--- trunk/OOPSE-2.0/src/visitors/AtomVisitor.cpp	2004/10/21 16:22:01	1625
+++ trunk/OOPSE-2.0/src/visitors/AtomVisitor.cpp	2004/11/05 21:45:14	1718
@@ -174,6 +174,139 @@ const string SSDAtomVisitor::toString(){
   return result;
 }
 
+bool LinearAtomVisitor::isLinearAtom(const string& atomType){
+  vector<string>::iterator strIter;
+  
+  for(strIter = linearAtomType.begin(); strIter != linearAtomType.end(); 
+      ++strIter)
+    if(*strIter == atomType)
+      return true;
+  
+  return false;  
+}
+
+void LinearAtomVisitor::visit(DirectionalAtom* datom){
+
+  vector<AtomInfo*> atoms;
+
+  //we need to convert linear into 4 different atoms
+  double c1[3] = {0.0, 0.0, -1.8};
+  double c2[3] = {0.0, 0.0, -0.6};
+  double c3[3] = {0.0, 0.0,  0.6};
+  double c4[3] = {0.0, 0.0,  1.8};
+  double rotMatrix[3][3];
+  double rotTrans[3][3];
+  AtomInfo* atomInfo;
+  double pos[3];
+  double newVec[3];
+  double q[4];
+  AtomData* atomData;
+  GenericData* data;
+  bool haveAtomData;
+  
+  //if atom is not SSD atom, just skip it
+  if(!isLinearAtom(datom->getType()))
+    return;
+  
+  data = datom->getProperty("ATOMDATA");
+  if(data != NULL){
+
+    atomData = dynamic_cast<AtomData*>(data);  
+    if(atomData == NULL){
+      cerr << "can not get Atom Data from " << datom->getType() << endl;
+      atomData = new AtomData; 
+      haveAtomData = false;      
+    }
+    else
+      haveAtomData = true;
+  }
+  else{
+    atomData = new AtomData;
+    haveAtomData = false;
+  }
+   
+  
+  datom->getPos(pos);
+  datom->getQ(q);
+  datom->getA(rotMatrix);
+
+  // We need A^T to convert from body-fixed to space-fixed:
+  transposeMat3(rotMatrix, rotTrans);
+  
+  matVecMul3(rotTrans, c1, newVec);
+  atomInfo = new AtomInfo;
+  atomInfo->AtomType = "C";
+  atomInfo->pos[0] = pos[0] + newVec[0];
+  atomInfo->pos[1] = pos[1] + newVec[1];
+  atomInfo->pos[2] = pos[2] + newVec[2];
+  atomInfo->dipole[0] = 0.0;
+  atomInfo->dipole[1] = 0.0;
+  atomInfo->dipole[2] = 0.0;
+  atomData->addAtomInfo(atomInfo);
+
+  matVecMul3(rotTrans, c2, newVec);
+  atomInfo = new AtomInfo;
+  atomInfo->AtomType = "C";
+  atomInfo->pos[0] = pos[0] + newVec[0];
+  atomInfo->pos[1] = pos[1] + newVec[1];
+  atomInfo->pos[2] = pos[2] + newVec[2];
+  atomInfo->dipole[0] = 0.0;
+  atomInfo->dipole[1] = 0.0;
+  atomInfo->dipole[2] = 0.0;
+  atomData->addAtomInfo(atomInfo);
+
+  matVecMul3(rotTrans, c3, newVec);
+  atomInfo = new AtomInfo;
+  atomInfo->AtomType = "C";
+  atomInfo->pos[0] = pos[0] + newVec[0];
+  atomInfo->pos[1] = pos[1] + newVec[1];
+  atomInfo->pos[2] = pos[2] + newVec[2];
+  atomInfo->dipole[0] = 0.0;
+  atomInfo->dipole[1] = 0.0;
+  atomInfo->dipole[2] = 0.0;
+  atomData->addAtomInfo(atomInfo);
+
+  matVecMul3(rotTrans, c4, newVec);
+  atomInfo = new AtomInfo;
+  atomInfo->AtomType = "C";
+  atomInfo->pos[0] = pos[0] + newVec[0];
+  atomInfo->pos[1] = pos[1] + newVec[1];
+  atomInfo->pos[2] = pos[2] + newVec[2];
+  atomInfo->dipole[0] = 0.0;
+  atomInfo->dipole[1] = 0.0;
+  atomInfo->dipole[2] = 0.0;
+  atomData->addAtomInfo(atomInfo);
+
+  //add atom data into atom's property
+
+  if(!haveAtomData){
+    atomData->setID("ATOMDATA");
+    datom->addProperty(atomData);
+  }
+
+  setVisited(datom);
+
+}
+
+const string LinearAtomVisitor::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: Convert linear into 4 different atoms\n");
+  result += buffer;
+
+  sprintf(buffer ,"------------------------------------------------------------------\n");
+  result += buffer;
+
+  return result;
+}
+
 //----------------------------------------------------------------------------//
 
 void DefaultAtomVisitor::visit(Atom* atom){