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#include "primitives/Molecule.hpp" |
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< |
#include "brans/SimInfo.hpp" |
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> |
#include "brains/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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+ |
// this routine is defined in BASS_interface.cpp |
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//another OOPS |
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extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
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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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> |
* The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo |
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* instance based on the information returned by parser. |
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*/ |
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class SimCreator { |
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public: |
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SimInfo* createSim(char* mdfile); |
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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(const std::string & mdFileName); |
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protected: |
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private: |
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void parseFile(char* mdfile, MakeStamps* stamps, Globals* globals); |
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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 simParams |
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*/ |
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> |
void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams); |
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< |
#ifdef IS_MPI |
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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(SimInfo* info); |
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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(SimInfo* info); |
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> |
|
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> |
void gatherParameters(SimInfo *info, const std::string& mdfile); |
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> |
|
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< |
virtual Molecule* createMolecule(); |
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> |
/** Extracts the molecules stamps and adds them into SimInfo class */ |
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> |
void compList(MakeStamps* stamps, Globals* simParams, |
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> |
std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ; |
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< |
void setGlobalIndices(); |
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private: |
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< |
void compList(MakeStamps* stamps,SimInfo* info) ; |
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> |
/** |
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> |
* Divide the molecules among the processors |
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> |
*/ |
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> |
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| 98 |
> |
void divideMolecules(SimInfo* info); |
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> |
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> |
/** Load initial coordinates */ |
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> |
void loadCoordinates(SimInfo* info); |
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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 |
