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"
#include "hydrodynamics/Shape.hpp"
#include "integrators/Velocitizer.hpp"

namespace oopse {
   
  struct SDShape{
    StuntDouble* sd;
    Shape* shape;
  };
    
  /**
   * @class LDForceManager
   * Force manager for Lagevin Dynamics applying friction and random 
   * forces as well as torques.
   */
  class LDForceManager : public ForceManager{
    
  public:
    LDForceManager(SimInfo * info);
    
    int getMaxIterationNumber() {
      return maxIterNum_;
    }
        
    void setMaxIterationNumber(int maxIter) {
      maxIterNum_ = maxIter;
    }

    RealType getForceTolerance() {
      return forceTolerance_;
    }

    void setForceTolerance(RealType tol) {
      forceTolerance_ = tol;
    }

    RealType getDt2() {
      return dt2_;
    }

    void setDt2(RealType dt2) {
      dt2_ = dt2;
    }


  protected:
    virtual void postCalculation(bool needStress);
    
  private:
    std::map<std::string, HydroProp*> parseFrictionFile(const std::string& filename);    
    void genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance);
    std::vector<HydroProp*> hydroProps_;
    SeqRandNumGen randNumGen_;    
    RealType variance_;
    RealType langevinBufferRadius_;
    RealType frozenBufferRadius_;
    bool sphericalBoundaryConditions_;
    Globals* simParams;
    Velocitizer* veloMunge;
    // convergence parameters:
    int maxIterNum_;
    RealType forceTolerance_;
    RealType dt2_;
  };
  
} //end namespace oopse
#endif //BRAINS_FORCEMANAGER_HPP

Revision:	3384
Committed:	Fri Apr 18 16:55:15 2008 UTC (17 years ago) by gezelter
File size:	3786 byte(s)
Log Message:	Adding iterative looping to get better estimates of friction forces from full-step velocities
#	Content
1	/*
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	#include "hydrodynamics/Shape.hpp"
49	#include "integrators/Velocitizer.hpp"
50
51	namespace oopse {
52
53	struct SDShape{
54	StuntDouble* sd;
55	Shape* shape;
56	};
57
58	/**
59	* @class LDForceManager
60	* Force manager for Lagevin Dynamics applying friction and random
61	* forces as well as torques.
62	*/
63	class LDForceManager : public ForceManager{
64
65	public:
66	LDForceManager(SimInfo * info);
67
68	int getMaxIterationNumber() {
69	return maxIterNum_;
70	}
71
72	void setMaxIterationNumber(int maxIter) {
73	maxIterNum_ = maxIter;
74	}
75
76	RealType getForceTolerance() {
77	return forceTolerance_;
78	}
79
80	void setForceTolerance(RealType tol) {
81	forceTolerance_ = tol;
82	}
83
84	RealType getDt2() {
85	return dt2_;
86	}
87
88	void setDt2(RealType dt2) {
89	dt2_ = dt2;
90	}
91
92
93	protected:
94	virtual void postCalculation(bool needStress);
95
96	private:
97	std::map<std::string, HydroProp*> parseFrictionFile(const std::string& filename);
98	void genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance);
99	std::vector<HydroProp*> hydroProps_;
100	SeqRandNumGen randNumGen_;
101	RealType variance_;
102	RealType langevinBufferRadius_;
103	RealType frozenBufferRadius_;
104	bool sphericalBoundaryConditions_;
105	Globals* simParams;
106	Velocitizer* veloMunge;
107	// convergence parameters:
108	int maxIterNum_;
109	RealType forceTolerance_;
110	RealType dt2_;
111	};
112
113	} //end namespace oopse
114	#endif //BRAINS_FORCEMANAGER_HPP
115