--- trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp	2004/07/29 18:16:16	1435
+++ trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp	2004/07/29 19:12:00	1436
@@ -29,6 +29,7 @@ int main( int argc, char* argv[]){
   string inputFileName;
   string outPrefix;
   string outMdFileName;
+  string outInitFileName;
   SimInfo* oldInfo;
   SimSetup* oldSimSetup;
   BaseLattice* simpleLat;
@@ -50,24 +51,9 @@ int main( int argc, char* argv[]){
   // parse command line arguments
   if (cmdline_parser (argc, argv, &args_info) != 0)
     exit(1) ;
+  
+  density = args_info.density_arg;
 
-  //process density
-  if(!args_info.density_given && !args_info.ndensity_given){
-    cerr << "SimpleBuilder Error: density or number density must be given" << endl;
-    cmdline_parser_print_help();
-    exit(1);
-  }
-  else if(args_info.density_given){
-    if( args_info.ndensity_given)
-      cerr << "SimpleBuilder Warning: both of density and number density are given, use density" << endl;
-    
-    density = args_info.density_arg;
-  }
-  else if(args_info.ndensity_given){
-    //convert number density to density 
-  }
-
-
   //get lattice type
   latticeType = UpperCase(args_info.latticetype_arg);
   if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){
@@ -104,16 +90,7 @@ int main( int argc, char* argv[]){
     exit(1);
   }
 
-  //determine the output file names
   
-  if (args_info.output_given){
-    outPrefix = args_info.output_arg;
-  }
-  else
-    outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
-  
-  outMdFileName = outPrefix + ".md";
-
   //parse md file and set up the system
   oldInfo = new SimInfo;
   if(oldInfo == NULL){
@@ -161,13 +138,24 @@ int main( int argc, char* argv[]){
   numMol = nx * ny * nz * numMolPerCell;
 
   if (oldInfo->n_mol != numMol){
-    //creat new .md file on fly which corrects the number of molecule 
+
+    outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType;
+    outMdFileName = outPrefix + ".md";
+
+    //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);
   }
-
+  
+  //determine the output file names  
+  if (args_info.output_given)
+    outInitFileName = args_info.output_arg;
+  else
+    outInitFileName = getPrefix(inputFileName.c_str())  + ".in";
+  
+  
   //allocat memory for storing pos, vel and etc
   oldInfo->getConfiguration()->createArrays(oldInfo->n_atoms);
   for (int i = 0; i < oldInfo->n_atoms; i++)
@@ -214,13 +202,14 @@ int main( int argc, char* argv[]){
   }
 
   //create dumpwriter and write out the coordinates
+  oldInfo->finalName = outInitFileName;
   writer = new DumpWriter( oldInfo );
   if(writer == NULL){
     cerr << "error in creating DumpWriter" << endl;
     exit(1);    
   }
   writer->writeFinal(0);
-  
+  cout << "new initial configuration file: " << outInitFileName <<" is generated." << endl;
   //delete objects
 
   //delete oldInfo and oldSimSetup