| 3 |
|
|
| 4 |
|
#include "Atom.hpp" |
| 5 |
|
#include "SRI.hpp" |
| 6 |
+ |
#include "MoleculeStamp.hpp" |
| 7 |
+ |
#include "Exclude.hpp" |
| 8 |
|
|
| 9 |
+ |
typedef struct{ |
| 10 |
+ |
|
| 11 |
+ |
int stampID; // the ID in the BASS component stamp array |
| 12 |
+ |
int nAtoms; // the number of atoms in the molecule |
| 13 |
+ |
int nBonds; // ... .. .. . .bonds .. .. . . . . |
| 14 |
+ |
int nBends; // . . . . .. . .bends . . . . .. . |
| 15 |
+ |
int nTorsions; // .. . . .. . . torsions . . .. . . |
| 16 |
+ |
int nOriented; // .. . . . .. . oriented atoms . . . |
| 17 |
+ |
int nExcludes; // . . .. . . . .exclude pairs.. . . . |
| 18 |
+ |
|
| 19 |
+ |
double* COM; // the location of the center of mass of the molecule |
| 20 |
+ |
|
| 21 |
+ |
Atom** myAtoms; // the array of atoms |
| 22 |
+ |
Exclude** myExcludes;// the array of Excluded pairs |
| 23 |
+ |
Bond** myBonds; // arrays of all the short range interactions |
| 24 |
+ |
Bend** myBends; |
| 25 |
+ |
Torsion** myTorsions; |
| 26 |
+ |
|
| 27 |
+ |
|
| 28 |
+ |
} molInit; |
| 29 |
+ |
|
| 30 |
|
class Molecule{ |
| 31 |
|
|
| 32 |
|
public: |
| 33 |
|
|
| 34 |
< |
Molecule() {} |
| 35 |
< |
~Molecule() {} |
| 34 |
> |
Molecule( void ); |
| 35 |
> |
~Molecule( void ); |
| 36 |
|
|
| 37 |
< |
int getNMembers( void ) { return nMembers; } |
| 38 |
< |
int getStartAtom( void ) { return startAtom; } |
| 39 |
< |
int getEndAtom( void ) { return endAtom; } |
| 40 |
< |
int getStampID( void ) { return stampID; } |
| 37 |
> |
void initialize( molInit &theInit ); |
| 38 |
> |
|
| 39 |
> |
void setMyIndex( int theIndex ){ myIndex = theIndex;} |
| 40 |
> |
|
| 41 |
> |
int getNAtoms ( void ) {return nAtoms;} |
| 42 |
> |
int getNBonds ( void ) {return nBonds;} |
| 43 |
> |
int getNBends ( void ) {return nBends;} |
| 44 |
> |
int getNTorsions( void ) {return nTorsions;} |
| 45 |
> |
int getNOriented( void ) {return nOriented;} |
| 46 |
> |
int getNExcludes( void ) {return nExcludes;} |
| 47 |
> |
int getNMembers ( void ) {return nMembers;} |
| 48 |
> |
int getStampID ( void ) {return stampID;} |
| 49 |
> |
|
| 50 |
> |
Atom** getMyAtoms ( void ) {return myAtoms;} |
| 51 |
> |
Bond** getMyBonds ( void ) {return myBonds;} |
| 52 |
> |
Bend** getMyBends ( void ) {return myBends;} |
| 53 |
> |
Torsion** getMyTorsions( void ) {return myTorsions;} |
| 54 |
> |
Exclude** getMyExcludes( void ) {return myExcludes;} |
| 55 |
|
|
| 56 |
< |
void setNMembers( int info ) { nMembers = info; } |
| 57 |
< |
void setStartAtom( int info ) { startAtom = info; } |
| 58 |
< |
void setEndAtom( int info ) { endAtom = info; } |
| 59 |
< |
void setStampID( int info ) { stampID = info; } |
| 56 |
> |
void setStampID( int info ) {stampID = info;} |
| 57 |
> |
|
| 58 |
> |
void calcForces( void ); |
| 59 |
> |
double getPotential( void ); |
| 60 |
|
|
| 61 |
+ |
void printMe( void ); |
| 62 |
|
|
| 63 |
+ |
double* getCOM(); |
| 64 |
+ |
void moveCOM(double* delta); |
| 65 |
+ |
|
| 66 |
|
private: |
| 67 |
|
|
| 68 |
< |
int nMembers; |
| 69 |
< |
int startAtom; |
| 70 |
< |
int endAtom; |
| 68 |
> |
int stampID; // the ID in the BASS component stamp array |
| 69 |
> |
int nAtoms; // the number of atoms in the molecule |
| 70 |
> |
int nBonds; // ... .. .. . .bonds .. .. . . . . |
| 71 |
> |
int nBends; // . . . . .. . .bends . . . . .. . |
| 72 |
> |
int nTorsions; // .. . . .. . . torsions . . .. . . |
| 73 |
> |
int nOriented; // .. . . . .. . oriented atoms . . . |
| 74 |
> |
int nMembers; // .. . . . . . .atoms (legacy code) . . . |
| 75 |
> |
int nExcludes; // . . . . .. .. excludes .. . . |
| 76 |
|
|
| 77 |
< |
int stampID; |
| 77 |
> |
int myIndex; // mostly just for debug |
| 78 |
> |
|
| 79 |
> |
Atom** myAtoms; // the array of atoms |
| 80 |
> |
Bond** myBonds; // arrays of all the short range interactions |
| 81 |
> |
Bend** myBends; |
| 82 |
> |
Torsion** myTorsions; |
| 83 |
> |
Exclude** myExcludes; // array of the excluded pairs of long range forces |
| 84 |
> |
|
| 85 |
> |
double* COM; |
| 86 |
|
}; |
| 87 |
|
|
| 88 |
|
#endif |
