| 6 |
|
#include "ForceFields.hpp" |
| 7 |
|
#include "SimInfo.hpp" |
| 8 |
|
#include "ReadWrite.hpp" |
| 9 |
+ |
#include "AllIntegrator.hpp" |
| 10 |
|
|
| 11 |
|
// this routine is defined in BASS_interface.cpp |
| 12 |
< |
void set_interface_stamps( MakeStamps* ms, Globals* g ); |
| 12 |
> |
extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
| 13 |
|
|
| 14 |
|
class SimSetup{ |
| 15 |
|
|
| 17 |
|
SimSetup(); |
| 18 |
|
~SimSetup(); |
| 19 |
|
|
| 20 |
< |
void setSimInfo( SimInfo* the_simnfo ) { simnfo = the_simnfo; } |
| 20 |
> |
void setSimInfo( SimInfo* the_info ) { info = the_info; } |
| 21 |
> |
void setSimInfo( SimInfo* the_info, int theNinfo ); |
| 22 |
> |
void suspendInit( void ) { initSuspend = true; } |
| 23 |
|
void parseFile( char* fileName ); |
| 24 |
|
void createSim( void ); |
| 25 |
|
|
| 30 |
|
void receiveParse(void); |
| 31 |
|
#endif |
| 32 |
|
|
| 33 |
< |
void makeMolecules( void ); |
| 33 |
> |
void gatherInfo( void ); |
| 34 |
> |
void sysObjectsCreation( void ); |
| 35 |
> |
void finalInfoCheck( void ); |
| 36 |
> |
void initSystemCoords( void ); |
| 37 |
> |
void makeOutNames(void); |
| 38 |
> |
void makeIntegrator(void); |
| 39 |
> |
void initFortran(void); |
| 40 |
> |
void makeMinimizer(void); |
| 41 |
|
|
| 42 |
< |
void makeAtoms( void ); |
| 43 |
< |
void makeBonds( void ); |
| 44 |
< |
void makeBends( void ); |
| 45 |
< |
void makeTorsions( void ); |
| 42 |
> |
void createFF( void ); |
| 43 |
> |
void compList( void ); |
| 44 |
> |
void calcSysValues( void ); |
| 45 |
> |
void makeSysArrays( void ); |
| 46 |
|
|
| 47 |
+ |
#ifdef IS_MPI |
| 48 |
+ |
void mpiMolDivide( void ); |
| 49 |
+ |
|
| 50 |
+ |
int* mol2proc; |
| 51 |
+ |
int* molCompType; |
| 52 |
+ |
|
| 53 |
+ |
#endif //is_mpi |
| 54 |
+ |
|
| 55 |
|
void initFromBass( void ); |
| 56 |
+ |
void makeMolecules( void ); |
| 57 |
|
void makeElement( double x, double y, double z ); |
| 58 |
|
|
| 59 |
+ |
int ensembleCase; |
| 60 |
+ |
int ffCase; |
| 61 |
+ |
|
| 62 |
|
MakeStamps* stamps; |
| 63 |
|
Globals* globals; |
| 64 |
|
char* inFileName; |
| 65 |
|
|
| 66 |
< |
SimInfo* simnfo; |
| 66 |
> |
SimInfo* info; |
| 67 |
> |
int isInfoArray; |
| 68 |
> |
int nInfo; |
| 69 |
> |
|
| 70 |
> |
bool initSuspend; |
| 71 |
|
|
| 72 |
|
int n_components; |
| 73 |
+ |
int globalAtomCounter; |
| 74 |
+ |
int globalMolCounter; |
| 75 |
|
|
| 76 |
|
char force_field[100]; |
| 77 |
|
char ensemble[100]; |
| 81 |
|
MoleculeStamp** comp_stamps; //the stamps matching the components |
| 82 |
|
int tot_nmol; |
| 83 |
|
int tot_atoms; |
| 84 |
+ |
int tot_rigid; |
| 85 |
|
int tot_bonds; |
| 86 |
|
int tot_bends; |
| 87 |
|
int tot_torsions; |
| 88 |
|
int tot_SRI; |
| 89 |
|
|
| 61 |
– |
Atom** the_atoms; |
| 62 |
– |
SRI** the_sris; |
| 63 |
– |
int *the_excludes; |
| 64 |
– |
Molecule* the_molecules; |
| 90 |
|
ForceFields* the_ff; |
| 91 |
|
|
| 92 |
|
// needed by makeElement |
| 96 |
|
int current_comp; |
| 97 |
|
int current_atom_ndx; |
| 98 |
|
|
| 99 |
< |
#ifdef IS_MPI |
| 100 |
< |
int* globalIndex; |
| 76 |
< |
#endif //is_mpi |
| 99 |
> |
vector<int> globalAtomIndex; |
| 100 |
> |
void setupZConstraint(SimInfo& theInfo); //setup parameters for zconstraint method |
| 101 |
|
|
| 102 |
|
}; |
| 103 |
|
#endif |
