1 |
mmeineke |
10 |
#ifndef __SIMSETUP_H__ |
2 |
|
|
#define __SIMSETUP_H__ |
3 |
|
|
|
4 |
|
|
#include "MakeStamps.hpp" |
5 |
|
|
#include "Globals.hpp" |
6 |
|
|
#include "ForceFields.hpp" |
7 |
|
|
#include "SimInfo.hpp" |
8 |
|
|
#include "ReadWrite.hpp" |
9 |
|
|
|
10 |
|
|
// this routine is defined in BASS_interface.cpp |
11 |
|
|
void set_interface_stamps( MakeStamps* ms, Globals* g ); |
12 |
|
|
|
13 |
|
|
class SimSetup{ |
14 |
|
|
|
15 |
|
|
public: |
16 |
|
|
SimSetup(); |
17 |
|
|
~SimSetup(); |
18 |
|
|
|
19 |
|
|
void setSimInfo( SimInfo* the_simnfo ) { simnfo = the_simnfo; } |
20 |
|
|
void parseFile( char* fileName ); |
21 |
|
|
void createSim( void ); |
22 |
chuckv |
127 |
void testMe(void); |
23 |
mmeineke |
10 |
|
24 |
chuckv |
125 |
#ifdef MPI |
25 |
|
|
void receveParse(void); |
26 |
|
|
void testMe(void); |
27 |
|
|
#endif |
28 |
mmeineke |
10 |
|
29 |
chuckv |
125 |
|
30 |
|
|
private: |
31 |
|
|
|
32 |
mmeineke |
10 |
void makeAtoms( void ); |
33 |
|
|
void makeBonds( void ); |
34 |
|
|
void makeBends( void ); |
35 |
|
|
void makeTorsions( void ); |
36 |
|
|
|
37 |
|
|
void initFromBass( void ); |
38 |
|
|
void makeElement( double x, double y, double z ); |
39 |
|
|
|
40 |
|
|
MakeStamps* stamps; |
41 |
|
|
Globals* globals; |
42 |
|
|
char* inFileName; |
43 |
chuckv |
125 |
|
44 |
mmeineke |
10 |
SimInfo* simnfo; |
45 |
chuckv |
125 |
|
46 |
mmeineke |
10 |
int n_components; |
47 |
|
|
|
48 |
|
|
char force_field[100]; |
49 |
|
|
char ensemble[100]; |
50 |
|
|
Component** the_components; |
51 |
|
|
|
52 |
|
|
int* components_nmol; |
53 |
|
|
MoleculeStamp** comp_stamps; //the stamps matching the components |
54 |
|
|
int tot_nmol; |
55 |
|
|
int tot_atoms; |
56 |
|
|
int tot_bonds; |
57 |
|
|
int tot_bends; |
58 |
|
|
int tot_torsions; |
59 |
|
|
int tot_SRI; |
60 |
|
|
|
61 |
|
|
Atom** the_atoms; |
62 |
|
|
SRI** the_sris; |
63 |
|
|
LRI* longRange; |
64 |
|
|
ex_pair *the_excludes; |
65 |
|
|
Molecule* the_molecules; |
66 |
|
|
ForceFields* the_ff; |
67 |
|
|
|
68 |
|
|
// needed by makeElement |
69 |
|
|
|
70 |
|
|
int current_mol; |
71 |
|
|
int current_comp_mol; |
72 |
|
|
int current_comp; |
73 |
|
|
int current_atom_ndx; |
74 |
|
|
}; |
75 |
|
|
#endif |