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. 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).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#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/PhysicalConstants.hpp"

namespace OpenMD {
  
  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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	3505 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	tim	891	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	891	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	891	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	891	*/
42			#ifndef APPLICATION_HYDRODYNAMICS_HYDRODYNAMICSMODEL_HPP
43			#define APPLICATION_HYDRODYNAMICS_HYDRODYNAMICSMODEL_HPP
44			#include <vector>
45
46			#include "math/Vector3.hpp"
47			#include "math/SquareMatrix3.hpp"
48			#include "math/DynamicRectMatrix.hpp"
49			#include "primitives/Molecule.hpp"
50	gezelter	981	#include "hydrodynamics/HydroProp.hpp"
51	gezelter	1390	#include "utils/PhysicalConstants.hpp"
52	gezelter	972
53	gezelter	1390	namespace OpenMD {
54	gezelter	972
55			struct BeadParam {
56	tim	891	std::string atomName;
57			Vector3d pos;
58	tim	977	RealType radius;
59	gezelter	972	};
60
61			class Shape;
62			class Sphere;
63			class Ellipsoid;
64			class CompositeShape;
65
66			class HydrodynamicsModel {
67			public:
68			HydrodynamicsModel(StuntDouble* sd, SimInfo* info) : sd_(sd), info_(info) {}
69			virtual ~HydrodynamicsModel() {}
70	tim	891
71	gezelter	972	virtual bool calcHydroProps(Shape* shape, RealType viscosity, RealType temperature);
72
73			virtual void init() {};
74			virtual void writeBeads(std::ostream& os) = 0;
75			void writeHydroProps(std::ostream& os);
76	gezelter	981	HydroProp* getHydroPropsAtCR() {return cr_;}
77			HydroProp* getHydroPropsAtCD() {return cd_;}
78	gezelter	972
79	gezelter	981	void setCR(HydroProp* cr) {cr_ = cr;}
80			void setCD(HydroProp* cd) {cd_ = cd;}
81	gezelter	972	std::string getStuntDoubleName() { return sd_->getType();}
82			protected:
83			StuntDouble* sd_;
84			SimInfo* info_;
85			private:
86	gezelter	981	HydroProp* cr_;
87			HydroProp* cd_;
88	gezelter	972	std::vector<BeadParam> beads_;
89			};
90
91	tim	891	}
92
93			#endif