--- trunk/OOPSE/libmdtools/NVT.cpp	2003/06/24 22:51:57	565
+++ trunk/OOPSE/libmdtools/NVT.cpp	2003/07/14 22:38:13	600
@@ -21,13 +21,14 @@ void NVT::moveA() {
 
 void NVT::moveA() {
   
-  int i,j,k;
-  int atomIndex, aMatIndex;
+  int i, j;
   DirectionalAtom* dAtom;
-  double Tb[3];
-  double ji[3];
+  double Tb[3], ji[3];
+  double A[3][3], I[3][3];
+  double angle, mass;
+  double vel[3], pos[3], frc[3];
+
   double instTemp;
-  double angle;
 
   instTemp = tStats->getTemperature();
 
@@ -36,17 +37,22 @@ void NVT::moveA() {
   chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
 
   for( i=0; i<nAtoms; i++ ){
-    atomIndex = i * 3;
-    aMatIndex = i * 9;
-    
-    // velocity half step
-    for( j=atomIndex; j<(atomIndex+3); j++ )
-      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
 
-    // position whole step    
-    for( j=atomIndex; j<(atomIndex+3); j++ )
+    atoms[i]->getVel( vel );
+    atoms[i]->getPos( pos );
+    atoms[i]->getFrc( frc );
+
+    mass = atoms[i]->getMass();
+
+    for (j=0; j < 3; j++) {
+      // velocity half step
+      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
+      // position whole step
       pos[j] += dt * vel[j];
+    }
 
+    atoms[i]->setVel( vel );
+    atoms[i]->setPos( pos );
    
     if( atoms[i]->isDirectional() ){
 
@@ -54,97 +60,91 @@ void NVT::moveA() {
 	  
       // get and convert the torque to body frame
       
-      Tb[0] = dAtom->getTx();
-      Tb[1] = dAtom->getTy();
-      Tb[2] = dAtom->getTz();
-      
+      dAtom->getTrq( Tb );
       dAtom->lab2Body( Tb );
       
       // get the angular momentum, and propagate a half step
 
-      ji[0] = dAtom->getJx();
-      ji[1] = dAtom->getJy();
-      ji[2] = dAtom->getJz();
+      dAtom->getJ( ji );
+
+      for (j=0; j < 3; j++) 
+        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
       
-      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
-      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
-      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
-      
       // use the angular velocities to propagate the rotation matrix a
       // full time step
-      
+
+      dAtom->getA(A);
+      dAtom->getI(I);
+    
       // rotate about the x-axis      
-      angle = dt2 * ji[0] / dAtom->getIxx();
-      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); 
-      
+      angle = dt2 * ji[0] / I[0][0];
+      this->rotate( 1, 2, angle, ji, A ); 
+
       // rotate about the y-axis
-      angle = dt2 * ji[1] / dAtom->getIyy();
-      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
+      angle = dt2 * ji[1] / I[1][1];
+      this->rotate( 2, 0, angle, ji, A );
       
       // rotate about the z-axis
-      angle = dt * ji[2] / dAtom->getIzz();
-      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
+      angle = dt * ji[2] / I[2][2];
+      this->rotate( 0, 1, angle, ji, A);
       
       // rotate about the y-axis
-      angle = dt2 * ji[1] / dAtom->getIyy();
-      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
+      angle = dt2 * ji[1] / I[1][1];
+      this->rotate( 2, 0, angle, ji, A );
       
        // rotate about the x-axis
-      angle = dt2 * ji[0] / dAtom->getIxx();
-      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
+      angle = dt2 * ji[0] / I[0][0];
+      this->rotate( 1, 2, angle, ji, A );
       
-      dAtom->setJx( ji[0] );
-      dAtom->setJy( ji[1] );
-      dAtom->setJz( ji[2] );
-    }
-    
+      dAtom->setJ( ji );
+      dAtom->setA( A  );    
+    }    
   }
 }
 
 void NVT::moveB( void ){
-  int i,j,k;
-  int atomIndex;
+  int i, j;
   DirectionalAtom* dAtom;
-  double Tb[3];
-  double ji[3];
+  double Tb[3], ji[3];
+  double vel[3], frc[3];
+  double mass;
+
   double instTemp;
   
   instTemp = tStats->getTemperature();
   chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
   
   for( i=0; i<nAtoms; i++ ){
-    atomIndex = i * 3;
-    
+
+    atoms[i]->getVel( vel );
+    atoms[i]->getFrc( frc );
+
+    mass = atoms[i]->getMass();
+
     // velocity half step
-    for( j=atomIndex; j<(atomIndex+3); j++ )
-      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*chi);
+    for (j=0; j < 3; j++) 
+      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
     
+    atoms[i]->setVel( vel );
+
     if( atoms[i]->isDirectional() ){
-      
+
       dAtom = (DirectionalAtom *)atoms[i];
-      
-      // get and convert the torque to body frame
-      
-      Tb[0] = dAtom->getTx();
-      Tb[1] = dAtom->getTy();
-      Tb[2] = dAtom->getTz();
-      
+
+      // get and convert the torque to body frame      
+
+      dAtom->getTrq( Tb );
       dAtom->lab2Body( Tb );
+
+      // get the angular momentum, and propagate a half step
+
+      dAtom->getJ( ji );
+
+      for (j=0; j < 3; j++) 
+        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
       
-      // get the angular momentum, and complete the angular momentum
-      // half step
-      
-      ji[0] = dAtom->getJx();
-      ji[1] = dAtom->getJy();
-      ji[2] = dAtom->getJz();
-      
-      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*chi);
-      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*chi);
-      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*chi);
-      
-      dAtom->setJx( ji[0] );
-      dAtom->setJy( ji[1] );
-      dAtom->setJz( ji[2] );
+
+      dAtom->setJ( ji );
     }
   }
 }