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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 658 by tim, Thu Jul 31 15:35:07 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 +  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;}
# Line 45 | Line 52 | class Molecule{ (public)
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
# Line 65 | Line 82 | class Molecule{ (public)
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;

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