src/math/Triangle.hpp

/* Copyright (c) 2008 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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 *
 *
 *  Triangle.hpp
 *
 *  Purpose: Provide basic triangle class for OpenMD. Hates Particle class.
 *
 *  Created by Charles F. Vardeman II on 29 July 2008.
 *  @author  Charles F. Vardeman II
 *  @version $Id: Triangle.hpp,v 1.6 2009-11-25 20:02:01 gezelter Exp $
 *
 */


#ifndef MATH_FACET_HPP
#define MATH_FACET_HPP

#include "math/Vector3.hpp"
#include "math/SquareMatrix3.hpp"
#include "config.h"
#include "primitives/StuntDouble.hpp"

#include <vector>


namespace OpenMD {

/**
   * @class Triangle
   *
   * Triangle provides geometric data to OpenMD. Triangle includes
   * information about the normal, centroid and the atoms
   * that belong to this triangle.
   */
  class Triangle {

  public:
    Triangle();
    virtual ~Triangle() { };

    void setNormal(Vector3d normal) {
      normal_ = normal;
      HaveNormal_ = true;
    }

    void addVertices(Vector3d P1, Vector3d P2, Vector3d P3);

    void addVertexSD(StuntDouble* thisSD){
      vertexSD_.push_back(thisSD);
    }

    std::vector<StuntDouble*> getVertices(){return vertexSD_;}

    void setArea(RealType area) {
      area_ = area;
      HaveArea_ = true;
    }
    
    Vector3d getNormal() {
      if (HaveNormal_) {
        return normal_;
      } else {
        return computeNormal();
      }
    }
    
    RealType getArea() { 
      if(HaveArea_){
        return area_;
      }else{
        return computeArea();
      }
    }

    RealType computeArea();
    Vector3d computeNormal();
    Vector3d computeCentroid();

    void setCentroid(Vector3d centroid) { 
      centroid_ = centroid;
      HaveCentroid_ = true;
    }

    Vector3d getCentroid() {
      if (HaveCentroid_) {
        return centroid_;
      } else {
        return computeCentroid();
      }
    }
    
    Vector3d getFacetVelocity(){
      return facetVelocity_;
    }
    
    void setFacetVelocity(Vector3d facetVelocity){
      facetVelocity_ = facetVelocity;
    }

    void setFacetMass(RealType mass){
      mass_ = mass;
    }

    RealType getFacetMass(){
      return mass_;
    }

    RealType a(){
      return a_.length();
    }

    RealType b(){
      return b_.length();
    }

    RealType c(){
      return c_.length();
    }

    RealType getHydroLength() {
      RealType a1 = a();
      RealType b1 = b();
      RealType c1 = c();
      RealType t1 =  a1 + b1 + c1;
      RealType t4 =  a1 + b1 - c1;

      return 32.0 * c1 / log(t1*t1/t4/t4);
    }


    RealType getIncircleRadius() {
      return 2.0 * getArea() / (a() + b() + c());
    }

    RealType getCircumcircleRadius() {
      RealType a1 = a();
      RealType b1 = b();
      RealType c1 = c();
      RealType t1 =  a1 + b1 + c1;
      RealType t2 = -a1 + b1 + c1;
      RealType t3 =  a1 - b1 + c1;
      RealType t4 =  a1 + b1 - c1;
      RealType junk = t1*t2*t3*t4;
      return a1 * b1 * c1 / sqrt(t1 * t2 * t3 * t4);
    }
      
    Mat3x3d computeHydrodynamicTensor(RealType viscosity);


  private:
    Mat3x3d hydro_tensor(const Vector3d& ri, const Vector3d& rj0, const Vector3d& rj1, const Vector3d& rj2,RealType s, RealType viscosity);
    
    /* Local Indentity of vertex atoms in pos array*/
    std::vector <StuntDouble*> vertexSD_;
    Vector3d normal_;
    Vector3d centroid_;
    Vector3d vertices_[3];
    RealType area_;
    RealType mass_;
    Vector3d facetVelocity_;
    //Length of triangle sides
    Vector3d a_,b_,c_;
    RealType alpha_,beta_,gamma_;
    bool HaveArea_;
    bool HaveNormal_;
    bool HaveCentroid_;
    
  }; // End class Triangle
    
    
} //end namespace OpenMD


#endif // MATH_FACET_HPP


Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size:	5663 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	Content
1	/* Copyright (c) 2008 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. Redistributions of source code must retain the above copyright
9	* notice, this list of conditions and the following disclaimer.
10	*
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.
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	* 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 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 1.6 2009-11-25 20:02:01 gezelter Exp $
48	*
49	*/
50
51
52	#ifndef MATH_FACET_HPP
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 OpenMD {
64
65	/**
66	* @class Triangle
67	*
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();
76	virtual ~Triangle() { };
77
78	void setNormal(Vector3d normal) {
79	normal_ = normal;
80	HaveNormal_ = true;
81	}
82
83	void addVertices(Vector3d P1, Vector3d P2, Vector3d P3);
84
85	void addVertexSD(StuntDouble* thisSD){
86	vertexSD_.push_back(thisSD);
87	}
88
89	std::vector<StuntDouble*> getVertices(){return vertexSD_;}
90
91	void setArea(RealType area) {
92	area_ = area;
93	HaveArea_ = true;
94	}
95
96	Vector3d getNormal() {
97	if (HaveNormal_) {
98	return normal_;
99	} else {
100	return computeNormal();
101	}
102	}
103
104	RealType getArea() {
105	if(HaveArea_){
106	return area_;
107	}else{
108	return computeArea();
109	}
110	}
111
112	RealType computeArea();
113	Vector3d computeNormal();
114	Vector3d computeCentroid();
115
116	void setCentroid(Vector3d centroid) {
117	centroid_ = centroid;
118	HaveCentroid_ = true;
119	}
120
121	Vector3d getCentroid() {
122	if (HaveCentroid_) {
123	return centroid_;
124	} else {
125	return computeCentroid();
126	}
127	}
128
129	Vector3d getFacetVelocity(){
130	return facetVelocity_;
131	}
132
133	void setFacetVelocity(Vector3d facetVelocity){
134	facetVelocity_ = facetVelocity;
135	}
136
137	void setFacetMass(RealType mass){
138	mass_ = mass;
139	}
140
141	RealType getFacetMass(){
142	return mass_;
143	}
144
145	RealType a(){
146	return a_.length();
147	}
148
149	RealType b(){
150	return b_.length();
151	}
152
153	RealType c(){
154	return c_.length();
155	}
156
157	RealType getHydroLength() {
158	RealType a1 = a();
159	RealType b1 = b();
160	RealType c1 = c();
161	RealType t1 = a1 + b1 + c1;
162	RealType t4 = a1 + b1 - c1;
163
164	return 32.0 * c1 / log(t1*t1/t4/t4);
165	}
166
167
168	RealType getIncircleRadius() {
169	return 2.0 * getArea() / (a() + b() + c());
170	}
171
172	RealType getCircumcircleRadius() {
173	RealType a1 = a();
174	RealType b1 = b();
175	RealType c1 = c();
176	RealType t1 = a1 + b1 + c1;
177	RealType t2 = -a1 + b1 + c1;
178	RealType t3 = a1 - b1 + c1;
179	RealType t4 = a1 + b1 - c1;
180	RealType junk = t1t2t3*t4;
181	return a1 * b1 * c1 / sqrt(t1 * t2 * t3 * t4);
182	}
183
184	Mat3x3d computeHydrodynamicTensor(RealType viscosity);
185
186
187	private:
188	Mat3x3d hydro_tensor(const Vector3d& ri, const Vector3d& rj0, const Vector3d& rj1, const Vector3d& rj2,RealType s, RealType viscosity);
189
190	/* Local Indentity of vertex atoms in pos array*/
191	std::vector <StuntDouble*> vertexSD_;
192	Vector3d normal_;
193	Vector3d centroid_;
194	Vector3d vertices_[3];
195	RealType area_;
196	RealType mass_;
197	Vector3d facetVelocity_;
198	//Length of triangle sides
199	Vector3d a_,b_,c_;
200	RealType alpha_,beta_,gamma_;
201	bool HaveArea_;
202	bool HaveNormal_;
203	bool HaveCentroid_;
204
205	}; // End class Triangle
206
207
208
209	} //end namespace OpenMD
210
211
212
213	#endif // MATH_FACET_HPP
214
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218