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 parseFile( char* fileName ); |
23 |
|
void createSim( void ); |
24 |
|
|
29 |
|
void receiveParse(void); |
30 |
|
#endif |
31 |
|
|
32 |
< |
void makeMolecules( void ); |
32 |
> |
void gatherInfo( void ); |
33 |
> |
void sysObjectsCreation( void ); |
34 |
> |
void finalInfoCheck( void ); |
35 |
> |
void initSystemCoords( void ); |
36 |
> |
void makeOutNames(void); |
37 |
> |
void makeIntegrator(void); |
38 |
> |
void initFortran(void); |
39 |
|
|
40 |
+ |
void createFF( void ); |
41 |
+ |
void compList( void ); |
42 |
+ |
void calcSysValues( void ); |
43 |
+ |
void makeSysArrays( void ); |
44 |
+ |
|
45 |
+ |
#ifdef IS_MPI |
46 |
+ |
void mpiMolDivide( void ); |
47 |
+ |
|
48 |
+ |
int* mol2proc; |
49 |
+ |
int* molCompType; |
50 |
+ |
|
51 |
+ |
#endif //is_mpi |
52 |
+ |
|
53 |
|
void initFromBass( void ); |
54 |
+ |
void makeMolecules( void ); |
55 |
|
void makeElement( double x, double y, double z ); |
56 |
|
|
57 |
+ |
int ensembleCase; |
58 |
+ |
int ffCase; |
59 |
+ |
|
60 |
+ |
|
61 |
|
MakeStamps* stamps; |
62 |
|
Globals* globals; |
63 |
|
char* inFileName; |
64 |
|
|
65 |
< |
SimInfo* simnfo; |
65 |
> |
SimInfo* info; |
66 |
> |
int isInfoArray; |
67 |
> |
int nInfo; |
68 |
|
|
69 |
|
int n_components; |
70 |
+ |
int globalAtomIndex; |
71 |
|
|
72 |
|
char force_field[100]; |
73 |
|
char ensemble[100]; |
84 |
|
|
85 |
|
Atom** the_atoms; |
86 |
|
SRI** the_sris; |
87 |
< |
int *the_excludes; |
87 |
> |
Exclude** the_excludes; |
88 |
|
Molecule* the_molecules; |
89 |
|
ForceFields* the_ff; |
90 |
|
|