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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 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 234107 (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   #ifndef CONSTRAINTS_ZCONSTRAINTFORCEMANAGER_HPP
# Line 47 | Line 48
48   #include "brains/ForceManager.hpp"
49   #include "constraints/ZconsStruct.hpp"
50   #include "io/ZConsWriter.hpp"
51 < namespace oopse {
51 > namespace OpenMD {
52  
53 < class ZconstraintForceManager : public ForceManager {
54 <    public:
55 <        ZconstraintForceManager(SimInfo* info);
56 <        ~ZconstraintForceManager();
53 >  class ZconstraintForceManager : public ForceManager {
54 >  public:
55 >    ZconstraintForceManager(SimInfo* info);
56 >    ~ZconstraintForceManager();
57          
58 <        virtual void calcForces(bool needPotential, bool needStress);
58 >    virtual void calcForces();
59  
60 <        double getZConsTime() { return zconsTime_; }
61 <        std::string getZConsOutput() { return zconsOutput_; }    
60 >    RealType getZConsTime() { return zconsTime_; }
61 >    std::string getZConsOutput() { return zconsOutput_; }    
62  
63 <        void update();
64 <        virtual void init();
65 <    private:
63 >    void update();
64 >    virtual void init();
65 >  private:
66  
67 <        bool isZMol(Molecule* mol);
68 <        void thermalize(void);
67 >    bool isZMol(Molecule* mol);
68 >    void thermalize(void);
69  
70 <        void zeroVelocity();
71 <        void doZconstraintForce();
72 <        void doHarmonic();
73 <        bool checkZConsState();        
74 <        void updateZPos();
75 <        void updateCantPos();
76 <        void calcTotalMassMovingZMols();
77 <        bool haveMovingZMols();
78 <        bool haveFixedZMols();
79 <        double getZTargetPos(int index);        
80 <        double getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce) ;
81 <        double getZFOfMovingMols(Molecule* mol, double totalForce) ;
82 <        double getHFOfFixedZMols(Molecule* mol, StuntDouble* sd, double totalForce);
83 <        double getHFOfUnconsMols(Molecule* mol, double totalForce);        
70 >    void zeroVelocity();
71 >    void doZconstraintForce();
72 >    void doHarmonic();
73 >    bool checkZConsState();        
74 >    void updateZPos();
75 >    void updateCantPos();
76 >    void calcTotalMassMovingZMols();
77 >    bool haveMovingZMols();
78 >    bool haveFixedZMols();
79 >    RealType getZTargetPos(int index);        
80 >    RealType getZFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce) ;
81 >    RealType getZFOfMovingMols(Molecule* mol, RealType totalForce) ;
82 >    RealType getHFOfFixedZMols(Molecule* mol, StuntDouble* sd, RealType totalForce);
83 >    RealType getHFOfUnconsMols(Molecule* mol, RealType totalForce);        
84  
85 <        std::list<ZconstraintMol> movingZMols_;  /**<   moving zconstraint molecules*/
86 <        std::list<ZconstraintMol> fixedZMols_;      /**< fixed zconstraint molecules*/
87 <        std::vector<Molecule*> unzconsMols_;    /**< free molecules*/
85 >    std::list<ZconstraintMol> movingZMols_;  /**<   moving zconstraint molecules*/
86 >    std::list<ZconstraintMol> fixedZMols_;      /**< fixed zconstraint molecules*/
87 >    std::vector<Molecule*> unzconsMols_;    /**< free molecules*/
88  
89 <        double zconsTime_;
90 <        std::string zconsOutput_;
91 <        double zconsTol_;
92 <        bool usingSMD_;
93 <        double zconsFixingTime_;  
94 <        double zconsGap_;
95 <        bool usingZconsGap_;
96 <        double dt_;
89 >    RealType zconsTime_;
90 >    std::string zconsOutput_;
91 >    RealType zconsTol_;
92 >    bool usingSMD_;
93 >    RealType zconsFixingTime_;  
94 >    RealType zconsGap_;
95 >    bool usingZconsGap_;
96 >    RealType dt_;
97  
98 <        const static int whichDirection = 2;
98 >    const static int whichDirection = 2;
99  
100 <        std::map<int, ZconstraintParam> allZMolIndices_;
100 >    std::map<int, ZconstraintParam> allZMolIndices_;
101  
102 <        Snapshot* currSnapshot_;
103 <        double currZconsTime_;
102 >    Snapshot* currSnapshot_;
103 >    RealType currZconsTime_;
104  
105 <        double totMassMovingZMols_;
106 <        double totMassUnconsMols_;  /**< mass of unconstraint molecules in the whole system (never change) */
105 >    RealType totMassMovingZMols_;
106 >    RealType totMassUnconsMols_;  /**< mass of unconstraint molecules in the whole system (never change) */
107  
108 <        ZConsWriter* fzOut;
109 <        const double infiniteTime;
110 < };
108 >    ZConsWriter* fzOut;
109 >    const RealType infiniteTime;
110 >  };
111  
112   }
113   #endif

Comparing trunk/src/constraints/ZconstraintForceManager.hpp (property svn:keywords):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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