--- trunk/OOPSE/libmdtools/Atom.cpp	2004/01/30 15:01:09	999
+++ trunk/OOPSE/libmdtools/Atom.cpp	2004/04/12 20:32:20	1097
@@ -6,15 +6,12 @@ Atom::Atom(int theIndex, SimState* theConfig) {
 #include "Atom.hpp"
 
 Atom::Atom(int theIndex, SimState* theConfig) {
-  
+
+  objType = OT_ATOM;
   myConfig = theConfig;
   hasCoords = false;
 
-  c_n_hyd = 0; 
   has_dipole = 0;
-  is_VDW = 0;
-  is_LJ = 0;
-  is_charged = 0;
   
   index = theIndex;
   offset = 0;
@@ -43,7 +40,6 @@ void Atom::setCoords(void){
 
   if( myConfig->isAllocated() ){
 
-
     myConfig->getAtomPointers( index,
 		     &pos, 
 		     &vel, 
@@ -60,150 +56,11 @@ void Atom::setCoords(void){
     painCave.isFatal = 1;
     simError();
   }
-
+  
   hasCoords = true;
-
+  
 }
 
-// void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, 
-//                    double* Atrq, double* AAmat, double* Amu, 
-//                    double* Aul) {
-
-//   int nNew = nElements+nAdded;
-
-//   double* new_pos = new double[nNew*3];
-//   double* new_vel = new double[nNew*3];
-//   double* new_frc = new double[nNew*3];
-//   double* new_trq = new double[nNew*3];
-//   double* new_Amat = new double[nNew*9];
-//   double* new_mu = new double[nNew];
-//   double* new_ul = new double[nNew*3];
-//   int i, j;
-  
-//   for (i = 0; i < 3*nElements; i++) {
-//     new_pos[i] = pos[i];
-//     new_vel[i] = vel[i];
-//     new_frc[i] = frc[i];
-//     new_trq[i] = trq[i];
-//     new_ul[i] = ul[i];
-//   }
-
-//   for(i = 0; i < 3*nAdded; i++) {
-//     j = i + 3*nElements;
-//     new_pos[j] = Apos[i];
-//     new_vel[j] = Avel[i];
-//     new_frc[j] = Afrc[i];
-//     new_trq[j] = Atrq[i];
-//     new_ul[j] = Aul[i]; 
-//   }
-
-//   for (i = 0; i < 9*nElements; i++) {
-//     new_Amat[i] = Amat[i];
-//   }
-
-//   for(i = 0; i < 9*nAdded; i++) {
-//     j = i + 9*nElements;
-//     new_Amat[j] = AAmat[i];
-//   }
-
-//   for (i = 0; i < nElements; i++) {
-//     new_mu[i] = mu[i];
-//   }
-
-//   for(i = 0; i < nAdded; i++) {
-//     j = i + nElements;
-//     new_mu[j] = Amu[i];
-//   }
-
-//   delete[] pos;
-//   delete[] vel;
-//   delete[] frc;
-//   delete[] trq;
-//   delete[] Amat;
-//   delete[] mu;
-
-//   pos = new_pos;
-//   vel = new_vel;
-//   frc = new_frc;
-//   trq = new_trq;
-//   ul = new_ul;
-//   Amat = new_Amat;
-//   mu = new_mu;
-
-//   nElements = nNew;
-// }
-
-// void Atom::deleteAtom(int theIndex) {
-//   deleteRange(theIndex, theIndex);
-// }
-
-// void Atom::deleteRange(int startIndex, int stopIndex) {
- 
-//   int nNew = nElements-(stopIndex-startIndex+1);
-
-//   double* new_pos = new double[nNew*3];
-//   double* new_vel = new double[nNew*3];
-//   double* new_frc = new double[nNew*3];
-//   double* new_trq = new double[nNew*3];
-//   double* new_Amat = new double[nNew*9];
-//   double* new_mu = new double[nNew];
-//   double* new_ul = new double[nNew*3];
-//   int i, j;
-  
-//   for (i = 0; i < 3*startIndex; i++) {
-//     new_pos[i] = pos[i];
-//     new_vel[i] = vel[i];
-//     new_frc[i] = frc[i];
-//     new_trq[i] = trq[i];
-//     new_ul[i] = ul[i];
-//   }
-
-//   for(i = 3*(stopIndex + 1); i < 3*nElements; i++) {
-//     j = i - 3*startIndex + 1;
-//     new_pos[j] = pos[i];
-//     new_vel[j] = vel[i];
-//     new_frc[j] = frc[i];
-//     new_trq[j] = trq[i];
-//     new_ul[j] = ul[i]; 
-//   }
-
-//   for (i = 0; i < 9*startIndex; i++) {
-//     new_Amat[i] = Amat[i];
-//   }
-
-//   for(i = 9*(stopIndex + 1); i < 9*nElements; i++) {
-//     j = i - 9*startIndex + 1;
-//     new_Amat[j] = Amat[i];
-//   }
-
-//   for (i = 0; i < startIndex; i++) {
-//     new_mu[i] = mu[i];
-//   }
-
-//   for(i = (stopIndex+1); i < nElements; i++) {
-//     j = i - startIndex + 1;
-//     new_mu[j] = mu[i];
-//   }
-
-//   delete[] pos;
-//   delete[] vel;
-//   delete[] frc;
-//   delete[] trq;
-//   delete[] Amat;
-//   delete[] mu;
-
-//   pos = new_pos;
-//   vel = new_vel;
-//   frc = new_frc;
-//   trq = new_trq;
-//   ul = new_ul;
-//   Amat = new_Amat;
-//   mu = new_mu;
-
-//   nElements = nNew;
-// }
-
-
 void Atom::getPos( double theP[3] ){
   
   if( hasCoords ){
@@ -222,7 +79,7 @@ void Atom::setPos( double theP[3] ){
 }
 
 void Atom::setPos( double theP[3] ){
-  
+
   if( hasCoords ){
     pos[offsetX] = theP[0];
     pos[offsetY] = theP[1];
@@ -308,9 +165,8 @@ void GeneralAtom::zeroForces( void ){
 }
 
 
-void GeneralAtom::zeroForces( void ){
+void Atom::zeroForces( void ){
   
-  
   if( hasCoords ){
     frc[offsetX] = 0.0; 
     frc[offsetY] = 0.0;