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root/OpenMD/branches/development/src/math/Triangle.cpp

Comparing:
trunk/src/math/Triangle.cpp (file contents), Revision 1316 by chuckv, Fri Nov 14 15:44:34 2008 UTC vs.
branches/development/src/math/Triangle.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 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 $Id$
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	+	}

Comparing:
trunk/src/math/Triangle.cpp (property svn:keywords), Revision 1316 by chuckv, Fri Nov 14 15:44:34 2008 UTC vs.
branches/development/src/math/Triangle.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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