src/visitors/AtomVisitor.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#ifndef VISITORS_BASEATOMVISITOR_HPP
#define VISITORS_BASEATOMVISITOR_HPP

#include <set>

#include "visitors/BaseVisitor.hpp"
#include "visitors/AtomData.hpp"

namespace OpenMD {

  /**
   * @class BaseAtomVisitor
   * @todo document
   */
  class BaseAtomVisitor : public BaseVisitor{
  public:
    virtual void visit(Atom* atom) {}
    virtual void visit(DirectionalAtom* datom) {}
    virtual void visit(RigidBody* rb);
    void setVisited(Atom* atom);
    bool isVisited(Atom* atom);

  protected:
    BaseAtomVisitor(SimInfo* info) : BaseVisitor() {}    
    SimInfo* info;
  };

  /**
   * @class SSDAtomVisitor
   * @todo document
   */
  class SSDAtomVisitor : public BaseAtomVisitor{
  public:
    SSDAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
      visitorName = "SSDAtomVisitor";
      ssdAtomType.insert("SSD");
      ssdAtomType.insert("SSD_E");
      ssdAtomType.insert("SSD_RF");
      ssdAtomType.insert("SSD1");
      ssdAtomType.insert("TAP");
    }

    virtual void visit(Atom* atom) {}
    virtual void visit(DirectionalAtom* datom);       
    virtual void visit(RigidBody* rb) {}

    virtual const std::string toString();
  private:
    inline bool isSSDAtom(const std::string& atomType);
    std::set<std::string> ssdAtomType;   
  };

  class TREDAtomVisitor : public BaseAtomVisitor{
  public:
    TREDAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
      visitorName = "TREDAtomVisitor";
      tredAtomType.insert("TRED");
    }

    virtual void visit(Atom* atom) {}
    virtual void visit(DirectionalAtom* datom);       
    virtual void visit(RigidBody* rb) {}

    virtual const std::string toString();
  private:
    inline bool isTREDAtom(const std::string& atomType);
    std::set<std::string> tredAtomType;   
  };

  class LinearAtomVisitor : public BaseAtomVisitor{
  public:
    LinearAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
      visitorName = "LinearAtomVisitor";
      linearAtomType.insert("GBlinear");
    }

    void addGayBerneAtomType(const std::string& atomType); 
    virtual void visit(Atom* atom) {}
    virtual void visit(DirectionalAtom* datom);       
    virtual void visit(RigidBody* rb) {}

    virtual const std::string toString();
  private:
    inline bool isLinearAtom(const std::string& atomType);
    std::set<std::string> linearAtomType;   
  };

  class GBLipidAtomVisitor : public BaseAtomVisitor{
  public:
    GBLipidAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
      visitorName = "GBLipidAtomVisitor";
      GBLipidAtomType.insert("GBlipid");
    }

    virtual void visit(Atom* atom) {}
    virtual void visit(DirectionalAtom* datom);       
    virtual void visit(RigidBody* rb) {}

    virtual const std::string toString();
  private:
    inline bool isGBLipidAtom(const std::string& atomType);
    std::set<std::string> GBLipidAtomType;   
  };

  class Ring5gbAtomVisitor : public BaseAtomVisitor{
  public:
    Ring5gbAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
      visitorName = "Ring5gbAtomVisitor";
      Ring5gbAtomType.insert("Ring5GB");
    }

    virtual void visit(Atom* atom) {}
    virtual void visit(DirectionalAtom* datom);       
    virtual void visit(RigidBody* rb) {}

    virtual const std::string toString();
  private:
    inline bool isRing5gbAtom(const std::string& atomType);
    std::set<std::string> Ring5gbAtomType;   
  };

  class HeadAtomVisitor : public BaseAtomVisitor{
  public:
    HeadAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
      visitorName = "HeadAtomVisitor";
      HeadAtomType.insert("HEAD");
    }

    virtual void visit(Atom* atom) {}
    virtual void visit(DirectionalAtom* datom);       
    virtual void visit(RigidBody* rb) {}

    virtual const std::string toString();
  private:
    inline bool isHeadAtom(const std::string& atomType);
    std::set<std::string> HeadAtomType;   
  };

  class DefaultAtomVisitor : public BaseAtomVisitor{
  public:
    DefaultAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) { visitorName = "DefaultAtomVisitor";}

    virtual void visit(Atom* atom);    
    virtual void visit(DirectionalAtom* datom);    
    virtual void visit(RigidBody* rb) {}

    virtual const std::string toString();

  };

}//namespace OpenMD
#endif
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/visitors/AtomVisitor.hpp*
File size:	6362 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1390	*
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	gezelter	246	*/
41
42			#ifndef VISITORS_BASEATOMVISITOR_HPP
43			#define VISITORS_BASEATOMVISITOR_HPP
44	gezelter	2
45	tim	247	#include <set>
46	tim	132
47	tim	3	#include "visitors/BaseVisitor.hpp"
48	tim	132	#include "visitors/AtomData.hpp"
49
50	gezelter	1390	namespace OpenMD {
51	gezelter	2
52	gezelter	507	/**
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	gezelter	246
64	gezelter	507	protected:
65			BaseAtomVisitor(SimInfo* info) : BaseVisitor() {}
66			SimInfo* info;
67			};
68	gezelter	2
69	gezelter	507	/**
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	chrisfen	527	ssdAtomType.insert("TAP");
82	gezelter	507	}
83	gezelter	2
84	gezelter	507	virtual void visit(Atom* atom) {}
85			virtual void visit(DirectionalAtom* datom);
86			virtual void visit(RigidBody* rb) {}
87	gezelter	246
88	gezelter	507	virtual const std::string toString();
89			private:
90			inline bool isSSDAtom(const std::string& atomType);
91			std::set<std::string> ssdAtomType;
92			};
93	gezelter	2
94	chrisfen	1008	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	gezelter	507	class LinearAtomVisitor : public BaseAtomVisitor{
112			public:
113			LinearAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
114			visitorName = "LinearAtomVisitor";
115	gezelter	983	linearAtomType.insert("GBlinear");
116	gezelter	507	}
117	chrisfen	211
118	tim	954	void addGayBerneAtomType(const std::string& atomType);
119	gezelter	507	virtual void visit(Atom* atom) {}
120			virtual void visit(DirectionalAtom* datom);
121			virtual void visit(RigidBody* rb) {}
122	tim	247
123	gezelter	507	virtual const std::string toString();
124			private:
125			inline bool isLinearAtom(const std::string& atomType);
126			std::set<std::string> linearAtomType;
127			};
128	chrisfen	211
129	xsun	881	class GBLipidAtomVisitor : public BaseAtomVisitor{
130			public:
131			GBLipidAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
132			visitorName = "GBLipidAtomVisitor";
133			GBLipidAtomType.insert("GBlipid");
134			}
135	chrisfen	211
136	xsun	881	virtual void visit(Atom* atom) {}
137			virtual void visit(DirectionalAtom* datom);
138			virtual void visit(RigidBody* rb) {}
139	chrisfen	211
140	xsun	881	virtual const std::string toString();
141			private:
142			inline bool isGBLipidAtom(const std::string& atomType);
143			std::set<std::string> GBLipidAtomType;
144			};
145	chrisfen	211
146	xsun	1219	class Ring5gbAtomVisitor : public BaseAtomVisitor{
147			public:
148			Ring5gbAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) {
149			visitorName = "Ring5gbAtomVisitor";
150			Ring5gbAtomType.insert("Ring5GB");
151			}
152	xsun	881
153	xsun	1219	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	gezelter	507	class DefaultAtomVisitor : public BaseAtomVisitor{
181			public:
182			DefaultAtomVisitor(SimInfo* info) : BaseAtomVisitor(info) { visitorName = "DefaultAtomVisitor";}
183	gezelter	2
184	gezelter	507	virtual void visit(Atom* atom);
185			virtual void visit(DirectionalAtom* datom);
186			virtual void visit(RigidBody* rb) {}
187	gezelter	246
188	gezelter	507	virtual const std::string toString();
189	gezelter	246
190	gezelter	507	};
191	tim	132
192	gezelter	1390	}//namespace OpenMD
193	gezelter	2	#endif