src/math/Triangle.cpp

/* 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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 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.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * 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 OpenMD
 *
 *  Created by Charles F. Vardeman II on 29 July 2008.
 *  @author  Charles F. Vardeman II
 *  @version $Id$
 *
 */

#include "math/Triangle.hpp"

using namespace OpenMD;


Triangle::Triangle() : HaveNormal_(false), HaveUnitNormal_(false), HaveCentroid_(false),
                       HaveArea_(false), area_(0.0), normal_(V3Zero), 
                       centroid_(V3Zero), facetVelocity_(V3Zero), mass_(0.0),
                       a_(V3Zero), b_(V3Zero), c_(V3Zero){
}

void Triangle::addVertices(Vector3d P1, Vector3d P2, Vector3d P3){
  vertices_[0] = P1;
  vertices_[1] = P2;
  vertices_[2] = P3;

  // Compute some quantites like a,b,c
  a_ = P1-P2;
  b_ = P1-P3;
  c_ = P2-P3;  
}


RealType Triangle::computeArea(){
  HaveArea_ = true;
  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])/RealType(3.0);
  return centroid_;
}


Mat3x3d Triangle::computeHydrodynamicTensor(RealType viscosity) {
  
  Vector3d u0 = -a_;
  Vector3d v0 = centroid_ - vertices_[0];
  RealType s0 = 0.5*cross(u0,v0).length();
  
  Vector3d u1 = -c_;
  Vector3d v1 = centroid_ - vertices_[1];
  RealType s1 = 0.5*cross(u1,v1).length();
  
  Vector3d u2 = b_;
  Vector3d v2 = centroid_ - vertices_[2];
  RealType s2 = 0.5*cross(u2,v2).length();
  
  Mat3x3d H;
  H = hydro_tensor(centroid_,centroid_,vertices_[1],vertices_[0],s0,viscosity)+
    hydro_tensor(centroid_,centroid_,vertices_[1],vertices_[2],s1,viscosity)+
    hydro_tensor(centroid_,centroid_,vertices_[2],vertices_[0],s2,viscosity);

  return H.inverse();
}

Mat3x3d Triangle::hydro_tensor(
                               const Vector3d& ri,
                               const Vector3d& rj0,
                               const Vector3d& rj1,
                               const Vector3d& rj2,
                               RealType s, RealType viscosity){
  
  Vector3d v2 = (rj0 + rj1 + rj2) / RealType(3.0);  // sub-centroid
  Vector3d dr = ri - v2;                // real centroid to sub-centroid
  RealType l2 = RealType(1.0)/dr.lengthSquare();  
 
  Mat3x3d G;
  G = (SquareMatrix3<RealType>::identity() + outProduct(dr,dr)*l2)*RealType(sqrt(l2));

  G *= 0.125/3.14159285358979;
  G *= s/viscosity;
  return G;
}
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	4884 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	User	Rev	Content
1	chuckv	1404	/* Copyright (c) 2008, 2010 The University of Notre Dame. All Rights Reserved.
2	chuckv	1316	*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
9	chuckv	1316	* notice, this list of conditions and the following disclaimer.
10			*
11	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
12	chuckv	1316	* notice, this list of conditions and the following disclaimer in the
13			* documentation and/or other materials provided with the
14			* distribution.
15			*
16			* This software is provided "AS IS," without a warranty of any
17			* kind. All express or implied conditions, representations and
18			* warranties, including any implied warranty of merchantability,
19			* fitness for a particular purpose or non-infringement, are hereby
20			* excluded. The University of Notre Dame and its licensors shall not
21			* be liable for any damages suffered by licensee as a result of
22			* using, modifying or distributing the software or its
23			* derivatives. In no event will the University of Notre Dame or its
24			* licensors be liable for any lost revenue, profit or data, or for
25			* direct, indirect, special, consequential, incidental or punitive
26			* damages, however caused and regardless of the theory of liability,
27			* arising out of the use of or inability to use software, even if the
28			* University of Notre Dame has been advised of the possibility of
29			* such damages.
30			*
31	gezelter	1390	* 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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40	chuckv	1316	*
41			* Triangle.cpp
42			*
43	gezelter	1390	* Purpose: Provide basic triangle object for OpenMD
44	chuckv	1316	*
45			* Created by Charles F. Vardeman II on 29 July 2008.
46			* @author Charles F. Vardeman II
47	gezelter	1442	* @version $Id$
48	chuckv	1316	*
49			*/
50
51			#include "math/Triangle.hpp"
52
53	gezelter	1390	using namespace OpenMD;
54	chuckv	1316
55
56	chuckv	1404	Triangle::Triangle() : HaveNormal_(false), HaveUnitNormal_(false), HaveCentroid_(false),
57	gezelter	1344	HaveArea_(false), area_(0.0), normal_(V3Zero),
58			centroid_(V3Zero), facetVelocity_(V3Zero), mass_(0.0),
59			a_(V3Zero), b_(V3Zero), c_(V3Zero){
60	chuckv	1316	}
61
62			void Triangle::addVertices(Vector3d P1, Vector3d P2, Vector3d P3){
63			vertices_[0] = P1;
64			vertices_[1] = P2;
65			vertices_[2] = P3;
66
67			// Compute some quantites like a,b,c
68			a_ = P1-P2;
69			b_ = P1-P3;
70	chuckv	1325	c_ = P2-P3;
71	chuckv	1316	}
72
73
74			RealType Triangle::computeArea(){
75			HaveArea_ = true;
76			area_ = getNormal().length() * 0.5;
77			return area_;
78			}
79	chuckv	1404	// This should return the normal for our calculations.
80	chuckv	1316	Vector3d Triangle::computeNormal(){
81			HaveNormal_ = true;
82			normal_ = cross(a_,b_);
83			return normal_;
84			}
85	chuckv	1404	// 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	chuckv	1316
93			Vector3d Triangle::computeCentroid(){
94			HaveCentroid_ = true;
95	gezelter	1782	centroid_ = (vertices_[0] + vertices_[1] + vertices_[2])/RealType(3.0);
96	chuckv	1316	return centroid_;
97			}
98	gezelter	1344
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	gezelter	1782	Vector3d v2 = (rj0 + rj1 + rj2) / RealType(3.0); // sub-centroid
130	gezelter	1344	Vector3d dr = ri - v2; // real centroid to sub-centroid
131	gezelter	1782	RealType l2 = RealType(1.0)/dr.lengthSquare();
132	gezelter	1344
133			Mat3x3d G;
134	gezelter	1782	G = (SquareMatrix3<RealType>::identity() + outProduct(dr,dr)l2)RealType(sqrt(l2));
135	gezelter	1344
136			G *= 0.125/3.14159285358979;
137			G *= s/viscosity;
138			return G;
139			}