--- trunk/OOPSE/libmdtools/ExtendedSystem.cpp	2003/04/04 19:16:11	457
+++ trunk/OOPSE/libmdtools/ExtendedSystem.cpp	2003/04/04 19:47:19	458
@@ -10,19 +10,17 @@ ExtendedSystem::ExtendedSystem( SimInfo &info ) {
   // get what information we need from the SimInfo object
   
   entry_plug = &info;
-  nAtoms = info.n_atoms;
-  atoms = info.atoms;
-  nMols = info.n_mol;
-  molecules = info.molecules;
+  nAtoms = entry_plug->n_atoms;
+  atoms = entry_plug->atoms;
+  nMols = entry_plug->n_mol;
+  molecules = entry_plug->molecules;
+  nOriented = entry_plug->n_oriented;
+  ndf = entry_plug->ndf;
   zeta = 0.0;
   epsilonDot = 0.0;
 
 }
 
-ExtendedSystem::~ExtendedSystem() {  
-}
-
-
 void ExtendedSystem::NoseHooverNVT( double dt, double ke ){
 
   // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
@@ -33,9 +31,11 @@ void ExtendedSystem::NoseHooverNVT( double dt, double 
   const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
   const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to 
                                         // amu*Ang^2*fs^-2/K
-    
+  DirectionalAtom* dAtom;    
+
+
   ke_temp = ke * e_convert;
-  NkBT = (double)getNDF() * kB * targetTemp;
+  NkBT = (double)ndf * kB * targetTemp;
 
   // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
   // qmass is set in the parameter file
@@ -44,7 +44,7 @@ void ExtendedSystem::NoseHooverNVT( double dt, double 
   zetaScale = zeta * dt;
 
   // perform thermostat scaling on linear velocities and angular momentum
-  for(i = 0; i < n_atoms; i++){
+  for(i = 0; i < nAtoms; i++){
     
     vx = atoms[i]->get_vx();
     vy = atoms[i]->get_vy();
@@ -54,9 +54,9 @@ void ExtendedSystem::NoseHooverNVT( double dt, double 
     atoms[i]->set_vy(vy * (1.0 - zetaScale));
     atoms[i]->set_vz(vz * (1.0 - zetaScale));
   }
-  if( n_oriented ){
+  if( nOriented ){
     
-    for( i=0; i < n_atoms; i++ ){
+    for( i=0; i < nAtoms; i++ ){
       
       if( atoms[i]->isDirectional() ){
 	
@@ -89,17 +89,21 @@ void ExtendedSystem::NoseHooverAndersonNPT( double dt,
   const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to 
                                         // amu*Ang^2*fs^-2/K
 
-  double p_ext;
+  double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
+  double volume, p_mol;
+  double vx, vy, vz, jx, jy, jz;
+  DirectionalAtom* dAtom;
+  int i;
 
   p_ext = targetPressure * p_units;
   p_mol = p_int * p_units;
 
-  getBox(oldBox);
+  entry_plug->getBox(oldBox);
 
   volume = oldBox[0]*oldBox[1]*oldBox[2];
 
   ke_temp = ke * e_convert;
-  NkBT = (double)getNDF() * kB * targetTemp;
+  NkBT = (double)ndf * kB * targetTemp;
 
   // propogate the strain rate
 
@@ -114,6 +118,8 @@ void ExtendedSystem::NoseHooverAndersonNPT( double dt,
   newBox[2] = oldBox[2] * scale;
   volume = newBox[0]*newBox[1]*newBox[2];
 
+  entry_plug->setBox(newBox);
+
   // perform affine transform to update positions with volume fluctuations
   this->AffineTransform( oldBox, newBox );
 
@@ -126,7 +132,7 @@ void ExtendedSystem::NoseHooverAndersonNPT( double dt,
   zetaScale = zeta * dt;
   
   // apply barostating and thermostating to velocities and angular momenta
-  for(i = 0; i < n_atoms; i++){
+  for(i = 0; i < nAtoms; i++){
     
     vx = atoms[i]->get_vx();
     vy = atoms[i]->get_vy();
@@ -136,9 +142,9 @@ void ExtendedSystem::NoseHooverAndersonNPT( double dt,
     atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
     atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
   }
-  if( n_oriented ){
+  if( nOriented ){
     
-    for( i=0; i < n_atoms; i++ ){
+    for( i=0; i < nAtoms; i++ ){
       
       if( atoms[i]->isDirectional() ){
 	
@@ -171,7 +177,7 @@ void ExtendedSystem::AffineTransform( double oldBox[3]
   
   for (i=0; i < nMols; i++) {
     
-    molecules[i]->getCOM(r);
+    molecules[i].getCOM(r);
     
     // find the minimum image coordinates of the molecular centers of mass:    
     
@@ -197,6 +203,6 @@ void ExtendedSystem::AffineTransform( double oldBox[3]
     r[1] = ryi + boxNum[1];
     r[2] = rzi + boxNum[2];
 
-    molecules[i]->moveCOM(r);
+    molecules[i].moveCOM(r);
   }
 }