applications/hydrodynamics/HydrodynamicsModel.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_HYDRODYNAMICSMODEL_HPP
#define APPLICATION_HYDRODYNAMICS_HYDRODYNAMICSMODEL_HPP
#include <vector>

#include "math/Vector3.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/DynamicRectMatrix.hpp"
#include "primitives/Molecule.hpp"
#include "applications/hydrodynamics/StuntDoubleShape.hpp"
#include "utils/any.hpp"
namespace oopse {
struct HydrodynamicProps {
    Vector3d diffCenter;
    Mat3x3d Ddtt;
    Mat3x3d Ddtr;
    Mat3x3d Ddrr;
    Mat3x3d Xidtt;
    Mat3x3d Xidrt;
    Mat3x3d Xidtr;
    Mat3x3d Xidrr;
};

struct BeadParam {
    std::string atomName;
    Vector3d pos;
    double radius;
};

typedef std::map<std::string, boost::any> DynamicProperty;

class HydrodynamicsModel {
    public:
        HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams);
        bool calcHydrodyanmicsProps();

        Vector3d getDiffCenter();
        Mat3x3d getTransDiff();
        Mat3x3d getRotDiff();
        Mat3x3d getTransRotDiff();
        void writeBeads(std::ostream& os);
        void writeDiffCenterAndDiffTensor(std::ostream& os);
    protected:
        StuntDouble* sd_;
    private:
        virtual bool createBeads(std::vector<BeadParam>& beads) = 0;

        void calcResistanceTensor();
        void calcDiffusionTensor();
        HydrodynamicProps props_;
        std::vector<BeadParam> beads_;
        double viscosity_;
        double temperature_;
        
};


}

#endif
Revision:	2611
Committed:	Mon Mar 13 22:42:40 2006 UTC (18 years, 3 months ago) by tim
File size:	3521 byte(s)
Log Message:	LangevinDynamics in progress
#	User	Rev	Content
1	tim	2596	/*
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			#ifndef APPLICATION_HYDRODYNAMICS_HYDRODYNAMICSMODEL_HPP
42			#define APPLICATION_HYDRODYNAMICS_HYDRODYNAMICSMODEL_HPP
43			#include <vector>
44
45			#include "math/Vector3.hpp"
46			#include "math/SquareMatrix3.hpp"
47			#include "math/DynamicRectMatrix.hpp"
48			#include "primitives/Molecule.hpp"
49	tim	2597	#include "applications/hydrodynamics/StuntDoubleShape.hpp"
50	tim	2596	#include "utils/any.hpp"
51			namespace oopse {
52			struct HydrodynamicProps {
53			Vector3d diffCenter;
54	tim	2611	Mat3x3d Ddtt;
55			Mat3x3d Ddtr;
56			Mat3x3d Ddrr;
57			Mat3x3d Xidtt;
58			Mat3x3d Xidrt;
59			Mat3x3d Xidtr;
60			Mat3x3d Xidrr;
61	tim	2596	};
62
63			struct BeadParam {
64			std::string atomName;
65			Vector3d pos;
66			double radius;
67			};
68
69			typedef std::map<std::string, boost::any> DynamicProperty;
70
71			class HydrodynamicsModel {
72			public:
73	tim	2597	HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams);
74			bool calcHydrodyanmicsProps();
75	tim	2596
76			Vector3d getDiffCenter();
77			Mat3x3d getTransDiff();
78			Mat3x3d getRotDiff();
79			Mat3x3d getTransRotDiff();
80			void writeBeads(std::ostream& os);
81			void writeDiffCenterAndDiffTensor(std::ostream& os);
82			protected:
83	tim	2597	StuntDouble* sd_;
84	tim	2596	private:
85			virtual bool createBeads(std::vector<BeadParam>& beads) = 0;
86
87	tim	2611	void calcResistanceTensor();
88			void calcDiffusionTensor();
89	tim	2596	HydrodynamicProps props_;
90			std::vector<BeadParam> beads_;
91	tim	2597	double viscosity_;
92			double temperature_;
93	tim	2596
94			};
95
96
97			}
98
99			#endif