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#include "ForceFields.hpp" |
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#include "SimInfo.hpp" |
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#include "ReadWrite.hpp" |
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#include "AllIntegrator.hpp" |
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// this routine is defined in BASS_interface.cpp |
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< |
void set_interface_stamps( MakeStamps* ms, Globals* g ); |
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> |
extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
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class SimSetup{ |
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SimSetup(); |
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~SimSetup(); |
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< |
void setSimInfo( SimInfo* the_simnfo ) { simnfo = the_simnfo; } |
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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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void receiveParse(void); |
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#endif |
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< |
void makeMolecules( void ); |
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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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< |
void makeAtoms( void ); |
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< |
void makeBonds( void ); |
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< |
void makeBends( void ); |
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< |
void makeTorsions( void ); |
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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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#ifdef IS_MPI |
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void mpiMolDivide( void ); |
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int* mol2proc; |
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int* molCompType; |
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#endif //is_mpi |
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|
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void initFromBass( void ); |
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void makeMolecules( void ); |
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void makeElement( double x, double y, double z ); |
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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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|
| 66 |
< |
SimInfo* simnfo; |
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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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int n_components; |
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int globalAtomCounter; |
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int globalMolCounter; |
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char force_field[100]; |
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char ensemble[100]; |
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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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Atom** the_atoms; |
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SRI** the_sris; |
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int *the_excludes; |
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Molecule* the_molecules; |
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ForceFields* the_ff; |
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// needed by makeElement |
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int current_comp; |
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int current_atom_ndx; |
| 99 |
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< |
#ifdef IS_MPI |
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< |
int* globalIndex; |
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< |
#endif //is_mpi |
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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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#endif |
