14 |
|
int nBends; // . . . . .. . .bends . . . . .. . |
15 |
|
int nTorsions; // .. . . .. . . torsions . . .. . . |
16 |
|
int nOriented; // .. . . . .. . oriented atoms . . . |
17 |
< |
|
17 |
> |
int nExcludes; // . . .. . . . .exclude pairs.. . . . |
18 |
> |
|
19 |
|
Atom** myAtoms; // the array of atoms |
20 |
|
Exclude** myExcludes;// the array of Excluded pairs |
21 |
|
Bond** myBonds; // arrays of all the short range interactions |
33 |
|
~Molecule( void ); |
34 |
|
|
35 |
|
void initialize( molInit &theInit ); |
36 |
+ |
|
37 |
+ |
void setMyIndex( int theIndex ){ myIndex = theIndex;} |
38 |
+ |
void setGlobalIndex( int theIndex ) { globalIndex = theIndex; } |
39 |
+ |
|
40 |
+ |
int getMyIndex( void ) { return myIndex; } |
41 |
+ |
int getGlobalIndex( void ) { return globalIndex; } |
42 |
|
|
43 |
|
int getNAtoms ( void ) {return nAtoms;} |
44 |
|
int getNBonds ( void ) {return nBonds;} |
52 |
|
Atom** getMyAtoms ( void ) {return myAtoms;} |
53 |
|
Bond** getMyBonds ( void ) {return myBonds;} |
54 |
|
Bend** getMyBends ( void ) {return myBends;} |
55 |
< |
Torsions** getmyTorsions( void ) {return myTorsions;} |
56 |
< |
Exclude** getmyExcludes( void ) {return myExcludes;} |
55 |
> |
Torsion** getMyTorsions( void ) {return myTorsions;} |
56 |
> |
Exclude** getMyExcludes( void ) {return myExcludes;} |
57 |
|
|
58 |
|
void setStampID( int info ) {stampID = info;} |
59 |
+ |
|
60 |
|
|
61 |
+ |
|
62 |
+ |
|
63 |
|
void calcForces( void ); |
64 |
|
double getPotential( void ); |
65 |
|
|
66 |
+ |
void printMe( void ); |
67 |
|
|
68 |
+ |
void getCOM( double COM[3] ); |
69 |
+ |
void moveCOM( double delta[3] ); |
70 |
+ |
double getCOMvel( double COMvel[3] ); |
71 |
+ |
|
72 |
+ |
double getTotalMass(); |
73 |
+ |
|
74 |
|
private: |
75 |
|
|
76 |
|
int stampID; // the ID in the BASS component stamp array |
82 |
|
int nMembers; // .. . . . . . .atoms (legacy code) . . . |
83 |
|
int nExcludes; // . . . . .. .. excludes .. . . |
84 |
|
|
85 |
+ |
int myIndex; // mostly just for debug (and for making pressure calcs work) |
86 |
+ |
int globalIndex; |
87 |
+ |
|
88 |
|
Atom** myAtoms; // the array of atoms |
89 |
|
Bond** myBonds; // arrays of all the short range interactions |
90 |
|
Bend** myBends; |