--- trunk/OOPSE-4/src/visitors/OtherVisitor.cpp	2005/04/15 22:04:00	2204
+++ trunk/OOPSE-4/src/visitors/OtherVisitor.cpp	2008/09/10 19:51:45	3446
@@ -5,7 +5,6 @@
  * non-exclusive, royalty free, license to use, modify and
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
- *
  * 1. Acknowledgement of the program authors must be made in any
  *    publication of scientific results based in part on use of the
  *    program.  An acceptable form of acknowledgement is citation of
@@ -77,10 +76,18 @@ namespace oopse {
     Snapshot* currSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
     
     for( atomInfo = atomData->beginAtomInfo(i); atomInfo; atomInfo = atomData->nextAtomInfo(i) ) {
-      currSnapshot->wrapVector(atomInfo->pos);
+      Vector3d newPos = atomInfo->pos - origin_;
+      currSnapshot->wrapVector(newPos);
+      atomInfo->pos = newPos;
     }
   }
 
+  void WrappingVisitor::update() {
+    if (useCom_){
+      origin_ = info->getCom();
+    }
+  }
+  
   const std::string WrappingVisitor::toString() {
     char        buffer[65535];
     std::string result;
@@ -227,7 +234,7 @@ namespace oopse {
       if (!evaluator.isDynamic()) {
         seleMan.setSelectionSet(evaluator.evaluate());
       }
-
+      posOnly_ = false;
     }
 
   XYZVisitor::XYZVisitor(SimInfo *info, const std::string& script) :
@@ -240,7 +247,7 @@ namespace oopse {
       if (!evaluator.isDynamic()) {
         seleMan.setSelectionSet(evaluator.evaluate());
       }
-          
+      posOnly_ = false;
     }
     
   void XYZVisitor::visit(Atom *atom) {
@@ -283,18 +290,57 @@ namespace oopse {
     } else
       return;
 
-    for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
-	 atomInfo = atomData->nextAtomInfo(i) ) {
-      sprintf(buffer,
-	      "%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
-	      atomInfo->atomTypeName.c_str(),
-	      atomInfo->pos[0],
-	      atomInfo->pos[1],
-	      atomInfo->pos[2],
-	      atomInfo->dipole[0],
-	      atomInfo->dipole[1],
-	      atomInfo->dipole[2]); 
-      frame.push_back(buffer);
+    AtomType* at = dynamic_cast<Atom *>(sd)->getAtomType();
+    std::string bn = baseTypeName(at);
+
+    if (posOnly_){
+      for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
+	   atomInfo = atomData->nextAtomInfo(i) ) {
+        if (atomInfo->hasCharge) {
+	  sprintf(buffer,
+		  "%s%15.8f%15.8f%15.8f%15.8f",
+		  bn.c_str(),
+		  atomInfo->pos[0],
+		  atomInfo->pos[1],
+		  atomInfo->pos[2],
+		  atomInfo->charge); 
+        } else {
+	  sprintf(buffer,
+		"%s%15.8f%15.8f%15.8f",
+		  bn.c_str(),
+		  atomInfo->pos[0],
+		  atomInfo->pos[1],
+		  atomInfo->pos[2]); 
+        }
+	frame.push_back(buffer);
+      }
+    }else{
+      for( atomInfo = atomData->beginAtomInfo(i); atomInfo;
+	   atomInfo = atomData->nextAtomInfo(i) ) {
+        if (atomInfo->hasCharge) {
+	sprintf(buffer,
+		"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
+		bn.c_str(),
+		atomInfo->pos[0],
+		atomInfo->pos[1],
+		atomInfo->pos[2],
+                atomInfo->charge,
+		atomInfo->dipole[0],
+		atomInfo->dipole[1],
+		atomInfo->dipole[2]); 
+        } else {
+	sprintf(buffer,
+		"%s%15.8f%15.8f%15.8f%15.8f%15.8f%15.8f",
+		bn.c_str(),
+		atomInfo->pos[0],
+		atomInfo->pos[1],
+		atomInfo->pos[2],
+		atomInfo->dipole[0],
+		atomInfo->dipole[1],
+		atomInfo->dipole[2]); 
+        }
+	frame.push_back(buffer);
+      }
     }
   }
 
@@ -329,6 +375,15 @@ namespace oopse {
       outStream << *i << std::endl;
   }
 
+  std::string XYZVisitor::trimmedName(const std::string&atomTypeName) {    
+    return atomTypeName.substr(0, atomTypeName.find('-'));
+  }
+
+  std::string XYZVisitor::baseTypeName(AtomType* at) {
+    std::vector<AtomType*> ayb = at->allYourBase();
+    return ayb[ayb.size()-1]->getName();
+  }
+
   const std::string XYZVisitor::toString() {
     char        buffer[65535];
     std::string result;