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 "io/RestWriter.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;
    RestWriter* restWriter;
    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:	1329
Committed:	Sat Mar 14 01:23:53 2009 UTC (16 years, 1 month ago) by gezelter
Original Path:	*trunk/src/integrators/Integrator.hpp*
File size:	4516 byte(s)
Log Message:	Adding RNEMD
#	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	chrisfen	417	#include "io/RestWriter.hpp"
58	gezelter	246	#include "integrators/Velocitizer.hpp"
59	gezelter	1329	#include "integrators/RNEMD.hpp"
60	gezelter	2
61	gezelter	246	namespace oopse {
62	gezelter	2
63
64	gezelter	507	/**
65			* @class Integrator Integrator.hpp "integrators/Integrator.hpp"
66			* @brief Base class of Integrator
67			* @todo document
68			*/
69			class Integrator {
70			public:
71	gezelter	2
72	gezelter	507	virtual ~Integrator();
73	gezelter	2
74	gezelter	507	//avoid public virtual function
75			void integrate() {
76			doIntegrate();
77			}
78	gezelter	2
79	gezelter	507	void update() {
80			doUpdate();
81			}
82	gezelter	2
83	gezelter	507	void setForceManager(ForceManager* forceMan) {
84			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			RestWriter* restWriter;
132			Thermo thermo;
133	gezelter	2
134	tim	963	RealType runTime;
135			RealType sampleTime;
136			RealType statusTime;
137			RealType thermalTime;
138			RealType resetTime;
139	gezelter	1329	RealType RNEMD_swapTime;
140	tim	963	RealType dt;
141	gezelter	2
142	gezelter	507	Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change
143	gezelter	2
144	gezelter	246
145	gezelter	507	private:
146	gezelter	246
147	tim	963	virtual RealType calcConservedQuantity() = 0;
148	gezelter	246
149	gezelter	507	virtual DumpWriter* createDumpWriter() = 0;
150	tim	276
151	gezelter	507	virtual StatWriter* createStatWriter() = 0;
152			};
153	gezelter	2
154
155	gezelter	246	}
156			#endif //INTEGRATORS_INTEGRATOR_HPP