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Comparing trunk/src/applications/hydrodynamics/RoughShell.hpp (file contents):
Revision 898 by tim, Wed Mar 15 15:51:44 2006 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   #ifndef APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP
42   #define APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP
43  
44 < #include "applications/hydrodynamics/HydrodynamicsModel.hpp"
45 <
46 < namespace oopse {
47 < /**
48 < * @class Grid3d
49 < * A generic 3d grid class
50 < */
51 < template<class Elem>
52 < class Grid3D {
53 <    public:
54 <        Grid3D(unsigned int dim1, unsigned int dim2, unsigned int dim3) : dim1_(dim1), dim2_(dim2), dim3_(dim3) {
55 <            data_.resize(dim1_*dim2_*dim3_);
56 <        }
57 <        Elem& operator ()(unsigned int i, unsigned int j, unsigned int k) {
58 <            int index = isValidGrid(i, j , k);
59 <            assert(index != -1);
60 <            return data_[index];
61 <        }
62 <
63 <        const Elem& operator () (unsigned int i, unsigned int j, unsigned int k) const {
64 <            int index = isValidGrid(i, j , k);
65 <            assert(index != -1);
66 <            return data_[index];
67 <        }
68 <        
69 <        std::vector<Elem> getAllNeighbors(unsigned int i, unsigned int j, unsigned int k) {
70 <            std::vector<Elem> result;
71 <            int index;
72 <            index = isValidGrid(i-1, j, k);
73 <            if (index != -1)
74 <                result.push_back(data_[index]);
75 <
76 <            index = isValidGrid(i+1, j, k);
77 <            if (index != -1)
78 <                result.push_back(data_[index]);
79 <
80 <            index = isValidGrid(i, j-1, k);
81 <            if (index != -1)
82 <                result.push_back(data_[index]);
83 <
84 <            index = isValidGrid(i, j+1, k);
85 <            if (index != -1)
86 <                result.push_back(data_[index]);
87 <
88 <            index = isValidGrid(i, j, k-1);
89 <            if (index != -1)
90 <                result.push_back(data_[index]);
91 <
92 <            index = isValidGrid(i, j, k+1);
93 <            if (index != -1)
94 <                result.push_back(data_[index]);
95 <
96 <            return result;
97 <        }
98 <    private:
99 <
100 <        int isValidGrid(unsigned int i, unsigned int j, unsigned int k) {
101 <            int index = i * dim2_*dim3_ + j * dim3_ + k;
102 <            return index < data_.size() ? index : -1;
103 <        };
104 <        
105 <        unsigned int dim1_;
106 <        unsigned int dim2_;
107 <        unsigned int dim3_;
108 <        std::vector<Elem> data_;
109 <
110 < };
44 > #include "applications/hydrodynamics/ApproximationModel.hpp"
45 > #include "applications/hydrodynamics/CompositeShape.hpp"
46 > namespace OpenMD {
47 >  /**
48 >   * @class Grid3d
49 >   * A generic 3d grid class
50 >   */
51 >  template<class Elem>
52 >  class Grid3D {
53 >  public:
54 >    Grid3D(unsigned int dim1, unsigned int dim2, unsigned int dim3) : dim1_(dim1), dim2_(dim2), dim3_(dim3) {
55 >      data_.resize(dim1_*dim2_*dim3_);
56 >    }
57 >    Elem& operator ()(unsigned int i, unsigned int j, unsigned int k) {
58 >      int index = isValidGrid(i, j , k);
59 >      assert(index != -1);
60 >      return data_[index];
61 >    }
62      
63 +    const Elem& operator () (unsigned int i, unsigned int j, unsigned int k) const {
64 +      int index = isValidGrid(i, j , k);
65 +      assert(index != -1);
66 +      return data_[index];
67 +    }
68      
69 < class RoughShell : public HydrodynamicsModel {
70 <    public:
71 <        RoughShell(StuntDouble* sd, const DynamicProperty& extraParams);
72 <    private:
73 <        virtual bool createBeads(std::vector<BeadParam>& beads);
74 <        StuntDoubleShape sdShape_;
75 <        double sigma_;
76 < };
77 <
69 >    std::vector<Elem> getAllNeighbors(unsigned int i, unsigned int j, unsigned int k) {
70 >      std::vector<Elem> result;
71 >      int index;
72 >      index = isValidGrid(i-1, j, k);
73 >      if (index != -1)
74 >        result.push_back(data_[index]);
75 >      
76 >      index = isValidGrid(i+1, j, k);
77 >      if (index != -1)
78 >        result.push_back(data_[index]);
79 >      
80 >      index = isValidGrid(i, j-1, k);
81 >      if (index != -1)
82 >        result.push_back(data_[index]);
83 >      
84 >      index = isValidGrid(i, j+1, k);
85 >      if (index != -1)
86 >        result.push_back(data_[index]);
87 >      
88 >      index = isValidGrid(i, j, k-1);
89 >      if (index != -1)
90 >        result.push_back(data_[index]);
91 >      
92 >      index = isValidGrid(i, j, k+1);
93 >      if (index != -1)
94 >        result.push_back(data_[index]);
95 >      
96 >      return result;
97 >    }
98 >  private:
99 >    
100 >    int isValidGrid(unsigned int i, unsigned int j, unsigned int k) const {
101 >      int index = i * dim2_*dim3_ + j * dim3_ + k;
102 >      return index < data_.size() ? index : -1;
103 >    };
104 >    
105 >    unsigned int dim1_;
106 >    unsigned int dim2_;
107 >    unsigned int dim3_;
108 >    std::vector<Elem> data_;
109 >    
110 >  };
111 >  
112 >  
113 >  class RoughShell : public ApproximationModel {
114 >  public:
115 >    RoughShell(StuntDouble* sd, SimInfo* info);
116 >    virtual ~RoughShell() { delete shape_;}
117 >    void setSigma(RealType sigma) {sigma_ = sigma;}
118 >    RealType getSigma() {return sigma_;}
119 >  private:
120 >    virtual bool createBeads(std::vector<BeadParam>& beads);
121 >    //StuntDoubleShape sdShape_;
122 >    RealType sigma_;
123 >    Shape* shape_;
124 >  };
125 >  
126   }
127   #endif

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