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Comparing trunk/OOPSE-3.0/src/visitors/OtherVisitor.hpp (file contents):
Revision 1490 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 2097 by tim, Wed Mar 9 17:30:29 2005 UTC

# Line 1 | Line 1
1 < #ifndef _OTHERVISITOR_H_
2 < #define _OTHERVISITOR_H_
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. 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
19 > *    notice, this list of conditions and the following disclaimer.
20 > *
21 > * 3. Redistributions in binary form must reproduce the above copyright
22 > *    notice, this list of conditions and the following disclaimer in the
23 > *    documentation and/or other materials provided with the
24 > *    distribution.
25 > *
26 > * This software is provided "AS IS," without a warranty of any
27 > * kind. All express or implied conditions, representations and
28 > * warranties, including any implied warranty of merchantability,
29 > * fitness for a particular purpose or non-infringement, are hereby
30 > * excluded.  The University of Notre Dame and its licensors shall not
31 > * be liable for any damages suffered by licensee as a result of
32 > * using, modifying or distributing the software or its
33 > * derivatives. In no event will the University of Notre Dame or its
34 > * licensors be liable for any lost revenue, profit or data, or for
35 > * direct, indirect, special, consequential, incidental or punitive
36 > * damages, however caused and regardless of the theory of liability,
37 > * arising out of the use of or inability to use software, even if the
38 > * University of Notre Dame has been advised of the possibility of
39 > * such damages.
40 > */
41 >
42 > #ifndef VISITORS_OTHERVISITOR_HPP
43 > #define VISITORS_OTHERVISITOR_HPP
44   #include <set>
45   #include <string>
46   #include <vector>
47  
48 < #include "BaseVisitor.hpp"
49 < #include "StuntDouble.hpp"
50 < using namespace std;
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 < //IgnoreVisitor will turn on the ignoring flag of the stuntdouble
12 < class IgnoreVisitor : public BaseVisitor{
13 <  public:
14 <    IgnoreVisitor() : BaseVisitor() {visitorName = "IgnoreVisitor";}
54 > namespace oopse {
55  
56 <    virtual void visit(Atom* atom);
17 <    virtual void visit(DirectionalAtom* datom);
18 <    virtual void visit(RigidBody* rb);
19 <    
20 <    virtual const string toString();
56 > class SimInfo;
57  
22 –    void addIgnoreType(const string& type) {itList.insert(type);}
23 –    
24 –  protected:
25 –    bool isIgnoreType(const string& name);
26 –    void internalVisit(StuntDouble* sd);
27 –    set<string> itList; //ignore type list;
28 – };
58  
30 –
59   class WrappingVisitor : public BaseVisitor{
60    public:
61      WrappingVisitor(SimInfo* info) : BaseVisitor() {
# Line 38 | Line 66 | class WrappingVisitor : public BaseVisitor{
66      virtual void visit(DirectionalAtom* datom);
67      virtual void visit(RigidBody* rb);
68  
69 <    virtual const string toString();
69 >    virtual const std::string toString();
70  
71    protected:
72      void internalVisit(StuntDouble* sd);
# Line 46 | Line 74 | class IntVec3 {
74   };
75  
76  
49 – class IntVec3 {
50 –  public:
51 –    IntVec3(){}
52 –    IntVec3(int i, int j, int k){
53 –      vec[0] = i;
54 –      vec[1] = j;
55 –      vec[2] = k;
56 –    }
57 –    
58 –    int vec[3];
59 –    int& operator[](int index) {return vec[index];}  
60 – };
61 –
77   class ReplicateVisitor : public BaseVisitor{
78    public:
79 <    ReplicateVisitor(SimInfo* info, IntVec3 opt);
79 >    ReplicateVisitor(SimInfo* info, Vector3i opt);
80      virtual void visit(Atom* atom);
81      virtual void visit(DirectionalAtom* datom);
82      virtual void visit(RigidBody* rb);
83  
84 <    virtual const string toString();
84 >    virtual const std::string toString();
85    protected:
86      void internalVisit(StuntDouble* sd);
87 <    void replicate(vector<AtomInfo*>& infoList,  AtomData* data, double boxM[3][3]);
87 >    void replicate(std::vector<AtomInfo*>& infoList,  AtomData* data, const Mat3x3d& box);
88      
89    private:
90 <    vector<IntVec3> dir;
90 >    std::vector<Vector3i> dir;
91      SimInfo* info;
92 <    IntVec3 replicateOpt;
92 >    Vector3i replicateOpt;
93   };
94  
95   class XYZVisitor : public BaseVisitor{
96    public:
82 –    XYZVisitor(SimInfo* info, bool printDipole = true);
97      
98 +    XYZVisitor(SimInfo* info);
99 +    
100 +    XYZVisitor(SimInfo* info, const std::string& script);
101 +    
102      virtual void visit(Atom* atom);
103      virtual void visit(DirectionalAtom* datom);
104      virtual void visit(RigidBody* rb);
105  
106 <    virtual const string toString();
106 >    virtual void update();
107 >
108 >    virtual const std::string toString();
109      
110 <    void writeFrame(ostream& outStream);    
110 >    void writeFrame(std::ostream& outStream);    
111      void clear() {frame.clear();}
112      
113    protected:
114      void internalVisit(StuntDouble* sd);
115 <    bool isIgnore(StuntDouble* sd);
115 >    bool isSelected(StuntDouble* sd);
116  
117    private:  
118      SimInfo* info;
119 <    vector<string> frame;
120 <    bool printDipole;
119 >    SelectionManager seleMan;
120 >    SelectionEvaluator evaluator;
121 >    std::vector<std::string> frame;
122 >
123   };
124  
125  
# Line 109 | Line 131 | class PrepareVisitor : public BaseVisitor{
131      virtual void visit(DirectionalAtom* datom) {internalVisit((Atom*)datom);}
132      virtual void visit(RigidBody* rb) {internalVisit(rb);}
133  
134 <    virtual const string toString();
134 >    virtual const std::string toString();
135  
136    protected:
137      void internalVisit(Atom* atom);
138      void internalVisit(RigidBody* rb);
139   };
140  
141 < class WaterTypeVisitor : public BaseVisitor{
141 >  class WaterTypeVisitor : public BaseVisitor{
142    public:
143      WaterTypeVisitor() ;
144      virtual void visit(Atom* atom) {}
145      virtual void visit(DirectionalAtom* datom) {}
146      virtual void visit(RigidBody* rb);
125 –
126 –    virtual const string toString();
147      
148 +    virtual const std::string toString();
149 +    
150    private:
151 <    void replaceType(string& atomType);
152 <      
153 <    set<string> waterTypeList;
151 >    std::string trimmedName(const std::string& atomType);
152 >    
153 >    std::set<std::string> waterTypeList;
154   };
155 +
156 +
157 + }//namespace oopse
158   #endif //_OTHERVISITOR_H_

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