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#define BRAINS_SIMCREATOR_HPP |
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#include "primitives/Molecule.hpp" |
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#include "brans/SimInfo.hpp" |
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#include "types/MakeStamps.hpp" |
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#include "io/Globals.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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namespace oopse { |
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/** |
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* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp" |
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< |
* @brief SimCreator is an abstract factory which is responsible for setting up the simulation. |
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> |
* @brief |
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*/ |
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class SimCreator { |
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public: |
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void parseFile(const string& mdfile); |
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void createSim(); |
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|
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/** |
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* Setup Simulation |
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> |
* @return a pointer to SimInfo |
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* @param mdfile the meta-data file name |
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*/ |
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SimInfo* createSim(char* mdfile); |
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protected: |
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virtual ForceFiled* createForceFiled(); |
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virtual Molecule* createMolecule(); |
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virtual Atom* createAtom(); |
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virtual RigidBody* createRigidBody(); |
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virtual Bond* createBond(); |
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virtual Bend* createBend(); |
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virtual Torsion* createTorsion(); |
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> |
/** |
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* Parses the meta-data file |
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> |
* @param mdfile |
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> |
* @param stamps |
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> |
* @param globals |
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> |
*/ |
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> |
void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* globals); |
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> |
|
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#ifdef IS_MPI |
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/** |
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* Divide the molecules among the processors |
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*/ |
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> |
void divideMolecules(); |
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#endif //is_mpi |
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> |
|
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> |
/** create the molecules belong to current processor*/ |
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virtual void createMolecules(); |
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> |
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> |
/** |
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> |
* Sets the global index for atoms, rigidbodies and cutoff groups and fill up |
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> |
* globalGroupMembership and globalMolMembership arrays which map atoms' |
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> |
* global index to the global index of the groups (or molecules) they belong to. |
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> |
* These array are never changed during the simulation. |
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> |
*/ |
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> |
void setGlobalIndex(); |
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> |
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> |
private: |
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+ |
/** Extracts the molecules stamps and adds them into SimInfo class */ |
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void compList(MakeStamps* stamps, Globals* globals, |
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std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ; |
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/** Initialize fortran, mainly set the cutoff radius and setup*/ |
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void initFortran(SimInfo* info); |
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/** Figure out the cutoff radius and pass it to fortran */ |
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void setCutoff(SimInfo* info); |
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< |
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< |
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> |
std::string mdFileName_; //save the meta-data file name which may be used later |
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}; |
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} //end namespace oopse |
