| 45 |
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| 46 |
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namespace oopse{ |
| 47 |
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| 48 |
+ |
class Constraint; |
| 49 |
+ |
|
| 50 |
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/** |
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* @class Molecule Molecule.hpp "primitives/Molecule.hpp" |
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* @brief |
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class Molecule { |
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public: |
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|
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< |
Molecule(); |
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> |
typedef std::vector<Atom*>::iterator AtomIterator; |
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> |
typedef std::vector<Bond*>::iterator BondIterator; |
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> |
typedef std::vector<Bend*>::iterator BendIterator; |
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> |
typedef std::vector<Torsion*>::iterator TorsionIterator; |
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> |
typedef std::vector<RigidBody*>::iterator RigidBodyIterator; |
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> |
typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator; |
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> |
typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
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> |
|
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> |
Molecule(int stampId, int globalIndex, const std::string& molName); |
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virtual ~Molecule(); |
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/** |
| 74 |
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} |
| 75 |
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| 76 |
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/** |
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+ |
* Returns the stamp id of this molecule |
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+ |
* @note Ideally, every molecule should keep a pointer of its molecule stamp instead of its |
| 79 |
+ |
* stamp id. However, the pointer will become invalid, if the molecule migrate to other processor. |
| 80 |
+ |
*/ |
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+ |
int getStampId() { |
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+ |
return stampId_; |
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+ |
} |
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+ |
|
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+ |
/** Returns the name of the molecule */ |
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+ |
std::string getType() { |
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+ |
return moleculeName_; |
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+ |
} |
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+ |
|
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+ |
/** |
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* Sets the global index of this molecule. |
| 92 |
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* @param new global index to be set |
| 93 |
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*/ |
| 94 |
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int setGlobalIndex(int index) { |
| 95 |
|
return globalIndex_; |
| 96 |
|
} |
| 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 |
– |
} |
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| 98 |
+ |
|
| 99 |
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/** add an atom into this molecule */ |
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void addAtom(Atom* atom); |
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|
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unsigned int getNConstraints() { |
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return constraints_.size(); |
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} |
| 159 |
< |
|
| 159 |
> |
|
| 160 |
> |
Atom* getAtomAt(unsigned int i) { |
| 161 |
> |
assert(i < atoms_.size()); |
| 162 |
> |
return atoms_[i]; |
| 163 |
> |
} |
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/** |
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* Returns the first atom in this molecule and initialize the iterator. |
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* @return the first atom, return NULL if there is not cut off group in this molecule |
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Constraint* nextConstraint(std::vector<Constraint*>::iterator& i); |
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– |
//void setStampID( int info ) {stampID = info;} |
| 235 |
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|
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– |
void calcForces( void ); |
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– |
|
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– |
void atoms2rigidBodies( void ); |
| 219 |
– |
|
| 236 |
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/** return the total potential energy of short range interaction of this molecule */ |
| 237 |
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double getPotential(); |
| 238 |
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|
| 252 |
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friend std::ostream& operator <<(std::ostream& o, Molecule& mol); |
| 253 |
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| 254 |
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private: |
| 255 |
< |
int localIndex_; |
| 255 |
> |
|
| 256 |
|
int globalIndex_; |
| 257 |
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|
| 258 |
|
std::vector<Atom*> atoms_; |
| 263 |
|
std::vector<StuntDouble*> integrableObjects_; |
| 264 |
|
std::vector<CutoffGroup*> cutoffGroups_; |
| 265 |
|
std::vector<Constraint*> constraints_; |
| 266 |
+ |
|
| 267 |
+ |
int stampId_; |
| 268 |
+ |
std::string moleculeName_; |
| 269 |
|
}; |
| 270 |
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|
| 271 |
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} //namespace oopse |
