src/hydrodynamics/HydroProp.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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#ifndef HYDRODYNAMICS_HYDROPROP_HPP
#define HYDRODYNAMICS_HYDROPROP_HPP
#include "math/Vector3.hpp"
#include "math/SquareMatrix3.hpp"
namespace OpenMD {

  /**
   * @class HydroProp HydroProp.hpp "hydrodynamics/HydroProp.hpp"
   * Container for information about the hydrodynamic behavior of objects
   * undergoing Langevin dynamics.
   * @note the units for the center of resistance (a location) are in Angstroms
   *
   * @note the units of Xi, the resistance tensor are:
   *    Xitt (Translation-translation) : kcal fs mol^-1 Angstroms^-2 
   *    Xirt (Rotation-translation) : kcal fs mol^-1 Angstroms^-1 radians^-1 
   *    Xitr (Translation-rotation) : kcal fs mol^-1 Angstroms^-1 radians^-1 
   *    Xirr (Rotation-rotation) : kcal fs mol^-1 radians^-2 
   *
   * @note the units of D, the diffusion tensor are:
   *    Dtt (Translation-translation) : Angstroms^2 fs^-1
   *    Drt (Rotation-translation) :    Angstroms fs^-1
   *    Dtr (Translation-rotation) :    Angstroms fs^-1
   *    Drr (Rotation-rotation) :       fs^-1
   *  
   * @note after setting the value of Xi manually, the complete() function 
   * should be called to perform the Cholesky Decomposition.
   */
  class HydroProp {

  public:
    HydroProp();
    HydroProp(Vector3d cor, Mat6x6d Xi, Mat6x6d D);
    HydroProp(const std::string &frictionLine);
    ~HydroProp() { } ;
    void complete();
    void setCOR(Vector3d cor) {cor_ = cor; hasCOR = true;}
    void setXi(Mat6x6d Xi) {Xi_ = Xi; hasXi = true;}
    void setD(Mat6x6d D) {D_ = D;}
    void setName(std::string name) {name_ = name;}

    Vector3d getCOR() {return cor_;}
    Mat3x3d getXitt() {return Xitt_;}
    Mat3x3d getXitr() {return Xitr_;}
    Mat3x3d getXirt() {return Xirt_;}
    Mat3x3d getXirr() {return Xirr_;}
    Mat6x6d getS() {return S_;}
    Mat6x6d getD() {return D_;}
    Mat6x6d getXi() {return Xi_;}
    std::string getName() {return name_;}    

  private:
    
    std::string name_;
    Vector3d cor_;
    Mat6x6d Xi_;
    Mat6x6d D_;
    Mat3x3d Xitt_;
    Mat3x3d Xirt_; //Xirrt == Xirtr
    Mat3x3d Xitr_;
    Mat3x3d Xirr_;
    Mat6x6d S_;
    bool hasCOR;
    bool hasXi;

  };
}

#endif
Revision:	1874
Committed:	Wed May 15 15:09:35 2013 UTC (11 years, 11 months ago) by gezelter
File size:	4344 byte(s)
Log Message:	Fixed a bunch of cppcheck warnings.
#	User	Rev	Content
1	gezelter	981	/*
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	gezelter	981	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	981	* 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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	gezelter	981	*/
42
43			#ifndef HYDRODYNAMICS_HYDROPROP_HPP
44			#define HYDRODYNAMICS_HYDROPROP_HPP
45			#include "math/Vector3.hpp"
46			#include "math/SquareMatrix3.hpp"
47	gezelter	1390	namespace OpenMD {
48	gezelter	981
49	xsun	1184	/**
50			* @class HydroProp HydroProp.hpp "hydrodynamics/HydroProp.hpp"
51			* Container for information about the hydrodynamic behavior of objects
52			* undergoing Langevin dynamics.
53			* @note the units for the center of resistance (a location) are in Angstroms
54			*
55			* @note the units of Xi, the resistance tensor are:
56			* Xitt (Translation-translation) : kcal fs mol^-1 Angstroms^-2
57			* Xirt (Rotation-translation) : kcal fs mol^-1 Angstroms^-1 radians^-1
58			* Xitr (Translation-rotation) : kcal fs mol^-1 Angstroms^-1 radians^-1
59			* Xirr (Rotation-rotation) : kcal fs mol^-1 radians^-2
60			*
61			* @note the units of D, the diffusion tensor are:
62			* Dtt (Translation-translation) : Angstroms^2 fs^-1
63			* Drt (Rotation-translation) : Angstroms fs^-1
64			* Dtr (Translation-rotation) : Angstroms fs^-1
65			* Drr (Rotation-rotation) : fs^-1
66			*
67			* @note after setting the value of Xi manually, the complete() function
68			* should be called to perform the Cholesky Decomposition.
69			*/
70	gezelter	981	class HydroProp {
71
72			public:
73			HydroProp();
74			HydroProp(Vector3d cor, Mat6x6d Xi, Mat6x6d D);
75	gezelter	1874	HydroProp(const std::string &frictionLine);
76	gezelter	981	~HydroProp() { } ;
77			void complete();
78			void setCOR(Vector3d cor) {cor_ = cor; hasCOR = true;}
79			void setXi(Mat6x6d Xi) {Xi_ = Xi; hasXi = true;}
80			void setD(Mat6x6d D) {D_ = D;}
81			void setName(std::string name) {name_ = name;}
82
83			Vector3d getCOR() {return cor_;}
84			Mat3x3d getXitt() {return Xitt_;}
85			Mat3x3d getXitr() {return Xitr_;}
86			Mat3x3d getXirt() {return Xirt_;}
87			Mat3x3d getXirr() {return Xirr_;}
88			Mat6x6d getS() {return S_;}
89			Mat6x6d getD() {return D_;}
90			Mat6x6d getXi() {return Xi_;}
91			std::string getName() {return name_;}
92
93			private:
94
95			std::string name_;
96			Vector3d cor_;
97			Mat6x6d Xi_;
98			Mat6x6d D_;
99			Mat3x3d Xitt_;
100			Mat3x3d Xirt_; //Xirrt == Xirtr
101			Mat3x3d Xitr_;
102			Mat3x3d Xirr_;
103			Mat6x6d S_;
104			bool hasCOR;
105			bool hasXi;
106
107			};
108			}
109
110			#endif