--- trunk/src/applications/dump2Xyz/Dump2XYZ.cpp	2005/03/09 17:30:29	413
+++ trunk/src/applications/dump2Xyz/Dump2XYZ.cpp	2006/08/30 21:04:04	1026
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -57,6 +57,7 @@
 #include "selection/SelectionEvaluator.hpp"
 #include "selection/SelectionManager.hpp"
 #include "visitors/LipidTransVisitor.hpp"
+#include "visitors/AtomNameVisitor.hpp"
 
 using namespace oopse;
 
@@ -67,7 +68,6 @@ int main(int argc, char* argv[]){
   
   gengetopt_args_info args_info;
   std::string dumpFileName;
-  std::string mdFileName;
   std::string xyzFileName;
   
   //parse the command line option
@@ -83,9 +83,6 @@ int main(int argc, char* argv[]){
     exit(1);
   }
   
-  mdFileName = dumpFileName;
-  mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
-
   if (args_info.output_given){
     xyzFileName = args_info.output_arg;
   } else {
@@ -95,35 +92,46 @@ int main(int argc, char* argv[]){
   
   //parse md file and set up the system
   SimCreator creator;
-  SimInfo* info = creator.createSim(mdFileName, false);
+  SimInfo* info = creator.createSim(dumpFileName, false);
   
-  
-  
-  //creat visitor list
+
+  //create visitor list
   CompositeVisitor* compositeVisitor = new CompositeVisitor();
     
-  //creat RigidBody Visitor
+  //create RigidBody Visitor
   if(args_info.rigidbody_flag){
     RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
     compositeVisitor->addVisitor(rbCOMVisitor, 900);
   }
   
-  //creat SSD atom visitor
+  //create SSD atom visitor
   SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
   compositeVisitor->addVisitor(ssdVisitor, 800);
   
   LinearAtomVisitor* linearVisitor = new LinearAtomVisitor(info);
   compositeVisitor->addVisitor(linearVisitor, 750);
+  if (args_info.gb_given) {
+    linearVisitor->addGayBerneAtomType(args_info.gb_arg);
+  }
   
-  //creat default atom visitor
+  GBLipidAtomVisitor* gbLipidVisitor = new GBLipidAtomVisitor(info);
+  compositeVisitor->addVisitor(gbLipidVisitor, 740);
+
+  //create default atom visitor
   DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
   compositeVisitor->addVisitor(defaultAtomVisitor, 700);
   
-  //creat waterType visitor
+  //create waterType visitor
   if(args_info.watertype_flag){
     WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
     compositeVisitor->addVisitor(waterTypeVisitor, 600);
   }
+
+  if (args_info.basetype_flag) {
+      AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
+      compositeVisitor->addVisitor(atomNameVisitor, 550);
+
+  }
   
   //create ZconsVisitor
   if(args_info.zconstraint_flag){
@@ -137,14 +145,14 @@ int main(int argc, char* argv[]){
     }
   }
   
-  //creat wrapping visitor
+  //create wrapping visitor
   
-  if(args_info.periodicBox_flag){
-    WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
-    compositeVisitor->addVisitor(wrappingVisitor, 400);
-  }
+  //if(args_info.periodicBox_flag){
+  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
+  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
+  //}
 
-  //creat replicate visitor
+  //create replicate visitor
   if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
     Vector3i replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
     ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info, replicateOpt);
@@ -160,7 +168,7 @@ int main(int argc, char* argv[]){
     exit(1);
   }
     
-  //creat xyzVisitor
+  //create xyzVisitor
   XYZVisitor* xyzVisitor;
   if (args_info.selection_given) {
     xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
@@ -171,7 +179,7 @@ int main(int argc, char* argv[]){
   
   std::cout << compositeVisitor->toString();
   
-  //creat prepareVisitor
+  //create prepareVisitor
   PrepareVisitor* prepareVisitor = new PrepareVisitor();
   
   //open dump file
@@ -189,10 +197,29 @@ int main(int argc, char* argv[]){
   Molecule* mol;
   StuntDouble* integrableObject;
   RigidBody* rb;
+  Vector3d molCom;
+  Vector3d newMolCom;
+  Vector3d displacement;
+  Mat3x3d hmat;
+  Snapshot* currentSnapshot;
        
   for (int i = 0; i < nframes; i += args_info.frame_arg){
     dumpReader->readFrame(i);
-    
+
+    //wrapping the molecule
+    if(args_info.periodicBox_flag) {
+      currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();    
+      for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
+          molCom = mol->getCom();
+          newMolCom = molCom;
+          currentSnapshot->wrapVector(newMolCom);
+          displacement = newMolCom - molCom;
+        for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
+             integrableObject = mol->nextIntegrableObject(iiter)) {  
+          integrableObject->setPos(integrableObject->getPos() + displacement);
+        }
+      }    
+    }
     //update atoms of rigidbody
     for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
       
@@ -229,7 +256,7 @@ int main(int argc, char* argv[]){
   
   xyzStream.close();
   
-  
+  delete prepareVisitor; 
   delete compositeVisitor;
   delete info;