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root/group/trunk/OOPSE/libmdtools/Molecule.hpp
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Comparing trunk/OOPSE/libmdtools/Molecule.hpp (file contents):
Revision 1140 by tim, Wed Apr 28 22:34:02 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    vector<RigidBody*>   myRigidBodies;
31    vector<StuntDouble*> myIntegrableObjects;
32 +  vector<CutoffGroup*> myCutoffGroups;
33   } molInit;
34  
35   class Molecule{
# Line 54 | Line 62 | class Molecule{ (public)
62    Torsion**   getMyTorsions( void )    {return myTorsions;}
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 79 | 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 89 | Line 114 | class Molecule{ (public)
114    Torsion** myTorsions;
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  
93 –  bool   hasMassRatio;
120  
121   };
122  

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