--- trunk/src/brains/SimCreator.cpp	2005/12/30 15:32:55	832
+++ trunk/src/brains/SimCreator.cpp	2006/05/17 21:51:42	963
@@ -46,7 +46,7 @@
  * @time 13:51am
  * @version 1.0
  */
-
+#include <exception>
 #include <iostream>
 #include <sstream>
 #include <string>
@@ -147,37 +147,88 @@ Globals* SimCreator::parseFile(const std::string mdFil
              simParams = treeParser.walkTree(parser.getAST());
 
         }
+
       
       catch(antlr::MismatchedCharException& e) {
-          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
+          sprintf(painCave.errMsg, 
+                  "parser exception: %s %s:%d:%d\n",
+                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
+          painCave.isFatal = 1;
+          simError();           
       }
       catch(antlr::MismatchedTokenException &e) {
-          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
+          sprintf(painCave.errMsg, 
+                  "parser exception: %s %s:%d:%d\n",
+                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
+          painCave.isFatal = 1;
+          simError();   
       }
       catch(antlr::NoViableAltForCharException &e) {
-          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
+          sprintf(painCave.errMsg, 
+                  "parser exception: %s %s:%d:%d\n",
+                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
+          painCave.isFatal = 1;
+          simError();   
       }
       catch(antlr::NoViableAltException &e) {
-          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
+          sprintf(painCave.errMsg, 
+                  "parser exception: %s %s:%d:%d\n",
+                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
+          painCave.isFatal = 1;
+          simError();   
       }
+      
 	catch(antlr::TokenStreamRecognitionException& e) {
-          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
+          sprintf(painCave.errMsg, 
+                  "parser exception: %s %s:%d:%d\n",
+                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
+          painCave.isFatal = 1;
+          simError();   
 	}
+	
 	catch(antlr::TokenStreamIOException& e) {
-          cerr<< "parser exception: " << e.getMessage() << endl;
+          sprintf(painCave.errMsg, 
+                  "parser exception: %s\n",
+                  e.getMessage().c_str());
+          painCave.isFatal = 1;
+          simError();
 	}
+	
 	catch(antlr::TokenStreamException& e) {
-          cerr<< "parser exception: " << e.getMessage() << endl;
+          sprintf(painCave.errMsg, 
+                  "parser exception: %s\n",
+                  e.getMessage().c_str());
+          painCave.isFatal = 1;
+          simError();
 	}        
        catch (antlr::RecognitionException& e) {
-          cerr<< "parser exception: " << e.getMessage() << " " <<  e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl;
+          sprintf(painCave.errMsg, 
+                  "parser exception: %s %s:%d:%d\n",
+                  e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn());
+          painCave.isFatal = 1;
+          simError();          
        }
        catch (antlr::CharStreamException& e) {
-            cerr << "parser exception: " << e.getMessage() << endl;
+          sprintf(painCave.errMsg, 
+                  "parser exception: %s\n",
+                  e.getMessage().c_str());
+          painCave.isFatal = 1;
+          simError();        
        }
-        catch (exception& e) {
-            cerr << "parser exception: " << e.what() << endl;
-        }
+       catch (OOPSEException& e) {
+          sprintf(painCave.errMsg, 
+                  "%s\n",
+                  e.getMessage().c_str());
+          painCave.isFatal = 1;
+          simError();
+       }
+       catch (std::exception& e) {
+          sprintf(painCave.errMsg, 
+                  "parser exception: %s\n",
+                  e.what());
+          painCave.isFatal = 1;
+          simError();
+       }
 
         return simParams;
   }
@@ -228,7 +279,8 @@ Globals* SimCreator::parseFile(const std::string mdFil
     //create SimInfo
     SimInfo * info = new SimInfo(ff, simParams);
      
-    //gather parameters (SimCreator only retrieves part of the parameters)
+    //gather parameters (SimCreator only retrieves part of the
+    //parameters)
     gatherParameters(info, mdFileName);
     
     //divide the molecules and determine the global index of molecules
@@ -240,18 +292,23 @@ Globals* SimCreator::parseFile(const std::string mdFil
     createMolecules(info);
     
     
-    //allocate memory for DataStorage(circular reference, need to break it)
+    //allocate memory for DataStorage(circular reference, need to
+    //break it)
     info->setSnapshotManager(new SimSnapshotManager(info));
     
-    //set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the
-    //global index will never change again). Local indices of atoms and rigidbodies are already set by 
-    //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. 
+    //set the global index of atoms, rigidbodies and cutoffgroups
+    //(only need to be set once, the global index will never change
+    //again). Local indices of atoms and rigidbodies are already set
+    //by MoleculeCreator class which actually delegates the
+    //responsibility to LocalIndexManager.
     setGlobalIndex(info);
     
-    //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point
-    //atoms don't have the global index yet  (their global index are all initialized to -1).
-    //Therefore we have to call addExcludePairs explicitly here. A way to work around is that
-    //we can determine the beginning global indices of atoms before they get created.
+    //Although addExcludePairs is called inside SimInfo's addMolecule
+    //method, at that point atoms don't have the global index yet
+    //(their global index are all initialized to -1).  Therefore we
+    //have to call addExcludePairs explicitly here. A way to work
+    //around is that we can determine the beginning global indices of
+    //atoms before they get created.
     SimInfo::MoleculeIterator mi;
     Molecule* mol;
     for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
@@ -295,12 +352,12 @@ Globals* SimCreator::parseFile(const std::string mdFil
   
 #ifdef IS_MPI
   void SimCreator::divideMolecules(SimInfo *info) {
-    double numerator;
-    double denominator;
-    double precast;
-    double x;
-    double y;
-    double a;
+    RealType numerator;
+    RealType denominator;
+    RealType precast;
+    RealType x;
+    RealType y;
+    RealType a;
     int old_atoms;
     int add_atoms;
     int new_atoms;
@@ -412,7 +469,7 @@ Globals* SimCreator::parseFile(const std::string mdFil
           //           Pacc(x) = exp(- a * x)
           // where a = penalty / (average atoms per molecule)
           
-          x = (double)(new_atoms - nTarget);
+          x = (RealType)(new_atoms - nTarget);
           y = myRandom->rand();
           
           if (y < exp(- a * x)) {