--- trunk/SHAPES/GridBuilder.cpp	2004/06/21 18:52:21	1284
+++ trunk/SHAPES/GridBuilder.cpp	2004/06/22 18:04:58	1285
@@ -3,10 +3,10 @@ GridBuilder::GridBuilder(RigidBody* rb, int bandWidth)
 #define PI 3.14159265359
 
 
-GridBuilder::GridBuilder(RigidBody* rb, int bandWidth) {
+GridBuilder::GridBuilder(RigidBody* rb, int gridWidth) {
   rbMol = rb;
-  bandwidth = bandWidth;
-  thetaStep = PI / bandwidth;
+  gridwidth = gridWidth;
+  thetaStep = PI / gridwidth;
   thetaMin = thetaStep / 2.0;
   phiStep = thetaStep * 2.0;
 }
@@ -22,40 +22,68 @@ void GridBuilder::launchProbe(int forceField, vector<d
   double startDist;
   double phiVal;
   double thetaVal;
+  double sigTemp, sTemp, epsTemp, sigProbe;
   double minDist = 10.0; //minimum start distance
 	
   sList = sGrid;
   sigList = sigmaGrid;
   epsList = epsGrid;
   forcefield = forceField;
+  
+  //load the probe atom parameters
+  switch(forcefield){
+    case 1:{
+      rparHe = 1.4800;
+      epsHe = -0.021270;
+    }; break;
+    case 2:{
+      rparHe = 1.14;
+      epsHe = 0.0203;
+    }; break;
+    case 3:{
+      rparHe = 2.28;
+      epsHe = 0.020269601874;
+    }; break;
+    case 4:{
+      rparHe = 2.5560;
+      epsHe = 0.0200;
+    }; break;
+    case 5:{
+      rparHe = 1.14;
+      epsHe = 0.0203;
+    }; break;
+  }
     
-  //first determine the start distance - we always start at least minDist away
+  if (rparHe < 2.2)
+    sigProbe = 2*rparHe/1.12246204831;
+  else
+    sigProbe = rparHe;
+  
+  //determine the start distance - we always start at least minDist away
   startDist = rbMol->findMaxExtent() + minDist;
   if (startDist < minDist)
     startDist = minDist;
 
-  printf("startDist = %lf\n", startDist);
-
   //set the initial orientation of the body and loop over theta values
 
-  for (k =0; k < bandwidth; k++) {
+  for (k =0; k < gridwidth; k++) {
     thetaVal = thetaMin + k*thetaStep;
-    for (j=0; j < bandwidth; j++) {
+    printf("Theta step %i\n", k);
+    for (j=0; j < gridwidth; 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);
-
+      //translate the values to sigma, s, and epsilon of the rigid body
+      sigTemp = 2*sigDist - sigProbe;
+      sTemp = (2*(sDist - sigDist))/(0.122462048309) - sigProbe;
+      epsTemp = pow(epsVal, 2)/fabs(epsHe);
+      
+      sigList.push_back(sigTemp);
+      sList.push_back(sTemp);
+      epsList.push_back(epsTemp);
     }
   }		
 }
@@ -113,42 +141,11 @@ void GridBuilder::calcEnergy(){
   double rXij, rYij, rZij;
   double rijSquared;
   double rValSquared, rValPowerSix;
-  double rparHe, epsHe;
   double atomRpar, atomEps;
   double rbAtomPos[3];
-  
-  //first get the probe atom parameters
-  switch(forcefield){
-    case 1:{
-      rparHe = 1.4800;
-      epsHe = -0.021270;
-    }; break;
-    case 2:{
-      rparHe = 1.14;
-      epsHe = 0.0203;
-    }; break;
-    case 3:{
-      rparHe = 2.28;
-      epsHe = 0.020269601874;
-    }; break;
-    case 4:{
-      rparHe = 2.5560;
-      epsHe = 0.0200;
-    }; break;
-    case 5:{
-      rparHe = 1.14;
-      epsHe = 0.0203;
-    }; break;
-  }
-  
+    
   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);
     
@@ -158,8 +155,8 @@ void GridBuilder::calcEnergy(){
     
     rijSquared = rXij * rXij + rYij * rYij + rZij * rZij;
     
-    //in the interest of keeping the code more compact, we are being less efficient by placing 
-    //a switch statement in the calculation loop
+    //in the interest of keeping the code more compact, we are being less 
+    //efficient by placing a switch statement in the calculation loop
     switch(forcefield){
       case 1:{
         //we are using the CHARMm force field