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Comparing trunk/src/integrators/NVT.hpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 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 NVT.hpp
44 <  * @author tlin
45 <  * @date 11/19/2004
46 <  * @time 13:25am
47 <  * @version 1.0
48 <  */
42 > /**
43 > * @file NVT.hpp
44 > * @author tlin
45 > * @date 11/19/2004
46 > * @time 13:25am
47 > * @version 1.0
48 > */
49  
50   #ifndef INTEGRATOR_NVT_HPP
51   #define INTEGRATOR_NVT_HPP
52  
53   #include "integrators/VelocityVerletIntegrator.hpp"
54  
55 < namespace oopse {
55 > namespace OpenMD {
56  
57 < /**
58 < * @class NVT NVT.hpp "integrators/NVT.hpp"
59 < * Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
60 < * @todo document
61 < */
62 < class NVT : public VelocityVerletIntegrator{
63 <    public:
64 <        NVT(SimInfo* info);
57 >  /**
58 >   * @class NVT NVT.hpp "integrators/NVT.hpp"
59 >   * Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
60 >   * @todo document
61 >   */
62 >  class NVT : public VelocityVerletIntegrator{
63 >  public:
64 >    NVT(SimInfo* info);
65  
66 <        int getMaxIterationNumber() {
67 <            return maxIterNum_;
68 <        }
66 >    int getMaxIterationNumber() {
67 >      return maxIterNum_;
68 >    }
69          
70 <        void setMaxIterationNumber(int maxIter) {
71 <            maxIterNum_ = maxIter;
72 <        }
70 >    void setMaxIterationNumber(int maxIter) {
71 >      maxIterNum_ = maxIter;
72 >    }
73  
74 <        double getTauThermostat() {
75 <            return tauThermostat_;
76 <        }
74 >    RealType getTauThermostat() {
75 >      return tauThermostat_;
76 >    }
77  
78 <        void setTauThermostat(double tt) {
79 <            tauThermostat_ = tt;
80 <        }
78 >    void setTauThermostat(RealType tt) {
79 >      tauThermostat_ = tt;
80 >    }
81  
82 <        double getTargetTemp() {
83 <            return targetTemp_;
84 <        }
82 >    RealType getTargetTemp() {
83 >      return targetTemp_;
84 >    }
85  
86 <        void setTargetTemp(double tt) {
87 <            targetTemp_ = tt;
88 <        }
86 >    void setTargetTemp(RealType tt) {
87 >      targetTemp_ = tt;
88 >    }
89  
90 <        double getChiTolerance() {
91 <            return chiTolerance_;
92 <        }
90 >    RealType getChiTolerance() {
91 >      return chiTolerance_;
92 >    }
93  
94 <        void setChiTolerance(double tol) {
95 <            chiTolerance_ = tol;
96 <        }
94 >    void setChiTolerance(RealType tol) {
95 >      chiTolerance_ = tol;
96 >    }
97  
98          
99 <    protected:
100 <        virtual void moveA();
99 >  protected:
100 >    virtual void moveA();
101  
102 <        virtual void moveB();
102 >    virtual void moveB();
103  
104 <        virtual void doUpdate() ;
105 <        
106 <    private:
107 <        virtual double calcConservedQuantity();              
104 >    virtual void doUpdate() ;
105  
106 <        int maxIterNum_;
107 <        double targetTemp_;
108 <        double tauThermostat_;
109 <        double chiTolerance_;
106 >    virtual void resetIntegrator();
107 >    
108 >  private:
109 >    virtual RealType calcConservedQuantity();              
110  
111 <        std::vector<Vector3d> oldVel_;
112 <        std::vector<Vector3d> oldJi_;
113 < };
111 >    int maxIterNum_;
112 >    RealType targetTemp_;
113 >    RealType tauThermostat_;
114 >    RealType chiTolerance_;
115  
116 +    std::vector<Vector3d> oldVel_;
117 +    std::vector<Vector3d> oldJi_;
118 +  };
119  
119 – } //end namespace oopse
120  
121 + } //end namespace OpenMD
122 +
123   #endif //INTEGRATOR_NVT_HPP

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