--- trunk/src/primitives/DirectionalAtom.cpp	2009/11/25 20:02:06	1390
+++ trunk/src/primitives/DirectionalAtom.cpp	2013/06/16 15:15:42	1879
@@ -35,21 +35,32 @@
  *                                                                      
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
- * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include "primitives/DirectionalAtom.hpp"
+#include "types/DirectionalAdapter.hpp"
+#include "types/MultipoleAdapter.hpp"
 #include "utils/simError.h"
 namespace OpenMD {
   
-  DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType) 
-    : Atom(dAtomType){
+  DirectionalAtom::DirectionalAtom(AtomType* dAtomType) 
+    : Atom(dAtomType) {
     objType_= otDAtom;
-    if (dAtomType->isMultipole()) {
-      electroBodyFrame_ = dAtomType->getElectroBodyFrame();
+
+    DirectionalAdapter da = DirectionalAdapter(dAtomType);
+    I_ = da.getI();
+
+    MultipoleAdapter ma = MultipoleAdapter(dAtomType);
+    if (ma.isDipole()) {
+      dipole_ = ma.getDipole();
     }
-    
+    if (ma.isQuadrupole()) {
+      quadrupole_ = ma.getQuadrupole();
+    }
+
     // Check if one of the diagonal inertia tensor of this directional
     // atom is zero:
     int nLinearAxis = 0;
@@ -73,31 +84,58 @@ namespace OpenMD {
   }
   
   Mat3x3d DirectionalAtom::getI() {
-    return static_cast<DirectionalAtomType*>(getAtomType())->getI();
+    return I_;     
   }    
   
   void DirectionalAtom::setPrevA(const RotMat3x3d& a) {
     ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
+
     if (atomType_->isMultipole()) {
-      ((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
+      RotMat3x3d atrans = a.transpose();
+      
+      if (atomType_->isDipole()) {
+        ((snapshotMan_->getPrevSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_;
+      }
+
+      if (atomType_->isQuadrupole()) {
+        ((snapshotMan_->getPrevSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
+      }
     }
   }
   
   
   void DirectionalAtom::setA(const RotMat3x3d& a) {
     ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
-    
+
     if (atomType_->isMultipole()) {
-      ((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;
+      RotMat3x3d atrans = a.transpose();
+
+      if (atomType_->isDipole()) {
+        ((snapshotMan_->getCurrentSnapshot())->*storage_).dipole[localIndex_] = atrans * dipole_;
+      }
+
+      if (atomType_->isQuadrupole()) {
+        ((snapshotMan_->getCurrentSnapshot())->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
+      }
     }
+   
   }    
   
   void DirectionalAtom::setA(const RotMat3x3d& a, int snapshotNo) {
     ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
-    
+
     if (atomType_->isMultipole()) {
-      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * electroBodyFrame_;    
+      RotMat3x3d atrans = a.transpose();
+      
+      if (atomType_->isDipole()) {
+        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).dipole[localIndex_] = atrans * dipole_;
+      }
+
+      if (atomType_->isQuadrupole()) {
+        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).quadrupole[localIndex_] = atrans * quadrupole_ * a;
+      }
     }
+
   }    
   
   void DirectionalAtom::rotateBy(const RotMat3x3d& m) {
@@ -109,7 +147,8 @@ namespace OpenMD {
     Vector3d force;
     Vector3d torque;
     Vector3d myEuler;
-    RealType phi, theta, psi;
+    RealType phi, theta;
+    // RealType psi;
     RealType cphi, sphi, ctheta, stheta;
     Vector3d ephi;
     Vector3d etheta;
@@ -121,7 +160,7 @@ namespace OpenMD {
     
     phi = myEuler[0];
     theta = myEuler[1];
-    psi = myEuler[2];
+    // psi = myEuler[2];
     
     cphi = cos(phi);
     sphi = sin(phi);
@@ -134,10 +173,14 @@ namespace OpenMD {
     ephi[1] = 0.0;
     ephi[2] = 1.0;
     
-    etheta[0] = -sphi;
-    etheta[1] =  cphi;
-    etheta[2] =  0.0;
+    //etheta[0] = -sphi;
+    //etheta[1] =  cphi;
+    //etheta[2] =  0.0;
     
+    etheta[0] = cphi;
+    etheta[1] = sphi;
+    etheta[2] = 0.0;
+    
     epsi[0] = stheta * cphi;
     epsi[1] = stheta * sphi;
     epsi[2] = ctheta;