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Comparing trunk/src/integrators/LDForceManager.hpp (file contents):
Revision 906 by tim, Fri Mar 17 23:20:35 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 45 | Line 46
46   #include "brains/ForceManager.hpp"
47   #include "primitives/Molecule.hpp"
48   #include "math/SeqRandNumGen.hpp"
49 + #include "hydrodynamics/Shape.hpp"
50 + #include "integrators/Velocitizer.hpp"
51  
52 < namespace oopse {
53 <
54 <
55 < struct HydroProp{
56 <    Vector3d cor;
57 <    Mat3x3d Xirtt;
58 <    Mat3x3d Xirrt; //Xirrt == Xirtr
56 <    Mat3x3d Xirtr;
57 <    Mat3x3d Xirrr;
58 <    Mat6x6d S;
59 < };
60 <
52 > namespace OpenMD {
53 >  
54 >  struct SDShape{
55 >    StuntDouble* sd;
56 >    Shape* shape;
57 >  };
58 >    
59    /**
60     * @class LDForceManager
61 <   * Force manager for Lagevin Dynamics applying friction and random forces as well as torques.
61 >   * Force manager for Lagevin Dynamics applying friction and random
62 >   * forces as well as torques.
63     */
64 < class LDForceManager : public ForceManager{
65 <
64 >  class LDForceManager : public ForceManager{
65 >    
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 <
96 >    
97    private:
98 <    std::map<std::string, HydroProp> parseFrictionFile(const std::string& filename);    
99 <    void genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance);
100 <    std::vector<HydroProp> hydroProps_;
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_;
101      SeqRandNumGen randNumGen_;    
102 <    double variance_;
103 < };
104 <
105 < } //end namespace oopse
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 OpenMD
115   #endif //BRAINS_FORCEMANAGER_HPP
116  

Comparing trunk/src/integrators/LDForceManager.hpp (property svn:keywords):
Revision 906 by tim, Fri Mar 17 23:20:35 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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