| 35 |
|
#include <vector> |
| 36 |
|
#include <iostream> |
| 37 |
|
|
| 38 |
+ |
#include "constraints/ConstraintPair.hpp" |
| 39 |
|
#include "math/Vector3.hpp" |
| 40 |
|
#include "primitives/Atom.hpp" |
| 41 |
|
#include "primitives/RigidBody.hpp" |
| 42 |
< |
//#include "primitives/Bond.hpp" |
| 43 |
< |
//#include "primitives/Bend.hpp" |
| 44 |
< |
//#include "primitives/Torsion.hpp" |
| 44 |
< |
#include "primitives/SRI.hpp" |
| 42 |
> |
#include "primitives/Bond.hpp" |
| 43 |
> |
#include "primitives/Bend.hpp" |
| 44 |
> |
#include "primitives/Torsion.hpp" |
| 45 |
|
#include "primitives/CutoffGroup.hpp" |
| 46 |
|
|
| 47 |
|
namespace oopse{ |
| 63 |
|
typedef std::vector<CutoffGroup*>::iterator CutoffGroupIterator; |
| 64 |
|
typedef std::vector<StuntDouble*>::iterator IntegrableObjectIterator; |
| 65 |
|
|
| 66 |
< |
Molecule(int stampId, int globalIndex); |
| 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 |
|
*/ |
| 96 |
|
return globalIndex_; |
| 97 |
|
} |
| 98 |
|
|
| 99 |
+ |
|
| 100 |
|
/** add an atom into this molecule */ |
| 101 |
|
void addAtom(Atom* atom); |
| 102 |
|
|
| 113 |
|
void addRigidBody(RigidBody *rb); |
| 114 |
|
|
| 115 |
|
/** add a cutoff group into this molecule */ |
| 116 |
< |
void addCutoffGroup(CutoffGroup* cp); |
| 116 |
> |
void addCutoffGroup(CutoffGroup* cp); |
| 117 |
|
|
| 118 |
+ |
void addConstraintPair(ConstraintPair* consPair); |
| 119 |
+ |
|
| 120 |
|
/** */ |
| 121 |
|
void complete(); |
| 122 |
|
|
| 156 |
|
} |
| 157 |
|
|
| 158 |
|
/** Returns the total number of constraints in this molecule */ |
| 159 |
< |
unsigned int getNConstraints() { |
| 160 |
< |
return constraints_.size(); |
| 159 |
> |
unsigned int getNConstraintPairs() { |
| 160 |
> |
return constraintPairs_.size(); |
| 161 |
|
} |
| 162 |
|
|
| 163 |
|
Atom* getAtomAt(unsigned int i) { |
| 231 |
|
*/ |
| 232 |
|
CutoffGroup* nextCutoffGroup(std::vector<CutoffGroup*>::iterator& i); |
| 233 |
|
|
| 234 |
< |
Constraint* beginConstraint(std::vector<Constraint*>::iterator& i); |
| 234 |
> |
ConstraintPair* beginConstraintPair(std::vector<ConstraintPair*>::iterator& i); |
| 235 |
|
|
| 236 |
< |
Constraint* nextConstraint(std::vector<Constraint*>::iterator& i); |
| 236 |
> |
ConstraintPair* nextConstraintPair(std::vector<ConstraintPair*>::iterator& i); |
| 237 |
|
|
| 221 |
– |
//void setStampID( int info ) {stampID = info;} |
| 238 |
|
|
| 223 |
– |
void calcForces( void ); |
| 224 |
– |
|
| 225 |
– |
void atoms2rigidBodies( void ); |
| 226 |
– |
|
| 239 |
|
/** return the total potential energy of short range interaction of this molecule */ |
| 240 |
|
double getPotential(); |
| 241 |
|
|
| 242 |
+ |
/** get total mass of this molecule */ |
| 243 |
+ |
double getMass(); |
| 244 |
|
|
| 245 |
|
/** return the center of mass of this molecule */ |
| 246 |
|
Vector3d getCom(); |
| 267 |
|
std::vector<RigidBody*> rigidBodies_; |
| 268 |
|
std::vector<StuntDouble*> integrableObjects_; |
| 269 |
|
std::vector<CutoffGroup*> cutoffGroups_; |
| 270 |
< |
std::vector<Constraint*> constraints_; |
| 270 |
> |
std::vector<ConstraintPair*> constraintPairs_; |
| 271 |
|
|
| 272 |
< |
int stampID; |
| 272 |
> |
int stampId_; |
| 273 |
> |
std::string moleculeName_; |
| 274 |
|
}; |
| 275 |
|
|
| 276 |
|
} //namespace oopse |
