--- trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp	2004/07/28 04:59:35	1424
+++ trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp	2004/07/28 18:42:59	1427
@@ -14,6 +14,7 @@
 #include "simpleBuilderCmd.hpp"
 #include "StringUtils.hpp"
 #include "LatticeFactory.hpp"
+#include "Vector3d.hpp"
 
 using namespace std;
 
@@ -33,14 +34,14 @@ int main( int argc, char* argv[]){
   BaseLattice* simpleLat;
   int numMol;
   double latticeConstant;
+  vector lc;
   double mass;
   double density;
   int nx, ny, nz;
   double Hmat[3][3];
   MoLocator *locator;
-  double* posX;
-  double* posY;
-  double* posZ;
+  vector<Vector3d> latticePos;
+  vector<Vector3d> latticeOrt;
   int numMolPerCell;
   int curMolIndex;
   DumpWriter* writer;
@@ -125,7 +126,7 @@ int main( int argc, char* argv[]){
   }
 
   //creat lattice
-	simpleLat = LatticeFactory::getInstance()	->createLattice(latticeType);
+	simpleLat = LatticeFactory::getInstance()->createLattice(latticeType);
 	if(simpleLat == NULL){
 		cerr << "Error in creating lattice" << endl;
  		exit(1);
@@ -137,7 +138,8 @@ int main( int argc, char* argv[]){
   latticeConstant = pow(numMolPerCell * mass /density, 1.0/3.0);
   
   //set lattice constant
-  simpleLat->setLatticeConstant(latticeConstant);
+  lc.push_back(latticeConstant);
+  simpleLat->setLatticeConstant(lc);
   
   //calculate the total
   numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell;
@@ -175,7 +177,7 @@ int main( int argc, char* argv[]){
   newSimSetup->parseFile(&outMdFileName[0] );
   newSimSetup->createSim(); 
 
-  //set Hamt
+  //set Hmat
   newInfo->setBoxM(Hmat);
 
   //allocat memory for storing pos, vel and etc
@@ -184,39 +186,25 @@ int main( int argc, char* argv[]){
     newInfo.atoms[i]->setCoords();  
 
   //creat Molocator
-  locator = new MoLocator(newInfo->compStamps[0]);
-
-  //allocate memory for posX, posY, posZ
-
-  posX = new doule[numMolPerCell];
-  if(posX == NULL){
-    cerr << "memory allocation error" << endl;
-    exit(1);
-  }
-
-  posY = new doule[numMolPerCell];
-  if(posX == NULL){
-    cerr << "memory allocation error" << endl;
-    exit(1);
-  }
+  locator = new MoLocator(newInfo->compStamps[0], newSimSetup->the_ff);
 
-  posZ = new doule[numMolPerCell];
-  if(posX == NULL){
-    cerr << "memory allocation error" << endl;
-    exit(1);
-  }
-
   //place the molecules
 
   curMolIndex = 0;
+
+  //get the orientation of the cell sites
+  //for the same type of molecule in same lattice, it will not change
+  latticeOrt = simpleLat->getLatticePointsOrt();
+
   for(int i =0; i < nx; i++){
     for(int j=0; j < ny; j++){
        for(int k = 0; k < nz; k++){
-        
-          simpleLat->getLatticePoints(&posX, &posY, &posZ, i, j, k);
 
+          //get the position of the cell sites
+          simpleLat->getLatticePointsPos(latticePos, i, j, k);
+
           for(int l = 0; l < numMolPerCell; l++)
-            locator->placeMol(posX[l], posY[l], posZ[l], newInfo->molecules[curMolIndex++]);
+            locator->placeMol(latticePos[l], latticeOrt[l], newInfo->molecules[curMolIndex++]);
        }
     }
   }
@@ -243,15 +231,6 @@ int main( int argc, char* argv[]){
   if(!newSimSetup)
      delete newSimSetup;
 
-  if (posX)
-     delete[] posX;
-
-  if (posY)
-     delete[] posY;
-
-  if (posZ)
-   delete[] posZ;
-
   if (writer != NULL)
     delete writer;
   return 0;