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. 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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#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 OpenMD {
   
  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();
    
  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 OpenMD
#endif //BRAINS_FORCEMANAGER_HPP

Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	3814 byte(s)
Log Message:	Creating busticated version of OpenMD
#	User	Rev	Content
1	tim	895	/*
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	895	* 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	895	* 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			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	895	*/
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	gezelter	956	#include "hydrodynamics/Shape.hpp"
49	gezelter	983	#include "integrators/Velocitizer.hpp"
50	tim	895
51	gezelter	1390	namespace OpenMD {
52	gezelter	956
53			struct SDShape{
54			StuntDouble* sd;
55			Shape* shape;
56			};
57	gezelter	981
58	tim	895	/**
59			* @class LDForceManager
60	gezelter	945	* Force manager for Lagevin Dynamics applying friction and random
61			* forces as well as torques.
62	tim	895	*/
63	gezelter	945	class LDForceManager : public ForceManager{
64
65	tim	895	public:
66			LDForceManager(SimInfo * info);
67	gezelter	945
68	gezelter	1237	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	tim	895	protected:
94	gezelter	1464	virtual void postCalculation();
95	gezelter	945
96	tim	895	private:
97	gezelter	981	std::map<std::string, HydroProp*> parseFrictionFile(const std::string& filename);
98	tim	963	void genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance);
99	gezelter	981	std::vector<HydroProp*> hydroProps_;
100	tim	895	SeqRandNumGen randNumGen_;
101	tim	963	RealType variance_;
102			RealType langevinBufferRadius_;
103			RealType frozenBufferRadius_;
104	gezelter	945	bool sphericalBoundaryConditions_;
105	gezelter	983	Globals* simParams;
106			Velocitizer* veloMunge;
107	gezelter	1237	// convergence parameters:
108			int maxIterNum_;
109			RealType forceTolerance_;
110			RealType dt2_;
111	gezelter	945	};
112
113	gezelter	1390	} //end namespace OpenMD
114	tim	895	#endif //BRAINS_FORCEMANAGER_HPP
115