--- trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp	2006/03/22 20:57:09	911
+++ trunk/src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp	2006/03/30 19:37:48	925
@@ -147,18 +147,23 @@ int main(int argc, char *argv []) {
     outInitFileName = getPrefix(inputFileName.c_str()) + ".in";
   }
    
+  std::cout <<"Before build shaped lattice. "<<std::endl;
   
-  
   /* create Molocators */
   locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField());
   
   /* Create nanoparticle */
   shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius);
+  
+  std::cout <<"Before build getPoints. "<<std::endl;
   /* Build a lattice and get lattice points for this lattice constant */
   vector<Vector3d> nanoParticleSites = nanoParticle.getPoints();
+  
   /* Get number of lattice sites */
   numSites = nanoParticleSites.size();
  
+ //std::cout <<"numSites are %d "<<numSites<<std::endl;
+// std::cout <<"nComponents are %d "<<nComponents<<std::endl;
   numMol = new int[nComponents];
  
   
@@ -166,17 +171,19 @@ int main(int argc, char *argv []) {
   if (!args_info.ShellRadius_given){
     std::cout << "Creating a random nanoparticle" << std::endl;
     /* Check to see if we have enough components */
-    if (nComponents != args_info.molFraction_given + 1){
+    if (nComponents != args_info.molFraction_given && nComponents != 1){
       std::cerr << "Number of components does not equal molFraction occurances." << std::endl;
       exit(1);
     }
     /* Build the mole fractions and number of molecules of each type */   
     int totComponents = 0;
-    for (int i = 0;i<nComponents-2;i++){ /* Figure out Percent for each component */
+    for (int i = 0;i<nComponents-1;i++){ /* Figure out Percent for each component */
       numMol[i] = int((double)numSites * args_info.molFraction_arg[i]);
+      std::cout<<numMol[i]<<std::endl;
       totComponents += numMol[i];
     }
     numMol[nComponents-1] = numSites - totComponents;
+   
 	/* do the iPod thing, Shuffle da vector */
 	std::random_shuffle(nanoParticleSites.begin(), nanoParticleSites.end());
   } else{ /*Handle core-shell with multiple components.*/
@@ -192,9 +199,11 @@ int main(int argc, char *argv []) {
    //get the orientation of the cell sites
   //for the same type of molecule in same lattice, it will not change
    latticeOrt = nanoParticle.getPointsOrt();
-  
-  
+std::cout<<"Orientational vector Size: "<< std::endl;
+std::cout<<latticeOrt.size()<< std::endl;
+ 
   
+
   // needed for writing out new md file.
   
     outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
@@ -210,24 +219,22 @@ int main(int argc, char *argv []) {
   // We need to read in new siminfo object.	
   //parse md file and set up the system
   //SimCreator NewCreator;
+   SimCreator newCreator;
+  SimInfo* NewInfo = newCreator.createSim(outMdFileName, false);
   
-  SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false);
   
-  
   // Place molecules
   Molecule* mol;
   SimInfo::MoleculeIterator mi;
   mol = NewInfo->beginMolecule(mi);
  int l = 0;
  for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) {
-  	locator->placeMol(latticePos[l], latticeOrt[l], mol);
+  	locator->placeMol(nanoParticleSites[l], latticeOrt[l], mol);
   	l++;
   }
+ 
 
 
-
-
-
   
   //fill Hmat
   hmat(0, 0)=  latticeConstant;