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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 1157 by tim, Tue May 11 20:33:41 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 >  int nCutoffGroups;
25 >  
26    Atom** myAtoms;      // the array of atoms
27    Bond** myBonds;      // arrays of all the short range interactions
28    Bend** myBends;
29    Torsion** myTorsions;
30 <  RigidBody** myRigidBodies;
30 >  vector<RigidBody*>   myRigidBodies;
31 >  vector<StuntDouble*> myIntegrableObjects;
32 >  vector<CutoffGroup*> myCutoffGroups;
33   } molInit;
34  
35   class Molecule{
# Line 33 | Line 42 | class Molecule{ (public)
42    void initialize( molInit &theInit );
43  
44    void setMyIndex( int theIndex ){ myIndex = theIndex;}
36 –  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
37 –
45    int getMyIndex( void ) { return myIndex; }
46 +
47    int getGlobalIndex( void ) { return globalIndex; }
48 <
48 >  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
49 >
50    int getNAtoms   ( void )    {return nAtoms;}
51    int getNBonds   ( void )    {return nBonds;}
52    int getNBends   ( void )    {return nBends;}
53    int getNTorsions( void )    {return nTorsions;}
54 <  int getNRigidBodies( void ) {return nRigidBodies;}
54 >  int getNRigidBodies( void ) {return myRigidBodies.size();}
55    int getNOriented( void )    {return nOriented;}
56    int getNMembers ( void )    {return nMembers;}
57    int getStampID  ( void )    {return stampID;}
# Line 51 | Line 60 | class Molecule{ (public)
60    Bond**      getMyBonds   ( void )    {return myBonds;}
61    Bend**      getMyBends   ( void )    {return myBends;}
62    Torsion**   getMyTorsions( void )    {return myTorsions;}
63 <  RigidBody** getMyRigidBodies( void ) {return myRigidBodies;}
63 >  vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
64 >  vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
65 >
66 >  CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
67 >    i = myCutoffGroups.begin();
68 >    return i != myCutoffGroups.end()? *i : NULL;
69 >  }
70 >
71 >  CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
72 >    i++;
73 >    return i != myCutoffGroups.end()? *i : NULL;
74 >  }
75 >
76 >  bool belongToCutoffGroup(int index){
77 >    return cutoffAtomSet.find(index) != cutoffAtomSet.end()? true: false;
78 >  }
79 >
80 >  int getNCutoffGroups() {return nCutoffGroups;}
81    
82    void setStampID( int info ) {stampID = info;}
83  
# Line 77 | Line 103 | class Molecule{ (public)
103    int nRigidBodies; // .. . . .. .rigid bodies . . .. . .
104    int nOriented; // .. . . . .. . oriented atoms . . .
105    int nMembers;  // .. . . . . . .atoms (legacy code) . . .
106 <
106 >  int nCutoffGroups;
107 >  
108    int myIndex; // mostly just for debug (and for making pressure calcs work)
109    int globalIndex;
110  
# Line 85 | Line 112 | class Molecule{ (public)
112    Bond** myBonds;     // arrays of all the short range interactions
113    Bend** myBends;
114    Torsion** myTorsions;
115 <  RigidBody** myRigidBodies;
116 <  
115 >  vector<RigidBody*>   myRigidBodies;
116 >  vector<StuntDouble*> myIntegrableObjects;
117 >  vector<CutoffGroup*> myCutoffGroups;
118 >  set<int> cutoffAtomSet;  //global index of atoms belonging to cutoff group
119 >
120 >
121   };
122  
123   #endif

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