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Comparing trunk/OOPSE-3.0/src/visitors/OtherVisitor.hpp (file contents):
Revision 1625 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 1930 by gezelter, Wed Jan 12 22:41:40 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>
# Line 8 | Line 49 | using namespace std;
49   #include "primitives/StuntDouble.hpp"
50   #include "visitors/AtomData.hpp"
51  
11 – using namespace std;
52  
53   namespace oopse {
54  
55 + class SimInfo;
56 +
57   //IgnoreVisitor will turn on the ignoring flag of the stuntdouble
58   class IgnoreVisitor : public BaseVisitor{
59    public:
# Line 21 | Line 63 | class IgnoreVisitor : public BaseVisitor{
63      virtual void visit(DirectionalAtom* datom);
64      virtual void visit(RigidBody* rb);
65      
66 <    virtual const string toString();
66 >    virtual const std::string toString();
67  
68 <    void addIgnoreType(const string& type) {itList.insert(type);}
68 >    void addIgnoreType(const std::string& type) {itList.insert(type);}
69      
70    protected:
71 <    bool isIgnoreType(const string& name);
71 >    bool isIgnoreType(const std::string& name);
72      void internalVisit(StuntDouble* sd);
73 <    set<string> itList; //ignore type list;
73 >    std::set<std::string> itList; //ignore type list;
74   };
75  
76  
# Line 42 | Line 84 | class WrappingVisitor : public BaseVisitor{
84      virtual void visit(DirectionalAtom* datom);
85      virtual void visit(RigidBody* rb);
86  
87 <    virtual const string toString();
87 >    virtual const std::string toString();
88  
89    protected:
90      void internalVisit(StuntDouble* sd);
# Line 50 | Line 92 | class IntVec3 {
92   };
93  
94  
53 – class IntVec3 {
54 –  public:
55 –    IntVec3(){}
56 –    IntVec3(int i, int j, int k){
57 –      vec[0] = i;
58 –      vec[1] = j;
59 –      vec[2] = k;
60 –    }
61 –    
62 –    int vec[3];
63 –    int& operator[](int index) {return vec[index];}  
64 – };
65 –
95   class ReplicateVisitor : public BaseVisitor{
96    public:
97 <    ReplicateVisitor(SimInfo* info, IntVec3 opt);
97 >    ReplicateVisitor(SimInfo* info, Vector3i opt);
98      virtual void visit(Atom* atom);
99      virtual void visit(DirectionalAtom* datom);
100      virtual void visit(RigidBody* rb);
101  
102 <    virtual const string toString();
102 >    virtual const std::string toString();
103    protected:
104      void internalVisit(StuntDouble* sd);
105 <    void replicate(vector<AtomInfo*>& infoList,  AtomData* data, double boxM[3][3]);
105 >    void replicate(std::vector<AtomInfo*>& infoList,  AtomData* data, const Mat3x3d& box);
106      
107    private:
108 <    vector<IntVec3> dir;
108 >    std::vector<Vector3i> dir;
109      SimInfo* info;
110 <    IntVec3 replicateOpt;
110 >    Vector3i replicateOpt;
111   };
112  
113   class XYZVisitor : public BaseVisitor{
# Line 89 | Line 118 | class XYZVisitor : public BaseVisitor{
118      virtual void visit(DirectionalAtom* datom);
119      virtual void visit(RigidBody* rb);
120  
121 <    virtual const string toString();
121 >    virtual const std::string toString();
122      
123 <    void writeFrame(ostream& outStream);    
123 >    void writeFrame(std::ostream& outStream);    
124      void clear() {frame.clear();}
125      
126    protected:
# Line 100 | Line 129 | class XYZVisitor : public BaseVisitor{
129  
130    private:  
131      SimInfo* info;
132 <    vector<string> frame;
132 >    std::vector<std::string> frame;
133      bool printDipole;
134   };
135  
# Line 113 | Line 142 | class PrepareVisitor : public BaseVisitor{
142      virtual void visit(DirectionalAtom* datom) {internalVisit((Atom*)datom);}
143      virtual void visit(RigidBody* rb) {internalVisit(rb);}
144  
145 <    virtual const string toString();
145 >    virtual const std::string toString();
146  
147    protected:
148      void internalVisit(Atom* atom);
# Line 127 | Line 156 | class WaterTypeVisitor : public BaseVisitor{
156      virtual void visit(DirectionalAtom* datom) {}
157      virtual void visit(RigidBody* rb);
158  
159 <    virtual const string toString();
159 >    virtual const std::string toString();
160      
161    private:
162 <    void replaceType(string& atomType);
162 >    void replaceType(std::string& atomType);
163        
164 <    set<string> waterTypeList;
164 >    std::set<std::string> waterTypeList;
165   };
166  
167  

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