--- branches/mmeineke/OOPSE/libmdtools/Atom.hpp	2003/03/21 17:42:12	377
+++ trunk/OOPSE/libmdtools/Atom.hpp	2004/04/12 20:32:20	1097
@@ -1,147 +1,38 @@
 #ifndef _ATOM_H_
 #define _ATOM_H_
 
-#include <cstring>
-#include <cstdlib>
+#include <string.h>
+#include <stdlib.h>
 #include <iostream>
 
-class Atom{
+#include "SimState.hpp"
+#include "StuntDouble.hpp"
+
+class Atom : public StuntDouble {
 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, SimState* theConfig );
+  virtual ~Atom() {} 
 
-    Axx = index*9;
-    Axy = Axx+1;
-    Axz = Axx+2;
-    
-    Ayx = Axx+3;
-    Ayy = Axx+4;
-    Ayz = Axx+5;
+  virtual void setCoords(void);
 
-    Azx = Axx+6;
-    Azy = Axx+7;
-    Azz = Axx+8;
-  }
-  virtual ~Atom() {}
+  void getPos( double theP[3] );
+  void setPos( double theP[3] );
 
-  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];
+  void getVel( double theV[3] );
+  void setVel( double theV[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;
-  }
+  void getFrc( double theF[3] );
+  void addFrc( double theF[3] );
 
-  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; }
-  
-  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[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;
+  virtual void zeroForces();
 
-  double getMass() const {return c_mass;}
+  double getMass() {return c_mass;}
   void setMass(double mass) {c_mass = mass;}
   
-  double getSigma() const {return c_sigma;}
-  void setSigma(double sigma) {c_sigma = sigma;}
-
-  double getEpslon() const {return c_epslon;}
-  void setEpslon(double epslon) {c_epslon = epslon;}
-  
-  double getCovalent() const {return c_covalent;}
-  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;
+  void setIndex(int theIndex);
 
-    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;
-  }
-
   char *getType() {return c_name;}
   void setType(char * name) {strcpy(c_name,name);}
   
@@ -153,34 +44,22 @@ class Atom{ (public)
   void setGlobalIndex( int info ) { myGlobalIndex = info; }
 #endif // is_mpi
 
-  void set_n_hydrogens( int n_h ) {c_n_hyd = n_h;}
-  int get_n_hydrogens() const {return c_n_hyd;}
-
   void setHasDipole( int value ) { has_dipole = value; }
   int hasDipole( void ) { return has_dipole; }
 
-  void setLJ( void )        { is_LJ = 1; is_VDW = 0; }
-  int isLJ( void )    { return is_LJ; }
-
-  void seVDW( void )        { is_VDW = 1; is_LJ = 0; }
-  int isVDW( void )    { return is_VDW; }
-
-  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:
   
+  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 */
-  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
@@ -192,142 +71,15 @@ class Atom{ (public)
 
   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 
   
   int has_dipole; // dipole boolean
-  int is_VDW;    // VDW boolean
-  int is_LJ;    // LJ boolean
 
+  bool hasCoords;
+
 #ifdef IS_MPI
   int myGlobalIndex;
 #endif
   
 };
 
-
-
-class GeneralAtom : public Atom{
-
-public:
-  GeneralAtom(int theIndex): Atom(theIndex){}
-  virtual ~GeneralAtom(){}
-
-  int isDirectional( void ){ return 0; }
-  void zeroForces() {
-    frc[offsetX] = 0.0; 
-    frc[offsetY] = 0.0; 
-    frc[offsetZ] = 0.0;
-  }
-};
-
-class DirectionalAtom : public Atom {
-  
-public:
-  DirectionalAtom(int theIndex) : Atom(theIndex)
-  { 
-    ssdIdentity = 0; 
-    sux = 0.0;
-    suy = 0.0;
-    suz = 0.0;
-  }
-  virtual ~DirectionalAtom() {}
-
-  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 );
-  
-  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; 
-    frc[offsetZ] = 0.0;
-
-    trq[offsetX] = 0.0; 
-    trq[offsetY] = 0.0; 
-    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
-
-  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 getQ( double the_q[4] ); // get the quanternions
- 
-  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]; }
-
-  double getIxx( void ) { return Ixx; } 
-  double getIxy( void ) { return Ixy; }
-  double getIxz( void ) { return Ixz; }
-  
-  double getIyx( void ) { return Iyx; } 
-  double getIyy( void ) { return Iyy; }
-  double getIyz( void ) { return Iyz; }
-  
-  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;
-
-  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 Iyx, Iyy, Iyz;
-  double Izx, Izy, Izz;
-
-  int ssdIdentity; // boolean of whether atom is ssd
-
-};
-
 #endif