--- branches/mmeineke/OOPSE/libmdtools/Atom.hpp	2003/03/21 17:42:12	377
+++ trunk/OOPSE/libmdtools/Atom.hpp	2003/08/07 00:47:33	669
@@ -7,78 +7,27 @@ 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 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);
 
-  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] = 0.0;
-      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 double* getPosArray( void ) { return pos; }
   static double* getVelArray( void ) { return vel; }
   static double* getFrcArray( void ) { return frc; }
@@ -87,6 +36,9 @@ class Atom{ (public)
   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];}
@@ -94,6 +46,9 @@ class Atom{ (public)
   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];}
@@ -101,6 +56,10 @@ class Atom{ (public)
   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];}
@@ -111,6 +70,9 @@ class Atom{ (public)
 
   double getMass() const {return c_mass;}
   void setMass(double mass) {c_mass = mass;}
+
+  double getEamRcut() const {return myEamRcut;}
+  void setEamRcut(double eamRcut) {myEamRcut = eamRcut;}
   
   double getSigma() const {return c_sigma;}
   void setSigma(double sigma) {c_sigma = sigma;}
@@ -122,26 +84,7 @@ 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);}
   
@@ -165,15 +108,11 @@ class Atom{ (public)
   void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
   int isVDW( void )    { return is_VDW; }
 
+  void setEAM( void ) { is_EAM = 1; }
+  int  isEAM( void ) { return is_EAM; }
+
   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:
   
@@ -182,6 +121,8 @@ class Atom{ (public)
   double c_epslon; /* the esplon parameter for VDW interactions */
   double c_covalent; // The covalent radius of the atom.
 
+  double myEamRcut; // Atom rcut for eam defined by the forcefield.
+
   int index; /* set the atom's index */
   int offset; // the atom's offset in the storage array
   int offsetX, offsetY, offsetZ;
@@ -198,6 +139,7 @@ class Atom{ (public)
   int has_dipole; // dipole boolean
   int is_VDW;    // VDW boolean
   int is_LJ;    // LJ boolean
+  int is_EAM; //EAM boolean
 
 #ifdef IS_MPI
   int myGlobalIndex;
@@ -205,8 +147,6 @@ class Atom{ (public)
   
 };
 
-
-
 class GeneralAtom : public Atom{
 
 public:
@@ -233,31 +173,24 @@ class DirectionalAtom : public Atom { (public)
   }
   virtual ~DirectionalAtom() {}
 
+  void printAmatIndex( void );
+
   int isDirectional(void) { return 1; }
   
   void setSSD( int value) { ssdIdentity = value; }
   int isSSD(void) {return ssdIdentity; }
 
-  void setA( double the_A[3][3] );
-
-  void setI( double the_I[3][3] );
-
-  void setQ( double the_q[4] );
   
   void setEuler( double phi, double theta, double psi );
+
+  double getSUx( void ) { return sux; }
+  double getSUy( void ) { return suy; }
+  double getSUz( void ) { return suz; }
   
   void setSUx( double the_sux ) { sux = the_sux; }
   void setSUy( double the_suy ) { suy = the_suy; }
   void setSUz( double the_suz ) { suz = the_suz; }
 
-  void setJx( double the_jx ) { jx = the_jx; }
-  void setJy( double the_jy ) { jy = the_jy; }
-  void setJz( double the_jz ) { jz = the_jz; }
-    
-  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 zeroForces() {
     frc[offsetX] = 0.0; 
     frc[offsetY] = 0.0; 
@@ -268,35 +201,40 @@ class DirectionalAtom : public Atom { (public)
     trq[offsetZ] = 0.0;
   }
 
-  double getAxx( void ) { return Amat[Axx]; } 
-  double getAxy( void ) { return Amat[Axy]; }
-  double getAxz( void ) { return Amat[Axz]; }
-  
-  double getAyx( void ) { return Amat[Ayx]; } 
-  double getAyy( void ) { return Amat[Ayy]; }
-  double getAyz( void ) { return Amat[Ayz]; }
-  
-  double getAzx( void ) { return Amat[Azx]; } 
-  double getAzy( void ) { return Amat[Azy]; }
-  double getAzz( void ) { return Amat[Azz]; }
-
   void getA( double the_A[3][3] ); // get the full rotation matrix
+  void setA( double the_A[3][3] );
 
-  double getSUx( void ) { return sux; }
-  double getSUy( void ) { return suy; }
-  double getSUz( void ) { return suz; }
-
   void getU( double the_u[3] ); // get the unit vetor
+  void updateU( void );
+
   void getQ( double the_q[4] ); // get the quanternions
+  void setQ( double the_q[4] );
  
+  void getJ( double theJ[3] );
+  void setJ( double theJ[3] );
+
   double getJx( void ) { return jx; } 
   double getJy( void ) { return jy; }
   double getJz( void ) { return jz; }
 
-  double getTx( void ) { return trq[offsetX];} 
-  double getTy( void ) { return trq[offsetY]; }
-  double getTz( void ) { return trq[offsetZ]; }
+  void setJx( double the_jx ) { jx = the_jx; }
+  void setJy( double the_jy ) { jy = the_jy; }
+  void setJz( double the_jz ) { jz = the_jz; }
 
+  void getTrq( double theT[3] );
+  void addTrq( double theT[3] );
+
+  //  double getTx( void ) { return trq[offsetX];} 
+  //  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] );
+  
   double getIxx( void ) { return Ixx; } 
   double getIxy( void ) { return Ixy; }
   double getIxz( void ) { return Ixz; }
@@ -308,14 +246,15 @@ 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; }
 
   void lab2Body( double r[3] );
   void body2Lab( double r[3] );
-  void updateU( void );
 
+
 private:
   int dIndex;