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root/group/trunk/OOPSE/libmdtools/Molecule.hpp
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Comparing trunk/OOPSE/libmdtools/Molecule.hpp (file contents):
Revision 422 by mmeineke, Thu Mar 27 19:21:42 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 4 | Line 4
4   #include "Atom.hpp"
5   #include "SRI.hpp"
6   #include "MoleculeStamp.hpp"
7 < #include "Exclude.hpp"
7 > #include "RigidBody.hpp"
8  
9   typedef struct{
10    
# Line 13 | Line 13 | typedef struct{
13    int nBonds;    // ... .. ..  . .bonds .. .. . . . .
14    int nBends;    // . . . . .. . .bends . . . . .. .
15    int nTorsions; // .. . . .. . . torsions . . .. . .
16 +  int nRigidBodies; // .. .. .. . rigid bodies ... ..
17    int nOriented; // .. . . . .. . oriented atoms . . .
18 <  
18 >
19    Atom** myAtoms;      // the array of atoms
19 –  Exclude** myExcludes;// the array of Excluded pairs
20    Bond** myBonds;      // arrays of all the short range interactions
21    Bend** myBends;
22    Torsion** myTorsions;
23 <
24 <
23 >  RigidBody** myRigidBodies;
24   } molInit;
25  
26   class Molecule{
# Line 33 | Line 32 | class Molecule{ (public)
32  
33    void initialize( molInit &theInit );
34  
35 <  int   getNMembers( void )  { return nMembers; }
36 <  int   getStartAtom( void ) { return startAtom; }
37 <  int   getEndAtom( void )   { return endAtom; }
38 <  int   getStampID( void )   { return stampID; }
35 >  void setMyIndex( int theIndex ){ myIndex = theIndex;}
36 >  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
37 >
38 >  int getMyIndex( void ) { return myIndex; }
39 >  int getGlobalIndex( void ) { return globalIndex; }
40 >
41 >  int getNAtoms   ( void )    {return nAtoms;}
42 >  int getNBonds   ( void )    {return nBonds;}
43 >  int getNBends   ( void )    {return nBends;}
44 >  int getNTorsions( void )    {return nTorsions;}
45 >  int getNRigidBodies( void ) {return nRigidBodies;}
46 >  int getNOriented( void )    {return nOriented;}
47 >  int getNMembers ( void )    {return nMembers;}
48 >  int getStampID  ( void )    {return stampID;}
49 >
50 >  Atom**      getMyAtoms   ( void )    {return myAtoms;}
51 >  Bond**      getMyBonds   ( void )    {return myBonds;}
52 >  Bend**      getMyBends   ( void )    {return myBends;}
53 >  Torsion**   getMyTorsions( void )    {return myTorsions;}
54 >  RigidBody** getMyRigidBodies( void ) {return myRigidBodies;}
55    
56 <  void   setStampID( int info )   { stampID = info; }
56 >  void setStampID( int info ) {stampID = info;}
57 >
58 >  void calcForces( void );
59 >  void atoms2rigidBodies( void );
60 >  double getPotential( void );
61    
62 +  void printMe( void );
63  
64 +  void getCOM( double COM[3] );
65 +  void moveCOM( double delta[3] );
66 +  double getCOMvel( double COMvel[3] );
67 +  
68 +  double getTotalMass();
69 +
70   private:
71  
72    int stampID;   // the ID in the BASS component stamp array
# Line 48 | Line 74 | class Molecule{ (public)
74    int nBonds;    // ... .. ..  . .bonds .. .. . . . .
75    int nBends;    // . . . . .. . .bends . . . . .. .
76    int nTorsions; // .. . . .. . . torsions . . .. . .
77 +  int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
78    int nOriented; // .. . . . .. . oriented atoms . . .
79 <  int nMembers;
79 >  int nMembers;  // .. . . . . . .atoms (legacy code) . . .
80  
81 +  int myIndex; // mostly just for debug (and for making pressure calcs work)
82 +  int globalIndex;
83 +
84    Atom** myAtoms;     // the array of atoms
85 <  Bond** myBonds;      // arrays of all the short range interactions
85 >  Bond** myBonds;     // arrays of all the short range interactions
86    Bend** myBends;
87    Torsion** myTorsions;
88 +  RigidBody** myRigidBodies;
89    
59 –  int startAtom;
60 –  int endAtom;
61 –
62 –
90   };
91  
92   #endif

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