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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 1692 by tim, Mon Nov 1 20:15:58 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"
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 48 | 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 60 | Line 75 | class Molecule {
75          }
76  
77          /**
78 <         * Sets the global index of this molecule.
79 <         * @param new global index to be set
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 <        void setGlobalIndex(int index) {
83 <            return globalIndex_;
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 <         * Returns the local index of this molecule
93 <         * @return the local index of this molecule
91 >        /**
92 >         * Sets the global index of this molecule.
93 >         * @param new global index to be set
94           */
95 <        int getLocalIndex() {
96 <            return localIndex_;
95 >        int setGlobalIndex(int index) {
96 >            return globalIndex_;
97          }
98  
99 +        
100          /** add an atom into this molecule */
101          void addAtom(Atom* atom);
102  
# Line 131 | 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 198 | 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  
205 –        void atoms2rigidBodies( void );
206 –
237          /** return the total potential energy of short range interaction of this molecule */
238          double getPotential();
239  
# Line 212 | Line 242 | class Molecule {
242          Vector3d getCom();
243  
244          /** Moves the center of this molecule */
245 <        void moveCom(const Vetor3d& delta);
245 >        void moveCom(const Vector3d& delta);
246  
247          /** Returns the velocity of center of mass of this molecule */
248          Vector3d getComVel();
# Line 220 | Line 250 | class Molecule {
250          /** Returns the total mass of this molecule */
251          double getTotalMass();
252  
253 <        friend std::ostream& operator <<(std::ostream& o, const Molecule& mol);
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 233 | 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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