src/integrators/VelocityVerletIntegrator.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.
 */
 
/**
 * @file VelocityVerletIntegrator.hpp
 * @author tlin
 * @date 11/08/2004
 * @time 13:25am
 * @version 1.0
 */

#ifndef INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP
#define INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP

#include "integrators/Integrator.hpp"
#include "integrators/RotationAlgorithm.hpp"
#include "constraints/Rattle.hpp"
namespace oopse {

  /**
   * @class VelocityVerletIntegrator VelocityVerletIntegrator.hpp "integrators/VelocityVerletIntegrator.hpp"
   * @brief  Velocity-Verlet Family Integrator
   * Template pattern is used in VelocityVerletIntegrator class. 
   */
  class VelocityVerletIntegrator : public Integrator {
  public:
    virtual ~VelocityVerletIntegrator();

    void setRotationAlgorithm(RotationAlgorithm* algo) {
      if (algo != rotAlgo && rotAlgo != NULL){            
        delete rotAlgo;
      }
            
      rotAlgo = algo;
    }
        
  protected:

    VelocityVerletIntegrator(SimInfo* info);

    virtual void doIntegrate();

    virtual void initialize();

    virtual void preStep();
        
    virtual void integrateStep();        

    virtual void postStep();

    virtual void finalize();

    virtual void resetIntegrator() {}
    
    RotationAlgorithm* rotAlgo;
    Rattle* rattle;
    RealType dt2;

    RealType currSample;
    RealType currStatus;
    RealType currThermal;
    RealType currReset;
    RealType currRNEMD;
        
  private:
        
    virtual void calcForce(bool needPotential, bool needStress);    
        
    virtual void moveA() = 0;
        
    virtual void moveB() = 0;        

    virtual RealType calcConservedQuantity() = 0;

    virtual DumpWriter* createDumpWriter();

    virtual StatWriter* createStatWriter();

  };

} //end namespace oopse
#endif //INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP
Revision:	3520
Committed:	Mon Sep 7 16:31:51 2009 UTC (15 years, 10 months ago) by cli2
File size:	3868 byte(s)
Log Message:	Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	/**
43			* @file VelocityVerletIntegrator.hpp
44			* @author tlin
45			* @date 11/08/2004
46			* @time 13:25am
47			* @version 1.0
48			*/
49	gezelter	1930
50			#ifndef INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP
51			#define INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP
52
53			#include "integrators/Integrator.hpp"
54			#include "integrators/RotationAlgorithm.hpp"
55			#include "constraints/Rattle.hpp"
56			namespace oopse {
57
58	gezelter	2204	/**
59			* @class VelocityVerletIntegrator VelocityVerletIntegrator.hpp "integrators/VelocityVerletIntegrator.hpp"
60			* @brief Velocity-Verlet Family Integrator
61			* Template pattern is used in VelocityVerletIntegrator class.
62			*/
63			class VelocityVerletIntegrator : public Integrator {
64			public:
65			virtual ~VelocityVerletIntegrator();
66	gezelter	1930
67	gezelter	2204	void setRotationAlgorithm(RotationAlgorithm* algo) {
68			if (algo != rotAlgo && rotAlgo != NULL){
69			delete rotAlgo;
70			}
71	gezelter	1930
72	gezelter	2204	rotAlgo = algo;
73			}
74	gezelter	1930
75	gezelter	2204	protected:
76	gezelter	1930
77	gezelter	2204	VelocityVerletIntegrator(SimInfo* info);
78	gezelter	1930
79	gezelter	2204	virtual void doIntegrate();
80	gezelter	1930
81	gezelter	2204	virtual void initialize();
82	gezelter	1930
83	gezelter	2204	virtual void preStep();
84	gezelter	1930
85	gezelter	2204	virtual void integrateStep();
86	gezelter	1930
87	gezelter	2204	virtual void postStep();
88	gezelter	1930
89	gezelter	2204	virtual void finalize();
90	gezelter	1930
91	tim	2243	virtual void resetIntegrator() {}
92
93	gezelter	2204	RotationAlgorithm* rotAlgo;
94			Rattle* rattle;
95	tim	2759	RealType dt2;
96	gezelter	1930
97	tim	2759	RealType currSample;
98			RealType currStatus;
99			RealType currThermal;
100			RealType currReset;
101	gezelter	3488	RealType currRNEMD;
102	gezelter	1930
103	gezelter	2204	private:
104	gezelter	1930
105	gezelter	2204	virtual void calcForce(bool needPotential, bool needStress);
106	gezelter	1930
107	gezelter	2204	virtual void moveA() = 0;
108	gezelter	1930
109	gezelter	2204	virtual void moveB() = 0;
110	gezelter	1930
111	tim	2759	virtual RealType calcConservedQuantity() = 0;
112	gezelter	1930
113	gezelter	2204	virtual DumpWriter* createDumpWriter();
114	tim	2008
115	gezelter	2204	virtual StatWriter* createStatWriter();
116	gezelter	1930
117	gezelter	2204	};
118	gezelter	1930
119			} //end namespace oopse
120			#endif //INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP