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