| 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" |
| 41 |
> |
#include "primitives/Bond.hpp" |
| 42 |
> |
#include "primitives/Bend.hpp" |
| 43 |
> |
#include "primitives/Torsion.hpp" |
| 44 |
|
#include "primitives/CutoffGroup.hpp" |
| 45 |
|
|
| 46 |
|
namespace oopse{ |
| 54 |
|
class Molecule { |
| 55 |
|
public: |
| 56 |
|
|
| 57 |
< |
Molecule(); |
| 57 |
> |
typedef std::vector<Atom*>::iterator AtomIterator; |
| 58 |
> |
typedef std::vector<Bond*>::iterator BondIterator; |
| 59 |
> |
typedef std::vector<Bend*>::iterator BendIterator; |
| 60 |
> |
typedef std::vector<Torsion*>::iterator TorsionIterator; |
| 61 |
> |
typedef std::vector<RigidBody*>::iterator RigidBodyIterator; |
| 62 |
> |
typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator; |
| 63 |
> |
typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
| 64 |
> |
|
| 65 |
> |
Molecule(int stampId, int globalIndex, const std::string& molName); |
| 66 |
|
virtual ~Molecule(); |
| 67 |
|
|
| 68 |
|
/** |
| 73 |
|
return globalIndex_; |
| 74 |
|
} |
| 75 |
|
|
| 76 |
+ |
/** |
| 77 |
+ |
* Returns the stamp id of this molecule |
| 78 |
+ |
* @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 |
+ |
*/ |
| 81 |
+ |
int getStampId() { |
| 82 |
+ |
return stampId_; |
| 83 |
+ |
} |
| 84 |
+ |
|
| 85 |
+ |
/** Returns the name of the molecule */ |
| 86 |
+ |
std::string getType() { |
| 87 |
+ |
return moleculeName_; |
| 88 |
+ |
} |
| 89 |
+ |
|
| 90 |
|
/** |
| 91 |
|
* Sets the global index of this molecule. |
| 92 |
|
* @param new global index to be set |
| 94 |
|
int setGlobalIndex(int index) { |
| 95 |
|
return globalIndex_; |
| 96 |
|
} |
| 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 |
– |
} |
| 97 |
|
|
| 98 |
+ |
|
| 99 |
|
/** add an atom into this molecule */ |
| 100 |
|
void addAtom(Atom* atom); |
| 101 |
|
|
| 156 |
|
unsigned int getNConstraints() { |
| 157 |
|
return constraints_.size(); |
| 158 |
|
} |
| 159 |
< |
|
| 159 |
> |
|
| 160 |
> |
Atom* getAtomAt(unsigned int i) { |
| 161 |
> |
assert(i < atoms_.size()); |
| 162 |
> |
return atoms_[i]; |
| 163 |
> |
} |
| 164 |
|
/** |
| 165 |
|
* Returns the first atom in this molecule and initialize the iterator. |
| 166 |
|
* @return the first atom, return NULL if there is not cut off group in this molecule |
| 232 |
|
|
| 233 |
|
Constraint* nextConstraint(std::vector<Constraint*>::iterator& i); |
| 234 |
|
|
| 217 |
– |
//void setStampID( int info ) {stampID = info;} |
| 235 |
|
|
| 219 |
– |
void calcForces( void ); |
| 220 |
– |
|
| 221 |
– |
void atoms2rigidBodies( void ); |
| 222 |
– |
|
| 236 |
|
/** return the total potential energy of short range interaction of this molecule */ |
| 237 |
|
double getPotential(); |
| 238 |
|
|
| 252 |
|
friend std::ostream& operator <<(std::ostream& o, Molecule& mol); |
| 253 |
|
|
| 254 |
|
private: |
| 255 |
< |
int localIndex_; |
| 255 |
> |
|
| 256 |
|
int globalIndex_; |
| 257 |
|
|
| 258 |
|
std::vector<Atom*> atoms_; |
| 264 |
|
std::vector<CutoffGroup*> cutoffGroups_; |
| 265 |
|
std::vector<Constraint*> constraints_; |
| 266 |
|
|
| 267 |
< |
int stampID; |
| 267 |
> |
int stampId_; |
| 268 |
> |
std::string moleculeName_; |
| 269 |
|
}; |
| 270 |
|
|
| 271 |
|
} //namespace oopse |
