src/visitors/OtherVisitor.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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#ifndef VISITORS_OTHERVISITOR_HPP
#define VISITORS_OTHERVISITOR_HPP
#include <set>
#include <string>
#include <vector>

#include "visitors/BaseVisitor.hpp"
#include "primitives/StuntDouble.hpp"
#include "visitors/AtomData.hpp"
#include "selection/SelectionManager.hpp"
#include "selection/SelectionEvaluator.hpp"

namespace OpenMD {

  class SimInfo;


  class WrappingVisitor : public BaseVisitor{
  public:
    WrappingVisitor(SimInfo* info, bool useCom = true) : BaseVisitor(), useCom_(useCom) {
      this->info = info;
      visitorName = "WrappingVisitor";
    }
    virtual void visit(Atom* atom);
    virtual void visit(DirectionalAtom* datom);
    virtual void visit(RigidBody* rb);

    virtual const std::string toString();

    virtual void update();
    
  private:
    void internalVisit(StuntDouble* sd);
    SimInfo* info;    
    Vector3d origin_;
    bool useCom_;
  };


  class ReplicateVisitor : public BaseVisitor{
  public:
    ReplicateVisitor(SimInfo* info, Vector3i opt);
    virtual void visit(Atom* atom);
    virtual void visit(DirectionalAtom* datom);
    virtual void visit(RigidBody* rb);

    virtual const std::string toString();
  protected:
    void internalVisit(StuntDouble* sd);
    void replicate(std::vector<AtomInfo*>& infoList,  AtomData* data, const Mat3x3d& box);
    
  private:
    std::vector<Vector3i> dir;
    SimInfo* info;
    Vector3i replicateOpt;
  };

  class XYZVisitor : public BaseVisitor{
  public:
    
    XYZVisitor(SimInfo* info);
    
    XYZVisitor(SimInfo* info, const std::string& script);
    
    virtual void visit(Atom* atom);
    virtual void visit(DirectionalAtom* datom);
    virtual void visit(RigidBody* rb);

    virtual void update();

    virtual const std::string toString();
    
    void writeFrame(std::ostream& outStream);    
    void clear() {frame.clear();}
    void doPositions(bool pos) {doPositions_  = pos;}
    void doVelocities(bool vel){doVelocities_ = vel;}
    void doForces(bool frc)    {doForces_     = frc;}
    void doVectors(bool vec)   {doVectors_    = vec;}
    void doCharges(bool chg)   {doCharges_    = chg;}

  protected:
    void internalVisit(StuntDouble* sd);
    bool isSelected(StuntDouble* sd);

  private:  
    std::string trimmedName(const std::string& atomType);

    SimInfo* info;
    SelectionManager seleMan;
    SelectionEvaluator evaluator; 
    std::vector<std::string> frame;
    bool doPositions_;
    bool doVelocities_;
    bool doForces_;
    bool doVectors_;
    bool doCharges_;
  };


  class PrepareVisitor : public BaseVisitor{
  public:
    PrepareVisitor() : BaseVisitor() {visitorName = "prepareVisitor";}

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

    virtual const std::string toString();

  protected:
    void internalVisit(Atom* atom);
    void internalVisit(RigidBody* rb);
  };

  class WaterTypeVisitor : public BaseVisitor{
  public:
    WaterTypeVisitor() ;
    virtual void visit(Atom* atom) {}
    virtual void visit(DirectionalAtom* datom) {}
    virtual void visit(RigidBody* rb);
    
    virtual const std::string toString();
    
  private:
    std::string trimmedName(const std::string& atomType);
    
    std::set<std::string> waterTypeList;
  };


}//namespace OpenMD
#endif //_OTHERVISITOR_H_
Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	5591 byte(s)
Log Message:	Fixed a widespread typo in the license
#	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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43			#ifndef VISITORS_OTHERVISITOR_HPP
44			#define VISITORS_OTHERVISITOR_HPP
45	gezelter	2	#include <set>
46			#include <string>
47			#include <vector>
48
49	tim	3	#include "visitors/BaseVisitor.hpp"
50			#include "primitives/StuntDouble.hpp"
51	tim	132	#include "visitors/AtomData.hpp"
52	tim	413	#include "selection/SelectionManager.hpp"
53			#include "selection/SelectionEvaluator.hpp"
54	tim	132
55	gezelter	1390	namespace OpenMD {
56	tim	132
57	gezelter	507	class SimInfo;
58	gezelter	246
59	gezelter	2
60	gezelter	507	class WrappingVisitor : public BaseVisitor{
61	gezelter	2	public:
62	tim	543	WrappingVisitor(SimInfo* info, bool useCom = true) : BaseVisitor(), useCom_(useCom) {
63	gezelter	2	this->info = info;
64			visitorName = "WrappingVisitor";
65			}
66			virtual void visit(Atom* atom);
67			virtual void visit(DirectionalAtom* datom);
68			virtual void visit(RigidBody* rb);
69
70	gezelter	246	virtual const std::string toString();
71	gezelter	2
72	tim	543	virtual void update();
73
74			private:
75	gezelter	2	void internalVisit(StuntDouble* sd);
76	tim	543	SimInfo* info;
77			Vector3d origin_;
78			bool useCom_;
79	gezelter	507	};
80	gezelter	2
81
82	gezelter	507	class ReplicateVisitor : public BaseVisitor{
83	gezelter	2	public:
84	gezelter	246	ReplicateVisitor(SimInfo* info, Vector3i opt);
85	gezelter	2	virtual void visit(Atom* atom);
86			virtual void visit(DirectionalAtom* datom);
87			virtual void visit(RigidBody* rb);
88
89	gezelter	246	virtual const std::string toString();
90	gezelter	2	protected:
91			void internalVisit(StuntDouble* sd);
92	gezelter	246	void replicate(std::vector<AtomInfo>& infoList, AtomData data, const Mat3x3d& box);
93	gezelter	2
94			private:
95	gezelter	246	std::vector<Vector3i> dir;
96	gezelter	2	SimInfo* info;
97	gezelter	246	Vector3i replicateOpt;
98	gezelter	507	};
99	gezelter	2
100	gezelter	507	class XYZVisitor : public BaseVisitor{
101	gezelter	2	public:
102
103	tim	413	XYZVisitor(SimInfo* info);
104
105			XYZVisitor(SimInfo* info, const std::string& script);
106
107	gezelter	2	virtual void visit(Atom* atom);
108			virtual void visit(DirectionalAtom* datom);
109			virtual void visit(RigidBody* rb);
110
111	tim	413	virtual void update();
112
113	gezelter	246	virtual const std::string toString();
114	gezelter	2
115	gezelter	246	void writeFrame(std::ostream& outStream);
116	gezelter	2	void clear() {frame.clear();}
117	gezelter	1456	void doPositions(bool pos) {doPositions_ = pos;}
118			void doVelocities(bool vel){doVelocities_ = vel;}
119			void doForces(bool frc) {doForces_ = frc;}
120			void doVectors(bool vec) {doVectors_ = vec;}
121			void doCharges(bool chg) {doCharges_ = chg;}
122
123	gezelter	2	protected:
124			void internalVisit(StuntDouble* sd);
125	tim	293	bool isSelected(StuntDouble* sd);
126	gezelter	2
127			private:
128	cli2	1290	std::string trimmedName(const std::string& atomType);
129
130	gezelter	2	SimInfo* info;
131	tim	413	SelectionManager seleMan;
132			SelectionEvaluator evaluator;
133	gezelter	246	std::vector<std::string> frame;
134	gezelter	1456	bool doPositions_;
135			bool doVelocities_;
136			bool doForces_;
137			bool doVectors_;
138			bool doCharges_;
139	gezelter	507	};
140	gezelter	2
141
142	gezelter	507	class PrepareVisitor : public BaseVisitor{
143	gezelter	2	public:
144			PrepareVisitor() : BaseVisitor() {visitorName = "prepareVisitor";}
145
146			virtual void visit(Atom* atom) {internalVisit(atom);}
147			virtual void visit(DirectionalAtom* datom) {internalVisit((Atom*)datom);}
148			virtual void visit(RigidBody* rb) {internalVisit(rb);}
149
150	gezelter	246	virtual const std::string toString();
151	gezelter	2
152			protected:
153			void internalVisit(Atom* atom);
154			void internalVisit(RigidBody* rb);
155	gezelter	507	};
156	gezelter	2
157	gezelter	407	class WaterTypeVisitor : public BaseVisitor{
158	gezelter	2	public:
159			WaterTypeVisitor() ;
160			virtual void visit(Atom* atom) {}
161			virtual void visit(DirectionalAtom* datom) {}
162			virtual void visit(RigidBody* rb);
163	gezelter	407
164	gezelter	246	virtual const std::string toString();
165	gezelter	2
166			private:
167	gezelter	407	std::string trimmedName(const std::string& atomType);
168
169	gezelter	246	std::set<std::string> waterTypeList;
170	gezelter	507	};
171	tim	132
172
173	gezelter	1390	}//namespace OpenMD
174	gezelter	2	#endif //_OTHERVISITOR_H_