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Comparing trunk/src/visitors/AtomVisitor.hpp (file contents):
Revision 247 by tim, Wed Jan 12 23:15:37 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# 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 VISITORS_BASEATOMVISITOR_HPP
# Line 47 | Line 47
47   #include "visitors/BaseVisitor.hpp"
48   #include "visitors/AtomData.hpp"
49  
50 < namespace oopse {
50 > namespace OpenMD {
51  
52 < /**
53 < * @class BaseAtomVisitor
54 < * @todo document
55 < */
56 < class BaseAtomVisitor : public BaseVisitor{
57 <    public:
58 <        virtual void visit(Atom* atom) {}
59 <        virtual void visit(DirectionalAtom* datom) {}
60 <        virtual void visit(RigidBody* rb);
61 <        void setVisited(Atom* atom);
62 <        bool isVisited(Atom* atom);
52 >  /**
53 >   * @class BaseAtomVisitor
54 >   * @todo document
55 >   */
56 >  class BaseAtomVisitor : public BaseVisitor{
57 >  public:
58 >    virtual void visit(Atom* atom) {}
59 >    virtual void visit(DirectionalAtom* datom) {}
60 >    virtual void visit(RigidBody* rb);
61 >    void setVisited(Atom* atom);
62 >    bool isVisited(Atom* atom);
63  
64 <    protected:
65 <        BaseAtomVisitor(SimInfo* info) : BaseVisitor() {}    
66 <        SimInfo* info;
67 < };
64 >  protected:
65 >    BaseAtomVisitor(SimInfo* info) : BaseVisitor() {}    
66 >    SimInfo* info;
67 >  };
68  
69 < /**
70 < * @class SSDAtomVisitor
71 < * @todo document
72 < */
73 < class SSDAtomVisitor : public BaseAtomVisitor{
74 <        public:
75 <            SSDAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
76 <                visitorName = "SSDAtomVisitor";
77 <                ssdAtomType.insert("SSD");
78 <                ssdAtomType.insert("SSD_E");
79 <                ssdAtomType.insert("SSD_RF");
80 <                ssdAtomType.insert("SSD1");
81 <            }
69 >  /**
70 >   * @class SSDAtomVisitor
71 >   * @todo document
72 >   */
73 >  class SSDAtomVisitor : public BaseAtomVisitor{
74 >  public:
75 >    SSDAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
76 >      visitorName = "SSDAtomVisitor";
77 >      ssdAtomType.insert("SSD");
78 >      ssdAtomType.insert("SSD_E");
79 >      ssdAtomType.insert("SSD_RF");
80 >      ssdAtomType.insert("SSD1");
81 >      ssdAtomType.insert("TAP");
82 >    }
83  
84 <            virtual void visit(Atom* atom) {}
85 <            virtual void visit(DirectionalAtom* datom);      
86 <            virtual void visit(RigidBody* rb) {}
84 >    virtual void visit(Atom* atom) {}
85 >    virtual void visit(DirectionalAtom* datom);      
86 >    virtual void visit(RigidBody* rb) {}
87  
88 <            virtual const std::string toString();
89 <        private:
90 <            inline bool isSSDAtom(const std::string& atomType);
91 <            std::set<std::string> ssdAtomType;  
92 < };
88 >    virtual const std::string toString();
89 >  private:
90 >    inline bool isSSDAtom(const std::string& atomType);
91 >    std::set<std::string> ssdAtomType;  
92 >  };
93  
94 < class LinearAtomVisitor : public BaseAtomVisitor{
95 <    public:
96 <        LinearAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
97 <            visitorName = "LinearAtomVisitor";
98 <            linearAtomType.insert("linear");
99 <        }
94 >  class TREDAtomVisitor : public BaseAtomVisitor{
95 >  public:
96 >    TREDAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
97 >      visitorName = "TREDAtomVisitor";
98 >      tredAtomType.insert("TRED");
99 >    }
100  
101 <        virtual void visit(Atom* atom) {}
102 <        virtual void visit(DirectionalAtom* datom);      
103 <        virtual void visit(RigidBody* rb) {}
101 >    virtual void visit(Atom* atom) {}
102 >    virtual void visit(DirectionalAtom* datom);      
103 >    virtual void visit(RigidBody* rb) {}
104  
105 <        virtual const std::string toString();
106 <    private:
107 <        inline bool isLinearAtom(const std::string& atomType);
108 <        std::set<std::string> linearAtomType;  
109 < };
105 >    virtual const std::string toString();
106 >  private:
107 >    inline bool isTREDAtom(const std::string& atomType);
108 >    std::set<std::string> tredAtomType;  
109 >  };
110  
111 +  class LinearAtomVisitor : public BaseAtomVisitor{
112 +  public:
113 +    LinearAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
114 +      visitorName = "LinearAtomVisitor";
115 +      linearAtomType.insert("GBlinear");
116 +    }
117  
118 +    void addGayBerneAtomType(const std::string& atomType);
119 +    virtual void visit(Atom* atom) {}
120 +    virtual void visit(DirectionalAtom* datom);      
121 +    virtual void visit(RigidBody* rb) {}
122  
123 +    virtual const std::string toString();
124 +  private:
125 +    inline bool isLinearAtom(const std::string& atomType);
126 +    std::set<std::string> linearAtomType;  
127 +  };
128  
129 < class DefaultAtomVisitor : public BaseAtomVisitor{
130 <    public:
131 <        DefaultAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) { visitorName = "DefaultAtomVisitor";}
129 >  class GBLipidAtomVisitor : public BaseAtomVisitor{
130 >  public:
131 >    GBLipidAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
132 >      visitorName = "GBLipidAtomVisitor";
133 >      GBLipidAtomType.insert("GBlipid");
134 >    }
135  
136 <        virtual void visit(Atom* atom);    
137 <        virtual void visit(DirectionalAtom* datom);    
138 <        virtual void visit(RigidBody* rb) {}
136 >    virtual void visit(Atom* atom) {}
137 >    virtual void visit(DirectionalAtom* datom);      
138 >    virtual void visit(RigidBody* rb) {}
139  
140 <        virtual const std::string toString();
140 >    virtual const std::string toString();
141 >  private:
142 >    inline bool isGBLipidAtom(const std::string& atomType);
143 >    std::set<std::string> GBLipidAtomType;  
144 >  };
145  
146 < };
146 >  class Ring5gbAtomVisitor : public BaseAtomVisitor{
147 >  public:
148 >    Ring5gbAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
149 >      visitorName = "Ring5gbAtomVisitor";
150 >      Ring5gbAtomType.insert("Ring5GB");
151 >    }
152  
153 < }//namespace oopse
153 >    virtual void visit(Atom* atom) {}
154 >    virtual void visit(DirectionalAtom* datom);      
155 >    virtual void visit(RigidBody* rb) {}
156 >
157 >    virtual const std::string toString();
158 >  private:
159 >    inline bool isRing5gbAtom(const std::string& atomType);
160 >    std::set<std::string> Ring5gbAtomType;  
161 >  };
162 >
163 >  class HeadAtomVisitor : public BaseAtomVisitor{
164 >  public:
165 >    HeadAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
166 >      visitorName = "HeadAtomVisitor";
167 >      HeadAtomType.insert("HEAD");
168 >    }
169 >
170 >    virtual void visit(Atom* atom) {}
171 >    virtual void visit(DirectionalAtom* datom);      
172 >    virtual void visit(RigidBody* rb) {}
173 >
174 >    virtual const std::string toString();
175 >  private:
176 >    inline bool isHeadAtom(const std::string& atomType);
177 >    std::set<std::string> HeadAtomType;  
178 >  };
179 >
180 >  class DefaultAtomVisitor : public BaseAtomVisitor{
181 >  public:
182 >    DefaultAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) { visitorName = "DefaultAtomVisitor";}
183 >
184 >    virtual void visit(Atom* atom);    
185 >    virtual void visit(DirectionalAtom* datom);    
186 >    virtual void visit(RigidBody* rb) {}
187 >
188 >    virtual const std::string toString();
189 >
190 >  };
191 >
192 > }//namespace OpenMD
193   #endif

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