--- trunk/OOPSE-2.0/src/visitors/RigidBodyVisitor.cpp	2004/10/21 16:22:01	1625
+++ trunk/OOPSE-2.0/src/visitors/RigidBodyVisitor.cpp	2005/01/12 22:41:40	1930
@@ -1,143 +1,329 @@
+ /*
+ * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ *
+ * The University of Notre Dame grants you ("Licensee") a
+ * 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
+ *    the article in which the program was described (Matthew
+ *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
+ *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
+ *    Parallel Simulation Engine for Molecular Dynamics,"
+ *    J. Comput. Chem. 26, pp. 252-271 (2005))
+ *
+ * 2. Redistributions of source code must retain the above copyright
+ *    notice, this list of conditions and the following disclaimer.
+ *
+ * 3. Redistributions in binary form must reproduce the above copyright
+ *    notice, this list of conditions and the following disclaimer in the
+ *    documentation and/or other materials provided with the
+ *    distribution.
+ *
+ * This software is provided "AS IS," without a warranty of any
+ * kind. All express or implied conditions, representations and
+ * warranties, including any implied warranty of merchantability,
+ * fitness for a particular purpose or non-infringement, are hereby
+ * excluded.  The University of Notre Dame and its licensors shall not
+ * be liable for any damages suffered by licensee as a result of
+ * using, modifying or distributing the software or its
+ * derivatives. In no event will the University of Notre Dame or its
+ * licensors be liable for any lost revenue, profit or data, or for
+ * direct, indirect, special, consequential, incidental or punitive
+ * damages, however caused and regardless of the theory of liability,
+ * arising out of the use of or inability to use software, even if the
+ * University of Notre Dame has been advised of the possibility of
+ * such damages.
+ */
+ 
 #include "visitors/RigidBodyVisitor.hpp"
+
 #include "primitives/RigidBody.hpp"
+
 #include "math/MatVec3.h"
 
+
+
 namespace oopse {
 
+
+
 void LipidHeadVisitor::visit(RigidBody* rb){
-  double pos[3];
-  double u[3] = {0, 0, 1};
-  double newVec[3];
+
+  Vector3d pos;
+
+  Vector3d u(0, 0, 1);
+
+  Vector3d newVec;
+
   GenericData* data;
+
   AtomData* atomData;
+
   AtomInfo* atomInfo;
+
   bool haveAtomData;
-  double rotMatrix[3][3];
 
+  RotMat3x3d rotMatrix;
+
+
+
   if(!canVisit(rb->getType()))
+
     return;
 
-  rb->getPos(pos);
-  rb->getA(rotMatrix);
-  matVecMul3(rotMatrix, u, newVec);
 
-  data = rb->getProperty("ATOMDATA");
+
+  pos = rb->getPos();
+
+  rotMatrix = rb->getA();
+
+  //matVecMul3(rotMatrix, u, newVec);
+
+  newVec = rotMatrix * u;
+
+  
+
+  data = rb->getPropertyByName("ATOMDATA");
+
   if(data != NULL){
 
+
+
     atomData = dynamic_cast<AtomData*>(data);  
+
     if(atomData == NULL){
-      cerr << "can not get Atom Data from " << rb->getType() << endl;
+
+      std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
+
       atomData = new AtomData; 
+
       haveAtomData = false;      
+
     }
+
     else
+
       haveAtomData = true;
+
   }
+
   else{
+
     atomData = new AtomData;
+
     haveAtomData = false;
+
   }
 
+
+
   atomInfo = new AtomInfo;
+
   atomInfo->AtomType = "X";
+
   atomInfo->pos[0] = pos[0];
+
   atomInfo->pos[1] = pos[1];
+
   atomInfo->pos[2] = pos[2];
+
   atomInfo->dipole[0] = newVec[0];
+
   atomInfo->dipole[1] = newVec[1];
+
   atomInfo->dipole[2] = newVec[2];
 
+
+
   atomData->addAtomInfo(atomInfo);
 
+
+
   if(!haveAtomData){
+
     atomData->setID("ATOMDATA");
+
     rb->addProperty(atomData);
+
   }
+
     
+
 }
 
-void LipidHeadVisitor::addLipidHeadName(const string& name){
+
+
+void LipidHeadVisitor::addLipidHeadName(const std::string& name){
+
   lipidHeadName.insert(name);
 
+
+
 }
 
-bool LipidHeadVisitor::canVisit(const string& name){
+
+
+bool LipidHeadVisitor::canVisit(const std::string& name){
+
   return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
 
+
+
 }
 
-const string LipidHeadVisitor::toString(){
+
+
+const  std::string LipidHeadVisitor::toString(){
+
   char buffer[65535];
-  string result;
-  set<string>::iterator i;
+
+   std::string result;
+
+   std::set<std::string>::iterator i;
+
   
+
   sprintf(buffer ,"------------------------------------------------------------------\n");
+
   result += buffer;
+
   
+
   sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
+
   result += buffer;
 
+
+
   //print the ignore type list
+
   sprintf(buffer , "lipidHeadName list contains below types:\n");
+
   result += buffer;
 
+
+
   for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
+
     sprintf(buffer ,"%s\t", i->c_str());
+
     result += buffer;
+
   }
 
+
+
   sprintf(buffer ,"\n");
+
   result += buffer;
 
+
+
   sprintf(buffer ,"------------------------------------------------------------------\n");
+
   result += buffer;
 
+
+
   return result;
 
+
+
 }
 
+
+
 void RBCOMVisitor::visit(RigidBody* rb){
+
   AtomData* atomData;
+
   AtomInfo* atomInfo;
-  double pos[3];
+
+  Vector3d pos;
+
   
-  rb->getPos(pos);
+
+  pos = rb->getPos();
+
   atomInfo = new AtomInfo;
+
   atomInfo->AtomType = "X";
+
   atomInfo->pos[0] = pos[0];
+
   atomInfo->pos[1] = pos[1];
+
   atomInfo->pos[2] = pos[2];
+
   atomInfo->dipole[0] = 0;
+
   atomInfo->dipole[1] = 0;
+
   atomInfo->dipole[2] = 0;
 
+
+
   atomData = new AtomData; 
+
   atomData->setID("ATOMDATA");
+
   atomData->addAtomInfo(atomInfo);
 
+
+
   rb->addProperty(atomData);
+
 }
 
-const string RBCOMVisitor::toString(){
+
+
+const  std::string RBCOMVisitor::toString(){
+
   char buffer[65535];
-  string result;
+
+   std::string result;
+
   
+
   sprintf(buffer ,"------------------------------------------------------------------\n");
+
   result += buffer;
+
   
+
   sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
+
   result += buffer;
 
+
+
   //print the ignore type list
+
   sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
+
   result += buffer;
 
+
+
   sprintf(buffer ,"------------------------------------------------------------------\n");
+
   result += buffer;
 
+
+
   return result;
 
+
+
 }
 
 
+
+
+
 }//namespace oopse
+