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

#ifndef INTEGRATORS_INTEGRATOR_HPP
#define INTEGRATORS_INTEGRATOR_HPP

#include "brains/ForceManager.hpp"
#include "restraints/ThermoIntegrationForceManager.hpp"
#include "io/DumpWriter.hpp"
#include "io/StatWriter.hpp"
#include "integrators/Velocitizer.hpp"
#include "integrators/RNEMD.hpp"

namespace oopse {


  /**
   * @class Integrator Integrator.hpp "integrators/Integrator.hpp"
   * @brief Base class of Integrator
   * @todo document
   */
  class Integrator {
  public:

    virtual ~Integrator();

    //avoid public virtual function        
    void integrate() {
      doIntegrate();
    }

    void update() {
      doUpdate();
    }

    void setForceManager(ForceManager* forceMan) {

      if (forceMan_ != forceMan && forceMan_  != NULL) {
        delete forceMan_;
      }
      forceMan_ = forceMan;
    }

    void setVelocitizer(Velocitizer* velocitizer) {
      if (velocitizer_ != velocitizer && velocitizer_  != NULL) {
        delete velocitizer_;
      }
      velocitizer_  = velocitizer;
    }

    void setRNEMD(RNEMD* rnemd) {
      if (rnemd_ != rnemd && rnemd_  != NULL) {
        delete rnemd_;
      }
      rnemd_  = rnemd;
    }
        
  protected:

    Integrator(SimInfo* info);

    virtual void doIntegrate() = 0;

    virtual void doUpdate() {}
        
    void saveConservedQuantity() {
      currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = calcConservedQuantity();
    }
        
    SimInfo* info_;
    Globals* simParams;
    ForceManager* forceMan_;
    bool needPotential;
    bool needStress;
    bool needReset;    
    Velocitizer* velocitizer_;
    RNEMD* rnemd_;
    bool needVelocityScaling;
    RealType targetScalingTemp;

    bool useRNEMD;    
    
    DumpWriter* dumpWriter;
    StatWriter* statWriter;
    Thermo thermo;

    RealType runTime;
    RealType sampleTime;
    RealType statusTime;
    RealType thermalTime;
    RealType resetTime;
    RealType RNEMD_swapTime;
    RealType dt;

    Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change

        
  private:
        
    virtual RealType calcConservedQuantity() = 0;
        
    virtual DumpWriter* createDumpWriter() = 0;

    virtual StatWriter* createStatWriter() = 0;
  };

    
}
#endif //INTEGRATORS_INTEGRATOR_HPP
Revision:	1360
Committed:	Mon Sep 7 16:31:51 2009 UTC (15 years, 7 months ago) by cli2
Original Path:	*trunk/src/integrators/Integrator.hpp*
File size:	4460 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	507	/*
2	gezelter	246	* 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	507	/**
43			* @file Integrator.hpp
44			* @author tlin
45			* @date 11/08/2004
46			* @time 13:25am
47			* @version 1.0
48			*/
49	gezelter	2
50	gezelter	246	#ifndef INTEGRATORS_INTEGRATOR_HPP
51			#define INTEGRATORS_INTEGRATOR_HPP
52	gezelter	2
53	gezelter	246	#include "brains/ForceManager.hpp"
54	chrisfen	417	#include "restraints/ThermoIntegrationForceManager.hpp"
55	gezelter	246	#include "io/DumpWriter.hpp"
56			#include "io/StatWriter.hpp"
57			#include "integrators/Velocitizer.hpp"
58	gezelter	1329	#include "integrators/RNEMD.hpp"
59	gezelter	2
60	gezelter	246	namespace oopse {
61	gezelter	2
62
63	gezelter	507	/**
64			* @class Integrator Integrator.hpp "integrators/Integrator.hpp"
65			* @brief Base class of Integrator
66			* @todo document
67			*/
68			class Integrator {
69			public:
70	gezelter	2
71	gezelter	507	virtual ~Integrator();
72	gezelter	2
73	gezelter	507	//avoid public virtual function
74			void integrate() {
75			doIntegrate();
76			}
77	gezelter	2
78	gezelter	507	void update() {
79			doUpdate();
80			}
81	gezelter	2
82	gezelter	507	void setForceManager(ForceManager* forceMan) {
83	cli2	1360
84	gezelter	507	if (forceMan_ != forceMan && forceMan_ != NULL) {
85			delete forceMan_;
86			}
87			forceMan_ = forceMan;
88			}
89	gezelter	2
90	gezelter	507	void setVelocitizer(Velocitizer* velocitizer) {
91			if (velocitizer_ != velocitizer && velocitizer_ != NULL) {
92			delete velocitizer_;
93			}
94			velocitizer_ = velocitizer;
95			}
96	gezelter	1329
97			void setRNEMD(RNEMD* rnemd) {
98			if (rnemd_ != rnemd && rnemd_ != NULL) {
99			delete rnemd_;
100			}
101			rnemd_ = rnemd;
102			}
103	gezelter	246
104	gezelter	507	protected:
105	gezelter	2
106	gezelter	507	Integrator(SimInfo* info);
107	gezelter	2
108	gezelter	507	virtual void doIntegrate() = 0;
109	gezelter	2
110	gezelter	507	virtual void doUpdate() {}
111	gezelter	246
112	gezelter	507	void saveConservedQuantity() {
113			currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = calcConservedQuantity();
114			}
115	gezelter	246
116	gezelter	507	SimInfo* info_;
117			Globals* simParams;
118			ForceManager* forceMan_;
119			bool needPotential;
120			bool needStress;
121	tim	546	bool needReset;
122	gezelter	507	Velocitizer* velocitizer_;
123	gezelter	1329	RNEMD* rnemd_;
124	gezelter	507	bool needVelocityScaling;
125	tim	963	RealType targetScalingTemp;
126	gezelter	1329
127			bool useRNEMD;
128	gezelter	246
129	gezelter	507	DumpWriter* dumpWriter;
130			StatWriter* statWriter;
131			Thermo thermo;
132	gezelter	2
133	tim	963	RealType runTime;
134			RealType sampleTime;
135			RealType statusTime;
136			RealType thermalTime;
137			RealType resetTime;
138	gezelter	1329	RealType RNEMD_swapTime;
139	tim	963	RealType dt;
140	gezelter	2
141	gezelter	507	Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change
142	gezelter	2
143	gezelter	246
144	gezelter	507	private:
145	gezelter	246
146	tim	963	virtual RealType calcConservedQuantity() = 0;
147	gezelter	246
148	gezelter	507	virtual DumpWriter* createDumpWriter() = 0;
149	tim	276
150	gezelter	507	virtual StatWriter* createStatWriter() = 0;
151			};
152	gezelter	2
153
154	gezelter	246	}
155			#endif //INTEGRATORS_INTEGRATOR_HPP