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Comparing trunk/src/visitors/OtherVisitor.hpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 6 | Line 6
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
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
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.
# Line 37 | Line 28
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
# Line 51 | Line 51
51   #include "selection/SelectionManager.hpp"
52   #include "selection/SelectionEvaluator.hpp"
53  
54 < namespace oopse {
54 > namespace OpenMD {
55  
56 < class SimInfo;
56 >  class SimInfo;
57  
58  
59 < class WrappingVisitor : public BaseVisitor{
59 >  class WrappingVisitor : public BaseVisitor{
60    public:
61 <    WrappingVisitor(SimInfo* info) : BaseVisitor() {
61 >    WrappingVisitor(SimInfo* info, bool useCom = true) : BaseVisitor(), useCom_(useCom) {
62        this->info = info;
63        visitorName = "WrappingVisitor";
64      }
# Line 68 | Line 68 | class WrappingVisitor : public BaseVisitor{
68  
69      virtual const std::string toString();
70  
71 <  protected:
71 >    virtual void update();
72 >    
73 >  private:
74      void internalVisit(StuntDouble* sd);
75 <    SimInfo* info;
76 < };
75 >    SimInfo* info;    
76 >    Vector3d origin_;
77 >    bool useCom_;
78 >  };
79  
80  
81 < class ReplicateVisitor : public BaseVisitor{
81 >  class ReplicateVisitor : public BaseVisitor{
82    public:
83      ReplicateVisitor(SimInfo* info, Vector3i opt);
84      virtual void visit(Atom* atom);
# Line 90 | Line 94 | class ReplicateVisitor : public BaseVisitor{
94      std::vector<Vector3i> dir;
95      SimInfo* info;
96      Vector3i replicateOpt;
97 < };
97 >  };
98  
99 < class XYZVisitor : public BaseVisitor{
99 >  class XYZVisitor : public BaseVisitor{
100    public:
101      
102      XYZVisitor(SimInfo* info);
# Line 109 | Line 113 | class XYZVisitor : public BaseVisitor{
113      
114      void writeFrame(std::ostream& outStream);    
115      void clear() {frame.clear();}
116 <    
116 >    void setPosOnly(bool posOnly){posOnly_ = posOnly;}
117    protected:
118      void internalVisit(StuntDouble* sd);
119      bool isSelected(StuntDouble* sd);
120  
121    private:  
122 +    std::string trimmedName(const std::string& atomType);
123 +
124      SimInfo* info;
125      SelectionManager seleMan;
126      SelectionEvaluator evaluator;
127      std::vector<std::string> frame;
128 +    bool posOnly_;
129 +  };
130  
123 – };
131  
132 <
126 < class PrepareVisitor : public BaseVisitor{
132 >  class PrepareVisitor : public BaseVisitor{
133    public:
134      PrepareVisitor() : BaseVisitor() {visitorName = "prepareVisitor";}
135  
# Line 136 | Line 142 | class PrepareVisitor : public BaseVisitor{
142    protected:
143      void internalVisit(Atom* atom);
144      void internalVisit(RigidBody* rb);
145 < };
145 >  };
146  
147    class WaterTypeVisitor : public BaseVisitor{
148    public:
# Line 151 | Line 157 | class PrepareVisitor : public BaseVisitor{
157      std::string trimmedName(const std::string& atomType);
158      
159      std::set<std::string> waterTypeList;
160 < };
160 >  };
161  
162  
163 < }//namespace oopse
163 > }//namespace OpenMD
164   #endif //_OTHERVISITOR_H_

Comparing trunk/src/visitors/OtherVisitor.hpp (property svn:keywords):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

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