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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#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:	1456
Committed:	Fri Jun 25 17:40:24 2010 UTC (15 years, 1 month ago) by gezelter
File size:	5524 byte(s)
Log Message:	more changes to make Dump2XYZ do velocities & forces
#	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_OTHERVISITOR_HPP
43	#define VISITORS_OTHERVISITOR_HPP
44	#include <set>
45	#include <string>
46	#include <vector>
47
48	#include "visitors/BaseVisitor.hpp"
49	#include "primitives/StuntDouble.hpp"
50	#include "visitors/AtomData.hpp"
51	#include "selection/SelectionManager.hpp"
52	#include "selection/SelectionEvaluator.hpp"
53
54	namespace OpenMD {
55
56	class SimInfo;
57
58
59	class WrappingVisitor : public BaseVisitor{
60	public:
61	WrappingVisitor(SimInfo* info, bool useCom = true) : BaseVisitor(), useCom_(useCom) {
62	this->info = info;
63	visitorName = "WrappingVisitor";
64	}
65	virtual void visit(Atom* atom);
66	virtual void visit(DirectionalAtom* datom);
67	virtual void visit(RigidBody* rb);
68
69	virtual const std::string toString();
70
71	virtual void update();
72
73	private:
74	void internalVisit(StuntDouble* sd);
75	SimInfo* info;
76	Vector3d origin_;
77	bool useCom_;
78	};
79
80
81	class ReplicateVisitor : public BaseVisitor{
82	public:
83	ReplicateVisitor(SimInfo* info, Vector3i opt);
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	protected:
90	void internalVisit(StuntDouble* sd);
91	void replicate(std::vector<AtomInfo>& infoList, AtomData data, const Mat3x3d& box);
92
93	private:
94	std::vector<Vector3i> dir;
95	SimInfo* info;
96	Vector3i replicateOpt;
97	};
98
99	class XYZVisitor : public BaseVisitor{
100	public:
101
102	XYZVisitor(SimInfo* info);
103
104	XYZVisitor(SimInfo* info, const std::string& script);
105
106	virtual void visit(Atom* atom);
107	virtual void visit(DirectionalAtom* datom);
108	virtual void visit(RigidBody* rb);
109
110	virtual void update();
111
112	virtual const std::string toString();
113
114	void writeFrame(std::ostream& outStream);
115	void clear() {frame.clear();}
116	void doPositions(bool pos) {doPositions_ = pos;}
117	void doVelocities(bool vel){doVelocities_ = vel;}
118	void doForces(bool frc) {doForces_ = frc;}
119	void doVectors(bool vec) {doVectors_ = vec;}
120	void doCharges(bool chg) {doCharges_ = chg;}
121
122	protected:
123	void internalVisit(StuntDouble* sd);
124	bool isSelected(StuntDouble* sd);
125
126	private:
127	std::string trimmedName(const std::string& atomType);
128
129	SimInfo* info;
130	SelectionManager seleMan;
131	SelectionEvaluator evaluator;
132	std::vector<std::string> frame;
133	bool doPositions_;
134	bool doVelocities_;
135	bool doForces_;
136	bool doVectors_;
137	bool doCharges_;
138	};
139
140
141	class PrepareVisitor : public BaseVisitor{
142	public:
143	PrepareVisitor() : BaseVisitor() {visitorName = "prepareVisitor";}
144
145	virtual void visit(Atom* atom) {internalVisit(atom);}
146	virtual void visit(DirectionalAtom* datom) {internalVisit((Atom*)datom);}
147	virtual void visit(RigidBody* rb) {internalVisit(rb);}
148
149	virtual const std::string toString();
150
151	protected:
152	void internalVisit(Atom* atom);
153	void internalVisit(RigidBody* rb);
154	};
155
156	class WaterTypeVisitor : public BaseVisitor{
157	public:
158	WaterTypeVisitor() ;
159	virtual void visit(Atom* atom) {}
160	virtual void visit(DirectionalAtom* datom) {}
161	virtual void visit(RigidBody* rb);
162
163	virtual const std::string toString();
164
165	private:
166	std::string trimmedName(const std::string& atomType);
167
168	std::set<std::string> waterTypeList;
169	};
170
171
172	}//namespace OpenMD
173	#endif //_OTHERVISITOR_H_