--- trunk/OOPSE/libmdtools/Atom.hpp	2003/08/07 00:47:33	669
+++ trunk/OOPSE/libmdtools/Atom.hpp	2003/08/07 21:47:18	670
@@ -5,67 +5,31 @@ class Atom{
 #include <cstdlib>
 #include <iostream>
 
+#include "SimState.hpp"
+
 class Atom{
 public:
 
-  Atom(int theIndex);
+  Atom(int theIndex, SimState* theConfig );
   virtual ~Atom() {} 
 
-  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;
+  void setCoords(void);
 
-  static void createArrays (int the_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);
+//   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; }
-  static double* getFrcArray( void ) { return frc; }
-  static double* getTrqArray( void ) { return trq; }
-  static double* getAmatArray( void ) { return Amat; }
-  static double* getMuArray( void ) { return mu; }
-  static double* getUlArray( void ) { return ul; }
-  
   void getPos( double theP[3] );
   void setPos( double theP[3] );
 
-  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;}
-  
   void getVel( double theV[3] );
   void setVel( double theV[3] );
 
-  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;}
-  
-
   void getFrc( double theF[3] );
   void addFrc( double theF[3] );
 
-  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;}
@@ -116,6 +80,16 @@ class Atom{ (protected)
 
 protected:
   
+  SimState* myConfig;
+
+  double* pos; // the position array
+  double* vel; // the velocity array
+  double* frc; // the forc array
+  double* trq; // the torque vector  ( space fixed )
+  double* Amat; // the rotation matrix
+  double* mu;   // the array of dipole moments
+  double* ul;   // the lab frame unit directional vector
+
   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 */
@@ -141,6 +115,8 @@ class Atom{ (protected)
   int is_LJ;    // LJ boolean
   int is_EAM; //EAM boolean
 
+  bool hasCoords;
+
 #ifdef IS_MPI
   int myGlobalIndex;
 #endif
@@ -150,21 +126,18 @@ class GeneralAtom : public Atom{ (public)
 class GeneralAtom : public Atom{
 
 public:
-  GeneralAtom(int theIndex): Atom(theIndex){}
+  GeneralAtom(int theIndex, SimState* theConfig): Atom(theIndex, theConfig){}
   virtual ~GeneralAtom(){}
 
   int isDirectional( void ){ return 0; }
-  void zeroForces() {
-    frc[offsetX] = 0.0; 
-    frc[offsetY] = 0.0; 
-    frc[offsetZ] = 0.0;
-  }
+  void zeroForces( void );
 };
 
 class DirectionalAtom : public Atom {
   
 public:
-  DirectionalAtom(int theIndex) : Atom(theIndex)
+  DirectionalAtom(int theIndex, SimState* theConfig) : Atom(theIndex, 
+							    theConfig)
   { 
     ssdIdentity = 0; 
     sux = 0.0;
@@ -191,16 +164,8 @@ class DirectionalAtom : public Atom { (public)
   void setSUy( double the_suy ) { suy = the_suy; }
   void setSUz( double the_suz ) { suz = the_suz; }
 
-  void zeroForces() {
-    frc[offsetX] = 0.0; 
-    frc[offsetY] = 0.0; 
-    frc[offsetZ] = 0.0;
+  void zeroForces();
 
-    trq[offsetX] = 0.0; 
-    trq[offsetY] = 0.0; 
-    trq[offsetZ] = 0.0;
-  }
-
   void getA( double the_A[3][3] ); // get the full rotation matrix
   void setA( double the_A[3][3] );
 
@@ -228,10 +193,6 @@ class DirectionalAtom : public Atom { (public)
   //  double getTy( void ) { return trq[offsetY]; }
   //  double getTz( void ) { return trq[offsetZ]; }
 
-  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 setI( double the_I[3][3] );
   void getI( double the_I[3][3] );
   
@@ -246,10 +207,9 @@ class DirectionalAtom : public Atom { (public)
   double getIzx( void ) { return Izx; } 
   double getIzy( void ) { return Izy; }
   double getIzz( void ) { return Izz; }
-  
 
-  double getMu( void ) { return mu[index]; }
-  void setMu( double the_mu ) { mu[index] = the_mu; }
+  double getMu( void );
+  void setMu( double the_mu );
 
   void lab2Body( double r[3] );
   void body2Lab( double r[3] );