--- trunk/src/utils/MoLocator.cpp	2005/04/15 22:04:00	507
+++ trunk/src/utils/MoLocator.cpp	2006/10/10 02:44:13	1062
@@ -58,6 +58,7 @@ namespace oopse {
   }
   
   void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){
+
     Vector3d newCoor;
     Vector3d curRefCoor;  
     RotMat3x3d rotMat = latVec2RotMat(ort);
@@ -78,8 +79,8 @@ namespace oopse {
       
       newCoor = rotMat * refCoords[i];
       newCoor += offset;
-      
-      integrableObject->setPos( newCoor);
+     
+      integrableObject->setPos(newCoor);
       integrableObject->setVel(V3Zero);
       
       if(integrableObject->isDirectional()){
@@ -94,28 +95,28 @@ namespace oopse {
     RigidBodyStamp* rbStamp;
     int nAtoms; 
     int nRigidBodies;
-    std::vector<double> mass;
+    std::vector<RealType> mass;
     Vector3d coor;
     Vector3d refMolCom;  
     int nAtomsInRb;
-    double totMassInRb;
-    double currAtomMass;
-    double molMass;
+    RealType totMassInRb;
+    RealType currAtomMass;
+    RealType molMass;
     
     nAtoms= myStamp->getNAtoms();
     nRigidBodies = myStamp->getNRigidBodies();
     
     for(size_t i=0; i<nAtoms; i++){
       
-      currAtomStamp = myStamp->getAtom(i);
+      currAtomStamp = myStamp->getAtomStamp(i);
       
       if( !currAtomStamp->havePosition() ){
         sprintf( painCave.errMsg,
                  "MoLocator error.\n"
                  "  Component %s, atom %s does not have a position specified.\n"
                  "  This means MoLocator cannot initalize it's position.\n",
-                 myStamp->getID(),
-                 currAtomStamp->getType() );
+                 myStamp->getName().c_str(),
+                 currAtomStamp->getType().c_str());
         
         painCave.isFatal = 1;
         simError();
@@ -138,7 +139,7 @@ namespace oopse {
     
     for(int i = 0; i < nRigidBodies; i++){
       
-      rbStamp = myStamp->getRigidBody(i);
+      rbStamp = myStamp->getRigidBodyStamp(i);
       nAtomsInRb = rbStamp->getNMembers();
       
       coor.x() = 0.0;
@@ -148,7 +149,7 @@ namespace oopse {
       
       for(int j = 0; j < nAtomsInRb; j++){
         
-        currAtomStamp = myStamp->getAtom(rbStamp->getMember(j));
+        currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j));
         currAtomMass = getAtomMass(currAtomStamp->getType(), myFF);
         totMassInRb +=  currAtomMass;
         
@@ -182,8 +183,8 @@ namespace oopse {
       refCoords[i] -= refMolCom;
   }
   
-  double getAtomMass(const std::string& at, ForceField* myFF) {
-    double mass;
+  RealType getAtomMass(const std::string& at, ForceField* myFF) {
+    RealType mass;
     AtomType* atomType= myFF->getAtomType(at);
     if (atomType != NULL) {
       mass =     atomType->getMass();
@@ -194,22 +195,22 @@ namespace oopse {
     return mass;
   }
   
-  double getMolMass(MoleculeStamp *molStamp, ForceField *myFF) {
+  RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) {
     int nAtoms;
-    double totMass = 0;
+    RealType totMass = 0;
     nAtoms = molStamp->getNAtoms();
     
     for(size_t i = 0; i < nAtoms; i++) {
-      AtomStamp *currAtomStamp = molStamp->getAtom(i);
+      AtomStamp *currAtomStamp = molStamp->getAtomStamp(i);
       totMass += getAtomMass(currAtomStamp->getType(), myFF);         
     }
     return totMass;
   }
   RotMat3x3d latVec2RotMat(const Vector3d& lv){
     
-    double theta =acos(lv[2]);
-    double phi = atan2(lv[1], lv[0]);
-    double psi = 0;
+    RealType theta =acos(lv[2]);
+    RealType phi = atan2(lv[1], lv[0]);
+    RealType psi = 0;
     
     return RotMat3x3d(phi, theta, psi);