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Comparing trunk/src/math/Triangle.cpp (file contents):
Revision 1316 by chuckv, Fri Nov 14 15:44:34 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.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 1.1 2008-11-14 15:44:34 chuckv 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),HaveArea_(false), area_(0.0), normal_(V3Zero),
57 <                       centroid_(V3Zero),facetVelocity_(V3Zero), mass_(0.0),
58 <                       a_(V3Zero),b_(V3Zero),c_(V3Zero){
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){
60   }
61  
62   void Triangle::addVertices(Vector3d P1, Vector3d P2, Vector3d P3){
# Line 66 | Line 67 | void Triangle::addVertices(Vector3d P1, Vector3d P2, V
67    // Compute some quantites like a,b,c
68    a_ = P1-P2;
69    b_ = P1-P3;
70 <  c_ = P1-P3;  
70 >  c_ = P2-P3;  
71   }
72  
73  
# Line 75 | Line 76 | RealType Triangle::computeArea(){
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;
96    return centroid_;
97   }
98 +
99 +
100 + Mat3x3d Triangle::computeHydrodynamicTensor(RealType viscosity) {
101 +  
102 +  Vector3d u0 = -a_;
103 +  Vector3d v0 = centroid_ - vertices_[0];
104 +  RealType s0 = 0.5*cross(u0,v0).length();
105 +  
106 +  Vector3d u1 = -c_;
107 +  Vector3d v1 = centroid_ - vertices_[1];
108 +  RealType s1 = 0.5*cross(u1,v1).length();
109 +  
110 +  Vector3d u2 = b_;
111 +  Vector3d v2 = centroid_ - vertices_[2];
112 +  RealType s2 = 0.5*cross(u2,v2).length();
113 +  
114 +  Mat3x3d H;
115 +  H = hydro_tensor(centroid_,centroid_,vertices_[1],vertices_[0],s0,viscosity)+
116 +    hydro_tensor(centroid_,centroid_,vertices_[1],vertices_[2],s1,viscosity)+
117 +    hydro_tensor(centroid_,centroid_,vertices_[2],vertices_[0],s2,viscosity);
118 +
119 +  return H.inverse();
120 + }
121 +
122 + Mat3x3d Triangle::hydro_tensor(
123 +                               const Vector3d& ri,
124 +                               const Vector3d& rj0,
125 +                               const Vector3d& rj1,
126 +                               const Vector3d& rj2,
127 +                               RealType s, RealType viscosity){
128 +  
129 +  Vector3d v2 = (rj0 + rj1 + rj2)/3.0;  // sub-centroid
130 +  Vector3d dr = ri - v2;                // real centroid to sub-centroid
131 +  RealType l2 = 1.0/dr.lengthSquare();  
132 +
133 +  Mat3x3d G;
134 +  G = (SquareMatrix3<RealType>::identity() + outProduct(dr,dr)*l2)*sqrt(l2);
135 +
136 +  G *= 0.125/3.14159285358979;
137 +  G *= s/viscosity;
138 +  return G;
139 + }

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