--- trunk/src/applications/dump2Xyz/Dump2XYZ.cpp	2005/01/12 22:41:40	246
+++ trunk/src/applications/dump2Xyz/Dump2XYZ.cpp	2006/05/23 18:46:11	968
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -54,6 +54,11 @@
 #include "visitors/RigidBodyVisitor.hpp"
 #include "visitors/OtherVisitor.hpp"
 #include "visitors/ZconsVisitor.hpp"
+#include "selection/SelectionEvaluator.hpp"
+#include "selection/SelectionManager.hpp"
+#include "visitors/LipidTransVisitor.hpp"
+#include "visitors/AtomNameVisitor.hpp"
+
 using namespace oopse;
 
 int main(int argc, char* argv[]){
@@ -81,7 +86,7 @@ int main(int argc, char* argv[]){
   
   mdFileName = dumpFileName;
   mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
-  
+
   if (args_info.output_given){
     xyzFileName = args_info.output_arg;
   } else {
@@ -91,61 +96,47 @@ int main(int argc, char* argv[]){
   
   //parse md file and set up the system
   SimCreator creator;
-  SimInfo* info = creator.createSim(mdFileName);
+  SimInfo* info = creator.createSim(mdFileName, false);
   
   
   
-  //creat visitor list
+  //create visitor list
   CompositeVisitor* compositeVisitor = new CompositeVisitor();
-  
-  //creat ignore visitor
-  if(args_info.ignore_given ||args_info.water_flag){
     
-    IgnoreVisitor* ignoreVisitor = new IgnoreVisitor();
-    
-    for(int i = 0; i < args_info.ignore_given; i++)
-      ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
-    
-    //ignore water 
-    if(args_info.water_flag){
-      ignoreVisitor->addIgnoreType("SSD");
-      ignoreVisitor->addIgnoreType("SSD1");
-      ignoreVisitor->addIgnoreType("SSD_E");
-      ignoreVisitor->addIgnoreType("SSD_RF");
-      ignoreVisitor->addIgnoreType("TIP3P_RB_0");
-      ignoreVisitor->addIgnoreType("TIP4P_RB_0");
-      ignoreVisitor->addIgnoreType("TIP5P_RB_0");
-      ignoreVisitor->addIgnoreType("SPCE_RB_0");      
-      ignoreVisitor->addIgnoreType("DPD_RB_0");
-    }
-    
-    compositeVisitor->addVisitor(ignoreVisitor, 1000);
-  }
-  
-  //creat RigidBody Visitor
+  //create RigidBody Visitor
   if(args_info.rigidbody_flag){
     RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
     compositeVisitor->addVisitor(rbCOMVisitor, 900);
   }
   
-  //compositeVisitor->addVisitor(lipidVisitor, 900);
-  
-  //creat SSD atom visitor
+  //create SSD atom visitor
   SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
   compositeVisitor->addVisitor(ssdVisitor, 800);
   
-  LinearVisitor* linearVisitor = new LinearAtomVisitor(info);
+  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){
@@ -159,27 +150,41 @@ 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);
-  }
-  
-  //creat replicate visitor
+  //if(args_info.periodicBox_flag){
+  //  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
+  //  compositeVisitor->addVisitor(wrappingVisitor, 400);
+  //}
+
+  //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);
     compositeVisitor->addVisitor(replicateVisitor, 300);
   }
-  
-  //creat xyzVisitor
-  XYZVisitor* xyzVisitor = new XYZVisitor(info);
+
+
+  //create rotation visitor
+  if (args_info.refsele_given&& args_info.originsele_given) {
+    compositeVisitor->addVisitor(new LipidTransVisitor(info, args_info.originsele_arg, args_info.refsele_arg), 250); 
+  } else if (args_info.refsele_given || args_info.originsele_given) {
+    std::cerr << "Both of --refsele and --originsele should appear by pair" << std::endl;
+    exit(1);
+  }
+    
+  //create xyzVisitor
+  XYZVisitor* xyzVisitor;
+  if (args_info.selection_given) {
+    xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
+  } else {
+    xyzVisitor = new XYZVisitor(info);
+  }
   compositeVisitor->addVisitor(xyzVisitor, 200);
   
   std::cout << compositeVisitor->toString();
   
-  //creat prepareVisitor
+  //create prepareVisitor
   PrepareVisitor* prepareVisitor = new PrepareVisitor();
   
   //open dump file
@@ -197,10 +202,29 @@ 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)) {
       
@@ -220,7 +244,8 @@ int main(int argc, char* argv[]){
     
     //update visitor
     compositeVisitor->update();
-    
+
+
     //visit stuntdouble
     for (mol = info->beginMolecule(miter); mol != NULL; mol = info->nextMolecule(miter)) {
       for (integrableObject = mol->beginIntegrableObject(iiter); integrableObject != NULL;
@@ -236,7 +261,7 @@ int main(int argc, char* argv[]){
   
   xyzStream.close();
   
-  
+  delete prepareVisitor; 
   delete compositeVisitor;
   delete info;