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 "utils/HydroProps.hpp"
#include "utils/OOPSEConstant.hpp"
#include "utils/HydroProps.hpp"
namespace oopse {

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

class Spheric;
class Ellipsoid;
class CompositeShape;

class HydrodynamicsModel {
    public:
        HydrodynamicsModel(StuntDouble* sd, SimInfo* info) : sd_(sd), info_(info) {}
        virtual ~HydrodynamicsModel() {}
        virtual bool calcHydroProps(Spheric* spheric, double viscosity, double temperature);
        virtual bool calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature);
        virtual bool calcHydroProps(CompositeShape* compositexShape, double viscosity, double temperature);

        virtual void init() {};
        virtual void writeBeads(std::ostream& os) = 0;
        void writeHydroProps(std::ostream& os);
        HydroProps getHydroPropsAtCR() {return cr_;}
        HydroProps getHydroPropsAtCD() {return cd_;}
        
        void setCR(const HydroProps cr) {cr_ = cr;}
        void setCD(const HydroProps cd) { cd_ = cd;}
        std::string getStuntDoubleName() { return sd_->getType();}
    protected:
        StuntDouble* sd_;
        SimInfo* info_;
    private:
        HydroProps cr_;
        HydroProps cd_;
        std::vector<BeadParam> beads_;
};

}

#endif
Revision:	2675
Committed:	Wed Mar 29 18:09:26 2006 UTC (18 years, 3 months ago) by tim
File size:	3666 byte(s)
Log Message:	(1) RoughShell Model is working; (20)Adding a new option into Hydro which allows user to generate the beads only
#	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	2634	#include "utils/HydroProps.hpp"
50			#include "utils/OOPSEConstant.hpp"
51			#include "utils/HydroProps.hpp"
52	tim	2596	namespace oopse {
53
54			struct BeadParam {
55			std::string atomName;
56			Vector3d pos;
57			double radius;
58			};
59
60	tim	2634	class Spheric;
61			class Ellipsoid;
62			class CompositeShape;
63	tim	2596
64			class HydrodynamicsModel {
65			public:
66	tim	2634	HydrodynamicsModel(StuntDouble* sd, SimInfo* info) : sd_(sd), info_(info) {}
67			virtual ~HydrodynamicsModel() {}
68			virtual bool calcHydroProps(Spheric* spheric, double viscosity, double temperature);
69			virtual bool calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature);
70			virtual bool calcHydroProps(CompositeShape* compositexShape, double viscosity, double temperature);
71	tim	2596
72	tim	2675	virtual void init() {};
73	tim	2665	virtual void writeBeads(std::ostream& os) = 0;
74	tim	2634	void writeHydroProps(std::ostream& os);
75			HydroProps getHydroPropsAtCR() {return cr_;}
76			HydroProps getHydroPropsAtCD() {return cd_;}
77
78			void setCR(const HydroProps cr) {cr_ = cr;}
79			void setCD(const HydroProps cd) { cd_ = cd;}
80			std::string getStuntDoubleName() { return sd_->getType();}
81	tim	2596	protected:
82	tim	2597	StuntDouble* sd_;
83	tim	2634	SimInfo* info_;
84	tim	2596	private:
85	tim	2634	HydroProps cr_;
86			HydroProps cd_;
87	tim	2596	std::vector<BeadParam> beads_;
88			};
89
90			}
91
92			#endif