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root/group/trunk/OOPSE/libmdtools/Molecule.hpp
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Comparing trunk/OOPSE/libmdtools/Molecule.hpp (file contents):
Revision 423 by mmeineke, Thu Mar 27 20:12:15 2003 UTC vs.
Revision 468 by gezelter, Mon Apr 7 16:56:38 2003 UTC

# Line 14 | Line 14 | typedef struct{
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
# Line 32 | Line 33 | class Molecule{ (public)
33    ~Molecule( void );
34  
35    void initialize( molInit &theInit );
36 +
37 +  void setMyIndex( int theIndex ){ myIndex = theIndex;}
38  
39    int getNAtoms   ( void ) {return nAtoms;}
40    int getNBonds   ( void ) {return nBonds;}
# Line 45 | Line 48 | class Molecule{ (public)
48    Atom**     getMyAtoms   ( void ) {return myAtoms;}
49    Bond**     getMyBonds   ( void ) {return myBonds;}
50    Bend**     getMyBends   ( void ) {return myBends;}
51 <  Torsions** getmyTorsions( void ) {return myTorsions;}
52 <  Exclude**  getmyExcludes( void ) {return myExcludes;}
51 >  Torsion**  getMyTorsions( void ) {return myTorsions;}
52 >  Exclude**  getMyExcludes( void ) {return myExcludes;}
53    
54    void setStampID( int info ) {stampID = info;}
55  
56    void calcForces( void );
57    double getPotential( void );
58    
59 +  void printMe( void );
60  
61 +  void getCOM( double COM[3] );
62 +  void moveCOM( double delta[3] );
63 +  void getCOMvel( double mtot, double COMvel[3] );
64 +
65   private:
66  
67    int stampID;   // the ID in the BASS component stamp array
# Line 65 | Line 73 | class Molecule{ (public)
73    int nMembers;  // .. . . . . . .atoms (legacy code) . . .
74    int nExcludes; // . . . . .. .. excludes .. . .
75  
76 +  int myIndex; // mostly just for debug
77 +
78    Atom** myAtoms;     // the array of atoms
79    Bond** myBonds;     // arrays of all the short range interactions
80    Bend** myBends;

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