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root/group/trunk/OOPSE/libmdtools/Molecule.hpp
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Comparing trunk/OOPSE/libmdtools/Molecule.hpp (file contents):
Revision 446 by gezelter, Thu Apr 3 20:19:50 2003 UTC vs.
Revision 490 by gezelter, Fri Apr 11 15:16:59 2003 UTC

# Line 16 | Line 16 | typedef struct{
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 –  
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 37 | Line 35 | class Molecule{ (public)
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 54 | 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 <  double* getCOM();
69 <  void moveCOM(double* delta);
68 >  void getCOM( double COM[3] );
69 >  void moveCOM( double delta[3] );
70 >  double getCOMvel( double COMvel[3] );
71  
72   private:
73  
# Line 74 | Line 80 | class Molecule{ (public)
80    int nMembers;  // .. . . . . . .atoms (legacy code) . . .
81    int nExcludes; // . . . . .. .. excludes .. . .
82  
83 <  int myIndex; // mostly just for debug
83 >  int myIndex; // mostly just for debug (and for making pressure calcs work)
84 >  int globalIndex;
85  
86    Atom** myAtoms;     // the array of atoms
87    Bond** myBonds;     // arrays of all the short range interactions
# Line 82 | Line 89 | class Molecule{ (public)
89    Torsion** myTorsions;
90    Exclude** myExcludes; // array of the excluded pairs of long range forces
91    
85 –  double* COM;
92   };
93  
94   #endif

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