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root/OpenMD/trunk/src/constraints/ZconstraintForceManager.hpp
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Comparing trunk/src/constraints/ZconstraintForceManager.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   #ifndef CONSTRAINTS_ZCONSTRAINTFORCEMANAGER_HPP
# Line 47 | Line 47
47   #include "brains/ForceManager.hpp"
48   #include "constraints/ZconsStruct.hpp"
49   #include "io/ZConsWriter.hpp"
50 < namespace oopse {
50 > namespace OpenMD {
51  
52 < class ZconstraintForceManager : public ForceManager {
53 <    public:
54 <        ZconstraintForceManager(SimInfo* info);
55 <        ~ZconstraintForceManager();
52 >  class ZconstraintForceManager : public ForceManager {
53 >  public:
54 >    ZconstraintForceManager(SimInfo* info);
55 >    ~ZconstraintForceManager();
56          
57 <        virtual void calcForces(bool needPotential, bool needStress);
57 >    virtual void calcForces(bool needPotential, bool needStress);
58  
59 <        double getZConsTime() { return zconsTime_; }
60 <        std::string getZConsOutput() { return zconsOutput_; }    
59 >    RealType getZConsTime() { return zconsTime_; }
60 >    std::string getZConsOutput() { return zconsOutput_; }    
61  
62 <        void update();
63 <        virtual void init();
64 <    private:
62 >    void update();
63 >    virtual void init();
64 >  private:
65  
66 <        bool isZMol(Molecule* mol);
67 <        void thermalize(void);
66 >    bool isZMol(Molecule* mol);
67 >    void thermalize(void);
68  
69 <        void zeroVelocity();
70 <        void doZconstraintForce();
71 <        void doHarmonic();
72 <        bool checkZConsState();        
73 <        void updateZPos();
74 <        void updateCantPos();
75 <        void calcTotalMassMovingZMols();
76 <        bool haveMovingZMols();
77 <        bool haveFixedZMols();
78 <        double getZTargetPos(int index);        
79 <        double getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce) ;
80 <        double getZFOfMovingMols(Molecule* mol, double totalForce) ;
81 <        double getHFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce);
82 <        double getHFOfUnconsMols(Molecule* mol, double totalForce);        
69 >    void zeroVelocity();
70 >    void doZconstraintForce();
71 >    void doHarmonic();
72 >    bool checkZConsState();        
73 >    void updateZPos();
74 >    void updateCantPos();
75 >    void calcTotalMassMovingZMols();
76 >    bool haveMovingZMols();
77 >    bool haveFixedZMols();
78 >    RealType getZTargetPos(int index);        
79 >    RealType getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce) ;
80 >    RealType getZFOfMovingMols(Molecule* mol, RealType totalForce) ;
81 >    RealType getHFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce);
82 >    RealType getHFOfUnconsMols(Molecule* mol, RealType totalForce);        
83  
84 <        std::list<ZconstraintMol> movingZMols_;  /**<   moving zconstraint molecules*/
85 <        std::list<ZconstraintMol> fixedZMols_;      /**< fixed zconstraint molecules*/
86 <        std::vector<Molecule*> unzconsMols_;    /**< free molecules*/
84 >    std::list<ZconstraintMol> movingZMols_;  /**<   moving zconstraint molecules*/
85 >    std::list<ZconstraintMol> fixedZMols_;      /**< fixed zconstraint molecules*/
86 >    std::vector<Molecule*> unzconsMols_;    /**< free molecules*/
87  
88 <        double zconsTime_;
89 <        std::string zconsOutput_;
90 <        double zconsTol_;
91 <        bool usingSMD_;
92 <        double zconsFixingTime_;  
93 <        double zconsGap_;
94 <        bool usingZconsGap_;
95 <        double dt_;
88 >    RealType zconsTime_;
89 >    std::string zconsOutput_;
90 >    RealType zconsTol_;
91 >    bool usingSMD_;
92 >    RealType zconsFixingTime_;  
93 >    RealType zconsGap_;
94 >    bool usingZconsGap_;
95 >    RealType dt_;
96  
97 <        const static int whichDirection = 2;
97 >    const static int whichDirection = 2;
98  
99 <        std::map<int, ZconstraintParam> allZMolIndices_;
99 >    std::map<int, ZconstraintParam> allZMolIndices_;
100  
101 <        Snapshot* currSnapshot_;
102 <        double currZconsTime_;
101 >    Snapshot* currSnapshot_;
102 >    RealType currZconsTime_;
103  
104 <        double totMassMovingZMols_;
105 <        double totMassUnconsMols_;  /**< mass of unconstraint molecules in the whole system (never change) */
104 >    RealType totMassMovingZMols_;
105 >    RealType totMassUnconsMols_;  /**< mass of unconstraint molecules in the whole system (never change) */
106  
107 <        ZConsWriter* fzOut;
108 <        const double infiniteTime;
109 < };
107 >    ZConsWriter* fzOut;
108 >    const RealType infiniteTime;
109 >  };
110  
111   }
112   #endif

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