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root/group/trunk/OOPSE/libmdtools/Molecule.hpp
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Comparing trunk/OOPSE/libmdtools/Molecule.hpp (file contents):
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC vs.
Revision 1167 by tim, Wed May 12 16:38:45 2004 UTC

# Line 1 | Line 1
1   #ifndef _MOLECULE_H_
2   #define _MOLECULE_H_
3  
4 + #include <set>
5 + #include <vector>
6 +
7   #include "Atom.hpp"
8   #include "SRI.hpp"
9   #include "MoleculeStamp.hpp"
10   #include "RigidBody.hpp"
11 + #include "CutoffGroup.hpp"
12  
13 + using namespace std;
14 +
15   typedef struct{
16    
17    int stampID;   // the ID in the BASS component stamp array
# Line 15 | Line 21 | typedef struct{
21    int nTorsions; // .. . . .. . . torsions . . .. . .
22    int nRigidBodies; // .. .. .. . rigid bodies ... ..
23    int nOriented; // .. . . . .. . oriented atoms . . .
24 <
24 >  
25    Atom** myAtoms;      // the array of atoms
26    Bond** myBonds;      // arrays of all the short range interactions
27    Bend** myBends;
28    Torsion** myTorsions;
29 <  RigidBody** myRigidBodies;
29 >  vector<RigidBody*>   myRigidBodies;
30 >  vector<StuntDouble*> myIntegrableObjects;
31 >  vector<CutoffGroup*> myCutoffGroups;
32   } molInit;
33  
34   class Molecule{
# Line 33 | Line 41 | class Molecule{ (public)
41    void initialize( molInit &theInit );
42  
43    void setMyIndex( int theIndex ){ myIndex = theIndex;}
36 –  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
37 –
44    int getMyIndex( void ) { return myIndex; }
45 +
46    int getGlobalIndex( void ) { return globalIndex; }
47 <
47 >  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
48 >
49    int getNAtoms   ( void )    {return nAtoms;}
50    int getNBonds   ( void )    {return nBonds;}
51    int getNBends   ( void )    {return nBends;}
52    int getNTorsions( void )    {return nTorsions;}
53 <  int getNRigidBodies( void ) {return nRigidBodies;}
53 >  int getNRigidBodies( void ) {return myRigidBodies.size();}
54    int getNOriented( void )    {return nOriented;}
55    int getNMembers ( void )    {return nMembers;}
56    int getStampID  ( void )    {return stampID;}
# Line 51 | Line 59 | class Molecule{ (public)
59    Bond**      getMyBonds   ( void )    {return myBonds;}
60    Bend**      getMyBends   ( void )    {return myBends;}
61    Torsion**   getMyTorsions( void )    {return myTorsions;}
62 <  RigidBody** getMyRigidBodies( void ) {return myRigidBodies;}
62 >  vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
63 >  vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
64 >
65 >  CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
66 >    i = myCutoffGroups.begin();
67 >    return i != myCutoffGroups.end()? *i : NULL;
68 >  }
69 >
70 >  CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
71 >    i++;
72 >    return i != myCutoffGroups.end()? *i : NULL;
73 >  }
74 >
75 >  int getNCutoffGroups() {return nCutoffGroups;}
76    
77    void setStampID( int info ) {stampID = info;}
78  
# Line 77 | Line 98 | class Molecule{ (public)
98    int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
99    int nOriented; // .. . . . .. . oriented atoms . . .
100    int nMembers;  // .. . . . . . .atoms (legacy code) . . .
101 <
101 >  int nCutoffGroups;
102 >  
103    int myIndex; // mostly just for debug (and for making pressure calcs work)
104    int globalIndex;
105  
# Line 85 | Line 107 | class Molecule{ (public)
107    Bond** myBonds;     // arrays of all the short range interactions
108    Bend** myBends;
109    Torsion** myTorsions;
110 <  RigidBody** myRigidBodies;
111 <  
110 >  vector<RigidBody*>   myRigidBodies;
111 >  vector<StuntDouble*> myIntegrableObjects;
112 >  vector<CutoffGroup*> myCutoffGroups;
113 >
114 >
115   };
116  
117   #endif

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