--- trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp	2004/07/28 18:42:59	1427
+++ trunk/OOPSE-1.0/utils/sysbuilder/simpleBuilder.cpp	2004/07/28 20:29:49	1429
@@ -7,17 +7,19 @@
 #include <map>
 #include <fstream>
 
-#include "simError.h"
 #include "Globals.hpp"
 #include "SimInfo.hpp"
 #include "SimSetup.hpp"
-#include "simpleBuilderCmd.hpp"
+#include "simpleBuilderCmd.h"
 #include "StringUtils.hpp"
 #include "LatticeFactory.hpp"
 #include "Vector3d.hpp"
+#include "MoLocator.hpp"
+#include "Lattice.hpp"
 
 using namespace std;
 
+void createMdFile(const string& oldMdFileName, const string& newMdFileName, int numMol);
 
 int main( int argc, char* argv[]){
 
@@ -34,7 +36,7 @@ int main( int argc, char* argv[]){
   BaseLattice* simpleLat;
   int numMol;
   double latticeConstant;
-  vector lc;
+  vector<double> lc;
   double mass;
   double density;
   int nx, ny, nz;
@@ -59,32 +61,31 @@ int main( int argc, char* argv[]){
   latticeType = UpperCase(args_info.latticetype_arg);
   if(!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)){
     cerr << latticeType << " is an invalid lattice type" << endl;
-    cerr << LatticeFactory::getInstance()->oString << endl;
+    cerr << LatticeFactory::getInstance()->toString() << endl;
     exit(1);
   }
 	
-  nx = args_info.nx_args;
+  nx = args_info.nx_arg;
   if(nx <= 0){
     cerr << "The number of unit cell in h direction must be greater than 0" << endl;
     exit(1);
   }
 
-  nx = args_info.nx_args;
-  if(nx <= 0){
+  ny = args_info.ny_arg;
+  if(ny <= 0){
     cerr << "The number of unit cell in l direction must be greater than 0" << endl;
     exit(1);
   }
 
-  nx = args_info.nx_args;
-  if(nx <= 0){
+  nz = args_info.nz_arg;
+  if(nz <= 0){
     cerr << "The number of unit cell in k direction must be greater than 0" << endl;
     exit(1);
   }
 	
   //get input file name
-  if (args_info.inputs_num) {
+  if (args_info.inputs_num) 
     inputFileName = args_info.inputs[0];
-    cerr << in_name << "\n";      }
   else {		 
     cerr <<"You must specify a input file name.\n" << endl;
     cmdline_parser_print_help();
@@ -109,7 +110,7 @@ int main( int argc, char* argv[]){
      exit(1);
   }
 
-  oldSimSetup = new SimSetup(oldInfo);  
+  oldSimSetup = new SimSetup();  
   if(oldSimSetup == NULL){
      cerr << "error in creating SimSetup" << endl;
      exit(1);
@@ -117,10 +118,9 @@ int main( int argc, char* argv[]){
     
   oldSimSetup->setSimInfo(oldInfo );
   oldSimSetup->parseFile(&inputFileName[0] );
-  oldSimSetup->createSim();
 
 
-  if(oldInfo->nComponets >=2){
+  if(oldInfo->nComponents >=2){
       cerr << "can not build the system with more than two components" << endl;
       exit(1);
   }
@@ -133,7 +133,7 @@ int main( int argc, char* argv[]){
 	}
 
 
-  numMolPerCell = simpleLat->getNpoints();
+  numMolPerCell = simpleLat->getNumSitesPerCell();
   //calculate lattice constant 
   latticeConstant = pow(numMolPerCell * mass /density, 1.0/3.0);
   
@@ -167,7 +167,7 @@ int main( int argc, char* argv[]){
      exit(1);
   }
 
-  newSimSetup = new SimSetup(newInfo);  
+  newSimSetup = new SimSetup();  
   if(newSimSetup == NULL){
      cerr << "error in creating SimSetup" << endl;
      exit(1);
@@ -181,12 +181,12 @@ int main( int argc, char* argv[]){
   newInfo->setBoxM(Hmat);
 
   //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();  
+  newInfo->getConfiguration()->createArrays(newInfo->n_atoms);
+  for (int i = 0; i < newInfo->n_atoms; i++)
+    newInfo->atoms[i]->setCoords();  
 
   //creat Molocator
-  locator = new MoLocator(newInfo->compStamps[0], newSimSetup->the_ff);
+  locator = new MoLocator(newInfo->compStamps[0], newSimSetup->getForceField());
 
   //place the molecules
 
@@ -204,7 +204,7 @@ 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], &(newInfo->molecules[curMolIndex++]));
        }
     }
   }
@@ -215,7 +215,7 @@ int main( int argc, char* argv[]){
     cerr << "error in creating DumpWriter" << endl;
     exit(1);    
   }
-  writer->writeFinal();
+  writer->writeFinal(0);
 
   
   //delete objects
@@ -241,17 +241,20 @@ 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())
-  newMdFile.open(newMdFileName);
+  oldMdFile.open(oldMdFileName.c_str());
+  newMdFile.open(newMdFileName.c_str());
 
   oldMdFile.getline(buffer, MAXLEN);
   while(!oldMdFile.eof()){
 
-    if(line.find("nMol") < line.size())
-      sprintf(buffer, "nMol = %s;", numMol);
+    if(line.find("nMol") < line.size()){
+      
+      sprintf(buffer, "\t\tnMol = %d;", numMol);
+      newMdFile << buffer << endl;
+    }
     else
       newMdFile << buffer << endl;