--- trunk/SHAPES/GridBuilder.cpp	2004/06/21 13:38:55	1281
+++ trunk/SHAPES/GridBuilder.cpp	2004/06/21 15:54:27	1283
@@ -9,26 +9,19 @@ GridBuilder::GridBuilder(RigidBody* rb, int bandWidth)
   thetaStep = PI / bandwidth;
   thetaMin = thetaStep / 2.0;
   phiStep = thetaStep * 2.0;
-	
-  //zero out the rot mats
-  for (i=0; i<3; i++) {
-    for (j=0; j<3; j++) {
-      rotX[i][j] = 0.0;
-      rotZ[i][j] = 0.0;
-      rbMatrix[i][j] = 0.0;
-    }
-  }
 }
 
 GridBuilder::~GridBuilder() {
 }
 
-void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid, vector<double> sGrid,
-                              vector<double> epsGrid){
+void GridBuilder::launchProbe(int forceField, vector<double> sigmaGrid, 
+                              vector<double> sGrid, vector<double> epsGrid){
   ofstream sigmaOut("sigma.grid");
   ofstream sOut("s.grid");
   ofstream epsOut("eps.grid");
   double startDist;
+  double phiVal;
+  double thetaVal;
   double minDist = 10.0; //minimum start distance
 	
   sList = sGrid;
@@ -41,36 +34,32 @@ void GridBuilder::launchProbe(int forceField, vector<d
   if (startDist < minDist)
     startDist = minDist;
 
-  initBody();
-  for (k=0; k<bandwidth; k++){		
-    printf("step theta...\n");
-    for (j=0; j<bandwidth; j++){
+  printf("startDist = %lf\n", startDist);
+
+  //set the initial orientation of the body and loop over theta values
+
+  for (k =0; k < bandwidth; k++) {
+    thetaVal = thetaMin + k*thetaStep;
+    for (j=0; j < bandwidth; j++) {
+      phiVal = j*phiStep;
+
+      printf("setting Euler, phi = %lf\ttheta = %lf\n", phiVal, thetaVal);
+
+      rbMol->setEuler(0.0, thetaVal, phiVal);
+
       releaseProbe(startDist);
 
+      printf("found sigDist = %lf\t sDist = %lf \t epsVal = %lf\n", 
+             sigDist, sDist, epsVal);
+
       sigList.push_back(sigDist);
       sList.push_back(sDist);
       epsList.push_back(epsVal);
-			
-      stepPhi(phiStep);
+
     }
-    stepTheta(thetaStep);
   }		
-  /*
-  //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){
   int tooClose;
   double tempPotEnergy;
@@ -83,8 +72,7 @@ void GridBuilder::releaseProbe(double farPos){
   tooClose = 0;
   epsVal = 0;
   rhoStep = 0.1; //the distance the probe atom moves between steps
-	
-	
+		
   while (!tooClose){
     calcEnergy();
     potProgress.push_back(potEnergy);
@@ -154,6 +142,12 @@ void GridBuilder::calcEnergy(){
   }
   
   potEnergy = 0.0;
+
+  rbMol->getAtomPos(rbAtomPos, 0);
+
+  printf("atom0 pos = %lf\t%lf\t%lf\n", rbAtomPos[0], rbAtomPos[1], rbAtomPos[2]);
+
+
   
   for(i=0; i<rbMol->getNumAtoms(); i++){
     rbMol->getAtomPos(rbAtomPos, i);
@@ -197,7 +191,6 @@ void GridBuilder::calcEnergy(){
         potEnergy += 4*sqrt(epsHe*atomEps)*(rValPowerSix * (rValPowerSix - 1.0));
         
       }; break;
-        
       
       case 4:{
         //we are using the OPLS force field
@@ -222,40 +215,6 @@ void GridBuilder::calcEnergy(){
   }
 } 
 
-void GridBuilder::stepTheta(double increment){
-  //zero out the euler angles
-  for (l=0; l<3; l++)
-    angles[i] = 0.0;
-	
-  //the second euler angle is for rotation about the x-axis (we use the zxz convention)
-  angles[1] = increment;
-	
-  //obtain the rotation matrix through the rigid body class
-  rbMol->doEulerToRotMat(angles, rotX);
-	
-  //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");
@@ -266,4 +225,4 @@ void GridBuilder::printGridFiles(){
     sOut << sList[k] << "\n0\n";    
     epsOut << epsList[k] << "\n0\n";
   }
-}
\ No newline at end of file
+}