--- trunk/OOPSE-1.0/libmdtools/SimSetup.cpp	2004/07/26 17:50:57	1415
+++ trunk/OOPSE-1.0/libmdtools/SimSetup.cpp	2004/07/27 15:41:17	1417
@@ -1003,7 +1003,7 @@ void SimSetup::gatherInfo(void){
                   "\tKeyword useSolidThermInt was set to 'true' but\n"
                   "\tthermodynamicIntegrationLambda (and/or\n"
                   "\tthermodynamicIntegrationK) was not specified.\n"
-                  "\tPlease provide a lambda value and k value in your .bass file.\n");
+                  "\tPlease provide a lambda value and k value in your .md file.\n");
           painCave.isFatal = 1;
           simError();    
         }
@@ -1012,12 +1012,12 @@ void SimSetup::gatherInfo(void){
         if (globals->getUseSolidThermInt()) {
           sprintf( painCave.errMsg,
                    "SimSetup Warning: It appears that you have both solid and\n"
-                   "\tliquid thermodynamic integration activated in your .bass\n"
+                   "\tliquid thermodynamic integration activated in your .md\n"
                    "\tfile. To avoid confusion, specify only one technique in\n"
-                   "\tyour .bass file. Liquid-state thermodynamic integration\n"
+                   "\tyour .md file. Liquid-state thermodynamic integration\n"
                    "\twill be assumed for the current simulation. If this is not\n"
                    "\twhat you desire, set useSolidThermInt to 'true' and\n"
-                   "\tuseLiquidThermInt to 'false' in your .bass file.\n");
+                   "\tuseLiquidThermInt to 'false' in your .md file.\n");
           painCave.isFatal = 0;
           simError();
         }
@@ -1032,7 +1032,7 @@ void SimSetup::gatherInfo(void){
                   "\tKeyword useLiquidThermInt was set to 'true' but\n"
                   "\tthermodynamicIntegrationLambda (and/or\n"
                   "\tthermodynamicIntegrationK) was not specified.\n"
-                  "\tPlease provide a lambda value and k value in your .bass file.\n");
+                  "\tPlease provide a lambda value and k value in your .md file.\n");
           painCave.isFatal = 1;
           simError();    
         }
@@ -1041,7 +1041,7 @@ void SimSetup::gatherInfo(void){
         sprintf(painCave.errMsg,
                 "SimSetup Warning: If you want to use Thermodynamic\n"
                 "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
-                "\t'true' in your .bass file.  These keywords are set to\n"
+                "\t'true' in your .md file.  These keywords are set to\n"
                 "\t'false' by default, so your lambda and/or k values are\n"
                 "\tbeing ignored.\n");
         painCave.isFatal = 0;
@@ -1305,7 +1305,7 @@ void SimSetup::initSystemCoords(void){
   }
   else{
     
-    // no init from bass
+    // no init from md file 
     
     sprintf(painCave.errMsg,
             "Cannot intialize a simulation without an initial configuration file.\n");
@@ -1323,109 +1323,21 @@ void SimSetup::makeOutNames(void){
 
 void SimSetup::makeOutNames(void){
   int k;
-
+  string prefix;
 
   for (k = 0; k < nInfo; k++){
 #ifdef IS_MPI
     if (worldRank == 0){
 #endif // is_mpi
-
-      if (globals->haveFinalConfig()){
-        strcpy(info[k].finalName, globals->getFinalConfig());
-      }
-      else{
-        strcpy(info[k].finalName, inFileName);
-        char* endTest;
-        int nameLength = strlen(info[k].finalName);
-        endTest = &(info[k].finalName[nameLength - 5]);
-        if (!strcmp(endTest, ".bass")){
-          strcpy(endTest, ".eor");
-        }
-        else if (!strcmp(endTest, ".BASS")){
-          strcpy(endTest, ".eor");
-        }
-        else{
-          endTest = &(info[k].finalName[nameLength - 4]);
-          if (!strcmp(endTest, ".bss")){
-            strcpy(endTest, ".eor");
-          }
-          else if (!strcmp(endTest, ".mdl")){
-            strcpy(endTest, ".eor");
-          }
-          else{
-            strcat(info[k].finalName, ".eor");
-          }
-        }
-      }
+      
+      if(globals->haveFinalConfig())
+	prefix = getPrefix(globals->getFinalConfig());   
+      else
+	prefix = getPrefix(info[k].finalName);
 
-      // make the sample and status out names
-
-      strcpy(info[k].sampleName, inFileName);
-      char* endTest;
-      int nameLength = strlen(info[k].sampleName);
-      endTest = &(info[k].sampleName[nameLength - 5]);
-      if (!strcmp(endTest, ".bass")){
-        strcpy(endTest, ".dump");
-      }
-      else if (!strcmp(endTest, ".BASS")){
-        strcpy(endTest, ".dump");
-      }
-      else{
-        endTest = &(info[k].sampleName[nameLength - 4]);
-        if (!strcmp(endTest, ".bss")){
-          strcpy(endTest, ".dump");
-        }
-        else if (!strcmp(endTest, ".mdl")){
-          strcpy(endTest, ".dump");
-        }
-        else{
-          strcat(info[k].sampleName, ".dump");
-        }
-      }
-
-      strcpy(info[k].statusName, inFileName);
-      nameLength = strlen(info[k].statusName);
-      endTest = &(info[k].statusName[nameLength - 5]);
-      if (!strcmp(endTest, ".bass")){
-        strcpy(endTest, ".stat");
-      }
-      else if (!strcmp(endTest, ".BASS")){
-        strcpy(endTest, ".stat");
-      }
-      else{
-        endTest = &(info[k].statusName[nameLength - 4]);
-        if (!strcmp(endTest, ".bss")){
-          strcpy(endTest, ".stat");
-        }
-        else if (!strcmp(endTest, ".mdl")){
-          strcpy(endTest, ".stat");
-        }
-        else{
-          strcat(info[k].statusName, ".stat");
-        }
-      }
-
-      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");
-        }
-      }
+      info[k].finalName = prefix + ".eor";	
+      info[k].sampleName = prefix + ".dump";
+      info[k].statusName = prefix + ".stat";
 
 #ifdef IS_MPI