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root/group/trunk/OOPSE/libmdtools/Molecule.hpp
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Comparing:
branches/mmeineke/OOPSE/libmdtools/Molecule.hpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/Molecule.hpp (file contents), Revision 1140 by tim, Wed Apr 28 22:34:02 2004 UTC

# Line 3 | Line 3
3  
4   #include "Atom.hpp"
5   #include "SRI.hpp"
6 + #include "MoleculeStamp.hpp"
7 + #include "RigidBody.hpp"
8  
9 + typedef struct{
10 +  
11 +  int stampID;   // the ID in the BASS component stamp array
12 +  int nAtoms;    // the number of atoms in the molecule
13 +  int nBonds;    // ... .. ..  . .bonds .. .. . . . .
14 +  int nBends;    // . . . . .. . .bends . . . . .. .
15 +  int nTorsions; // .. . . .. . . torsions . . .. . .
16 +  int nRigidBodies; // .. .. .. . rigid bodies ... ..
17 +  int nOriented; // .. . . . .. . oriented atoms . . .
18 +
19 +  Atom** myAtoms;      // the array of atoms
20 +  Bond** myBonds;      // arrays of all the short range interactions
21 +  Bend** myBends;
22 +  Torsion** myTorsions;
23 +  vector<RigidBody*>   myRigidBodies;
24 +  vector<StuntDouble*> myIntegrableObjects;
25 + } molInit;
26 +
27   class Molecule{
28  
29   public:
30    
31 <  Molecule() {}
32 <  ~Molecule() {}
31 >  Molecule( void );
32 >  ~Molecule( void );
33  
34 <  int   getNMembers( void )  { return nMembers; }
35 <  int   getStartAtom( void ) { return startAtom; }
36 <  int   getEndAtom( void )   { return endAtom; }
37 <  int   getStampID( void )   { return stampID; }
34 >  void initialize( molInit &theInit );
35 >
36 >  void setMyIndex( int theIndex ){ myIndex = theIndex;}
37 >  int getMyIndex( void ) { return myIndex; }
38 >
39 >  int getGlobalIndex( void ) { return globalIndex; }
40 >  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
41 >
42 >  int getNAtoms   ( void )    {return nAtoms;}
43 >  int getNBonds   ( void )    {return nBonds;}
44 >  int getNBends   ( void )    {return nBends;}
45 >  int getNTorsions( void )    {return nTorsions;}
46 >  int getNRigidBodies( void ) {return myRigidBodies.size();}
47 >  int getNOriented( void )    {return nOriented;}
48 >  int getNMembers ( void )    {return nMembers;}
49 >  int getStampID  ( void )    {return stampID;}
50 >
51 >  Atom**      getMyAtoms   ( void )    {return myAtoms;}
52 >  Bond**      getMyBonds   ( void )    {return myBonds;}
53 >  Bend**      getMyBends   ( void )    {return myBends;}
54 >  Torsion**   getMyTorsions( void )    {return myTorsions;}
55 >  vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
56 >  vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
57    
58 <  void   setNMembers( int info )  { nMembers = info; }
59 <  void   setStartAtom( int info ) { startAtom = info; }
60 <  void   setEndAtom( int info )   { endAtom = info; }
61 <  void   setStampID( int info )   { stampID = info; }
58 >  void setStampID( int info ) {stampID = info;}
59 >
60 >  void calcForces( void );
61 >  void atoms2rigidBodies( void );
62 >  double getPotential( void );
63    
64 +  void printMe( void );
65  
66 +  void getCOM( double COM[3] );
67 +  void moveCOM( double delta[3] );
68 +  double getCOMvel( double COMvel[3] );
69 +  
70 +  double getTotalMass();
71 +
72   private:
73  
74 <  int nMembers;
75 <  int startAtom;
76 <  int endAtom;
74 >  int stampID;   // the ID in the BASS component stamp array
75 >  int nAtoms;    // the number of atoms in the molecule
76 >  int nBonds;    // ... .. ..  . .bonds .. .. . . . .
77 >  int nBends;    // . . . . .. . .bends . . . . .. .
78 >  int nTorsions; // .. . . .. . . torsions . . .. . .
79 >  int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
80 >  int nOriented; // .. . . . .. . oriented atoms . . .
81 >  int nMembers;  // .. . . . . . .atoms (legacy code) . . .
82  
83 <  int stampID;
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
88 >  Bend** myBends;
89 >  Torsion** myTorsions;
90 >  vector<RigidBody*>   myRigidBodies;
91 >  vector<StuntDouble*> myIntegrableObjects;
92 >
93 >  bool   hasMassRatio;
94 >
95   };
96  
97   #endif

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