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 "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;
    }

    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;
    }

    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() {
      currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = 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;    
    
    DumpWriter* dumpWriter;
    StatWriter* statWriter;
    Thermo thermo;

    RealType runTime;
    RealType sampleTime;
    RealType statusTime;
    RealType thermalTime;
    RealType resetTime;
    RealType RNEMD_exchangeTime;
    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:	1731
Committed:	Thu May 31 12:25:30 2012 UTC (12 years, 11 months ago) by gezelter
File size:	5226 byte(s)
Log Message:	Reorganized source directories, added RNEMD and flucQ blocks for options parsing.
#	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 "io/DumpWriter.hpp"
57	#include "io/StatWriter.hpp"
58	#include "integrators/RotationAlgorithm.hpp"
59	#include "flucq/FluctuatingChargePropagator.hpp"
60	#include "integrators/Velocitizer.hpp"
61	#include "rnemd/RNEMD.hpp"
62	#include "constraints/Rattle.hpp"
63
64	namespace OpenMD {
65
66
67	/**
68	* @class Integrator Integrator.hpp "integrators/Integrator.hpp"
69	* @brief Base class of Integrator
70	* @todo document
71	*/
72	class Integrator {
73	public:
74
75	virtual ~Integrator();
76
77	//avoid public virtual function
78	void integrate() {
79	doIntegrate();
80	}
81
82	void updateSizes() {
83	doUpdateSizes();
84	flucQ_->updateSizes();
85	}
86
87	void setForceManager(ForceManager* forceMan) {
88
89	if (forceMan_ != forceMan && forceMan_ != NULL) {
90	delete forceMan_;
91	}
92	forceMan_ = forceMan;
93	}
94
95	void setVelocitizer(Velocitizer* velocitizer) {
96	if (velocitizer_ != velocitizer && velocitizer_ != NULL) {
97	delete velocitizer_;
98	}
99	velocitizer_ = velocitizer;
100	}
101
102	void setFluctuatingChargePropagator(FluctuatingChargePropagator* prop) {
103	if (prop != flucQ_ && flucQ_ != NULL){
104	delete flucQ_;
105	}
106	flucQ_ = prop;
107	}
108
109	void setRotationAlgorithm(RotationAlgorithm* algo) {
110	if (algo != rotAlgo_ && rotAlgo_ != NULL){
111	delete rotAlgo_;
112	}
113
114	rotAlgo_ = algo;
115	}
116
117	void setRNEMD(RNEMD* rnemd) {
118	if (rnemd_ != rnemd && rnemd_ != NULL) {
119	delete rnemd_;
120	}
121	rnemd_ = rnemd;
122	}
123
124	protected:
125
126	Integrator(SimInfo* info);
127
128	virtual void doIntegrate() = 0;
129
130	virtual void doUpdateSizes() {}
131
132	void saveConservedQuantity() {
133	currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = calcConservedQuantity();
134	}
135
136	SimInfo* info_;
137	Globals* simParams;
138	ForceManager* forceMan_;
139	RotationAlgorithm* rotAlgo_;
140	FluctuatingChargePropagator* flucQ_;
141	Rattle* rattle_;
142	Velocitizer* velocitizer_;
143	RNEMD* rnemd_;
144
145	bool needPotential;
146	bool needStress;
147	bool needReset;
148	bool needVelocityScaling;
149	RealType targetScalingTemp;
150
151	bool useRNEMD;
152
153	DumpWriter* dumpWriter;
154	StatWriter* statWriter;
155	Thermo thermo;
156
157	RealType runTime;
158	RealType sampleTime;
159	RealType statusTime;
160	RealType thermalTime;
161	RealType resetTime;
162	RealType RNEMD_exchangeTime;
163	RealType dt;
164
165	Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change
166
167
168	private:
169
170	virtual RealType calcConservedQuantity() = 0;
171
172	virtual DumpWriter* createDumpWriter() = 0;
173
174	virtual StatWriter* createStatWriter() = 0;
175	};
176
177
178	}
179	#endif //INTEGRATORS_INTEGRATOR_HPP