--- trunk/src/primitives/RigidBody.cpp	2005/04/15 22:04:00	507
+++ trunk/src/primitives/RigidBody.cpp	2006/05/17 21:51:42	963
@@ -51,11 +51,10 @@ namespace oopse {
 
   void RigidBody::setPrevA(const RotMat3x3d& a) {
     ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
-    //((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;
 
     for (int i =0 ; i < atoms_.size(); ++i){
       if (atoms_[i]->isDirectional()) {
-	atoms_[i]->setPrevA(a * refOrients_[i]);
+	atoms_[i]->setPrevA(refOrients_[i].transpose() * a);
       }
     }
 
@@ -64,11 +63,10 @@ namespace oopse {
       
   void RigidBody::setA(const RotMat3x3d& a) {
     ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
-    //((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;
 
     for (int i =0 ; i < atoms_.size(); ++i){
       if (atoms_[i]->isDirectional()) {
-	atoms_[i]->setA(a * refOrients_[i]);
+	atoms_[i]->setA(refOrients_[i].transpose() * a);
       }
     }
   }    
@@ -79,7 +77,7 @@ namespace oopse {
 
     for (int i =0 ; i < atoms_.size(); ++i){
       if (atoms_[i]->isDirectional()) {
-	atoms_[i]->setA(a * refOrients_[i], snapshotNo);
+	atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo);
       }
     }
 
@@ -89,13 +87,13 @@ namespace oopse {
     return inertiaTensor_;
   }    
 
-  std::vector<double> RigidBody::getGrad() {
-    std::vector<double> grad(6, 0.0);
+  std::vector<RealType> RigidBody::getGrad() {
+    std::vector<RealType> grad(6, 0.0);
     Vector3d force;
     Vector3d torque;
     Vector3d myEuler;
-    double phi, theta, psi;
-    double cphi, sphi, ctheta, stheta;
+    RealType phi, theta, psi;
+    RealType cphi, sphi, ctheta, stheta;
     Vector3d ephi;
     Vector3d etheta;
     Vector3d epsi;
@@ -148,7 +146,7 @@ namespace oopse {
 
   /**@todo need modification */
   void  RigidBody::calcRefCoords() {
-    double mtmp;
+    RealType mtmp;
     Vector3d refCOM(0.0);
     mass_ = 0.0;
     for (std::size_t i = 0; i < atoms_.size(); ++i) {
@@ -164,26 +162,24 @@ namespace oopse {
     }
 
     // Moment of Inertia calculation
-    Mat3x3d Itmp(0.0);
-  
+    Mat3x3d Itmp(0.0);    
     for (std::size_t i = 0; i < atoms_.size(); i++) {
+      Mat3x3d IAtom(0.0);  
       mtmp = atoms_[i]->getMass();
-      Itmp -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
-      double r2 = refCoords_[i].lengthSquare();
-      Itmp(0, 0) += mtmp * r2;
-      Itmp(1, 1) += mtmp * r2;
-      Itmp(2, 2) += mtmp * r2;
-    }
+      IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
+      RealType r2 = refCoords_[i].lengthSquare();
+      IAtom(0, 0) += mtmp * r2;
+      IAtom(1, 1) += mtmp * r2;
+      IAtom(2, 2) += mtmp * r2;
+      Itmp += IAtom;
 
-    //project the inertial moment of directional atoms into this rigid body
-    for (std::size_t i = 0; i < atoms_.size(); i++) {
+      //project the inertial moment of directional atoms into this rigid body
       if (atoms_[i]->isDirectional()) {
-	RectMatrix<double, 3, 3> Iproject = refOrients_[i].transpose() * atoms_[i]->getI();
-	Itmp(0, 0) += Iproject(0, 0);
-	Itmp(1, 1) += Iproject(1, 1);
-	Itmp(2, 2) += Iproject(2, 2);
-      }
+        Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i];
+      } 
     }
+
+    //    std::cout << Itmp << std::endl;
 
     //diagonalize 
     Vector3d evals;
@@ -249,8 +245,8 @@ namespace oopse {
         
     }
     
-    setFrc(frc);
-    setTrq(trq);
+    addFrc(frc);
+    addTrq(trq);
     
   }
 
@@ -273,8 +269,7 @@ namespace oopse {
       if (atoms_[i]->isDirectional()) {
           
 	dAtom = (DirectionalAtom *) atoms_[i];
-	dAtom->setA(a * refOrients_[i]);
-	//dAtom->rotateBy( A );      
+	dAtom->setA(refOrients_[i].transpose() * a);
       }
 
     }
@@ -301,7 +296,7 @@ namespace oopse {
       if (atoms_[i]->isDirectional()) {
           
 	dAtom = (DirectionalAtom *) atoms_[i];
-	dAtom->setA(a * refOrients_[i], frame);
+	dAtom->setA(refOrients_[i].transpose() * a, frame);
       }
 
     }
@@ -486,7 +481,7 @@ namespace oopse {
 	       "RigidBody error.\n"
 	       "\tAtom %s does not have a position specified.\n"
 	       "\tThis means RigidBody cannot set up reference coordinates.\n",
-	       ats->getType() );
+	       ats->getType().c_str() );
       painCave.isFatal = 1;
       simError();
     }
@@ -506,7 +501,7 @@ namespace oopse {
 		 "RigidBody error.\n"
 		 "\tAtom %s does not have an orientation specified.\n"
 		 "\tThis means RigidBody cannot set up reference orientations.\n",
-		 ats->getType() );
+		 ats->getType().c_str() );
 	painCave.isFatal = 1;
 	simError();
       }