--- trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp	2004/07/29 18:01:05	1434
+++ trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp	2004/07/29 18:16:16	1435
@@ -29,11 +29,8 @@ int main( int argc, char* argv[]){
   string inputFileName;
   string outPrefix;
   string outMdFileName;
-  string outInitFileName;
   SimInfo* oldInfo;
-  SimInfo* newInfo;
   SimSetup* oldSimSetup;
-  SimSetup* newSimSetup;
   BaseLattice* simpleLat;
   int numMol;
   double latticeConstant;
@@ -116,7 +113,6 @@ int main( int argc, char* argv[]){
     outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
   
   outMdFileName = outPrefix + ".md";
-  outInitFileName = outPrefix + ".in";
 
   //parse md file and set up the system
   oldInfo = new SimInfo;
@@ -130,15 +126,16 @@ int main( int argc, char* argv[]){
      cerr << "error in creating SimSetup" << endl;
      exit(1);
   }
-    
+
+  oldSimSetup->suspendInit();
   oldSimSetup->setSimInfo(oldInfo );
   oldSimSetup->parseFile(&inputFileName[0] );
   oldSimSetup->createSim(); 
+  
   if(oldInfo->nComponents >=2){
       cerr << "can not build the system with more than two components" << endl;
       exit(1);
   }
-
   
   //get mass of molecule. 
   //Due to the design of OOPSE, given atom type, we have to query forcefiled to get the mass
@@ -161,51 +158,39 @@ int main( int argc, char* argv[]){
   simpleLat->setLatticeConstant(lc);
   
   //calculate the total number of molecules
-  numMol = args_info.nx_arg * args_info.ny_arg * args_info.nz_arg * numMolPerCell;
-  
-  //creat new .md file on fly 
-  createMdFile(inputFileName, outMdFileName, numMol);
+  numMol = nx * ny * nz * numMolPerCell;
 
-  //parse new .md file and set up the system
-  newInfo = new SimInfo;
-  if(newInfo == NULL){
-     cerr << "error in creating SimInfo" << endl;
-     exit(1);
+  if (oldInfo->n_mol != numMol){
+    //creat new .md file on fly which corrects the number of molecule 
+    createMdFile(inputFileName, outMdFileName, numMol);
+    cerr << "SimpleBuilder Error: the number of molecule and the density are not matched" <<endl;
+    cerr << "A new .md file: " << outMdFileName << " is generated, use it to rerun the simpleBuilder" << endl;
+    exit(1);
   }
-  
-  newSimSetup = new SimSetup();  
-  if(newSimSetup == NULL){
-     cerr << "error in creating SimSetup" << endl;
-     exit(1);
-  }
-    
-  newSimSetup->setSimInfo(newInfo );
-  newSimSetup->parseFile(&outMdFileName[0] );
-  newSimSetup->createSim(); 
 
   //allocat memory for storing pos, vel and etc
-  newInfo->getConfiguration()->createArrays(newInfo->n_atoms);
-  for (int i = 0; i < newInfo->n_atoms; i++)
-    newInfo->atoms[i]->setCoords();  
+  oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms);
+  for (int i = 0; i < oldInfo->n_atoms; i++)
+    oldInfo->atoms[i]->setCoords();  
 
   //creat Molocator
-  locator = new MoLocator(newInfo->compStamps[0], newSimSetup->getForceField());
+  locator = new MoLocator(oldInfo->compStamps[0], oldSimSetup->getForceField());
 
   //fill Hmat
   Hmat[0][0] = nx * latticeConstant;
   Hmat[0][1] = 0.0;
   Hmat[0][2] = 0.0;
 
-  Hmat[1][0] = ny * latticeConstant;
-  Hmat[1][1] = 0.0;
+  Hmat[1][0] = 0.0;
+  Hmat[1][1] = ny * latticeConstant;
   Hmat[1][2] = 0.0;
 
-  Hmat[2][0] = nz * latticeConstant;
+  Hmat[2][0] = 0.0;
   Hmat[2][1] = 0.0;
-  Hmat[2][2] = 0.0;
+  Hmat[2][2] = nz * latticeConstant ;
 
   //set Hmat
-  newInfo->setBoxM(Hmat);
+  oldInfo->setBoxM(Hmat);
   
   //place the molecules
 
@@ -223,13 +208,13 @@ int main( int argc, char* argv[]){
           simpleLat->getLatticePointsPos(latticePos, i, j, k);
 
           for(int l = 0; l < numMolPerCell; l++)
-            locator->placeMol(latticePos[l], latticeOrt[l], &(newInfo->molecules[curMolIndex++]));
+            locator->placeMol(latticePos[l], latticeOrt[l], &(oldInfo->molecules[curMolIndex++]));
        }
     }
   }
 
   //create dumpwriter and write out the coordinates
-  writer = new DumpWriter( newInfo );
+  writer = new DumpWriter( oldInfo );
   if(writer == NULL){
     cerr << "error in creating DumpWriter" << endl;
     exit(1);    
@@ -237,18 +222,14 @@ int main( int argc, char* argv[]){
   writer->writeFinal(0);
   
   //delete objects
-  if(!oldInfo)
+
+  //delete oldInfo and oldSimSetup
+  if(oldInfo != NULL)
      delete oldInfo;
   
-  if(!oldSimSetup)
-     delete oldSimSetup;
-
-  if(!newInfo)
-     delete newInfo;
+  if(oldSimSetup != NULL)
+     delete oldSimSetup; 
   
-  if(!newSimSetup)
-     delete newSimSetup;
-
   if (writer != NULL)
     delete writer;
   return 0;
@@ -259,7 +240,6 @@ void createMdFile(const string& oldMdFileName, const s
   ofstream newMdFile;
   const int MAXLEN = 65535;
   char buffer[MAXLEN];
-  string line;
 
   //create new .md file based on old .md file
   oldMdFile.open(oldMdFileName.c_str());
@@ -268,8 +248,8 @@ void createMdFile(const string& oldMdFileName, const s
   oldMdFile.getline(buffer, MAXLEN);
   while(!oldMdFile.eof()){
 
-    if(line.find("nMol") < line.size()){
-      
+    //correct molecule number
+    if(strstr(buffer, "nMol") !=NULL){      
       sprintf(buffer, "\t\tnMol = %d;", numMol);
       newMdFile << buffer << endl;
     }