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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 1695 by tim, Mon Nov 1 22:52:57 2004 UTC vs.
Revision 1738 by tim, Sat Nov 13 05:08:12 2004 UTC

# Line 38 | Line 38
38   #include "math/Vector3.hpp"
39   #include "primitives/Atom.hpp"
40   #include "primitives/RigidBody.hpp"
41 < #include "primitives/Bond.hpp"
42 < #include "primitives/Bend.hpp"
43 < #include "primitives/Torsion.hpp"
41 > //#include "primitives/Bond.hpp"
42 > //#include "primitives/Bend.hpp"
43 > //#include "primitives/Torsion.hpp"
44 > #include "primitives/SRI.hpp"
45   #include "primitives/CutoffGroup.hpp"
46  
47   namespace oopse{
48  
49 + class Constraint;
50 +
51   /**
52   * @class Molecule Molecule.hpp "primitives/Molecule.hpp"
53   * @brief
# Line 52 | Line 55 | class Molecule {
55   class Molecule {
56      public:
57  
58 <        Molecule();
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 63 | Line 74 | class Molecule {
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 70 | Line 95 | class Molecule {
95          int setGlobalIndex(int index) {
96              return globalIndex_;
97          }
73 –        
74 –        /**
75 –         * Returns the local index of this molecule
76 –         * @return the local index of this molecule
77 –         */
78 –        int getLocalIndex() {
79 –            return localIndex_;
80 –        }
98  
99 +        
100          /** add an atom into this molecule */
101          void addAtom(Atom* atom);
102  
# Line 135 | Line 153 | class Molecule {
153              return cutoffGroups_.size();
154          }
155  
156 +        /** Returns the total number of constraints in this molecule */
157 +        unsigned int getNConstraints() {
158 +            return constraints_.size();
159 +        }
160 +
161 +        Atom* getAtomAt(unsigned int i) {
162 +            assert(i < atoms_.size());
163 +            return atoms_[i];
164 +        }
165          /**
166           * Returns the first atom in this molecule and initialize the iterator.
167           * @return the first atom, return NULL if there is not cut off group in this molecule
# Line 202 | Line 229 | class Molecule {
229           */        
230          CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i);
231  
232 <        //void setStampID( int info ) {stampID = info;}
232 >        Constraint* beginConstraint(std::vector<Constraint*>::iterator& i);
233  
234 <        void calcForces( void );
234 >        Constraint* nextConstraint(std::vector<Constraint*>::iterator& i);
235 >        
236  
209 –        void atoms2rigidBodies( void );
210 –
237          /** return the total potential energy of short range interaction of this molecule */
238          double getPotential();
239  
# Line 227 | Line 253 | class Molecule {
253          friend std::ostream& operator <<(std::ostream& o, Molecule& mol);
254          
255      private:
256 <        int localIndex_;
256 >        
257          int globalIndex_;
258  
259          std::vector<Atom*> atoms_;
# Line 237 | Line 263 | class Molecule {
263          std::vector<RigidBody*> rigidBodies_;
264          std::vector<StuntDouble*> integrableObjects_;
265          std::vector<CutoffGroup*> cutoffGroups_;
266 +        std::vector<Constraint*> constraints_;
267 +
268 +        int stampId_;
269 +        std::string moleculeName_;
270   };
271  
272   } //namespace oopse

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