applications/hydrodynamics/StuntDoubleShape.hpp

/*
 * Copyright (c) 2005 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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */

#ifndef APPLICATION_HYDRODYNAMICS_MOLECULESHAPE_HPP
#define APPLICATION_HYDRODYNAMICS_MOLECULESHAPE_HPP

#include "math/Vector3.hpp"
#include "primitives/Molecule.hpp"
namespace oopse {

/** @class Shape*/
class Shape {
    public:
        virtual bool isInterior(Vector3d pos) = 0;
        virtual std::pair<Vector3d, Vector3d> getBox() = 0;
        virtual bool hasAnalyticalSolution() = 0;
        //virtual Mat3x3d getTranslationalFriction() = 0;
        //virtual Mat3x3d getRotationalFriction() = 0 ;
};

/** @class Spheric */
class Spheric : public Shape {
    public:
        Spheric(Vector3d origin, double radius);
        virtual bool isInterior(Vector3d pos);
        virtual std::pair<Vector3d, Vector3d> getBox();
        virtual bool hasAnalyticalSolution() {return true;}
        //virtual Mat3x3d getTranslationalFriction();
        //virtual Mat3x3d getRotationalFriction();

    private:
        Vector3d origin_;
        double radius_;
};

/** @class Ellipsoid */
class Ellipsoid : public Shape{
    public:
        Ellipsoid(Vector3d origin, double radius, double ratio, Mat3x3d rotMat);
        virtual bool isInterior(Vector3d pos);
        virtual std::pair<Vector3d, Vector3d> getBox();
        virtual bool hasAnalyticalSolution() {return true;}
        //virtual Mat3x3d getTranslationalFriction() {
        //    Mat3x3d Xirr;
        //}
        
        //virtual Mat3x3d getFrictionCoff() {

        //}

     private:


        /**
         * calculate the ratio of friction coeffiction constant between ellipsoid and spheric 
         * with same volume.
         * @param m
         * @param n 
         * @note 
         * Reference:
         *
         * (1) Victor A. Bloomfield, On-Line Biophysics Textbook, Volume: Separations and Hydrodynamics
         * Chapter 1,Survey of Biomolecular Hydrodynamics
         * http://www.biophysics.org/education/vbloomfield.pdf 
         * (2) F. Perrin , J. Phys. Radium, [7] 5, 497-511, 1934
         * (3) F. Perrin, J. Phys. Radium, [7] 7, 1-11, 1936
         */
        void calcFrictionRatio(double m, double n, double& Ft, double& Frm, double& Frn) {
            double q = n/m;
            if (q > 1.0) {//prolate
                Ft = sqrt(1-q*q)/(pow(q, 2.0/3.0)*log((1 + sqrt(1-q*q))/q));
                Frm = 4*(1-q*q)/(3*(2 - 2*pow(q, 4.0/3.0)/Ft)); //not sure
                Frn = 4*(1-q*q*q*q) /(3*q*q*(2*pow(q, -2.0/3.0)*(2-q*q)/Ft-2));
            } else {//oblate
                Ft = sqrt(1-q*q)/(pow(q, 2.0/3.0)*atan(sqrt(q*q-1)));
                Frm = 4*(1-q*q)/(3*(2 - 2*pow(q, 4.0/3.0)/Ft)); //not sure
                Frn = 4*(1-q*q*q*q) /(3*q*q*(2*pow(q, -2.0/3.0)*(2-q*q)/Ft-2));
            }
        }
        Vector3d origin_;
        double a_;
        double b_;
        Mat3x3d rotMat_;
};

/** @class StuntDoubleShape */
class StuntDoubleShape {
    public:
        StuntDoubleShape(StuntDouble* sd);
        ~StuntDoubleShape();
        bool hasAnalyticalSolution();
        std::pair<Vector3d, Vector3d> getBox();
        bool isInterior(Vector3d pos);
    private:
        Shape* createShape(Atom* atom);
        std::vector<Shape*> shapes_;
};


class ShapeBuilder {
    public:
        
};


}

#endif
Revision:	2611
Committed:	Mon Mar 13 22:42:40 2006 UTC (18 years, 6 months ago) by tim
File size:	5295 byte(s)
Log Message:	LangevinDynamics in progress
#	User	Rev	Content
1	tim	2597	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#ifndef APPLICATION_HYDRODYNAMICS_MOLECULESHAPE_HPP
43			#define APPLICATION_HYDRODYNAMICS_MOLECULESHAPE_HPP
44
45			#include "math/Vector3.hpp"
46			#include "primitives/Molecule.hpp"
47			namespace oopse {
48
49			/** @class Shape*/
50			class Shape {
51			public:
52			virtual bool isInterior(Vector3d pos) = 0;
53			virtual std::pair<Vector3d, Vector3d> getBox() = 0;
54	tim	2611	virtual bool hasAnalyticalSolution() = 0;
55			//virtual Mat3x3d getTranslationalFriction() = 0;
56			//virtual Mat3x3d getRotationalFriction() = 0 ;
57	tim	2597	};
58
59			/** @class Spheric */
60			class Spheric : public Shape {
61			public:
62			Spheric(Vector3d origin, double radius);
63			virtual bool isInterior(Vector3d pos);
64			virtual std::pair<Vector3d, Vector3d> getBox();
65	tim	2611	virtual bool hasAnalyticalSolution() {return true;}
66			//virtual Mat3x3d getTranslationalFriction();
67			//virtual Mat3x3d getRotationalFriction();
68
69	tim	2597	private:
70			Vector3d origin_;
71			double radius_;
72			};
73
74			/** @class Ellipsoid */
75			class Ellipsoid : public Shape{
76			public:
77			Ellipsoid(Vector3d origin, double radius, double ratio, Mat3x3d rotMat);
78			virtual bool isInterior(Vector3d pos);
79			virtual std::pair<Vector3d, Vector3d> getBox();
80	tim	2611	virtual bool hasAnalyticalSolution() {return true;}
81			//virtual Mat3x3d getTranslationalFriction() {
82			// Mat3x3d Xirr;
83			//}
84
85			//virtual Mat3x3d getFrictionCoff() {
86
87			//}
88
89	tim	2597	private:
90	tim	2611
91
92			/**
93			* calculate the ratio of friction coeffiction constant between ellipsoid and spheric
94			* with same volume.
95			* @param m
96			* @param n
97			* @note
98			* Reference:
99			*
100			* (1) Victor A. Bloomfield, On-Line Biophysics Textbook, Volume: Separations and Hydrodynamics
101			* Chapter 1,Survey of Biomolecular Hydrodynamics
102			* http://www.biophysics.org/education/vbloomfield.pdf
103			* (2) F. Perrin , J. Phys. Radium, [7] 5, 497-511, 1934
104			* (3) F. Perrin, J. Phys. Radium, [7] 7, 1-11, 1936
105			*/
106			void calcFrictionRatio(double m, double n, double& Ft, double& Frm, double& Frn) {
107			double q = n/m;
108			if (q > 1.0) {//prolate
109			Ft = sqrt(1-qq)/(pow(q, 2.0/3.0)log((1 + sqrt(1-q*q))/q));
110			Frm = 4(1-qq)/(3(2 - 2pow(q, 4.0/3.0)/Ft)); //not sure
111			Frn = 4(1-qqqq) /(3qq(2pow(q, -2.0/3.0)(2-qq)/Ft-2));
112			} else {//oblate
113			Ft = sqrt(1-qq)/(pow(q, 2.0/3.0)atan(sqrt(q*q-1)));
114			Frm = 4(1-qq)/(3(2 - 2pow(q, 4.0/3.0)/Ft)); //not sure
115			Frn = 4(1-qqqq) /(3qq(2pow(q, -2.0/3.0)(2-qq)/Ft-2));
116			}
117			}
118	tim	2597	Vector3d origin_;
119			double a_;
120			double b_;
121			Mat3x3d rotMat_;
122			};
123
124			/** @class StuntDoubleShape */
125			class StuntDoubleShape {
126			public:
127			StuntDoubleShape(StuntDouble* sd);
128			~StuntDoubleShape();
129	tim	2611	bool hasAnalyticalSolution();
130	tim	2597	std::pair<Vector3d, Vector3d> getBox();
131			bool isInterior(Vector3d pos);
132			private:
133			Shape* createShape(Atom* atom);
134			std::vector<Shape*> shapes_;
135			};
136
137	tim	2611
138			class ShapeBuilder {
139			public:
140
141			};
142
143
144	tim	2597	}
145
146			#endif