src/integrators/SMIPDForceManager.hpp

/*
 * Copyright (c) 2008 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_SMIPDFORCEMANAGER_HPP
#define INTEGRATOR_SMIPDFORCEMANAGER_HPP

#include "brains/ForceManager.hpp"
#include "primitives/Molecule.hpp"
#include "math/SeqRandNumGen.hpp"
#include "hydrodynamics/Shape.hpp"
#include "integrators/Velocitizer.hpp"
#include "math/Hull.hpp"
#include "math/Triangle.hpp"

namespace oopse {
   
  struct SDShape{
    StuntDouble* sd;
    Shape* shape;
  };
    
  /**
   * @class SMIDForceManager
   * Force manager for Surface Mesh Implicit Pressure Dynamics
   * applying friction and random forces as well as torques. 
   * Stochasitc force is determined by area of surface triangles 
   * on the convex hull. See: Kohanoff et al. CHEMPHYSCHEM 2005, 6, 1848-1852.
   */
  class SMIPDForceManager : public ForceManager{
    
  public:
    SMIPDForceManager(SimInfo * info);
    

    RealType getGamma() {
      return gamma_t_;
    }

  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<RealType> genTriangleForces(int nTriangles, RealType variance);
    std::vector<HydroProp*> hydroProps_;
    SeqRandNumGen randNumGen_;    
    RealType variance_;
    RealType langevinBufferRadius_;
    Globals* simParams;
    Velocitizer* veloMunge;
    // convergence parameters:
    int maxIterNum_;
    RealType forceTolerance_;
    RealType dt_;

    RealType gamma_t_; /*Gamma at time t*/
    RealType targetTemp_;
    RealType viscosity_;
    RealType targetPressure_; /* External Pressure */
    Hull* surfaceMesh_;
    RealType Area0_;
    RealType gamma_0_;
    std::vector<StuntDouble*> localSites_;
  };
  
} //end namespace oopse
#endif //SIMPD_FORCEMANAGER

Revision:	1323
Committed:	Tue Nov 25 16:32:47 2008 UTC (16 years, 5 months ago) by chuckv
Original Path:	*trunk/src/integrators/SMIPDForceManager.hpp*
File size:	3920 byte(s)
Log Message:	Code clean-up. Removed old langevin code.
#	User	Rev	Content
1	chuckv	1293	/*
2			* Copyright (c) 2008 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_SMIPDFORCEMANAGER_HPP
43			#define INTEGRATOR_SMIPDFORCEMANAGER_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			#include "math/Hull.hpp"
51			#include "math/Triangle.hpp"
52
53			namespace oopse {
54
55			struct SDShape{
56			StuntDouble* sd;
57			Shape* shape;
58			};
59
60			/**
61			* @class SMIDForceManager
62			* Force manager for Surface Mesh Implicit Pressure Dynamics
63			* applying friction and random forces as well as torques.
64			* Stochasitc force is determined by area of surface triangles
65			* on the convex hull. See: Kohanoff et al. CHEMPHYSCHEM 2005, 6, 1848-1852.
66			*/
67			class SMIPDForceManager : public ForceManager{
68
69			public:
70			SMIPDForceManager(SimInfo * info);
71
72
73			RealType getGamma() {
74			return gamma_t_;
75			}
76
77			protected:
78			virtual void postCalculation(bool needStress);
79
80			private:
81			std::map<std::string, HydroProp*> parseFrictionFile(const std::string& filename);
82			void genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance);
83			std::vector<RealType> genTriangleForces(int nTriangles, RealType variance);
84			std::vector<HydroProp*> hydroProps_;
85			SeqRandNumGen randNumGen_;
86			RealType variance_;
87			RealType langevinBufferRadius_;
88			Globals* simParams;
89			Velocitizer* veloMunge;
90			// convergence parameters:
91			int maxIterNum_;
92			RealType forceTolerance_;
93	chuckv	1323	RealType dt_;
94
95	chuckv	1293	RealType gamma_t_; /Gamma at time t/
96			RealType targetTemp_;
97	chuckv	1323	RealType viscosity_;
98	chuckv	1293	RealType targetPressure_; /* External Pressure */
99			Hull* surfaceMesh_;
100			RealType Area0_;
101	chuckv	1307	RealType gamma_0_;
102	chuckv	1293	std::vector<StuntDouble*> localSites_;
103			};
104
105			} //end namespace oopse
106			#endif //SIMPD_FORCEMANAGER
107