--- trunk/mdtools/headers/Atom.hpp	2002/11/26 21:04:43	189
+++ trunk/mdtools/headers/Atom.hpp	2003/01/17 21:53:33	237
@@ -13,6 +13,9 @@ class Atom{ (public)
     is_LJ = 0;
     index = theIndex;
     offset = 3 * index;
+    offsetX = offset;
+    offsetY = offset+1;
+    offsetZ = offset+2;
   }
   virtual ~Atom() {}
 
@@ -28,27 +31,33 @@ class Atom{ (public)
     delete[] frc;
     delete[] trq;
   }
+
+  static double* getPosArray( void ) { return pos; }
+  static double* getVelArray( void ) { return vel; }
+  static double* getFrcArray( void ) { return frc; }
+  static double* getTrqArray( void ) { return trq; }
   
-  double getX() const {return pos[offset];}
-  double getY() const {return pos[offset+1];}
-  double getZ() const {return pos[offset+2];}
-  void setX(double x) {pos[offset]   = x;}
-  void setY(double y) {pos[offset+1] = y;}
-  void setZ(double z) {pos[offset+2] = z;}
   
-  double get_vx() const  {return vel[offset];}
-  double get_vy() const  {return vel[offset+1];}
-  double get_vz() const  {return vel[offset+2];}
-  void set_vx(double vx) {vel[offset]   = vx;}
-  void set_vy(double vy) {vel[offset+1] = vy;}
-  void set_vz(double vz) {vel[offset+2] = vz;}
+  double getX() const {return pos[offsetX];}
+  double getY() const {return pos[offsetY];}
+  double getZ() const {return pos[offsetZ];}
+  void setX(double x) {pos[offsetX] = x;}
+  void setY(double y) {pos[offsetY] = y;}
+  void setZ(double z) {pos[offsetZ] = z;}
   
-  double getFx() const   {return frc[offset];}
-  double getFy() const   {return frc[offset+1];}
-  double getFz() const   {return frc[offset+2];}
-  void addFx(double add) {frc[offset]   += add;}
-  void addFy(double add) {frc[offset+1] += add;}
-  void addFz(double add) {frc[offset+2] += add;}
+  double get_vx() const  {return vel[offsetX];}
+  double get_vy() const  {return vel[offsetY];}
+  double get_vz() const  {return vel[offsetZ];}
+  void set_vx(double vx) {vel[offsetX]   = vx;}
+  void set_vy(double vy) {vel[offsetY] = vy;}
+  void set_vz(double vz) {vel[offsetZ] = vz;}
+  
+  double getFx() const   {return frc[offsetX];}
+  double getFy() const   {return frc[offsetY];}
+  double getFz() const   {return frc[offsetZ];}
+  void addFx(double add) {frc[offsetX]   += add;}
+  void addFy(double add) {frc[offsetY] += add;}
+  void addFz(double add) {frc[offsetZ] += add;}
   virtual void zeroForces() = 0;
 
   double getMass() const {return c_mass;}
@@ -64,10 +73,19 @@ class Atom{ (public)
   void setCovalent(double covalent) {c_covalent = covalent;}
   
   int getIndex() const {return index;}
-  void setIndex(int theIndex) {index = theIndex; offset = index*3;}
-  
+  void setIndex(int theIndex) {
+    index = theIndex; 
+    offset = index*3;
+    offsetX = offset;
+    offsetY = offset+1;
+    offsetZ = offset+2;
+  }
+
   char *getType() {return c_name;}
   void setType(char * name) {strcpy(c_name,name);}
+  
+  int getIdent( void ) { return ident; }
+  void setIdent( int info ) { ident = info; }
 
   void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
   int get_n_hydrogens() const {return c_n_hyd;}
@@ -97,8 +115,10 @@ class Atom{ (public)
 
   int index; /* set the atom's index */
   int offset; // the atom's offset in the storage array
+  int offsetX, offsetY, offsetZ;
 
   char c_name[100]; /* it's name */
+  int ident;  // it's unique numeric identity.
 
   int c_n_hyd; // the number of hydrogens bonded to the atom 
   
@@ -118,9 +138,9 @@ class GeneralAtom : public Atom{ (public)
 
   int isDirectional( void ){ return 0; }
   void zeroForces() {
-    frc[offset]   = 0.0; 
-    frc[offset+1] = 0.0; 
-    frc[offset+2] = 0.0;
+    frc[offsetX]   = 0.0; 
+    frc[offsetY] = 0.0; 
+    frc[offsetZ] = 0.0;
   }
 };
 
@@ -161,20 +181,20 @@ class DirectionalAtom : public Atom { (public)
   void setJy( double the_jy ) { jy = the_jy; }
   void setJz( double the_jz ) { jz = the_jz; }
     
-  void addTx( double the_tx ) { trq[offset]   += the_tx;}
-  void addTy( double the_ty ) { trq[offset+1] += the_ty;}
-  void addTz( double the_tz ) { trq[offset+2] += the_tz;}
+  void addTx( double the_tx ) { trq[offsetX]   += the_tx;}
+  void addTy( double the_ty ) { trq[offsetY] += the_ty;}
+  void addTz( double the_tz ) { trq[offsetZ] += the_tz;}
 
   void setMu( double the_mu ) { mu = the_mu; }
 
   void zeroForces() {
-    frc[offset]   = 0.0; 
-    frc[offset+1] = 0.0; 
-    frc[offset+2] = 0.0;
+    frc[offsetX]   = 0.0; 
+    frc[offsetY] = 0.0; 
+    frc[offsetZ] = 0.0;
 
-    trq[offset]   = 0.0; 
-    trq[offset+1] = 0.0; 
-    trq[offset+2] = 0.0;
+    trq[offsetX]   = 0.0; 
+    trq[offsetY] = 0.0; 
+    trq[offsetZ] = 0.0;
   }
 
   double getAxx( void ) { return Axx; } 
@@ -202,9 +222,9 @@ class DirectionalAtom : public Atom { (public)
   double getJy( void ) { return jy; }
   double getJz( void ) { return jz; }
 
-  double getTx( void ) { return trq[offset];} 
-  double getTy( void ) { return trq[offset+1]; }
-  double getTz( void ) { return trq[offset+2]; }
+  double getTx( void ) { return trq[offsetX];} 
+  double getTy( void ) { return trq[offsetY]; }
+  double getTz( void ) { return trq[offsetZ]; }
 
   double getIxx( void ) { return Ixx; } 
   double getIxy( void ) { return Ixy; }