--- trunk/OOPSE/libmdtools/Molecule.hpp	2003/04/03 20:19:50	446
+++ trunk/OOPSE/libmdtools/Molecule.hpp	2003/07/31 15:35:07	658
@@ -16,8 +16,6 @@ typedef struct{
   int nOriented; // .. . . . .. . oriented atoms . . . 
   int nExcludes; // . . .. . . . .exclude pairs.. . . . 
 
-  double* COM;   // the location of the center of mass of the molecule
-  
   Atom** myAtoms;      // the array of atoms
   Exclude** myExcludes;// the array of Excluded pairs 
   Bond** myBonds;      // arrays of all the short range interactions
@@ -37,6 +35,10 @@ 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;}
@@ -54,14 +56,20 @@ class Molecule{ (public)
   Exclude**  getMyExcludes( void ) {return myExcludes;}
   
   void setStampID( int info ) {stampID = info;}
+  
 
+
+
   void calcForces( void );
   double getPotential( void );
   
   void printMe( void );
 
-  double* getCOM();
-  void moveCOM(double* delta);
+  void getCOM( double COM[3] );
+  void moveCOM( double delta[3] );
+  double getCOMvel( double COMvel[3] );
+  
+  double getTotalMass();
 
 private:
 
@@ -74,7 +82,8 @@ class Molecule{ (public)
   int nMembers;  // .. . . . . . .atoms (legacy code) . . . 
   int nExcludes; // . . . . .. .. excludes .. . . 
 
-  int myIndex; // mostly just for debug
+  int myIndex; // mostly just for debug (and for making pressure calcs work)
+  int globalIndex;
 
   Atom** myAtoms;     // the array of atoms
   Bond** myBonds;     // arrays of all the short range interactions
@@ -82,7 +91,6 @@ class Molecule{ (public)
   Torsion** myTorsions;
   Exclude** myExcludes; // array of the excluded pairs of long range forces
   
-  double* COM;
 };
 
 #endif