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. 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @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 "brains/Stats.hpp"
#include "io/DumpWriter.hpp"
#include "io/StatWriter.hpp"
#include "integrators/RotationAlgorithm.hpp"
#include "flucq/FluctuatingChargePropagator.hpp"
#include "integrators/Velocitizer.hpp"
#include "rnemd/RNEMD.hpp"
#include "constraints/Rattle.hpp"

namespace OpenMD {


  /**
   * @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 updateSizes() {
      doUpdateSizes();
      flucQ_->updateSizes();
    }

    void setForceManager(ForceManager* forceMan) {

      if (forceMan_ != forceMan && forceMan_  != NULL) {
        delete forceMan_;
      }
      forceMan_ = forceMan;
      // forward this on:
      if (flucQ_ != NULL) {
        flucQ_->setForceManager(forceMan_);
      }
    }

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

    void setFluctuatingChargePropagator(FluctuatingChargePropagator* prop) {
      if (prop != flucQ_ && flucQ_ != NULL){            
        delete flucQ_;
      }            
      flucQ_ = prop;
      if (forceMan_ != NULL) {
        flucQ_->setForceManager(forceMan_);
      }
    }

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

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

    Integrator(SimInfo* info);

    virtual void doIntegrate() = 0;

    virtual void doUpdateSizes() {}
        
    void saveConservedQuantity() {
      snap->setConservedQuantity( calcConservedQuantity() );
    }
        
    SimInfo* info_;
    Globals* simParams;
    ForceManager* forceMan_;
    RotationAlgorithm* rotAlgo_;
    FluctuatingChargePropagator* flucQ_;
    Rattle* rattle_;
    Velocitizer* velocitizer_;
    RNEMD* rnemd_;

    bool needPotential;
    bool needStress;
    bool needReset;    
    bool needVelocityScaling;
    RealType targetScalingTemp;

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

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

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

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

    virtual StatWriter* createStatWriter() = 0;
  };

    
}
#endif //INTEGRATORS_INTEGRATOR_HPP
Revision:	1764
Committed:	Tue Jul 3 18:32:27 2012 UTC (12 years, 10 months ago) by gezelter
File size:	5413 byte(s)
Log Message:	Refactored Snapshot and Stats to use the Accumulator classes. Collected a number of methods into Thermo that belonged there.
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	507	/**
44			* @file Integrator.hpp
45			* @author tlin
46			* @date 11/08/2004
47			* @time 13:25am
48			* @version 1.0
49			*/
50	gezelter	2
51	gezelter	246	#ifndef INTEGRATORS_INTEGRATOR_HPP
52			#define INTEGRATORS_INTEGRATOR_HPP
53	gezelter	2
54	gezelter	246	#include "brains/ForceManager.hpp"
55	chrisfen	417	#include "restraints/ThermoIntegrationForceManager.hpp"
56	gezelter	1764	#include "brains/Stats.hpp"
57	gezelter	246	#include "io/DumpWriter.hpp"
58			#include "io/StatWriter.hpp"
59	gezelter	1715	#include "integrators/RotationAlgorithm.hpp"
60	gezelter	1731	#include "flucq/FluctuatingChargePropagator.hpp"
61	gezelter	246	#include "integrators/Velocitizer.hpp"
62	gezelter	1731	#include "rnemd/RNEMD.hpp"
63	gezelter	1715	#include "constraints/Rattle.hpp"
64	gezelter	2
65	gezelter	1390	namespace OpenMD {
66	gezelter	2
67
68	gezelter	507	/**
69			* @class Integrator Integrator.hpp "integrators/Integrator.hpp"
70			* @brief Base class of Integrator
71			* @todo document
72			*/
73			class Integrator {
74			public:
75	gezelter	2
76	gezelter	507	virtual ~Integrator();
77	gezelter	2
78	gezelter	507	//avoid public virtual function
79			void integrate() {
80			doIntegrate();
81			}
82	gezelter	2
83	gezelter	1715	void updateSizes() {
84			doUpdateSizes();
85			flucQ_->updateSizes();
86	gezelter	507	}
87	gezelter	2
88	gezelter	507	void setForceManager(ForceManager* forceMan) {
89	cli2	1360
90	gezelter	507	if (forceMan_ != forceMan && forceMan_ != NULL) {
91			delete forceMan_;
92			}
93			forceMan_ = forceMan;
94	gezelter	1760	// forward this on:
95			if (flucQ_ != NULL) {
96			flucQ_->setForceManager(forceMan_);
97			}
98	gezelter	507	}
99	gezelter	2
100	gezelter	507	void setVelocitizer(Velocitizer* velocitizer) {
101	skuang	1368	if (velocitizer_ != velocitizer && velocitizer_ != NULL) {
102	gezelter	507	delete velocitizer_;
103			}
104	skuang	1368	velocitizer_ = velocitizer;
105	gezelter	507	}
106	gezelter	1329
107	gezelter	1715	void setFluctuatingChargePropagator(FluctuatingChargePropagator* prop) {
108			if (prop != flucQ_ && flucQ_ != NULL){
109			delete flucQ_;
110			}
111			flucQ_ = prop;
112	gezelter	1760	if (forceMan_ != NULL) {
113			flucQ_->setForceManager(forceMan_);
114			}
115	gezelter	1715	}
116
117			void setRotationAlgorithm(RotationAlgorithm* algo) {
118			if (algo != rotAlgo_ && rotAlgo_ != NULL){
119			delete rotAlgo_;
120			}
121
122			rotAlgo_ = algo;
123			}
124
125	gezelter	1329	void setRNEMD(RNEMD* rnemd) {
126			if (rnemd_ != rnemd && rnemd_ != NULL) {
127			delete rnemd_;
128			}
129	skuang	1368	rnemd_ = rnemd;
130	gezelter	1329	}
131	skuang	1368
132	gezelter	507	protected:
133	gezelter	2
134	gezelter	507	Integrator(SimInfo* info);
135	gezelter	2
136	gezelter	507	virtual void doIntegrate() = 0;
137	gezelter	2
138	gezelter	1715	virtual void doUpdateSizes() {}
139	gezelter	246
140	gezelter	507	void saveConservedQuantity() {
141	gezelter	1764	snap->setConservedQuantity( calcConservedQuantity() );
142	gezelter	507	}
143	gezelter	246
144	gezelter	507	SimInfo* info_;
145			Globals* simParams;
146			ForceManager* forceMan_;
147	gezelter	1715	RotationAlgorithm* rotAlgo_;
148			FluctuatingChargePropagator* flucQ_;
149			Rattle* rattle_;
150			Velocitizer* velocitizer_;
151			RNEMD* rnemd_;
152
153	gezelter	507	bool needPotential;
154			bool needStress;
155	tim	546	bool needReset;
156	gezelter	507	bool needVelocityScaling;
157	tim	963	RealType targetScalingTemp;
158	gezelter	1329
159			bool useRNEMD;
160	gezelter	246
161	gezelter	1764	Stats* stats;
162	gezelter	507	DumpWriter* dumpWriter;
163			StatWriter* statWriter;
164			Thermo thermo;
165	gezelter	2
166	tim	963	RealType runTime;
167			RealType sampleTime;
168			RealType statusTime;
169			RealType thermalTime;
170			RealType resetTime;
171	skuang	1368	RealType RNEMD_exchangeTime;
172	tim	963	RealType dt;
173	gezelter	2
174	gezelter	1764	Snapshot* snap; // During the integration, the address of snap Will not change
175	gezelter	2
176	gezelter	246
177	gezelter	507	private:
178	gezelter	246
179	tim	963	virtual RealType calcConservedQuantity() = 0;
180	gezelter	246
181	gezelter	507	virtual DumpWriter* createDumpWriter() = 0;
182	tim	276
183	gezelter	507	virtual StatWriter* createStatWriter() = 0;
184			};
185	gezelter	2
186
187	gezelter	246	}
188			#endif //INTEGRATORS_INTEGRATOR_HPP