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tim |
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#include <cstring>
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#include "visitors/AtomVisitor.hpp"
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#include "primitives/DirectionalAtom.hpp"
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#include "math/MatVec3.h"
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#include "primitives/RigidBody.hpp"
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namespace oopse {
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void BaseAtomVisitor::visit(RigidBody* rb){
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//vector<Atom*> myAtoms;
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//vector<Atom*>::iterator atomIter;
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//myAtoms = rb->getAtoms();
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//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
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// (*atomIter)->accept(this);
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}
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void BaseAtomVisitor::setVisited(Atom* atom){
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GenericData* data;
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data = atom->getPropertyByName("VISITED");
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tim |
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//if visited property is not existed, add it as new property
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if(data == NULL){
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data = new GenericData();
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data->setID("VISITED");
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atom->addProperty(data);
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}
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}
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bool BaseAtomVisitor::isVisited(Atom* atom){
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GenericData* data;
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data = atom->getPropertyByName("VISITED");
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return data == NULL ? false : true;
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}
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bool SSDAtomVisitor::isSSDAtom(const string& atomType){
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vector<string>::iterator strIter;
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for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter)
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if(*strIter == atomType)
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return true;
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return false;
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}
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void SSDAtomVisitor::visit(DirectionalAtom* datom){
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vector<AtomInfo*> atoms;
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//we need to convert SSD into 4 differnet atoms
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//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
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//of the water with a dipole moment
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Vector3d h1(0.0, -0.75695, 0.5206);
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Vector3d h2(0.0, 0.75695, 0.5206);
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Vector3d ox(0.0, 0.0, -0.0654);
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Vector3d u(0, 0, 1);
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RotMat3x3d rotMatrix;
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RotMat3x3d rotTrans;
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AtomInfo* atomInfo;
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Vector3d pos;
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Vector3d newVec;
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Quat4d q;
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AtomData* atomData;
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GenericData* data;
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bool haveAtomData;
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//if atom is not SSD atom, just skip it
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if(!isSSDAtom(datom->getType()))
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return;
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data = datom->getPropertyByName("ATOMDATA");
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if(data != NULL){
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atomData = dynamic_cast<AtomData*>(data);
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if(atomData == NULL){
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cerr << "can not get Atom Data from " << datom->getType() << endl;
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atomData = new AtomData;
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haveAtomData = false;
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}
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else
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haveAtomData = true;
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}
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else{
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atomData = new AtomData;
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haveAtomData = false;
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}
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pos = datom->getPos();
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q = datom->getQ();
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rotMatrix= datom->getA();
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// We need A^T to convert from body-fixed to space-fixed:
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//transposeMat3(rotMatrix, rotTrans);
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rotTrans = rotMatrix.transpose();
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//center of mass of the water molecule
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//matVecMul3(rotTrans, u, newVec);
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newVec = rotTrans * u;
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atomInfo = new AtomInfo;
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atomInfo->AtomType = "X";
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atomInfo->pos[0] = pos[0];
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atomInfo->pos[1] = pos[1];
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atomInfo->pos[2] = pos[2];
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atomInfo->dipole[0] = newVec[0];
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atomInfo->dipole[1] = newVec[1];
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atomInfo->dipole[2] = newVec[2];
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atomData->addAtomInfo(atomInfo);
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//oxygen
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//matVecMul3(rotTrans, ox, newVec);
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newVec = rotTrans * ox;
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atomInfo = new AtomInfo;
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atomInfo->AtomType = "O";
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atomInfo->pos[0] = pos[0] + newVec[0];
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atomInfo->pos[1] = pos[1] + newVec[1];
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atomInfo->pos[2] = pos[2] + newVec[2];
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atomInfo->dipole[0] = 0.0;
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atomInfo->dipole[1] = 0.0;
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atomInfo->dipole[2] = 0.0;
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atomData->addAtomInfo(atomInfo);
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//hydrogen1
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//matVecMul3(rotTrans, h1, newVec);
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newVec = rotTrans * h1;
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atomInfo = new AtomInfo;
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atomInfo->AtomType = "H";
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atomInfo->pos[0] = pos[0] + newVec[0];
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atomInfo->pos[1] = pos[1] + newVec[1];
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atomInfo->pos[2] = pos[2] + newVec[2];
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atomInfo->dipole[0] = 0.0;
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atomInfo->dipole[1] = 0.0;
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atomInfo->dipole[2] = 0.0;
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atomData->addAtomInfo(atomInfo);
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//hydrogen2
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//matVecMul3(rotTrans, h2, newVec);
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newVec = rotTrans * h2;
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atomInfo = new AtomInfo;
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atomInfo->AtomType = "H";
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atomInfo->pos[0] = pos[0] + newVec[0];
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atomInfo->pos[1] = pos[1] + newVec[1];
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atomInfo->pos[2] = pos[2] + newVec[2];
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atomInfo->dipole[0] = 0.0;
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atomInfo->dipole[1] = 0.0;
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atomInfo->dipole[2] = 0.0;
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atomData->addAtomInfo(atomInfo);
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//add atom data into atom's property
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if(!haveAtomData){
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atomData->setID("ATOMDATA");
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datom->addProperty(atomData);
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}
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setVisited(datom);
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}
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const string SSDAtomVisitor::toString(){
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char buffer[65535];
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string result;
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sprintf(buffer ,"------------------------------------------------------------------\n");
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result += buffer;
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
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result += buffer;
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sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
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result += buffer;
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sprintf(buffer ,"------------------------------------------------------------------\n");
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result += buffer;
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return result;
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}
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//----------------------------------------------------------------------------//
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void DefaultAtomVisitor::visit(Atom* atom){
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AtomData* atomData;
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AtomInfo* atomInfo;
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Vector3d pos;
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if(isVisited(atom))
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return;
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atomInfo =new AtomInfo;
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atomData = new AtomData;
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atomData->setID("ATOMDATA");
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pos = atom->getPos();
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atomInfo->AtomType = atom->getType();
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atomInfo->pos[0] = pos[0];
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atomInfo->pos[1] = pos[1];
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atomInfo->pos[2] = pos[2];
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atomInfo->dipole[0] = 0.0;
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atomInfo->dipole[1] = 0.0;
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atomInfo->dipole[2] = 0.0;
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atomData->addAtomInfo(atomInfo);
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atom->addProperty(atomData);
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setVisited(atom);
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}
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void DefaultAtomVisitor::visit(DirectionalAtom* datom){
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AtomData* atomData;
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AtomInfo* atomInfo;
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Vector3d pos;
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Vector3d u;
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if(isVisited(datom))
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return;
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pos = datom->getPos();
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u = datom->getUnitVector();
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atomData = new AtomData;
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atomData->setID("ATOMDATA");
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atomInfo =new AtomInfo;
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atomInfo->AtomType = datom->getType();
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atomInfo->pos[0] = pos[0];
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atomInfo->pos[1] = pos[1];
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atomInfo->pos[2] = pos[2];
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atomInfo->dipole[0] = u[0];
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atomInfo->dipole[1] = u[1];
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atomInfo->dipole[2] = u[2];
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atomData->addAtomInfo(atomInfo);
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datom->addProperty(atomData);
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setVisited(datom);
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}
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const string DefaultAtomVisitor::toString(){
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char buffer[65535];
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string result;
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sprintf(buffer ,"------------------------------------------------------------------\n");
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result += buffer;
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
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result += buffer;
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sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
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result += buffer;
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sprintf(buffer ,"------------------------------------------------------------------\n");
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result += buffer;
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return result;
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}
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}//namespace oopse
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