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root/group/trunk/OOPSE/libmdtools/Molecule.hpp
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Comparing trunk/OOPSE/libmdtools/Molecule.hpp (file contents):
Revision 435 by mmeineke, Fri Mar 28 19:33:37 2003 UTC vs.
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC

# Line 15 | Line 15 | typedef struct{
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
# Line 33 | 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 50 | Line 56 | class Molecule{ (public)
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  
# Line 68 | 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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