src/math/Triangle.hpp

/* 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, 24107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *
 *  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 $Id$
 *
 */


#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 setUnitNormal(Vector3d normal) {
      unitnormal_ = normal;
      HaveUnitNormal_ = 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();
      }
    }
   Vector3d getUnitNormal() {
      if (HaveUnitNormal_) {
        return unitnormal_;
      } else {
        return computeUnitNormal();
      }
    }
    
    RealType getArea() { 
      if(HaveArea_){
        return area_;
      }else{
        return computeArea();
      }
    }

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

    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 unitnormal_;
    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 HaveUnitNormal_;
    bool HaveCentroid_;
    
  }; // End class Triangle
    
    
} //end namespace OpenMD


#endif // MATH_FACET_HPP


Revision:	1782
Committed:	Wed Aug 22 02:28:28 2012 UTC (13 years, 2 months ago) by gezelter
File size:	6004 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	User	Rev	Content
1	chuckv	1404	/* Copyright (c) 2008, 2010 The University of Notre Dame. All Rights Reserved.
2	chuckv	1293	*
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	1293	* 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	1293	* 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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (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	1293	*
41			* Triangle.hpp
42			*
43	gezelter	1390	* Purpose: Provide basic triangle class for OpenMD. Hates Particle class.
44	chuckv	1293	*
45			* Created by Charles F. Vardeman II on 29 July 2008.
46			* @author Charles F. Vardeman II
47	gezelter	1442	* @version $Id$
48	chuckv	1293	*
49			*/
50
51
52			#ifndef MATH_FACET_HPP
53			#define MATH_FACET_HPP
54
55			#include "math/Vector3.hpp"
56	gezelter	1344	#include "math/SquareMatrix3.hpp"
57	chuckv	1293	#include "config.h"
58			#include "primitives/StuntDouble.hpp"
59
60			#include <vector>
61
62
63	gezelter	1390	namespace OpenMD {
64	chuckv	1293
65			/**
66			* @class Triangle
67			*
68	gezelter	1390	* Triangle provides geometric data to OpenMD. Triangle includes
69	chuckv	1293	* information about the normal, centroid and the atoms
70			* that belong to this triangle.
71			*/
72			class Triangle {
73
74			public:
75	chuckv	1316	Triangle();
76	chuckv	1293	virtual ~Triangle() { };
77
78			void setNormal(Vector3d normal) {
79			normal_ = normal;
80	chuckv	1316	HaveNormal_ = true;
81	chuckv	1293	}
82	chuckv	1404	void setUnitNormal(Vector3d normal) {
83			unitnormal_ = normal;
84			HaveUnitNormal_ = true;
85			}
86	chuckv	1293
87	chuckv	1316	void addVertices(Vector3d P1, Vector3d P2, Vector3d P3);
88
89			void addVertexSD(StuntDouble* thisSD){
90	chuckv	1293	vertexSD_.push_back(thisSD);
91			}
92	chuckv	1316
93	chuckv	1293	std::vector<StuntDouble*> getVertices(){return vertexSD_;}
94
95			void setArea(RealType area) {
96			area_ = area;
97	chuckv	1316	HaveArea_ = true;
98	chuckv	1293	}
99
100	chuckv	1316	Vector3d getNormal() {
101			if (HaveNormal_) {
102			return normal_;
103			} else {
104			return computeNormal();
105			}
106	chuckv	1293	}
107	chuckv	1404	Vector3d getUnitNormal() {
108			if (HaveUnitNormal_) {
109			return unitnormal_;
110			} else {
111			return computeUnitNormal();
112			}
113			}
114	chuckv	1293
115			RealType getArea() {
116	chuckv	1316	if(HaveArea_){
117			return area_;
118			}else{
119			return computeArea();
120			}
121	chuckv	1293	}
122
123	chuckv	1316	RealType computeArea();
124			Vector3d computeNormal();
125			Vector3d computeCentroid();
126	chuckv	1404	Vector3d computeUnitNormal();
127	chuckv	1316
128	chuckv	1293	void setCentroid(Vector3d centroid) {
129			centroid_ = centroid;
130	chuckv	1316	HaveCentroid_ = true;
131	chuckv	1293	}
132
133	chuckv	1316	Vector3d getCentroid() {
134			if (HaveCentroid_) {
135			return centroid_;
136			} else {
137			return computeCentroid();
138			}
139	chuckv	1293	}
140	chuckv	1316
141	chuckv	1307	Vector3d getFacetVelocity(){
142			return facetVelocity_;
143			}
144
145			void setFacetVelocity(Vector3d facetVelocity){
146			facetVelocity_ = facetVelocity;
147			}
148
149	chuckv	1316	void setFacetMass(RealType mass){
150			mass_ = mass;
151			}
152	chuckv	1307
153	chuckv	1316	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	chuckv	1325	RealType junk = t1t2t3*t4;
193	chuckv	1316	return a1 * b1 * c1 / sqrt(t1 * t2 * t3 * t4);
194			}
195
196	gezelter	1344	Mat3x3d computeHydrodynamicTensor(RealType viscosity);
197	chuckv	1316
198
199	chuckv	1293	private:
200	gezelter	1344	Mat3x3d hydro_tensor(const Vector3d& ri, const Vector3d& rj0, const Vector3d& rj1, const Vector3d& rj2,RealType s, RealType viscosity);
201
202	chuckv	1293	/* Local Indentity of vertex atoms in pos array*/
203			std::vector <StuntDouble*> vertexSD_;
204			Vector3d normal_;
205	chuckv	1404	Vector3d unitnormal_;
206	chuckv	1293	Vector3d centroid_;
207	chuckv	1316	Vector3d vertices_[3];
208	chuckv	1404	RealType area_;
209	chuckv	1316	RealType mass_;
210	chuckv	1307	Vector3d facetVelocity_;
211	chuckv	1316	//Length of triangle sides
212			Vector3d a_,b_,c_;
213			RealType alpha_,beta_,gamma_;
214			bool HaveArea_;
215			bool HaveNormal_;
216	chuckv	1404	bool HaveUnitNormal_;
217	chuckv	1316	bool HaveCentroid_;
218	chuckv	1293
219			}; // End class Triangle
220
221
222
223	gezelter	1390	} //end namespace OpenMD
224	chuckv	1293
225
226
227			#endif // MATH_FACET_HPP
228
229
230
231
232