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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 1464 by gezelter, Fri Jul 9 19:29:05 2010 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 INTEGRATOR_LDFORCEMANAGER_HPP
# Line 46 | Line 46
46   #include "primitives/Molecule.hpp"
47   #include "math/SeqRandNumGen.hpp"
48   #include "hydrodynamics/Shape.hpp"
49 + #include "integrators/Velocitizer.hpp"
50  
51 < namespace oopse {
51 > namespace OpenMD {
52    
53    struct SDShape{
54      StuntDouble* sd;
55      Shape* shape;
56    };
57 <  
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 <  
57 >    
58    /**
59     * @class LDForceManager
60     * Force manager for Lagevin Dynamics applying friction and random
# Line 73 | Line 65 | namespace oopse {
65    public:
66      LDForceManager(SimInfo * info);
67      
68 +    int getMaxIterationNumber() {
69 +      return maxIterNum_;
70 +    }
71 +        
72 +    void setMaxIterationNumber(int maxIter) {
73 +      maxIterNum_ = maxIter;
74 +    }
75 +
76 +    RealType getForceTolerance() {
77 +      return forceTolerance_;
78 +    }
79 +
80 +    void setForceTolerance(RealType tol) {
81 +      forceTolerance_ = tol;
82 +    }
83 +
84 +    RealType getDt2() {
85 +      return dt2_;
86 +    }
87 +
88 +    void setDt2(RealType dt2) {
89 +      dt2_ = dt2;
90 +    }
91 +
92 +
93    protected:
94      virtual void postCalculation();
95      
96    private:
97 <    std::map<std::string, HydroProp> parseFrictionFile(const std::string& filename);    
97 >    std::map<std::string, HydroProp*> parseFrictionFile(const std::string& filename);    
98      void genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance);
99 <    std::vector<HydroProp> hydroProps_;
99 >    std::vector<HydroProp*> hydroProps_;
100      SeqRandNumGen randNumGen_;    
101      RealType variance_;
102      RealType langevinBufferRadius_;
103      RealType frozenBufferRadius_;
104      bool sphericalBoundaryConditions_;
105 +    Globals* simParams;
106 +    Velocitizer* veloMunge;
107 +    // convergence parameters:
108 +    int maxIterNum_;
109 +    RealType forceTolerance_;
110 +    RealType dt2_;
111    };
112    
113 < } //end namespace oopse
113 > } //end namespace OpenMD
114   #endif //BRAINS_FORCEMANAGER_HPP
115  

Comparing trunk/src/integrators/LDForceManager.hpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1464 by gezelter, Fri Jul 9 19:29:05 2010 UTC

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