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root/group/branches/new_design/OOPSE-3.0/src/primitives/Molecule.hpp
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Comparing branches/new_design/OOPSE-3.0/src/primitives/Molecule.hpp (file contents):
Revision 1719 by tim, Fri Nov 5 23:38:27 2004 UTC vs.
Revision 1733 by tim, Fri Nov 12 06:19:04 2004 UTC

# Line 55 | Line 55 | class Molecule {
55   class Molecule {
56      public:
57  
58 <        Molecule(int stampId, int globalIndex);
58 >        typedef std::vector<Atom*>::iterator AtomIterator;
59 >        typedef std::vector<Bond*>::iterator BondIterator;
60 >        typedef std::vector<Bend*>::iterator BendIterator;
61 >        typedef std::vector<Torsion*>::iterator TorsionIterator;
62 >        typedef std::vector<RigidBody*>::iterator RigidBodyIterator;
63 >        typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator;
64 >        typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator;        
65 >
66 >        Molecule(int stampId, int globalIndex, const std::string& molName);
67          virtual ~Molecule();
68  
69          /**
# Line 64 | Line 72 | class Molecule {
72           */
73          int getGlobalIndex() {
74              return globalIndex_;
75 +        }
76 +
77 +        /**
78 +         * Returns the stamp id of this molecule
79 +         * @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its
80 +         * stamp id. However, the pointer will become invalid, if the molecule migrate to other processor.
81 +         */
82 +        int getStampId() {
83 +            return stampId_;
84          }
85  
86 +        /** Returns the name of the molecule */
87 +        std::string getType() {
88 +            return moleculeName_;
89 +        }
90 +        
91          /**
92           * Sets the global index of this molecule.
93           * @param new global index to be set
# Line 73 | Line 95 | class Molecule {
95          int setGlobalIndex(int index) {
96              return globalIndex_;
97          }
76 –        
77 –        /**
78 –         * Returns the local index of this molecule
79 –         * @return the local index of this molecule
80 –         */
81 –        int getLocalIndex() {
82 –            return localIndex_;
83 –        }
98  
99 +        
100          /** add an atom into this molecule */
101          void addAtom(Atom* atom);
102  
# Line 243 | Line 258 | class Molecule {
258          friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
259          
260      private:
261 <        int localIndex_;
261 >        
262          int globalIndex_;
263  
264          std::vector<Atom*> atoms_;
# Line 255 | Line 270 | class Molecule {
270          std::vector<CutoffGroup*> cutoffGroups_;
271          std::vector<Constraint*> constraints_;
272  
273 <        int stampID;
273 >        int stampId_;
274 >        std::string moleculeName_;
275   };
276  
277   } //namespace oopse

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