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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.
branches/development/src/visitors/OtherVisitor.hpp (file contents), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 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, 234107 (2008).          
39 + * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #ifndef VISITORS_OTHERVISITOR_HPP
# Line 51 | Line 52
52   #include "selection/SelectionManager.hpp"
53   #include "selection/SelectionEvaluator.hpp"
54  
55 < namespace oopse {
55 > namespace OpenMD {
56  
57 < class SimInfo;
57 >  class SimInfo;
58  
59  
60 < class WrappingVisitor : public BaseVisitor{
60 >  class WrappingVisitor : public BaseVisitor{
61    public:
62 <    WrappingVisitor(SimInfo* info) : BaseVisitor() {
62 >    WrappingVisitor(SimInfo* info, bool useCom = true) : BaseVisitor(), useCom_(useCom) {
63        this->info = info;
64        visitorName = "WrappingVisitor";
65      }
# Line 68 | Line 69 | class WrappingVisitor : public BaseVisitor{
69  
70      virtual const std::string toString();
71  
72 <  protected:
72 >    virtual void update();
73 >    
74 >  private:
75      void internalVisit(StuntDouble* sd);
76 <    SimInfo* info;
77 < };
76 >    SimInfo* info;    
77 >    Vector3d origin_;
78 >    bool useCom_;
79 >  };
80  
81  
82 < class ReplicateVisitor : public BaseVisitor{
82 >  class ReplicateVisitor : public BaseVisitor{
83    public:
84      ReplicateVisitor(SimInfo* info, Vector3i opt);
85      virtual void visit(Atom* atom);
# Line 90 | Line 95 | class ReplicateVisitor : public BaseVisitor{
95      std::vector<Vector3i> dir;
96      SimInfo* info;
97      Vector3i replicateOpt;
98 < };
98 >  };
99  
100 < class XYZVisitor : public BaseVisitor{
100 >  class XYZVisitor : public BaseVisitor{
101    public:
102      
103      XYZVisitor(SimInfo* info);
# Line 109 | Line 114 | class XYZVisitor : public BaseVisitor{
114      
115      void writeFrame(std::ostream& outStream);    
116      void clear() {frame.clear();}
117 <    
117 >    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 >    void doElectricFields(bool efl) {doElectricFields_ = efl;}
123 >
124    protected:
125      void internalVisit(StuntDouble* sd);
126      bool isSelected(StuntDouble* sd);
127  
128    private:  
129 +    std::string trimmedName(const std::string& atomType);
130 +
131      SimInfo* info;
132      SelectionManager seleMan;
133      SelectionEvaluator evaluator;
134      std::vector<std::string> frame;
135 +    bool doPositions_;
136 +    bool doVelocities_;
137 +    bool doForces_;
138 +    bool doVectors_;
139 +    bool doCharges_;
140 +    bool doElectricFields_;
141 +  };
142  
123 – };
143  
144 <
126 < class PrepareVisitor : public BaseVisitor{
144 >  class PrepareVisitor : public BaseVisitor{
145    public:
146      PrepareVisitor() : BaseVisitor() {visitorName = "prepareVisitor";}
147  
148      virtual void visit(Atom* atom) {internalVisit(atom);}
149 <    virtual void visit(DirectionalAtom* datom) {internalVisit((Atom*)datom);}
149 >    virtual void visit(DirectionalAtom* datom) {internalVisit(reinterpret_cast<Atom*>(datom));}
150      virtual void visit(RigidBody* rb) {internalVisit(rb);}
151  
152      virtual const std::string toString();
# Line 136 | Line 154 | class PrepareVisitor : public BaseVisitor{
154    protected:
155      void internalVisit(Atom* atom);
156      void internalVisit(RigidBody* rb);
157 < };
157 >  };
158  
159    class WaterTypeVisitor : public BaseVisitor{
160    public:
# Line 151 | Line 169 | class PrepareVisitor : public BaseVisitor{
169      std::string trimmedName(const std::string& atomType);
170      
171      std::set<std::string> waterTypeList;
172 < };
172 >  };
173  
174  
175 < }//namespace oopse
175 > }//namespace OpenMD
176   #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.
branches/development/src/visitors/OtherVisitor.hpp (property svn:keywords), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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