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root/OpenMD/trunk/src/integrators/VelocityVerletIntegrator.hpp
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Comparing trunk/src/integrators/VelocityVerletIntegrator.hpp (file contents):
Revision 276 by tim, Wed Jan 26 15:26:47 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 6 | Line 6
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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
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.
# Line 37 | Line 28
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]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42 < /**
43 <  * @file VelocityVerletIntegrator.hpp
44 <  * @author tlin
45 <  * @date 11/08/2004
46 <  * @time 13:25am
47 <  * @version 1.0
48 <  */
42 > /**
43 > * @file VelocityVerletIntegrator.hpp
44 > * @author tlin
45 > * @date 11/08/2004
46 > * @time 13:25am
47 > * @version 1.0
48 > */
49  
50   #ifndef INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP
51   #define INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP
# Line 53 | Line 53
53   #include "integrators/Integrator.hpp"
54   #include "integrators/RotationAlgorithm.hpp"
55   #include "constraints/Rattle.hpp"
56 < namespace oopse {
56 > namespace OpenMD {
57  
58 < /**
59 < * @class VelocityVerletIntegrator VelocityVerletIntegrator.hpp "integrators/VelocityVerletIntegrator.hpp"
60 < * @brief  Velocity-Verlet Family Integrator
61 < * Template pattern is used in VelocityVerletIntegrator class.
62 < */
63 < class VelocityVerletIntegrator : public Integrator {
64 <    public:
65 <        virtual ~VelocityVerletIntegrator();
58 >  /**
59 >   * @class VelocityVerletIntegrator VelocityVerletIntegrator.hpp "integrators/VelocityVerletIntegrator.hpp"
60 >   * @brief  Velocity-Verlet Family Integrator
61 >   * Template pattern is used in VelocityVerletIntegrator class.
62 >   */
63 >  class VelocityVerletIntegrator : public Integrator {
64 >  public:
65 >    virtual ~VelocityVerletIntegrator();
66  
67 <        void setRotationAlgorithm(RotationAlgorithm* algo) {
68 <            if (algo != rotAlgo && rotAlgo != NULL){            
69 <                delete rotAlgo;
70 <            }
67 >    void setRotationAlgorithm(RotationAlgorithm* algo) {
68 >      if (algo != rotAlgo && rotAlgo != NULL){            
69 >        delete rotAlgo;
70 >      }
71              
72 <            rotAlgo = algo;
73 <        }
72 >      rotAlgo = algo;
73 >    }
74          
75 <    protected:
75 >  protected:
76  
77 <        VelocityVerletIntegrator(SimInfo* info);
77 >    VelocityVerletIntegrator(SimInfo* info);
78  
79 <        virtual void doIntegrate();
79 >    virtual void doIntegrate();
80  
81 <        virtual void initialize();
81 >    virtual void initialize();
82  
83 <        virtual void preStep();
83 >    virtual void preStep();
84          
85 <        virtual void integrateStep();        
85 >    virtual void integrateStep();        
86  
87 <        virtual void postStep();
87 >    virtual void postStep();
88  
89 <        virtual void finalize();
89 >    virtual void finalize();
90  
91 <        RotationAlgorithm* rotAlgo;
92 <        Rattle* rattle;
93 <        double dt2;
91 >    virtual void resetIntegrator() {}
92 >    
93 >    RotationAlgorithm* rotAlgo;
94 >    Rattle* rattle;
95 >    RealType dt2;
96  
97 <        double currSample;
98 <        double currStatus;
99 <        double currThermal;
97 >    RealType currSample;
98 >    RealType currStatus;
99 >    RealType currThermal;
100 >    RealType currReset;
101 >    RealType currRNEMD;
102          
103 <    private:
103 >  private:
104          
105 <        virtual void calcForce(bool needPotential, bool needStress);    
105 >    virtual void calcForce(bool needPotential, bool needStress);    
106          
107 <        virtual void moveA() = 0;
107 >    virtual void moveA() = 0;
108          
109 <        virtual void moveB() = 0;        
109 >    virtual void moveB() = 0;        
110  
111 <        virtual double calcConservedQuantity() = 0;
111 >    virtual RealType calcConservedQuantity() = 0;
112  
113 <        virtual DumpWriter* createDumpWriter();
110 <        virtual DumpWriter* createEorWriter();
111 <        virtual StatWriter* createStatWriter();
113 >    virtual DumpWriter* createDumpWriter();
114  
115 < };
115 >    virtual StatWriter* createStatWriter();
116  
117 < } //end namespace oopse
117 >  };
118 >
119 > } //end namespace OpenMD
120   #endif //INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP

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