--- trunk/mdtools/headers/Atom.hpp	2002/07/09 18:40:59	11
+++ trunk/mdtools/headers/Atom.hpp	2002/10/17 21:58:55	143
@@ -6,34 +6,48 @@ class Atom{ (public)
 
 class Atom{
 public:
-  Atom() {
+  Atom(int theIndex) {
     c_n_hyd = 0; 
     has_dipole = 0;
     is_VDW = 0;
     is_LJ = 0;
+    index = theIndex;
   }
-  ~Atom() {}
+  virtual ~Atom() {}
+
+  static void createArrays (int nElements) {
+    pos = new double[nElements*3];
+    vel = new double[nElements*3];
+    frc = new double[nElements*3];
+    trq = new double[nElements*3];
+  }
+  static void destroyArrays(void) {
+    delete[] pos;
+    delete[] vel;
+    delete[] frc;
+    delete[] trq;
+  }
   
-  double getX() const {return c_x;}
-  double getY() const {return c_y;}
-  double getZ() const {return c_z;}
-  void setX(double x) {c_x = x;}
-  void setY(double y) {c_y = y;}
-  void setZ(double z) {c_z = z;}
+  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 get_vx() const {return c_vx;}
-  double get_vy() const {return c_vy;}
-  double get_vz() const {return c_vz;}
-  void set_vx(double vx) {c_vx = vx;}
-  void set_vy(double vy) {c_vy = vy;}
-  void set_vz(double vz) {c_vz = vz;}
+  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 getFx() const {return c_Fx;}
-  double getFy() const {return c_Fy;}
-  double getFz() const {return c_Fz;}
-  void addFx(double add) {c_Fx += add;}
-  void addFy(double add) {c_Fy += add;}
-  void addFz(double add) {c_Fz += add;}
+  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;}
   virtual void zeroForces() = 0;
 
   double getMass() const {return c_mass;}
@@ -48,8 +62,8 @@ class Atom{ (public)
   double getCovalent() const {return c_covalent;}
   void setCovalent(double covalent) {c_covalent = covalent;}
   
-  int getIndex() const {return c_index;}
-  void setIndex(int index) {c_index = index;}
+  int getIndex() const {return index;}
+  void setIndex(int theIndex) {index = theIndex;}
   
   char *getType() {return c_name;}
   void setType(char * name) {strcpy(c_name,name);}
@@ -58,64 +72,70 @@ class Atom{ (public)
   int get_n_hydrogens() const {return c_n_hyd;}
 
   void setHasDipole( int value ) { has_dipole = value; }
-  short int hasDipole( void ) { return has_dipole; }
+  int hasDipole( void ) { return has_dipole; }
 
   void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
-  short int isLJ( void )    { return is_LJ; }
+  int isLJ( void )    { return is_LJ; }
 
   void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
-  short int isVDW( void )    { return is_VDW; }
+  int isVDW( void )    { return is_VDW; }
 
   virtual int isDirectional( void ) = 0;
 
 protected:
-  double c_x; /*the atom's position */
-  double c_y;
-  double c_z;
-  	    
-  double c_vx; /*the atom's velocity */
-  double c_vy;
-  double c_vz;
-  	    
-  double c_Fx; /* the atom's forces */
-  double c_Fy;
-  double c_Fz;
   
+  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 )
+
   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 c_index; /* set the atom's index */
+  int index; /* set the atom's index */
 
   char c_name[100]; /* it's name */
 
   int c_n_hyd; // the number of hydrogens bonded to the atom 
   
-  short int has_dipole; // dipole boolean
-  short int is_VDW;    // VDW boolean
-  short int is_LJ;    // LJ boolean
+  int has_dipole; // dipole boolean
+  int is_VDW;    // VDW boolean
+  int is_LJ;    // LJ boolean
   
 };
 
 class GeneralAtom : public Atom{
 
 public:
-  GeneralAtom(){}
-  ~GeneralAtom(){}
+  GeneralAtom(int theIndex): Atom(theIndex){}
+  virtual ~GeneralAtom(){}
 
   int isDirectional( void ){ return 0; }
   void zeroForces() {
-    c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
+    frc[3*index]   = 0.0; 
+    frc[3*index+1] = 0.0; 
+    frc[3*index+2] = 0.0;
   }
 };
 
 class DirectionalAtom : public Atom {
   
 public:
-  DirectionalAtom() { ssdIdentity = 0; }
-  ~DirectionalAtom() {}
+  DirectionalAtom(int theIndex) : Atom(theIndex)
+  { 
+    ssdIdentity = 0; 
+  }
+  virtual ~DirectionalAtom() {}
 
+  static void createDArrays(int nElements){
+    trq = new double[nElements*3];
+  }
+  static void destroyDArrays(void){
+    delete[] trq;
+  }
+
   int isDirectional(void) { return 1; }
   
   void setSSD( int value) { ssdIdentity = value; }
@@ -137,15 +157,20 @@ 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 ) { tx += the_tx;}
-  void addTy( double the_ty ) { ty += the_ty;}
-  void addTz( double the_tz ) { tz += the_tz;}
+  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 setMu( double the_mu ) { mu = the_mu; }
 
   void zeroForces() {
-    c_Fx = 0.0; c_Fy = 0.0; c_Fz = 0.0;
-    tx = 0.0; ty = 0.0; tz = 0.0;
+    frc[3*index]   = 0.0; 
+    frc[3*index+1] = 0.0; 
+    frc[3*index+2] = 0.0;
+
+    trq[3*index]   = 0.0; 
+    trq[3*index+1] = 0.0; 
+    trq[3*index+2] = 0.0;
   }
 
   double getAxx( void ) { return Axx; } 
@@ -160,6 +185,8 @@ class DirectionalAtom : public Atom { (public)
   double getAzy( void ) { return Azy; }
   double getAzz( void ) { return Azz; }
 
+  void getA( double the_A[3][3] ); // get the full rotation matrix
+
   double getSUx( void ) { return sux; }
   double getSUy( void ) { return suy; }
   double getSUz( void ) { return suz; }
@@ -171,9 +198,9 @@ class DirectionalAtom : public Atom { (public)
   double getJy( void ) { return jy; }
   double getJz( void ) { return jz; }
 
-  double getTx( void ) { return tx; } 
-  double getTy( void ) { return ty; }
-  double getTz( void ) { return tz; }
+  double getTx( void ) { return trq[3*index];} 
+  double getTy( void ) { return trq[3*index+1]; }
+  double getTz( void ) { return trq[3*index+2]; }
 
   double getIxx( void ) { return Ixx; } 
   double getIxy( void ) { return Ixy; }
@@ -193,16 +220,16 @@ class DirectionalAtom : public Atom { (public)
   void body2Lab( double r[3] );
 
 private:
+  int dIndex;
 
-  double Axx, Axy, Axz;; // the rotational matrix 
+  double Axx, Axy, Axz; // the rotational matrix 
   double Ayx, Ayy, Ayz;
   double Azx, Azy, Azz;
 
-  double sux, suy, suz; // the standard unit vector ( body fixed )
-  double jx, jy, jz; // the angular momentum vector ( body fixed )
-  double tx, ty, tz; // the torque vector           ( space fixed )
+  double sux, suy, suz; // the standard unit vector    ( body fixed )
+  double jx, jy, jz;    // the angular momentum vector ( body fixed )
   
-  double Ixx, Ixy, Ixz; // the inertial tensor matrix ( body fixed )
+  double Ixx, Ixy, Ixz; // the inertial tensor matrix  ( body fixed )
   double Iyx, Iyy, Iyz;
   double Izx, Izy, Izz;