--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/05/12 16:38:45	1167
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/05/20 20:24:07	1180
@@ -226,17 +226,17 @@ void SimSetup::makeMolecules(void){
       molInfo.myAtoms = &(info[k].atoms[atomOffset]);
 
       if (molInfo.nBonds > 0) 
-        molInfo.myBonds = new (Bond *) [molInfo.nBonds];
+        molInfo.myBonds = new Bond*[molInfo.nBonds];
       else 
         molInfo.myBonds = NULL;
 
       if (molInfo.nBends > 0) 
-        molInfo.myBends = new (Bend *) [molInfo.nBends];
+        molInfo.myBends = new Bend*[molInfo.nBends];
       else 
         molInfo.myBends = NULL;
 
       if (molInfo.nTorsions > 0) 
-        molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
+        molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
       else 
         molInfo.myTorsions = NULL;
 
@@ -948,7 +948,16 @@ void SimSetup::gatherInfo(void){
 
     info[i].useInitXSstate = globals->getUseInitXSstate();
     info[i].orthoTolerance = globals->getOrthoBoxTolerance();
-    
+
+    // check for thermodynamic integration
+    if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
+      info[i].thermIntLambda = globals->getThermIntLambda();
+      info[i].thermIntK = globals->getThermIntK();
+      info[i].useThermInt = 1;
+      
+      Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
+      info[i].restraint = myRestraint;
+    }
   }
   
   //setup seed for random number generator
@@ -1261,6 +1270,28 @@ void SimSetup::makeOutNames(void){
         }
       }
 
+      strcpy(info[k].rawPotName, inFileName);
+      nameLength = strlen(info[k].rawPotName);
+      endTest = &(info[k].rawPotName[nameLength - 5]);
+      if (!strcmp(endTest, ".bass")){
+        strcpy(endTest, ".raw");
+      }
+      else if (!strcmp(endTest, ".BASS")){
+        strcpy(endTest, ".raw");
+      }
+      else{
+        endTest = &(info[k].rawPotName[nameLength - 4]);
+        if (!strcmp(endTest, ".bss")){
+          strcpy(endTest, ".raw");
+        }
+        else if (!strcmp(endTest, ".mdl")){
+          strcpy(endTest, ".raw");
+        }
+        else{
+          strcat(info[k].rawPotName, ".raw");
+        }
+      }
+
 #ifdef IS_MPI
 
     }