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Comparing trunk/src/visitors/AtomData.hpp (file contents):
Revision 407 by gezelter, Tue Mar 8 21:07:49 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 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 VISITOR_ATOMDATA_HPP
# Line 47 | Line 48
48   #include "utils/GenericData.hpp"
49   #include "math/Vector3.hpp"
50  
51 < namespace oopse {
51 > namespace OpenMD {
52  
53 < struct AtomInfo {
53 >  struct AtomInfo {
54 >    AtomInfo() : hasCharge(false), hasVector(false), hasVelocity(false),
55 >                 hasForce(false), hasElectricField(false),
56 >                 pos(V3Zero), vec(V3Zero), vel(V3Zero), frc(V3Zero),
57 >                 charge(0.0), eField(V3Zero) {}
58 >    
59      std::string atomTypeName;
60      Vector3d pos;
61 <    Vector3d dipole;  
62 < };
61 >    Vector3d vec;  
62 >    Vector3d vel;  
63 >    Vector3d frc;  
64 >    Vector3d eField;
65 >    RealType charge;
66 >    bool hasCharge;
67 >    bool hasVector;
68 >    bool hasVelocity;
69 >    bool hasForce;
70 >    bool hasElectricField;
71 >  };
72  
73 < class AtomData : public GenericData{
74 <    public:
73 >  class AtomData : public GenericData{
74 >  public:
75  
76 <        AtomData(const std::string& id = "ATOMDATA") : GenericData(id) {}
76 >    AtomData(const std::string& id = "ATOMDATA") : GenericData(id) {}
77  
78 <        ~AtomData() {
79 <            std::vector<AtomInfo*>::iterator i;
80 <            AtomInfo* atomInfo;
78 >    ~AtomData() {
79 >      std::vector<AtomInfo*>::iterator i;
80 >      AtomInfo* atomInfo;
81  
82 <            for(atomInfo = beginAtomInfo(i); atomInfo; atomInfo  = nextAtomInfo(i)) {
83 <                delete atomInfo;
84 <            }
85 <            data.clear();
86 <        }
82 >      for(atomInfo = beginAtomInfo(i); atomInfo; atomInfo  = nextAtomInfo(i)) {
83 >        delete atomInfo;
84 >      }
85 >      data.clear();
86 >    }
87          
88 <        void addAtomInfo(AtomInfo* info) {data.push_back(info);}
88 >    void addAtomInfo(AtomInfo* info) {data.push_back(info);}
89  
90 <        void clearAllAtomInfo();
90 >    void clearAllAtomInfo();
91  
92 <        AtomInfo* beginAtomInfo(std::vector<AtomInfo*>::iterator& i){
93 <            i = data.begin();
94 <            return i != data.end()? *i : NULL;
95 <        }
92 >    AtomInfo* beginAtomInfo(std::vector<AtomInfo*>::iterator& i){
93 >      i = data.begin();
94 >      return i != data.end()? *i : NULL;
95 >    }
96  
97 <        AtomInfo* nextAtomInfo(std::vector<AtomInfo*>::iterator& i){
98 <            ++i;
99 <            return i != data.end()? *i: NULL;
100 <        }
97 >    AtomInfo* nextAtomInfo(std::vector<AtomInfo*>::iterator& i){
98 >      ++i;
99 >      return i != data.end()? *i: NULL;
100 >    }
101  
102 <        std::vector<AtomInfo*> getData() {return data;}
102 >    std::vector<AtomInfo*> getData() {return data;}
103  
104 <        int getSize() {return data.size();}
104 >    int getSize() {return data.size();}
105  
106 <    protected:
106 >  protected:
107  
108 <        std::vector<AtomInfo*> data;
109 < };
108 >    std::vector<AtomInfo*> data;
109 >  };
110  
111  
112   }

Comparing trunk/src/visitors/AtomData.hpp (property svn:keywords):
Revision 407 by gezelter, Tue Mar 8 21:07:49 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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