--- trunk/SHAPES/GridBuilder.cpp	2004/06/21 13:38:55	1281
+++ trunk/SHAPES/GridBuilder.cpp	2004/06/21 15:10:29	1282
@@ -29,6 +29,8 @@ void GridBuilder::launchProbe(int forceField, vector<d
   ofstream sOut("s.grid");
   ofstream epsOut("eps.grid");
   double startDist;
+  double phiVal;
+  double thetaVal;
   double minDist = 10.0; //minimum start distance
 	
   sList = sGrid;
@@ -41,34 +43,27 @@ void GridBuilder::launchProbe(int forceField, vector<d
   if (startDist < minDist)
     startDist = minDist;
 
-  initBody();
-  for (k=0; k<bandwidth; k++){		
-    printf("step theta...\n");
+  //set the initial orientation of the body and loop over theta values
+  phiVal = 0.0;
+  thetaVal = thetaMin;
+  rotBody(phiVal, thetaVal);
+  for (k=0; k<bandwidth; k++){	
+	//loop over phi values starting with phi = 0.0
     for (j=0; j<bandwidth; j++){
       releaseProbe(startDist);
 
       sigList.push_back(sigDist);
       sList.push_back(sDist);
       epsList.push_back(epsVal);
-			
-      stepPhi(phiStep);
+      
+      phiVal += phiStep;
+      rotBody(phiVal, thetaVal);
     }
-    stepTheta(thetaStep);
+    phiVal = 0.0;
+    thetaVal += thetaStep;
+    rotBody(phiVal, thetaVal);
+    printf("step theta %i\n",k);
   }		
-  /*
-  //write out the grid files
-  printf("the grid size is %d\n",sigmaGrid.size());
-  for (k=0; k<sigmaGrid.size(); k++){
-    sigmaOut << sigmaGrid[k] << "\n0\n";
-    sOut << sGrid[k] << "\n0\n";
-    epsOut << epsGrid[k] << "\n0\n";
-  }
-   */
-}
-
-void GridBuilder::initBody(){
-  //set up the rigid body in the starting configuration
-  stepTheta(thetaMin);
 }
 
 void GridBuilder::releaseProbe(double farPos){
@@ -197,7 +192,6 @@ void GridBuilder::calcEnergy(){
         potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0));
         
       }; break;
-        
       
       case 4:{
         //we are using the OPLS force field
@@ -222,40 +216,28 @@ void GridBuilder::calcEnergy(){
   }
 } 
 
-void GridBuilder::stepTheta(double increment){
+void GridBuilder::rotBody(double pValue, double tValue){
   //zero out the euler angles
   for (l=0; l<3; l++)
     angles[i] = 0.0;
 	
+  //the phi euler angle is for rotation about the z-axis (we use the zxz convention)
+  angles[0] = pValue;
   //the second euler angle is for rotation about the x-axis (we use the zxz convention)
-  angles[1] = increment;
+  angles[1] = tValue;
 	
   //obtain the rotation matrix through the rigid body class
   rbMol->doEulerToRotMat(angles, rotX);
-	
+  
+  //start from the reference position
+  identityMat3(rbMatrix);
+  rbMol->setA(rbMatrix);
+  
   //rotate the rigid body
-  rbMol->getA(rbMatrix);
   matMul3(rotX, rbMatrix, rotatedMat);
   rbMol->setA(rotatedMat);	
 }
 
-void GridBuilder::stepPhi(double increment){
-  //zero out the euler angles
-  for (l=0; l<3; l++)
-    angles[i] = 0.0;
-	
-  //the phi euler angle is for rotation about the z-axis (we use the zxz convention)
-  angles[0] = increment;
-	
-  //obtain the rotation matrix through the rigid body class
-  rbMol->doEulerToRotMat(angles, rotZ);
-	
-  //rotate the rigid body
-  rbMol->getA(rbMatrix);
-  matMul3(rotZ, rbMatrix, rotatedMat);
-  rbMol->setA(rotatedMat);	
-}
-
 void GridBuilder::printGridFiles(){
   ofstream sigmaOut("sigma.grid");
   ofstream sOut("s.grid");