| 8 |
|
#include "ReadWrite.hpp" |
| 9 |
|
|
| 10 |
|
// this routine is defined in BASS_interface.cpp |
| 11 |
< |
void set_interface_stamps( MakeStamps* ms, Globals* g ); |
| 11 |
> |
extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
| 12 |
|
|
| 13 |
|
class SimSetup{ |
| 14 |
|
|
| 27 |
|
void receiveParse(void); |
| 28 |
|
#endif |
| 29 |
|
|
| 30 |
< |
void makeMolecules( void ); |
| 30 |
> |
void gatherInfo( void ); |
| 31 |
> |
void sysObjectsCreation( void ); |
| 32 |
> |
void finalInfoCheck( void ); |
| 33 |
> |
void initSystemCoords( void ); |
| 34 |
> |
void makeOutNames(void); |
| 35 |
|
|
| 36 |
< |
void makeAtoms( void ); |
| 37 |
< |
void makeBonds( void ); |
| 38 |
< |
void makeBends( void ); |
| 39 |
< |
void makeTorsions( void ); |
| 36 |
> |
void createFF( void ); |
| 37 |
> |
void compList( void ); |
| 38 |
> |
void calcSysValues( void ); |
| 39 |
> |
void makeSysArrays( void ); |
| 40 |
|
|
| 41 |
+ |
#ifdef IS_MPI |
| 42 |
+ |
void mpiMolDivide( void ); |
| 43 |
+ |
|
| 44 |
+ |
int* mol2proc; |
| 45 |
+ |
int* molCompType; |
| 46 |
+ |
|
| 47 |
+ |
#endif //is_mpi |
| 48 |
+ |
|
| 49 |
|
void initFromBass( void ); |
| 50 |
+ |
void makeMolecules( void ); |
| 51 |
|
void makeElement( double x, double y, double z ); |
| 52 |
|
|
| 53 |
+ |
int ensembleCase; |
| 54 |
+ |
int ffCase; |
| 55 |
+ |
|
| 56 |
+ |
|
| 57 |
|
MakeStamps* stamps; |
| 58 |
|
Globals* globals; |
| 59 |
|
char* inFileName; |
| 60 |
|
|
| 61 |
< |
SimInfo* simnfo; |
| 61 |
> |
SimInfo* info; |
| 62 |
|
|
| 63 |
|
int n_components; |
| 64 |
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|
| 77 |
|
|
| 78 |
|
Atom** the_atoms; |
| 79 |
|
SRI** the_sris; |
| 80 |
< |
int *the_excludes; |
| 80 |
> |
Exclude** the_excludes; |
| 81 |
|
Molecule* the_molecules; |
| 82 |
|
ForceFields* the_ff; |
| 83 |
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|
