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root/OpenMD/trunk/src/constraints/ZconstraintForceManager.hpp
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Comparing trunk/src/constraints/ZconstraintForceManager.hpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# 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:
# Line 56 | Line 56 | namespace oopse {
56          
57      virtual void calcForces(bool needPotential, bool needStress);
58  
59 <    double getZConsTime() { return zconsTime_; }
59 >    RealType getZConsTime() { return zconsTime_; }
60      std::string getZConsOutput() { return zconsOutput_; }    
61  
62      void update();
# Line 75 | Line 75 | namespace oopse {
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);        
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*/
87  
88 <    double zconsTime_;
88 >    RealType zconsTime_;
89      std::string zconsOutput_;
90 <    double zconsTol_;
90 >    RealType zconsTol_;
91      bool usingSMD_;
92 <    double zconsFixingTime_;  
93 <    double zconsGap_;
92 >    RealType zconsFixingTime_;  
93 >    RealType zconsGap_;
94      bool usingZconsGap_;
95 <    double dt_;
95 >    RealType dt_;
96  
97      const static int whichDirection = 2;
98  
99      std::map<int, ZconstraintParam> allZMolIndices_;
100  
101      Snapshot* currSnapshot_;
102 <    double currZconsTime_;
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;
108 >    const RealType infiniteTime;
109    };
110  
111   }

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