--- trunk/OOPSE/libmdtools/OtherVisitor.cpp	2004/04/19 20:54:58	1120
+++ trunk/OOPSE/libmdtools/OtherVisitor.cpp	2004/04/22 03:29:30	1129
@@ -15,8 +15,21 @@ void IgnoreVisitor::visit(RigidBody* rb){
 }
 
 void IgnoreVisitor::visit(RigidBody* rb){
-  if(isIgnoreType(rb->getType()))
+  vector<Atom*> myAtoms;
+  vector<Atom*>::iterator atomIter;
+  AtomInfo* atomInfo;
+  
+  if(isIgnoreType(rb->getType())){
+    
     internalVisit(rb);
+
+    myAtoms = rb->getAtoms();    
+    
+    for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
+      internalVisit(*atomIter);
+
+  }
+  
 }
 
 bool IgnoreVisitor::isIgnoreType(const string& name){
@@ -47,12 +60,15 @@ const string IgnoreVisitor::toString(){
   sprintf(buffer ,"Visitor name: %s", visitorName.c_str());
   result += buffer;
 
+  sprintf(buffer ,"Visitor Description: ignore  stuntdoubles\n");
+  result += buffer;
+
   //print the ignore type list
   sprintf(buffer , "Ignore type list contains below types:\n");
   result += buffer;
 
   for(i = itList.begin(); i != itList.end(); ++i){
-    sprintf(buffer ,"%s,\t", i->c_str());
+    sprintf(buffer ,"%s\t", i->c_str());
     result += buffer;
 
   }
@@ -62,7 +78,7 @@ const string IgnoreVisitor::toString(){
   sprintf(buffer ,"------------------------------------------------------------------\n");
   result += buffer;
 
-  return buffer;
+  return result;
 }
 
 //----------------------------------------------------------------------------//
@@ -82,32 +98,52 @@ void WrappingVisitor::internalVisit(StuntDouble* sd){
   GenericData* data;
   AtomData* atomData;
   AtomInfo* atomInfo;
-  double pos[3];
   vector<AtomInfo*>::iterator i;
 
   data = sd->getProperty("ATOMDATA");
-  if(data != NULL)
+  if(data != NULL){
     atomData = dynamic_cast<AtomData*>(data);  
     if(atomData == NULL)
       return;
+  }
   else
     return;
 
-  for(atomInfo = atomData->beginAtomInfo(i); atomInfo != NULL; atomData->nextAtomInfo(i))
+  for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i))
     info->wrapVector(atomInfo->pos);
+
    
 }
 
+const string WrappingVisitor::toString(){
+  char buffer[65535];
+  string result;
+  
+  sprintf(buffer ,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
+  result += buffer;
+
+  sprintf(buffer ,"Visitor Description: wrapping atoms back to periodic box\n");
+  result += buffer;
+ 
+  sprintf(buffer,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  return result;
+}
+
 //----------------------------------------------------------------------------//
 
-ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 replicateOpt) : BaseVisitor(){
+ReplicateVisitor::ReplicateVisitor(SimInfo* info, IntVec3 opt) : BaseVisitor(){
   this->info = info;
   visitorName = "ReplicateVisitor";
-  this->replicateOpt = replicateOpt;
+  this->replicateOpt = opt;
   //generate the replicate directions
-  for(int i = 0; i < replicateOpt[0]; i ++)
-    for(int j = 0; i < replicateOpt[1]; j ++)
-      for(int k = 0; i < replicateOpt[2]; k ++)
+  for(int i = 0; i <= replicateOpt[0]; i ++)
+    for(int j = 0; j <= replicateOpt[1]; j ++)
+      for(int k = 0; k <= replicateOpt[2]; k ++)
         //skip original frame
         if(i == 0 && j ==0 && k ==0)
           continue;
@@ -136,10 +172,11 @@ void ReplicateVisitor::internalVisit(StuntDouble* sd){
   
   //if there is not atom data, just skip it
   data = sd->getProperty("ATOMDATA");
-  if(data != NULL)
+  if(data != NULL){
     atomData = dynamic_cast<AtomData*>(data);  
     if(atomData == NULL)
       return;
+  }
   else
     return;
 
@@ -178,9 +215,12 @@ const string ReplicateVisitor::toString(){
   sprintf(buffer ,"------------------------------------------------------------------\n");
   result += buffer;
 
-  sprintf(buffer ,"Visitor name: %s", visitorName.c_str());
+  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
   result += buffer;
 
+  sprintf(buffer ,"Visitor Description: replicate the atoms in different direction\n");
+  result += buffer;
+  
   //print the replicate direction
   sprintf(buffer , "repeatX = %d:\n", replicateOpt[0]);
   result += buffer;
@@ -255,11 +295,12 @@ void XYZVisitor::internalVisit(StuntDouble* sd){
                   atomInfo->AtomType.c_str(),
                   atomInfo->pos[0],
                   atomInfo->pos[1],
-                  atomInfo->pos[2]);        
+                  atomInfo->pos[2]);   
+
+    frame.push_back(buffer);
+              
   }
 
-  frame.push_back(buffer);
-          
 }
 
 bool XYZVisitor::isIgnore(StuntDouble* sd){
@@ -294,6 +335,25 @@ void XYZVisitor::writeFrame(ostream& outStream){
     outStream << *i << endl;
 }
 
+const string XYZVisitor::toString(){
+  char buffer[65535];
+  string result;
+  
+  sprintf(buffer ,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
+  result += buffer;
+
+  sprintf(buffer ,"Visitor Description: assemble the atom data and output xyz file\n");
+  result += buffer;
+ 
+  sprintf(buffer,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  return result;
+}
+
 //----------------------------------------------------------------------------//
 
 void PrepareVisitor::internalVisit(Atom * atom){
@@ -340,4 +400,93 @@ void PrepareVisitor::internalVisit(RigidBody * rb){
     
   for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
    internalVisit (*atomIter);  
-}
\ No newline at end of file
+}
+
+const string PrepareVisitor::toString(){
+  char buffer[65535];
+  string result;
+  
+  sprintf(buffer ,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  sprintf(buffer ,"Visitor name: %s", visitorName.c_str());
+  result += buffer;
+
+  sprintf(buffer ,"Visitor Description: prepare for operation of other vistors\n");
+  result += buffer;
+
+  sprintf(buffer ,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  return result;
+}
+
+//----------------------------------------------------------------------------//
+
+WaterTypeVisitor:: WaterTypeVisitor(){
+  visitorName = "WaterTypeVisitor";
+  waterTypeList.insert("TIP3P_RB_0");
+  waterTypeList.insert("TIP4P_RB_0");
+  waterTypeList.insert("TIP5P_RB_0");
+  waterTypeList.insert("SPCE_RB_0");  
+}
+
+
+void WaterTypeVisitor:: visit(RigidBody* rb){
+  string rbName;
+  vector<Atom*> myAtoms;
+  vector<Atom*>::iterator atomIter;
+  GenericData* data;
+  AtomData* atomData;
+  AtomInfo* atomInfo;
+  vector<AtomInfo*>::iterator i;
+  
+  rbName = rb->getType();
+
+  if(waterTypeList.find(rbName) != waterTypeList.end()){
+
+    myAtoms = rb->getAtoms();    
+    for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter){
+
+      data = (*atomIter)->getProperty("ATOMDATA");
+      if(data != NULL){
+        atomData = dynamic_cast<AtomData*>(data);  
+        if(atomData == NULL)
+          continue;
+      }
+      else
+        continue;
+      
+      for(atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i)){
+        replaceType(atomInfo->AtomType);
+      }//end for(atomInfo)
+
+    }//end for(atomIter)
+      
+  }//end if (waterTypeList.find(rbName) != waterTypeList.end())
+  
+}
+
+void WaterTypeVisitor:: replaceType(string& atomType){
+  atomType = atomType.substr(0, atomType.find('_'));
+}
+
+const string WaterTypeVisitor:: toString(){
+  char buffer[65535];
+  string result;
+  
+  sprintf(buffer ,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
+  result += buffer;
+
+  sprintf(buffer ,"Visitor Description: Replace the atom type in water model\n");
+  result += buffer;
+
+  sprintf(buffer ,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  return result;
+}
+