--- trunk/OOPSE-1.0/utils/Dump2XYZ.cpp	2004/07/16 18:58:03	1334
+++ trunk/OOPSE-1.0/utils/Dump2XYZ.cpp	2004/07/27 15:41:17	1417
@@ -15,7 +15,7 @@ int main(int argc, char* argv[]){
 int main(int argc, char* argv[]){
   gengetopt_args_info args_info;
   string dumpFileName;
-  string bassFileName;
+  string mdFileName;
   char inFileName[2002];
   string xyzFileName;
   SimInfo* info;
@@ -47,7 +47,7 @@ int main(int argc, char* argv[]){
       exit(1) ;
 
 
-  //get the dumpfile name and bass file name
+  //get the dumpfile name and md file name
   if (args_info.input_given){
     dumpFileName = args_info.input_arg;
   }
@@ -55,8 +55,8 @@ int main(int argc, char* argv[]){
     cerr << "Does not have input file name" << endl;
     exit(1);
   }
-  bassFileName = dumpFileName;
-  bassFileName = bassFileName.substr(0, bassFileName.rfind(".")) + ".bass";
+  mdFileName = dumpFileName;
+  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
 
   if (args_info.output_given){
     xyzFileName = args_info.output_arg;
@@ -66,11 +66,11 @@ int main(int argc, char* argv[]){
     xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
   }
 
-  //parse bass file and set up the system
+  //parse md file and set up the system
   info = new SimInfo();
   startMe.setSimInfo(info );
 
-  strcpy(inFileName, bassFileName.c_str() );
+  strcpy(inFileName, mdFileName.c_str() );
   startMe.parseFile( inFileName );
 
   startMe.createSim();
@@ -108,13 +108,7 @@ int main(int argc, char* argv[]){
     rbCOMVisitor = new RBCOMVisitor(info);
     compositeVisitor->addVisitor(rbCOMVisitor, 900);
   }
-  //creat RigidBody Visitor
-  //lipidVisitor = new LipidHeadVisitor(info);
 
-  //adding names of lipid head group
-  //lipidVisitor->addLipidHeadName("PC_RB_0");
-  //lipidVisitor->addLipidHeadName("PE_RB_0");
-
   //compositeVisitor->addVisitor(lipidVisitor, 900);
 
   //creat SSD atom visitor