ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/Molecule.hpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/Molecule.hpp (file contents):
Revision 446 by gezelter, Thu Apr 3 20:19:50 2003 UTC vs.
Revision 489 by mmeineke, Thu Apr 10 20:08:56 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 +  void atomicRollCall(int* molMembership);
73 +
74   private:
75  
76    int stampID;   // the ID in the BASS component stamp array
# Line 74 | Line 82 | class Molecule{ (public)
82    int nMembers;  // .. . . . . . .atoms (legacy code) . . .
83    int nExcludes; // . . . . .. .. excludes .. . .
84  
85 <  int myIndex; // mostly just for debug
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
# Line 82 | Line 91 | class Molecule{ (public)
91    Torsion** myTorsions;
92    Exclude** myExcludes; // array of the excluded pairs of long range forces
93    
85 –  double* COM;
94   };
95  
96   #endif

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines