| 15 |
|
int nTorsions; // .. . . .. . . torsions . . .. . . |
| 16 |
|
int nOriented; // .. . . . .. . oriented atoms . . . |
| 17 |
|
int nExcludes; // . . .. . . . .exclude pairs.. . . . |
| 18 |
< |
|
| 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 |
| 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;} |
| 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 ); |
| 60 |
– |
|
| 67 |
|
|
| 68 |
+ |
void getCOM( double COM[3] ); |
| 69 |
+ |
void moveCOM( double delta[3] ); |
| 70 |
+ |
double getCOMvel( double COMvel[3] ); |
| 71 |
+ |
|
| 72 |
+ |
void atomicRollCall(int* molMembership); |
| 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 |
| 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 |
