--- trunk/OOPSE/libmdtools/Molecule.hpp	2003/04/10 20:08:56	489
+++ trunk/OOPSE/libmdtools/Molecule.hpp	2004/05/11 20:33:41	1157
@@ -1,11 +1,17 @@
 #ifndef _MOLECULE_H_
 #define _MOLECULE_H_
 
+#include <set>
+#include <vector>
+
 #include "Atom.hpp"
 #include "SRI.hpp"
 #include "MoleculeStamp.hpp"
-#include "Exclude.hpp"
+#include "RigidBody.hpp"
+#include "CutoffGroup.hpp"
 
+using namespace std;
+
 typedef struct{
   
   int stampID;   // the ID in the BASS component stamp array
@@ -13,16 +19,17 @@ typedef struct{
   int nBonds;    // ... .. ..  . .bonds .. .. . . . . 
   int nBends;    // . . . . .. . .bends . . . . .. . 
   int nTorsions; // .. . . .. . . torsions . . .. . . 
+  int nRigidBodies; // .. .. .. . rigid bodies ... .. 
   int nOriented; // .. . . . .. . oriented atoms . . . 
-  int nExcludes; // . . .. . . . .exclude pairs.. . . . 
-
+  int nCutoffGroups;
+  
   Atom** myAtoms;      // the array of atoms
-  Exclude** myExcludes;// the array of Excluded pairs 
   Bond** myBonds;      // arrays of all the short range interactions
   Bend** myBends;
   Torsion** myTorsions;
-
-
+  vector<RigidBody*>   myRigidBodies;
+  vector<StuntDouble*> myIntegrableObjects;
+  vector<CutoffGroup*> myCutoffGroups;
 } molInit;
 
 class Molecule{
@@ -35,32 +42,47 @@ class Molecule{ (public)
   void initialize( molInit &theInit );
 
   void setMyIndex( int theIndex ){ myIndex = theIndex;}
-  void setGlobalIndex( int theIndex ) {globalIndex = theIndex; }
-
   int getMyIndex( void ) { return myIndex; }
+
   int getGlobalIndex( void ) { return globalIndex; }
- 
-  int getNAtoms   ( void ) {return nAtoms;}
-  int getNBonds   ( void ) {return nBonds;}
-  int getNBends   ( void ) {return nBends;}
-  int getNTorsions( void ) {return nTorsions;}
-  int getNOriented( void ) {return nOriented;}
-  int getNExcludes( void ) {return nExcludes;}
-  int getNMembers ( void ) {return nMembers;}
-  int getStampID  ( void ) {return stampID;}
+  void setGlobalIndex( int theIndex ) { globalIndex = theIndex; }
 
-  Atom**     getMyAtoms   ( void ) {return myAtoms;}
-  Bond**     getMyBonds   ( void ) {return myBonds;}
-  Bend**     getMyBends   ( void ) {return myBends;}
-  Torsion**  getMyTorsions( void ) {return myTorsions;}
-  Exclude**  getMyExcludes( void ) {return myExcludes;}
-  
-  void setStampID( int info ) {stampID = info;}
-  
+  int getNAtoms   ( void )    {return nAtoms;}
+  int getNBonds   ( void )    {return nBonds;}
+  int getNBends   ( void )    {return nBends;}
+  int getNTorsions( void )    {return nTorsions;}
+  int getNRigidBodies( void ) {return myRigidBodies.size();}
+  int getNOriented( void )    {return nOriented;}
+  int getNMembers ( void )    {return nMembers;}
+  int getStampID  ( void )    {return stampID;}
 
+  Atom**      getMyAtoms   ( void )    {return myAtoms;}
+  Bond**      getMyBonds   ( void )    {return myBonds;}
+  Bend**      getMyBends   ( void )    {return myBends;}
+  Torsion**   getMyTorsions( void )    {return myTorsions;}
+  vector<RigidBody*> getMyRigidBodies( void ) {return myRigidBodies;}
+  vector<StuntDouble*>& getIntegrableObjects(void) {return myIntegrableObjects;}
 
+  CutoffGroup* beginCutoffGroup(vector<CutoffGroup*>::iterator& i){
+    i = myCutoffGroups.begin();
+    return i != myCutoffGroups.end()? *i : NULL;
+  }
 
+  CutoffGroup* nextCutoffGroup(vector<CutoffGroup*>::iterator& i){
+    i++;
+    return i != myCutoffGroups.end()? *i : NULL;
+  }
+
+  bool belongToCutoffGroup(int index){
+    return cutoffAtomSet.find(index) != cutoffAtomSet.end()? true: false;
+  }
+
+  int getNCutoffGroups() {return nCutoffGroups;}
+  
+  void setStampID( int info ) {stampID = info;} 
+
   void calcForces( void );
+  void atoms2rigidBodies( void );
   double getPotential( void );
   
   void printMe( void );
@@ -68,9 +90,9 @@ class Molecule{ (public)
   void getCOM( double COM[3] );
   void moveCOM( double delta[3] );
   double getCOMvel( double COMvel[3] );
+  
+  double getTotalMass();
 
-  void atomicRollCall(int* molMembership);
-
 private:
 
   int stampID;   // the ID in the BASS component stamp array
@@ -78,10 +100,11 @@ class Molecule{ (public)
   int nBonds;    // ... .. ..  . .bonds .. .. . . . . 
   int nBends;    // . . . . .. . .bends . . . . .. . 
   int nTorsions; // .. . . .. . . torsions . . .. . . 
+  int nRigidBodies; // .. . . .. .rigid bodies . . .. . . 
   int nOriented; // .. . . . .. . oriented atoms . . . 
   int nMembers;  // .. . . . . . .atoms (legacy code) . . . 
-  int nExcludes; // . . . . .. .. excludes .. . . 
-
+  int nCutoffGroups;
+  
   int myIndex; // mostly just for debug (and for making pressure calcs work)
   int globalIndex;
 
@@ -89,8 +112,12 @@ class Molecule{ (public)
   Bond** myBonds;     // arrays of all the short range interactions
   Bend** myBends;
   Torsion** myTorsions;
-  Exclude** myExcludes; // array of the excluded pairs of long range forces
-  
+  vector<RigidBody*>   myRigidBodies;
+  vector<StuntDouble*> myIntegrableObjects;
+  vector<CutoffGroup*> myCutoffGroups;
+  set<int> cutoffAtomSet;  //global index of atoms belonging to cutoff group
+
+
 };
 
 #endif