| 45 |
|
|
| 46 |
|
/** |
| 47 |
|
* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp" |
| 48 |
< |
* @brief SimCreator is an abstract factory which is responsible for setting up the simulation. |
| 48 |
> |
* @brief |
| 49 |
|
*/ |
| 50 |
|
class SimCreator { |
| 51 |
|
public: |
| 52 |
|
|
| 53 |
+ |
/** |
| 54 |
+ |
* Setup Simulation |
| 55 |
+ |
* @return a pointer to SimInfo |
| 56 |
+ |
* @param mdfile the meta-data file name |
| 57 |
+ |
*/ |
| 58 |
|
SimInfo* createSim(char* mdfile); |
| 59 |
|
|
| 60 |
|
protected: |
| 61 |
+ |
|
| 62 |
+ |
/** |
| 63 |
+ |
* Parses the meta-data file |
| 64 |
+ |
* @param mdfile |
| 65 |
+ |
* @param stamps |
| 66 |
+ |
* @param globals |
| 67 |
+ |
*/ |
| 68 |
+ |
void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* globals); |
| 69 |
+ |
|
| 70 |
+ |
#ifdef IS_MPI |
| 71 |
+ |
/** |
| 72 |
+ |
* Divide the molecules among the processors |
| 73 |
+ |
*/ |
| 74 |
+ |
void divideMolecules(); |
| 75 |
+ |
#endif //is_mpi |
| 76 |
+ |
|
| 77 |
+ |
/** create the molecules belong to current processor*/ |
| 78 |
+ |
virtual void createMolecules(); |
| 79 |
+ |
|
| 80 |
+ |
/** |
| 81 |
+ |
* Sets the global index for atoms, rigidbodies and cutoff groups and fill up |
| 82 |
+ |
* globalGroupMembership and globalMolMembership arrays which map atoms' |
| 83 |
+ |
* global index to the global index of the groups (or molecules) they belong to. |
| 84 |
+ |
* These array are never changed during the simulation. |
| 85 |
+ |
*/ |
| 86 |
+ |
void setGlobalIndex(); |
| 87 |
+ |
|
| 88 |
+ |
private: |
| 89 |
|
|
| 90 |
< |
void parseFile(char* mdfile, MakeStamps* stamps, Globals* globals); |
| 90 |
> |
/** Extracts the molecules stamps and adds them into SimInfo class */ |
| 91 |
> |
void compList(MakeStamps* stamps, Globals* globals, |
| 92 |
> |
std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ; |
| 93 |
> |
|
| 94 |
> |
/** Initialize fortran, mainly set the cutoff radius and setup*/ |
| 95 |
> |
void initFortran(SimInfo* info); |
| 96 |
> |
|
| 97 |
> |
/** Figure out the cutoff radius and pass it to fortran */ |
| 98 |
> |
void setCutoff(SimInfo* info); |
| 99 |
|
|
| 100 |
< |
virtual ForceField* createForceField(); |
| 60 |
< |
virtual Molecule* createMolecule(); |
| 61 |
< |
virtual Atom* createAtom(); |
| 62 |
< |
virtual RigidBody* createRigidBody(); |
| 63 |
< |
virtual Bond* createBond(); |
| 64 |
< |
virtual Bend* createBend(); |
| 65 |
< |
virtual Torsion* createTorsion(); |
| 66 |
< |
|
| 67 |
< |
|
| 100 |
> |
std::string mdFileName_; //save the meta-data file name which may be used later |
| 101 |
|
}; |
| 102 |
|
|
| 103 |
|
} //end namespace oopse |
