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