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, 9 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)
#	Content
1	/*
2	* 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	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
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	*
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
43	#define VISITORS_BASEATOMVISITOR_HPP
44
45	#include <set>
46
47	#include "visitors/BaseVisitor.hpp"
48	#include "visitors/AtomData.hpp"
49
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);
63
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	ssdAtomType.insert("TAP");
82	}
83
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	};
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("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 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";}
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