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 |
|
/** |
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 |
94 |
|
*/ |
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 |
|
|
157 |
|
unsigned int getNConstraints() { |
158 |
|
return constraints_.size(); |
159 |
|
} |
160 |
< |
|
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 |
233 |
|
|
234 |
|
Constraint* nextConstraint(std::vector<Constraint*>::iterator& i); |
235 |
|
|
217 |
– |
//void setStampID( int info ) {stampID = info;} |
236 |
|
|
219 |
– |
void calcForces( void ); |
220 |
– |
|
221 |
– |
void atoms2rigidBodies( void ); |
222 |
– |
|
237 |
|
/** return the total potential energy of short range interaction of this molecule */ |
238 |
|
double getPotential(); |
239 |
|
|
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_; |
265 |
|
std::vector<CutoffGroup*> cutoffGroups_; |
266 |
|
std::vector<Constraint*> constraints_; |
267 |
|
|
268 |
< |
int stampID; |
268 |
> |
int stampId_; |
269 |
> |
std::string moleculeName_; |
270 |
|
}; |
271 |
|
|
272 |
|
} //namespace oopse |