14 |
|
int nBends; // . . . . .. . .bends . . . . .. . |
15 |
|
int nTorsions; // .. . . .. . . torsions . . .. . . |
16 |
|
int nOriented; // .. . . . .. . oriented atoms . . . |
17 |
+ |
int nExcludes; // . . .. . . . .exclude pairs.. . . . |
18 |
|
|
19 |
|
Atom** myAtoms; // the array of atoms |
20 |
|
Exclude** myExcludes;// the array of Excluded pairs |
33 |
|
~Molecule( void ); |
34 |
|
|
35 |
|
void initialize( molInit &theInit ); |
36 |
+ |
|
37 |
+ |
int getNAtoms ( void ) {return nAtoms;} |
38 |
+ |
int getNBonds ( void ) {return nBonds;} |
39 |
+ |
int getNBends ( void ) {return nBends;} |
40 |
+ |
int getNTorsions( void ) {return nTorsions;} |
41 |
+ |
int getNOriented( void ) {return nOriented;} |
42 |
+ |
int getNExcludes( void ) {return nExcludes;} |
43 |
+ |
int getNMembers ( void ) {return nMembers;} |
44 |
+ |
int getStampID ( void ) {return stampID;} |
45 |
|
|
46 |
< |
int getNMembers( void ) { return nMembers; } |
47 |
< |
int getStartAtom( void ) { return startAtom; } |
48 |
< |
int getEndAtom( void ) { return endAtom; } |
49 |
< |
int getStampID( void ) { return stampID; } |
46 |
> |
Atom** getMyAtoms ( void ) {return myAtoms;} |
47 |
> |
Bond** getMyBonds ( void ) {return myBonds;} |
48 |
> |
Bend** getMyBends ( void ) {return myBends;} |
49 |
> |
Torsion** getMyTorsions( void ) {return myTorsions;} |
50 |
> |
Exclude** getMyExcludes( void ) {return myExcludes;} |
51 |
|
|
52 |
< |
void setStampID( int info ) { stampID = info; } |
52 |
> |
void setStampID( int info ) {stampID = info;} |
53 |
> |
|
54 |
> |
void calcForces( void ); |
55 |
> |
double getPotential( void ); |
56 |
|
|
57 |
+ |
void printMe( void ); |
58 |
+ |
|
59 |
|
|
60 |
|
private: |
61 |
|
|
65 |
|
int nBends; // . . . . .. . .bends . . . . .. . |
66 |
|
int nTorsions; // .. . . .. . . torsions . . .. . . |
67 |
|
int nOriented; // .. . . . .. . oriented atoms . . . |
68 |
< |
int nMembers; |
68 |
> |
int nMembers; // .. . . . . . .atoms (legacy code) . . . |
69 |
> |
int nExcludes; // . . . . .. .. excludes .. . . |
70 |
|
|
71 |
|
Atom** myAtoms; // the array of atoms |
72 |
< |
Bond** myBonds; // arrays of all the short range interactions |
72 |
> |
Bond** myBonds; // arrays of all the short range interactions |
73 |
|
Bend** myBends; |
74 |
|
Torsion** myTorsions; |
75 |
+ |
Exclude** myExcludes; // array of the excluded pairs of long range forces |
76 |
|
|
59 |
– |
int startAtom; |
60 |
– |
int endAtom; |
61 |
– |
|
62 |
– |
|
77 |
|
}; |
78 |
|
|
79 |
|
#endif |