214      bool HaveArea_;
215      bool HaveNormal_;
216 +    bool HaveUnitNormal_;
217      bool HaveCentroid_;
218      
219    }; // End class Triangle
220      
221      
222  
223 < } //End Namespace oopse
223 > } //end namespace OpenMD
224  
225  
226  

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