[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 1291 by gezelter, Thu Sep 11 19:40:59 2008 UTC

+  void SSDAtomVisitor::visit(DirectionalAtom *datom) {
+    std::vector<AtomInfo*>atoms;
-<
+    //we need to convert SSD into 4 differnet atoms
-<
+    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
-<
+    //of the water with a dipole moment
->
+    //we need to convert SSD into 4 different atoms
->
+    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of
->
+    //the mass of the water with a dipole moment
+    Vector3d h1(0.0, -0.75695, 0.5206);
+    Vector3d h2(0.0, 0.75695, 0.5206);
+    Vector3d ox(0.0, 0.0, -0.0654);
+    result += buffer;
+    return result;
-+
+  }
-+
-+
-+
+  bool TREDAtomVisitor::isTREDAtom(const std::string&atomType) {
-+
+    std::set<std::string>::iterator strIter;
-+
+    strIter = tredAtomType.find(atomType);
-+
+    return strIter != tredAtomType.end() ? true : false;
-+
+  }
-+
-+
+  void TREDAtomVisitor::visit(DirectionalAtom *datom) {
-+
+    std::vector<AtomInfo*>atoms;
-+
-+
+    // we need to convert a TRED into 4 different atoms:
-+
+    // one oxygen atom, two hydrogen atoms, and one atom which is the center of
-+
+    // the mass of the water with a dipole moment
-+
+    Vector3d h1(0.0, -0.75695, 0.5206);
-+
+    Vector3d h2(0.0, 0.75695, 0.5206);
-+
+    Vector3d ox(0.0, 0.0, -0.0654);
-+
+    Vector3d u(0, 0, 1);
-+
+    RotMat3x3d   rotMatrix;
-+
+    RotMat3x3d   rotTrans;
-+
+    AtomInfo *   atomInfo;
-+
+    Vector3d     pos;
-+
+    Vector3d     newVec;
-+
+    Quat4d       q;
-+
+    AtomData *   atomData;
-+
+    GenericData *data;
-+
+    bool         haveAtomData;
-+
-+
+    // if the atom is not a TRED atom, skip it
-+
+    if (!isTREDAtom(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:
-+
+    // transposeMat3(rotMatrix, rotTrans);
-+
+    rotTrans = rotMatrix.transpose();
-+
-+
+    // center of mass of the water molecule
-+
+    // matVecMul3(rotTrans, u, newVec);
-+
+    newVec = rotTrans * u;
-+
-+
+    atomInfo = new AtomInfo;
-+
+    atomInfo->atomTypeName = "TRED";
-+
+    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);
-+
-+
+    // oxygen
-+
+    // matVecMul3(rotTrans, ox, newVec);
-+
+    newVec = rotTrans * ox;
-+
-+
+    atomInfo = new AtomInfo;
-+
+    atomInfo->atomTypeName = "O";
-+
+    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);
-+
-+
+    // hydrogen1
-+
+    // matVecMul3(rotTrans, h1, newVec);
-+
+    newVec = rotTrans * h1;
-+
+    atomInfo = new AtomInfo;
-+
+    atomInfo->atomTypeName = "H";
-+
+    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);
-+
-+
+    // hydrogen2
-+
+    // matVecMul3(rotTrans, h2, newVec);
-+
+    newVec = rotTrans * h2;
-+
+    atomInfo = new AtomInfo;
-+
+    atomInfo->atomTypeName = "H";
-+
+    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 TREDAtomVisitor::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 the TRED atom into 4 different atoms\n");
-+
+    result += buffer;
-+
-+
+    sprintf(buffer,
-+
+            "------------------------------------------------------------------\n");
-+
+    result += buffer;
-+
-+
+    return result;
-+
+  }
-+
-+
+  bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
+    std::set<std::string>::iterator strIter;
+    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){
+    std::vector<AtomInfo*> atoms;
+    //we need to convert linear into 4 different atoms
+    AtomData* atomData;
+    GenericData* data;
+    bool haveAtomData;
-<
-<
+    //if atom is not SSD atom, just skip it
-<
+    if(!isLinearAtom(datom->getType()))
->
+    //if atom is not linear atom, just skip it
->
+    if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
+      return;
-+
+    //setup GayBerne type in fortran side
-+
+    data = datom->getAtomType()->getPropertyByName("GayBerne");
-+
+    if (data != NULL) {
-+
+       GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
-+
-+
+       if (gayBerneData != NULL) {
-+
+           GayBerneParam gayBerneParam = gayBerneData->getData();
-+
-+
+                          // double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
-+
+                          double halfLen = gayBerneParam.GB_l/2.0;
-+
+                          c1[2] = -halfLen;
-+
+              c2[2] = -halfLen /2;
-+
+              c3[2] = halfLen/2;
-+
+              c4[2] = halfLen;
-+
-+
+            }
-+
-+
+              else {
-+
+                    sprintf( painCave.errMsg,
-+
+                           "Can not cast GenericData to GayBerneParam\n");
-+
+                    painCave.severity = OOPSE_ERROR;
-+
+                    painCave.isFatal = 1;
-+
+                    simError();
-+
+        }
-+
+    }
-+
-+
+    data = datom->getPropertyByName("ATOMDATA");
+    if(data != NULL){
+      atomData = dynamic_cast<AtomData*>(data);
+    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;
-+
+    Vector3d c1(0.0, 0.0, 0.0);
-+
+    Vector3d c2(0.0, 0.0, 1.0);
-+
+    RotMat3x3d rotMatrix;
-+
+    RotMat3x3d rotTrans;
-+
+    AtomInfo* atomInfo;
-+
+    Vector3d pos;
-+
+    Vector3d newVec;
-+
+    Vector3d dVec;
-+
+    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;
-+
+    dVec = rotTrans * c2;
-+
+    atomInfo = new AtomInfo;
-+
+    atomInfo->atomTypeName = "GB";
-+
+    atomInfo->pos[0] = pos[0] + newVec[0];
-+
+    atomInfo->pos[1] = pos[1] + newVec[1];
-+
+    atomInfo->pos[2] = pos[2] + newVec[2];
-+
+    atomInfo->dipole[0] = dVec[0];
-+
+    atomInfo->dipole[1] = dVec[1];
-+
+    atomInfo->dipole[2] = dVec[2];
-+
+    atomInfo->hasVector = true;
-+
+    atomInfo->charge = 3.0;
-+
+    atomInfo->hasCharge = true;
-+
+    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 xyz-formatted atom for use with xyz2pov\n");
-+
+    result += buffer;
-+
-+
+    sprintf(buffer ,"------------------------------------------------------------------\n");
-+
+    result += buffer;
-+
-+
+    return result;
-+
+  }
-+
-+
+  bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
-+
+    std::set<std::string>::iterator strIter;
-+
+    strIter = Ring5gbAtomType.find(atomType);
-+
-+
+    return strIter != Ring5gbAtomType.end() ? true : false;
-+
+  }
-+
-+
+  void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
-+
+    std::vector<AtomInfo*> atoms;
-+
+    //we need to convert linear into 4 different atoms
-+
+    Vector3d c1(0.0, 0.0, -5.5);
-+
+    Vector3d c2(0.0, 0.0, -1.8);
-+
+    Vector3d c3(0.0, 0.0,  1.8);
-+
+    Vector3d c4(0.0, 0.0,  5.5);
-+
+    RotMat3x3d rotMatrix;
-+
+    RotMat3x3d rotTrans;
-+
+    AtomInfo* atomInfo;
-+
+    Vector3d pos;
-+
+    Vector3d newVec;
-+
+    Vector3d dVec;
-+
+    Quat4d q;
-+
+    AtomData* atomData;
-+
+    GenericData* data;
-+
+    bool haveAtomData;
-+
-+
+    //if atom is not Ring5GB atom, just skip it
-+
+    if(!isRing5gbAtom(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 Ring5gbAtomVisitor::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 Ring5GB into 4 different K atoms\n");
-+
+    result += buffer;
-+
-+
+    sprintf(buffer ,"------------------------------------------------------------------\n");
-+
+    result += buffer;
-+
-+
+    return result;
-+
+  }
-+
-+
+  bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
-+
+    std::set<std::string>::iterator strIter;
-+
+    strIter = HeadAtomType.find(atomType);
-+
-+
+    return strIter != HeadAtomType.end() ? true : false;
-+
+  }
-+
-+
+  void HeadAtomVisitor::visit(DirectionalAtom* datom){
-+
+    std::vector<AtomInfo*> atoms;
-+
+    //we need to convert linear into 2 different atoms
-+
+    Vector3d c1(0.0, 0.0, -1.5);
-+
+    Vector3d c2(0.0, 0.0, 1.5);
-+
+    RotMat3x3d rotMatrix;
-+
+    RotMat3x3d rotTrans;
-+
+    AtomInfo* atomInfo;
-+
+    Vector3d pos;
-+
+    Vector3d newVec;
-+
+    Vector3d dVec;
-+
+    Quat4d q;
-+
+    AtomData* atomData;
-+
+    GenericData* data;
-+
+    bool haveAtomData;
-+
-+
+    //if atom is not Head atom, just skip it
-+
+    if(!isHeadAtom(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 = "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);
-+
-+
+    newVec = rotTrans * c2;
-+
+    atomInfo = new AtomInfo;
-+
+    atomInfo->atomTypeName = "O";
-+
+    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 HeadAtomVisitor::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 HEAD into C atom and O atom\n");
-+
+    result += buffer;
-+
-+
+    sprintf(buffer ,"------------------------------------------------------------------\n");
-+
+    result += buffer;
-+
-+
+    return result;
-+
+  }
-+
-+
+  //----------------------------------------------------------------------------//
+  void DefaultAtomVisitor::visit(Atom *atom) {
+      return;
+    pos = datom->getPos();
-<
+    u = datom->getElectroFrame().getColumn(2);
-<
->
+    if (datom->getAtomType()->isGayBerne()) {
->
+        u = datom->getA().transpose()*V3Z;
->
+    } else if (datom->getAtomType()->isMultipole()) {
->
+        u = datom->getElectroFrame().getColumn(2);
->
+    }
+    atomData = new AtomData;
+    atomData->setID("ATOMDATA");
+    atomInfo = new AtomInfo;

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/src/visitors/AtomVisitor.cpp (file contents): Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs. Revision 1291 by gezelter, Thu Sep 11 19:40:59 2008 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 1291 by gezelter, Thu Sep 11 19:40:59 2008 UTC