--- trunk/src/brains/SimCreator.cpp	2005/03/11 17:50:11	436
+++ trunk/src/brains/SimCreator.cpp	2005/11/16 23:10:02	749
@@ -71,7 +71,6 @@ namespace oopse {
     if (worldRank == 0) {
 #endif // is_mpi
       
-      simParams->initalize();
       set_interface_stamps(stamps, simParams);
       
 #ifdef IS_MPI
@@ -96,7 +95,8 @@ namespace oopse {
     
   }
   
-  SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
+  SimInfo*  SimCreator::createSim(const std::string & mdFileName, 
+                                  bool loadInitCoords) {
     
     MakeStamps * stamps = new MakeStamps();
     
@@ -106,12 +106,13 @@ namespace oopse {
     parseFile(mdFileName, stamps, simParams);
     
     //create the force field
-    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
-                                                                         simParams->getForceField());
+    ForceField * ff = ForceFieldFactory::getInstance()
+      ->createForceField(simParams->getForceField());
     
     if (ff == NULL) {
-      sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
-              simParams->getForceField());
+      sprintf(painCave.errMsg, 
+              "ForceField Factory can not create %s force field\n",
+              simParams->getForceField().c_str());
       painCave.isFatal = 1;
       simError();
     }
@@ -146,8 +147,8 @@ namespace oopse {
     compList(stamps, simParams, moleculeStampPairs);
     
     //create SimInfo
-    SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
-    
+    SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams);
+     
     //gather parameters (SimCreator only retrieves part of the parameters)
     gatherParameters(info, mdFileName);
     
@@ -186,7 +187,7 @@ namespace oopse {
   
   void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
     
-    //figure out the ouput file names
+    //figure out the output file names
     std::string prefix;
     
 #ifdef IS_MPI
@@ -397,7 +398,6 @@ namespace oopse {
                             std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
     int i;
     char * id;
-    LinkedMolStamp* extractedStamp = NULL;
     MoleculeStamp * currentStamp;
     Component** the_components = simParams->getComponents();
     int n_components = simParams->getNComponents();
@@ -418,9 +418,9 @@ namespace oopse {
         }
         
         id = the_components[i]->getType();
-        
-        extractedStamp = stamps->extractMolStamp(id);
-        if (extractedStamp == NULL) {
+
+        currentStamp = stamps->getMolStamp(id);
+        if (currentStamp == NULL) {
           sprintf(painCave.errMsg,
                   "SimCreator error: Component \"%s\" was not found in the "
                   "list of declared molecules\n", id);
@@ -429,9 +429,6 @@ namespace oopse {
           simError();
         }
         
-        currentStamp = extractedStamp->getStamp();
-        
-        
         moleculeStampPairs.push_back(
                                      std::make_pair(currentStamp, the_components[i]->getNMol()));
       } //end for (i = 0; i < n_components; i++)
@@ -606,7 +603,7 @@ namespace oopse {
       //invalid initial coordinate file
       sprintf(painCave.errMsg, 
               "Initial configuration file %s should at least contain one frame\n",
-              simParams->getInitialConfig());
+              simParams->getInitialConfig().c_str());
       painCave.isFatal = 1;
       simError();
     }