src/integrators/LDForceManager.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 INTEGRATOR_LDFORCEMANAGER_HPP
#define INTEGRATOR_LDFORCEMANAGER_HPP

#include "brains/ForceManager.hpp"
#include "primitives/Molecule.hpp"
#include "math/SeqRandNumGen.hpp"

namespace oopse {
  
  
  struct HydroProp{
    Vector3d cor;
    Mat3x3d Xirtt;
    Mat3x3d Xirrt; //Xirrt == Xirtr
    Mat3x3d Xirtr;
    Mat3x3d Xirrr;
    Mat6x6d S;
  };
  
  /**
   * @class LDForceManager
   * Force manager for Lagevin Dynamics applying friction and random 
   * forces as well as torques.
   */
  class LDForceManager : public ForceManager{
    
  public:
    LDForceManager(SimInfo * info);
    
  protected:
    virtual void postCalculation();
    
  private:
    std::map<std::string, HydroProp> parseFrictionFile(const std::string& filename);    
    void genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance);
    std::vector<HydroProp> hydroProps_;
    SeqRandNumGen randNumGen_;    
    double variance_;
    double langevinBufferRadius_;
    double frozenBufferRadius_;
    bool sphericalBoundaryConditions_;
  };
  
} //end namespace oopse
#endif //BRAINS_FORCEMANAGER_HPP

Revision:	2733
Committed:	Tue Apr 25 02:09:01 2006 UTC (18 years, 2 months ago) by gezelter
File size:	3207 byte(s)
Log Message:	Adding spherical boundary conditions to LD integrator
#	User	Rev	Content
1	tim	2611	/*
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
42			#ifndef INTEGRATOR_LDFORCEMANAGER_HPP
43			#define INTEGRATOR_LDFORCEMANAGER_HPP
44
45			#include "brains/ForceManager.hpp"
46			#include "primitives/Molecule.hpp"
47			#include "math/SeqRandNumGen.hpp"
48
49			namespace oopse {
50	gezelter	2733
51
52			struct HydroProp{
53	tim	2634	Vector3d cor;
54			Mat3x3d Xirtt;
55			Mat3x3d Xirrt; //Xirrt == Xirtr
56			Mat3x3d Xirtr;
57			Mat3x3d Xirrr;
58			Mat6x6d S;
59	gezelter	2733	};
60
61	tim	2611	/**
62			* @class LDForceManager
63	gezelter	2733	* Force manager for Lagevin Dynamics applying friction and random
64			* forces as well as torques.
65	tim	2611	*/
66	gezelter	2733	class LDForceManager : public ForceManager{
67
68	tim	2611	public:
69			LDForceManager(SimInfo * info);
70	gezelter	2733
71	tim	2611	protected:
72			virtual void postCalculation();
73	gezelter	2733
74	tim	2611	private:
75			std::map<std::string, HydroProp> parseFrictionFile(const std::string& filename);
76			void genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance);
77			std::vector<HydroProp> hydroProps_;
78			SeqRandNumGen randNumGen_;
79			double variance_;
80	gezelter	2733	double langevinBufferRadius_;
81			double frozenBufferRadius_;
82			bool sphericalBoundaryConditions_;
83			};
84
85	tim	2611	} //end namespace oopse
86			#endif //BRAINS_FORCEMANAGER_HPP
87