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

Comparing:
trunk/src/math/Triangle.hpp (file contents), Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
branches/development/src/math/Triangle.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
39	+	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40		*
41		*  Triangle.hpp
42		*
43	<	*  Purpose: Provide facets from hull to oopse
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 1.1 2008-09-14 01:32:25 chuckv Exp $
47	>	*  @version $Id$
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		*/
72		class Triangle {
73
74		public:
75	<	Triangle(){};
75	>	Triangle();
76		virtual ~Triangle() { };
77
78		void setNormal(Vector3d normal) {
79		normal_ = normal;
80	+	HaveNormal_ = true;
81		}
82	+	void setUnitNormal(Vector3d normal) {
83	+	unitnormal_ = normal;
84	+	HaveUnitNormal_ = true;
85	+	}
86
87	<	void addVertex(StuntDouble* thisSD){
87	>	void addVertices(Vector3d P1, Vector3d P2, Vector3d P3);
88	>
89	>	void addVertexSD(StuntDouble* thisSD){
90		vertexSD_.push_back(thisSD);
91		}
92	<
92	>
93		std::vector<StuntDouble*> getVertices(){return vertexSD_;}
94
95		void setArea(RealType area) {
96		area_ = area;
97	+	HaveArea_ = true;
98		}
99
100	<	Vector3d getNormal() {
101	<	return normal_;
100	>	Vector3d getNormal() {
101	>	if (HaveNormal_) {
102	>	return normal_;
103	>	} else {
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	<	return area_;
116	>	if(HaveArea_){
117	>	return area_;
118	>	}else{
119	>	return computeArea();
120	>	}
121		}
122
123	+	RealType computeArea();
124	+	Vector3d computeNormal();
125	+	Vector3d computeCentroid();
126	+	Vector3d computeUnitNormal();
127	+
128		void setCentroid(Vector3d centroid) {
129		centroid_ = centroid;
130	+	HaveCentroid_ = true;
131		}
132
133	<	Vector3d getCentroid() {
134	<	return centroid_;
133	>	Vector3d getCentroid() {
134	>	if (HaveCentroid_) {
135	>	return centroid_;
136	>	} else {
137	>	return computeCentroid();
138	>	}
139		}
140	+
141	+	Vector3d getFacetVelocity(){
142	+	return facetVelocity_;
143	+	}
144	+
145	+	void setFacetVelocity(Vector3d facetVelocity){
146	+	facetVelocity_ = facetVelocity;
147	+	}
148
149	+	void setFacetMass(RealType mass){
150	+	mass_ = mass;
151	+	}
152	+
153	+	RealType getFacetMass(){
154	+	return mass_;
155	+	}
156	+
157	+	RealType a(){
158	+	return a_.length();
159	+	}
160	+
161	+	RealType b(){
162	+	return b_.length();
163	+	}
164	+
165	+	RealType c(){
166	+	return c_.length();
167	+	}
168	+
169	+	RealType getHydroLength() {
170	+	RealType a1 = a();
171	+	RealType b1 = b();
172	+	RealType c1 = c();
173	+	RealType t1 =  a1 + b1 + c1;
174	+	RealType t4 =  a1 + b1 - c1;
175	+
176	+	return 32.0 * c1 / log(t1*t1/t4/t4);
177	+	}
178	+
179	+
180	+	RealType getIncircleRadius() {
181	+	return 2.0 * getArea() / (a() + b() + c());
182	+	}
183	+
184	+	RealType getCircumcircleRadius() {
185	+	RealType a1 = a();
186	+	RealType b1 = b();
187	+	RealType c1 = c();
188	+	RealType t1 =  a1 + b1 + c1;
189	+	RealType t2 = -a1 + b1 + c1;
190	+	RealType t3 =  a1 - b1 + c1;
191	+	RealType t4 =  a1 + b1 - c1;
192	+	RealType junk = t1*t2*t3*t4;
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	<	RealType area_;
207	>	Vector3d vertices_[3];
208	>	RealType area_;
209	>	RealType mass_;
210	>	Vector3d facetVelocity_;
211	>	//Length of triangle sides
212	>	Vector3d a_,b_,c_;
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

Comparing:
trunk/src/math/Triangle.hpp (property svn:keywords), Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 UTC vs.
branches/development/src/math/Triangle.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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