# | Line 6 | Line 6 | |
---|---|---|
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 | extern void set_interface_stamps( MakeStamps* ms, Globals* g ); | |
# | Line 16 | Line 17 | class SimSetup{ (public) | |
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 | ||
# | Line 27 | Line 30 | class SimSetup{ (public) | |
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 | ||
41 | + | void createFF( void ); |
42 | + | void compList( void ); |
43 | + | void calcSysValues( void ); |
44 | + | void makeSysArrays( void ); |
45 | + | |
46 | + | #ifdef IS_MPI |
47 | + | void mpiMolDivide( void ); |
48 | + | |
49 | + | int* mol2proc; |
50 | + | int* molCompType; |
51 | + | |
52 | + | #endif //is_mpi |
53 | + | |
54 | void initFromBass( void ); | |
55 | + | void makeMolecules( void ); |
56 | void makeElement( double x, double y, double z ); | |
57 | ||
58 | + | int ensembleCase; |
59 | + | int ffCase; |
60 | + | |
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 globalAtomIndex; |
74 | ||
75 | char force_field[100]; | |
76 | char ensemble[100]; | |
# | Line 53 | Line 85 | class SimSetup{ (public) | |
85 | int tot_torsions; | |
86 | int tot_SRI; | |
87 | ||
56 | – | Atom** the_atoms; |
57 | – | SRI** the_sris; |
58 | – | Exclude** the_excludes; |
59 | – | Molecule* the_molecules; |
88 | ForceFields* the_ff; | |
89 | ||
90 | // needed by makeElement | |
# | Line 70 | Line 98 | class SimSetup{ (public) | |
98 | int* globalIndex; | |
99 | #endif //is_mpi | |
100 | ||
101 | + | void setupZConstraint(SimInfo& theInfo); //setup parameters for zconstraint method |
102 | + | |
103 | }; | |
104 | #endif |
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