--- trunk/OOPSE/libmdtools/Atom.hpp	2003/03/24 18:33:51	393
+++ trunk/OOPSE/libmdtools/Atom.hpp	2003/03/26 21:04:38	409
@@ -7,77 +7,26 @@ class Atom{ (public)
 
 class Atom{
 public:
-  Atom(int theIndex) {
-    c_n_hyd = 0; 
-    has_dipole = 0;
-    is_VDW = 0;
-    is_LJ = 0;
 
-    index = theIndex;
-    offset = 3 * index;
-    offsetX = offset;
-    offsetY = offset+1;
-    offsetZ = offset+2;
+  Atom(int theIndex);
+  virtual ~Atom() {} 
 
-    Axx = index*9;
-    Axy = Axx+1;
-    Axz = Axx+2;
-    
-    Ayx = Axx+3;
-    Ayy = Axx+4;
-    Ayz = Axx+5;
+  static double* pos; // the position array
+  static double* vel; // the velocity array
+  static double* frc; // the forc array
+  static double* trq; // the torque vector  ( space fixed )
+  static double* Amat; // the rotation matrix
+  static double* mu; // the dipole moment array
+  static double* ul; // the lab frame unit directional vector
+  static int nElements;
 
-    Azx = Axx+6;
-    Azy = Axx+7;
-    Azz = Axx+8;
-  }
-  virtual ~Atom() {}
-
-  static void createArrays (int nElements) {
-    int i;
-    
-    pos = new double[nElements*3];
-    vel = new double[nElements*3];
-    frc = new double[nElements*3];
-    trq = new double[nElements*3];
-    Amat = new double[nElements*9];
-    mu = new double[nElements];
-    ul = new double[nElements*3];
-
-    // init directional values to zero
-    
-    for( i=0; i<nElements; i++){
-      trq[i] = 0.0;
-      trq[i+1] = 0.0;
-      trq[i+2] = 0.0;
-      
-      Amat[i] = 1.0;
-      Amat[i+1] = 0.0;
-      Amat[i+2] = 0.0;
-      
-      Amat[i+3] = 0.0;
-      Amat[i+4] = 1.0;
-      Amat[i+5] = 0.0;
-      
-      Amat[i+6] = 0.0;
-      Amat[i+7] = 0.0;
-      Amat[i+8] = 1.0;
-      
-      mu[i] = 0.0;    
-      
-      ul[i] = 1.0;
-      ul[i+1] = 0.0;
-      ul[i+2] = 0.0;
-    }
-  }
-  static void destroyArrays(void) {
-    delete[] pos;
-    delete[] vel;
-    delete[] frc;
-    delete[] trq;
-    delete[] Amat;
-    delete[] mu;
-  }
+  static void createArrays (int nElements);
+  static void destroyArrays(void);
+  void addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, 
+                double* Atrq, double* AAmat, double* Amu, 
+                double* Aul);
+  void deleteAtom(int theIndex);
+  void deleteRange(int startIndex, int stopIndex);
 
   static double* getPosArray( void ) { return pos; }
   static double* getVelArray( void ) { return vel; }
@@ -122,26 +71,7 @@ class Atom{ (public)
   void setCovalent(double covalent) {c_covalent = covalent;}
   
   int getIndex() const {return index;}
-  void setIndex(int theIndex) {
-    index = theIndex; 
-    offset = index*3;
-    offsetX = offset;
-    offsetY = offset+1;
-    offsetZ = offset+2;
-
-    Axx = index*9;
-    Axy = Axx+1;
-    Axz = Axx+2;
-    
-    Ayx = Axx+3;
-    Ayy = Axx+4;
-    Ayz = Axx+5;
-
-    Azx = Axx+6;
-    Azy = Axx+7;
-    Azz = Axx+8;
-  }
-
+  void setIndex(int theIndex);
   char *getType() {return c_name;}
   void setType(char * name) {strcpy(c_name,name);}
   
@@ -167,13 +97,6 @@ class Atom{ (public)
 
   virtual int isDirectional( void ) = 0;
 
-  static double* pos; // the position array
-  static double* vel; // the velocity array
-  static double* frc; // the forc array
-  static double* trq; // the torque vector  ( space fixed )
-  static double* Amat; // the rotation matrix
-  static double* mu; // the dipole moment array
-  static double* ul; // the lab frame unit directional vector
 
 protected:
   
@@ -205,8 +128,6 @@ class Atom{ (public)
   
 };
 
-
-
 class GeneralAtom : public Atom{
 
 public: