[ViewVC] Diff of: OpenMD/branches/development/src/visitors/AtomVisitor.cpp

Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 954 by tim, Wed May 10 01:44:48 2006 UTC

+    strIter = linearAtomType.find(atomType);
+    return strIter != linearAtomType.end() ? true : false;
-+
+  }
-+
-+
+  void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
-+
+   linearAtomType.insert(atomType);
+  void LinearAtomVisitor::visit(DirectionalAtom* datom){
+    result += buffer;
+    return result;
-+
+  }
-+
-+
+  bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
-+
+    std::set<std::string>::iterator strIter;
-+
+    strIter = GBLipidAtomType.find(atomType);
-+
-+
+    return strIter != GBLipidAtomType.end() ? true : false;
-+
-+
+  void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
-+
+    std::vector<AtomInfo*> atoms;
-+
+    //we need to convert linear into 4 different atoms
-+
+    Vector3d c1(0.0, 0.0, -6.25);
-+
+    Vector3d c2(0.0, 0.0, -2.1);
-+
+    Vector3d c3(0.0, 0.0,  2.1);
-+
+    Vector3d c4(0.0, 0.0,  6.25);
-+
+    RotMat3x3d rotMatrix;
-+
+    RotMat3x3d rotTrans;
-+
+    AtomInfo* atomInfo;
-+
+    Vector3d pos;
-+
+    Vector3d newVec;
-+
+    Quat4d q;
-+
+    AtomData* atomData;
-+
+    GenericData* data;
-+
+    bool haveAtomData;
-+
-+
+    //if atom is not GBlipid atom, just skip it
-+
+    if(!isGBLipidAtom(datom->getType()))
-+
+      return;
-+
-+
+    data = datom->getPropertyByName("ATOMDATA");
-+
+    if(data != NULL){
-+
+      atomData = dynamic_cast<AtomData*>(data);
-+
+      if(atomData == NULL){
-+
+        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
-+
+        atomData = new AtomData;
-+
+        haveAtomData = false;
-+
+      } else {
-+
+        haveAtomData = true;
-+
+      }
-+
+    } else {
-+
+      atomData = new AtomData;
-+
+      haveAtomData = false;
-+
+    }
-+
-+
-+
+    pos = datom->getPos();
-+
+    q = datom->getQ();
-+
+    rotMatrix = datom->getA();
-+
+    // We need A^T to convert from body-fixed to space-fixed:
-+
+    rotTrans = rotMatrix.transpose();
-+
-+
+    newVec = rotTrans * c1;
-+
+    atomInfo = new AtomInfo;
-+
+    atomInfo->atomTypeName = "K";
-+
+    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);
-+
-+
+    newVec = rotTrans * c2;
-+
+    atomInfo = new AtomInfo;
-+
+    atomInfo->atomTypeName = "K";
-+
+    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);
-+
-+
+    newVec = rotTrans * c3;
-+
+    atomInfo = new AtomInfo;
-+
+    atomInfo->atomTypeName = "K";
-+
+    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);
-+
-+
+    newVec = rotTrans * c4;
-+
+    atomInfo = new AtomInfo;
-+
+    atomInfo->atomTypeName = "K";
-+
+    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 std::string GBLipidAtomVisitor::toString(){
-+
+    char buffer[65535];
-+
+    std::string result;
-+
-+
+    sprintf(buffer ,"------------------------------------------------------------------\n");
-+
+    result += buffer;
-+
-+
+    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
-+
+    result += buffer;
-+
-+
+    sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
-+
+    result += buffer;
-+
-+
+    sprintf(buffer ,"------------------------------------------------------------------\n");
-+
+    result += buffer;
-+
-+
+    return result;
-+
+  }
-+
+  //----------------------------------------------------------------------------//
+  void DefaultAtomVisitor::visit(Atom *atom) {

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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents): Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs. Revision 954 by tim, Wed May 10 01:44:48 2006 UTC

Diff Legend

Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 954 by tim, Wed May 10 01:44:48 2006 UTC