--- trunk/OOPSE/libmdtools/OOPSEMinimizer.cpp	2004/03/01 20:01:50	1074
+++ trunk/OOPSE/libmdtools/OOPSEMinimizer.cpp	2004/04/14 15:37:41	1108
@@ -5,8 +5,6 @@ OOPSEMinimizer::OOPSEMinimizer( SimInfo *theInfo, Forc
                                               MinimizerParameterSet * param)
                      :RealIntegrator(theInfo, the_ff), bVerbose(false), bShake(true){
 
-  atoms = info->atoms;
-
   tStats = new Thermo(info);
   dumpOut = new DumpWriter(info);
   statOut = new StatWriter(info);
@@ -54,12 +52,12 @@ void OOPSEMinimizer::calcEnergyGradient(vector<double>
 
   index = 0;
 
-  for(int i = 0; i < nAtoms; i++){
+  for(int i = 0; i < integrableObjects.size(); i++){
 
-    if(atoms[i]->isDirectional()){
-      dAtom = (DirectionalAtom*) atoms[i];
-      dAtom->getGrad(dAtomGrad);
+    if (integrableObjects[i]->isDirectional()) {
 
+      integrableObjects[i]->getGrad(dAtomGrad);
+
       //gradient is equal to -f
       grad[index++] = -dAtomGrad[0];
       grad[index++] = -dAtomGrad[1];
@@ -70,7 +68,7 @@ void OOPSEMinimizer::calcEnergyGradient(vector<double>
 
     }
     else{
-      atoms[i]->getFrc(force);
+      integrableObjects[i]->getFrc(force);
 
       grad[index++] = -force[0];
       grad[index++] = -force[1];
@@ -99,22 +97,23 @@ void OOPSEMinimizer::setCoor(vector<double>& x){
 
   index = 0;
   
-  for(int i = 0; i < nAtoms; i++){
+  for(int i = 0; i < integrableObjects.size(); i++){
     
     position[0] = x[index++];
     position[1] = x[index++];
     position[2] = x[index++];
 
-    atoms[i]->setPos(position);
+    integrableObjects[i]->setPos(position);
 
-    if (atoms[i]->isDirectional()){
-      dAtom = (DirectionalAtom*) atoms[i];
+    if (integrableObjects[i]->isDirectional()){
  
       eulerAngle[0] = x[index++];
       eulerAngle[1] = x[index++];
       eulerAngle[2] = x[index++];
 
-       dAtom->setEuler(eulerAngle[0], eulerAngle[1], eulerAngle[2]);
+      integrableObjects[i]->setEuler(eulerAngle[0], 
+                                     eulerAngle[1], 
+                                     eulerAngle[2]);
 
     }
     
@@ -137,17 +136,17 @@ vector<double> OOPSEMinimizer::getCoor(){
 
   index = 0;
   
-  for(int i = 0; i < nAtoms; i++){
-    atoms[i]->getPos(position);
+  for(int i = 0; i < integrableObjects.size(); i++){
+    integrableObjects[i]->getPos(position);
 
     x[index++] = position[0];
     x[index++] = position[1];
     x[index++] = position[2];
 
-    if (atoms[i]->isDirectional()){
-      dAtom = (DirectionalAtom*) atoms[i];
-      dAtom->getEulerAngles(eulerAngle);
+    if (integrableObjects[i]->isDirectional()){
 
+      integrableObjects[i]->getEulerAngles(eulerAngle);
+      
       x[index++] = eulerAngle[0];
       x[index++] = eulerAngle[1];
       x[index++] = eulerAngle[2];
@@ -425,9 +424,9 @@ void OOPSEMinimizer::calcDim(){
 
   ndim = 0;
 
-  for(int i = 0; i < nAtoms; i++){
+  for(int i = 0; i < integrableObjects.size(); i++){
     ndim += 3;
-    if (atoms[i]->isDirectional())
+    if (integrableObjects[i]->isDirectional())
       ndim += 3;      
   }
 }
@@ -484,7 +483,7 @@ void OOPSEMinimizer::printMinimizerInfo(){
 
 /**
  * In thoery, we need to find the minimum along the search direction
- * However, function evaluation is too expensive. I
+ * However, function evaluation is too expensive. 
  * At the very begining of the problem, we check the search direction and make sure
  * it is a descent direction
  * we will compare the energy of two end points,