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Comparing trunk/src/integrators/LDForceManager.hpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 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 INTEGRATOR_LDFORCEMANAGER_HPP
# Line 46 | Line 47
47   #include "primitives/Molecule.hpp"
48   #include "math/SeqRandNumGen.hpp"
49   #include "hydrodynamics/Shape.hpp"
50 + #include "integrators/Velocitizer.hpp"
51  
52 < namespace oopse {
52 > namespace OpenMD {
53    
54    struct SDShape{
55      StuntDouble* sd;
56      Shape* shape;
57    };
58 <  
57 <  struct HydroProp{
58 <    Vector3d cor;
59 <    Mat3x3d Xirtt;
60 <    Mat3x3d Xirrt; //Xirrt == Xirtr
61 <    Mat3x3d Xirtr;
62 <    Mat3x3d Xirrr;
63 <    Mat6x6d S;
64 <  };
65 <  
58 >    
59    /**
60     * @class LDForceManager
61     * Force manager for Lagevin Dynamics applying friction and random
# Line 73 | Line 66 | namespace oopse {
66    public:
67      LDForceManager(SimInfo * info);
68      
69 +    int getMaxIterationNumber() {
70 +      return maxIterNum_;
71 +    }
72 +        
73 +    void setMaxIterationNumber(int maxIter) {
74 +      maxIterNum_ = maxIter;
75 +    }
76 +
77 +    RealType getForceTolerance() {
78 +      return forceTolerance_;
79 +    }
80 +
81 +    void setForceTolerance(RealType tol) {
82 +      forceTolerance_ = tol;
83 +    }
84 +
85 +    RealType getDt2() {
86 +      return dt2_;
87 +    }
88 +
89 +    void setDt2(RealType dt2) {
90 +      dt2_ = dt2;
91 +    }
92 +
93 +
94    protected:
95      virtual void postCalculation();
96      
97    private:
98 <    std::map<std::string, HydroProp> parseFrictionFile(const std::string& filename);    
98 >    std::map<std::string, HydroProp*> parseFrictionFile(const std::string& filename);    
99      void genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance);
100 <    std::vector<HydroProp> hydroProps_;
100 >    std::vector<HydroProp*> hydroProps_;
101      SeqRandNumGen randNumGen_;    
102      RealType variance_;
103      RealType langevinBufferRadius_;
104      RealType frozenBufferRadius_;
105      bool sphericalBoundaryConditions_;
106 +    Globals* simParams;
107 +    Velocitizer* veloMunge;
108 +    // convergence parameters:
109 +    int maxIterNum_;
110 +    RealType forceTolerance_;
111 +    RealType dt2_;
112    };
113    
114 < } //end namespace oopse
114 > } //end namespace OpenMD
115   #endif //BRAINS_FORCEMANAGER_HPP
116  

Comparing trunk/src/integrators/LDForceManager.hpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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