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 "hydrodynamics/HydroProp.hpp"
#include "utils/OOPSEConstant.hpp"

namespace oopse {
  
  struct BeadParam {
    std::string atomName;
    Vector3d pos;
    RealType radius;
  };
  
  class Shape;
  class Sphere;
  class Ellipsoid;
  class CompositeShape;
  
  class HydrodynamicsModel {
  public:
    HydrodynamicsModel(StuntDouble* sd, SimInfo* info) : sd_(sd), info_(info) {}
    virtual ~HydrodynamicsModel() {}

    virtual bool calcHydroProps(Shape* shape, RealType viscosity, RealType temperature);
    
    virtual void init() {};
    virtual void writeBeads(std::ostream& os) = 0;
    void writeHydroProps(std::ostream& os);
    HydroProp* getHydroPropsAtCR() {return cr_;}
    HydroProp* getHydroPropsAtCD() {return cd_;}
    
    void setCR(HydroProp* cr) {cr_ = cr;}
    void setCD(HydroProp* cd) {cd_ = cd;}
    std::string getStuntDoubleName() { return sd_->getType();}
  protected:
    StuntDouble* sd_;
    SimInfo* info_;
  private:
    HydroProp* cr_;
    HydroProp* cd_;
    std::vector<BeadParam> beads_;
  };
  
}

#endif
Revision:	2787
Committed:	Mon Jun 5 18:24:45 2006 UTC (18 years, 1 month ago) by gezelter
File size:	3393 byte(s)
Log Message:	Massive changes for GB code with multiple ellipsoid types (a la Cleaver's paper). Also, changes in hydrodynamics code to make HydroProp a somewhat smarter class (rather than just a struct).
#	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	gezelter	2787	#include "hydrodynamics/HydroProp.hpp"
50	tim	2634	#include "utils/OOPSEConstant.hpp"
51	gezelter	2768
52	tim	2596	namespace oopse {
53	gezelter	2768
54			struct BeadParam {
55	tim	2596	std::string atomName;
56			Vector3d pos;
57	tim	2773	RealType radius;
58	gezelter	2768	};
59
60			class Shape;
61			class Sphere;
62			class Ellipsoid;
63			class CompositeShape;
64
65			class HydrodynamicsModel {
66			public:
67			HydrodynamicsModel(StuntDouble* sd, SimInfo* info) : sd_(sd), info_(info) {}
68			virtual ~HydrodynamicsModel() {}
69	tim	2596
70	gezelter	2768	virtual bool calcHydroProps(Shape* shape, RealType viscosity, RealType temperature);
71
72			virtual void init() {};
73			virtual void writeBeads(std::ostream& os) = 0;
74			void writeHydroProps(std::ostream& os);
75	gezelter	2787	HydroProp* getHydroPropsAtCR() {return cr_;}
76			HydroProp* getHydroPropsAtCD() {return cd_;}
77	gezelter	2768
78	gezelter	2787	void setCR(HydroProp* cr) {cr_ = cr;}
79			void setCD(HydroProp* cd) {cd_ = cd;}
80	gezelter	2768	std::string getStuntDoubleName() { return sd_->getType();}
81			protected:
82			StuntDouble* sd_;
83			SimInfo* info_;
84			private:
85	gezelter	2787	HydroProp* cr_;
86			HydroProp* cd_;
87	gezelter	2768	std::vector<BeadParam> beads_;
88			};
89
90	tim	2596	}
91
92			#endif