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Comparing trunk/src/visitors/AtomVisitor.hpp (file contents):
Revision 527 by chrisfen, Thu May 12 19:43:48 2005 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  
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
# Line 91 | Line 91 | namespace oopse {
91      std::set<std::string> ssdAtomType;  
92    };
93  
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) {}
104 +
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("linear");
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) {}
# Line 108 | Line 126 | namespace oopse {
126      std::set<std::string> linearAtomType;  
127    };
128  
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) {}
139  
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 +  class Ring5gbAtomVisitor : public BaseAtomVisitor{
147 +  public:
148 +    Ring5gbAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
149 +      visitorName = "Ring5gbAtomVisitor";
150 +      Ring5gbAtomType.insert("Ring5GB");
151 +    }
152 +
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";}
# Line 123 | Line 189 | namespace oopse {
189  
190    };
191  
192 < }//namespace oopse
192 > }//namespace OpenMD
193   #endif

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