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#ifndef __SIMSETUP_H__ |
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#define __SIMSETUP_H__ |
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#include <string> |
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#include "utils/StringUtils.hpp" |
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#include "types/MakeStamps.hpp" |
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#include "io/Globals.hpp" |
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#include "UseTheForce/ForceFields.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "io/ReadWrite.hpp" |
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#include "integrators/AllIntegrator.hpp" |
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|
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using namespace std; |
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using namespace oopse; |
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// this routine is defined in BASS_interface.cpp |
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extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
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|
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string getPrefix(const string& str ); |
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|
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class SimSetup{ |
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|
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public: |
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SimSetup(); |
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~SimSetup(); |
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|
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void setSimInfo( SimInfo* the_info ) { info = the_info; } |
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void setSimInfo( SimInfo* the_info, int theNinfo ); |
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void suspendInit( void ) { initSuspend = true; } |
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void parseFile( char* fileName ); |
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void createSim( void ); |
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|
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ForceFields* getForceField() {return the_ff;} |
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private: |
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|
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#ifdef IS_MPI |
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void receiveParse(void); |
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#endif |
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|
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void gatherInfo( void ); |
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void sysObjectsCreation( void ); |
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void finalInfoCheck( void ); |
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void initSystemCoords( void ); |
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void makeOutNames(void); |
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void makeIntegrator(void); |
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void initFortran(void); |
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void makeMinimizer(void); |
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|
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void createFF( void ); |
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void compList( void ); |
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void calcSysValues( void ); |
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void makeSysArrays( void ); |
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|
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#ifdef IS_MPI |
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void mpiMolDivide( void ); |
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|
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int* mol2proc; |
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int* molCompType; |
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|
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#endif //is_mpi |
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|
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void initFromMetaDataFile( void ); |
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void makeMolecules( void ); |
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void makeElement( double x, double y, double z ); |
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|
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int ensembleCase; |
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int ffCase; |
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|
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MakeStamps* stamps; |
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Globals* globals; |
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char* inFileName; |
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|
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SimInfo* info; |
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int isInfoArray; |
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int nInfo; |
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|
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bool initSuspend; |
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|
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int n_components; |
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int globalAtomCounter; |
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int globalMolCounter; |
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|
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char force_field[100]; |
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string forcefield_variant; |
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char ensemble[100]; |
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Component** the_components; |
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|
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int* components_nmol; |
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MoleculeStamp** comp_stamps; //the stamps matching the components |
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int tot_nmol; |
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int tot_atoms; |
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int tot_groups; |
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int tot_rigid; |
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int tot_bonds; |
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int tot_bends; |
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int tot_torsions; |
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int tot_SRI; |
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|
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ForceFields* the_ff; |
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|
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// needed by makeElement |
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|
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int current_mol; |
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int current_comp_mol; |
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int current_comp; |
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int current_atom_ndx; |
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short int has_forcefield_variant; |
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|
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vector<int> globalAtomIndex; |
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vector<int> globalGroupIndex; |
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void setupZConstraint(SimInfo& theInfo); //setup parameters for zconstraint method |
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|
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}; |
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#endif |
