--- trunk/mdtools/headers/Atom.hpp	2002/10/17 21:58:55	143
+++ trunk/mdtools/headers/Atom.hpp	2002/12/16 21:42:11	213
@@ -12,6 +12,10 @@ class Atom{ (public)
     is_VDW = 0;
     is_LJ = 0;
     index = theIndex;
+    offset = 3 * index;
+    offsetX = offset;
+    offsetY = offset+1;
+    offsetZ = offset+2;
   }
   virtual ~Atom() {}
 
@@ -28,26 +32,26 @@ class Atom{ (public)
     delete[] trq;
   }
   
-  double getX() const {return pos[3*index];}
-  double getY() const {return pos[3*index+1];}
-  double getZ() const {return pos[3*index+2];}
-  void setX(double x) {pos[3*index]   = x;}
-  void setY(double y) {pos[3*index+1] = y;}
-  void setZ(double z) {pos[3*index+2] = z;}
+  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 get_vx() const  {return vel[3*index];}
-  double get_vy() const  {return vel[3*index+1];}
-  double get_vz() const  {return vel[3*index+2];}
-  void set_vx(double vx) {vel[3*index]   = vx;}
-  void set_vy(double vy) {vel[3*index+1] = vy;}
-  void set_vz(double vz) {vel[3*index+2] = vz;}
+  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[3*index];}
-  double getFy() const   {return frc[3*index+1];}
-  double getFz() const   {return frc[3*index+2];}
-  void addFx(double add) {frc[3*index]   += add;}
-  void addFy(double add) {frc[3*index+1] += add;}
-  void addFz(double add) {frc[3*index+2] += add;}
+  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;}
@@ -63,8 +67,14 @@ class Atom{ (public)
   void setCovalent(double covalent) {c_covalent = covalent;}
   
   int getIndex() const {return index;}
-  void setIndex(int theIndex) {index = theIndex;}
-  
+  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);}
 
@@ -82,19 +92,21 @@ class Atom{ (public)
 
   virtual int isDirectional( void ) = 0;
 
-protected:
-  
   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 )
 
+protected:
+  
   double c_mass; /* the mass of the atom in amu */
   double c_sigma; /* the sigma parameter for van der walls interactions */
   double c_epslon; /* the esplon parameter for VDW interactions */
   double c_covalent; // The covalent radius of the atom.
 
   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 */
 
@@ -106,6 +118,8 @@ class Atom{ (public)
   
 };
 
+
+
 class GeneralAtom : public Atom{
 
 public:
@@ -114,9 +128,9 @@ class GeneralAtom : public Atom{ (public)
 
   int isDirectional( void ){ return 0; }
   void zeroForces() {
-    frc[3*index]   = 0.0; 
-    frc[3*index+1] = 0.0; 
-    frc[3*index+2] = 0.0;
+    frc[offsetX]   = 0.0; 
+    frc[offsetY] = 0.0; 
+    frc[offsetZ] = 0.0;
   }
 };
 
@@ -157,20 +171,20 @@ 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[3*index]   += the_tx;}
-  void addTy( double the_ty ) { trq[3*index+1] += the_ty;}
-  void addTz( double the_tz ) { trq[3*index+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[3*index]   = 0.0; 
-    frc[3*index+1] = 0.0; 
-    frc[3*index+2] = 0.0;
+    frc[offsetX]   = 0.0; 
+    frc[offsetY] = 0.0; 
+    frc[offsetZ] = 0.0;
 
-    trq[3*index]   = 0.0; 
-    trq[3*index+1] = 0.0; 
-    trq[3*index+2] = 0.0;
+    trq[offsetX]   = 0.0; 
+    trq[offsetY] = 0.0; 
+    trq[offsetZ] = 0.0;
   }
 
   double getAxx( void ) { return Axx; } 
@@ -198,9 +212,9 @@ class DirectionalAtom : public Atom { (public)
   double getJy( void ) { return jy; }
   double getJz( void ) { return jz; }
 
-  double getTx( void ) { return trq[3*index];} 
-  double getTy( void ) { return trq[3*index+1]; }
-  double getTz( void ) { return trq[3*index+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; }