| 6 |
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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 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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|
| 32 |
< |
void makeMolecules( void ); |
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> |
void gatherInfo( void ); |
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> |
void sysObjectsCreation( void ); |
| 34 |
> |
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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|
| 40 |
< |
void makeAtoms( void ); |
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< |
void makeBonds( void ); |
| 42 |
< |
void makeBends( void ); |
| 43 |
< |
void makeTorsions( void ); |
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> |
void createFF( void ); |
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> |
void compList( void ); |
| 42 |
> |
void calcSysValues( void ); |
| 43 |
> |
void makeSysArrays( void ); |
| 44 |
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|
| 45 |
+ |
#ifdef IS_MPI |
| 46 |
+ |
void mpiMolDivide( void ); |
| 47 |
+ |
|
| 48 |
+ |
int* mol2proc; |
| 49 |
+ |
int* molCompType; |
| 50 |
+ |
|
| 51 |
+ |
#endif //is_mpi |
| 52 |
+ |
|
| 53 |
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void initFromBass( void ); |
| 54 |
+ |
void makeMolecules( void ); |
| 55 |
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void makeElement( double x, double y, double z ); |
| 56 |
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|
| 57 |
+ |
int ensembleCase; |
| 58 |
+ |
int ffCase; |
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+ |
|
| 60 |
+ |
|
| 61 |
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MakeStamps* stamps; |
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Globals* globals; |
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char* inFileName; |
| 64 |
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|
| 65 |
< |
SimInfo* simnfo; |
| 65 |
> |
SimInfo* info; |
| 66 |
> |
int isInfoArray; |
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> |
int nInfo; |
| 68 |
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| 69 |
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int n_components; |
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+ |
int globalAtomIndex; |
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| 72 |
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char force_field[100]; |
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char ensemble[100]; |
| 84 |
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| 85 |
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Atom** the_atoms; |
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SRI** the_sris; |
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< |
int *the_excludes; |
| 87 |
> |
Exclude** the_excludes; |
| 88 |
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Molecule* the_molecules; |
| 89 |
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ForceFields* the_ff; |
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