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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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|
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namespace oopse { |
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|
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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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|
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//myAtoms = rb->getAtoms(); |
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|
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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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|
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void BaseAtomVisitor::setVisited(Atom* atom){ |
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GenericData* data; |
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data = atom->getProperty("VISITED"); |
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|
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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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|
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bool BaseAtomVisitor::isVisited(Atom* atom){ |
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GenericData* data; |
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data = atom->getProperty("VISITED"); |
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return data == NULL ? false : true; |
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} |
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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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|
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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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|
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return false; |
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} |
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|
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void SSDAtomVisitor::visit(DirectionalAtom* datom){ |
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|
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vector<AtomInfo*> atoms; |
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|
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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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double h1[3] = {0.0, -0.75695, 0.5206}; |
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double h2[3] = {0.0, 0.75695, 0.5206}; |
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double ox[3] = {0.0, 0.0, -0.0654}; |
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double u[3] = {0, 0, 1}; |
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double rotMatrix[3][3]; |
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double rotTrans[3][3]; |
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AtomInfo* atomInfo; |
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double pos[3]; |
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double newVec[3]; |
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double q[4]; |
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AtomData* atomData; |
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GenericData* data; |
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bool haveAtomData; |
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|
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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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|
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data = datom->getProperty("ATOMDATA"); |
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if(data != NULL){ |
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|
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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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|
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|
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datom->getPos(pos); |
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datom->getQ(q); |
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datom->getA(rotMatrix); |
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|
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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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|
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//center of mass of the water molecule |
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matVecMul3(rotTrans, u, newVec); |
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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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|
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atomData->addAtomInfo(atomInfo); |
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|
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//oxygen |
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matVecMul3(rotTrans, ox, newVec); |
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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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|
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|
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//hydrogen1 |
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matVecMul3(rotTrans, h1, newVec); |
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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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|
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//hydrogen2 |
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matVecMul3(rotTrans, h2, newVec); |
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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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|
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//add atom data into atom's property |
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|
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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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|
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setVisited(datom); |
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|
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} |
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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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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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|
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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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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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return result; |
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} |
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|
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bool LinearAtomVisitor::isLinearAtom(const string& atomType){ |
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vector<string>::iterator strIter; |
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|
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for(strIter = linearAtomType.begin(); strIter != linearAtomType.end(); |
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++strIter) |
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if(*strIter == atomType) |
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return true; |
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|
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return false; |
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} |
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|
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void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
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|
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vector<AtomInfo*> atoms; |
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|
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//we need to convert linear into 4 different atoms |
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double c1[3] = {0.0, 0.0, -1.8}; |
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double c2[3] = {0.0, 0.0, -0.6}; |
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double c3[3] = {0.0, 0.0, 0.6}; |
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double c4[3] = {0.0, 0.0, 1.8}; |
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double rotMatrix[3][3]; |
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double rotTrans[3][3]; |
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AtomInfo* atomInfo; |
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double pos[3]; |
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double newVec[3]; |
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double q[4]; |
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AtomData* atomData; |
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GenericData* data; |
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bool haveAtomData; |
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|
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//if atom is not SSD atom, just skip it |
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if(!isLinearAtom(datom->getType())) |
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return; |
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|
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data = datom->getProperty("ATOMDATA"); |
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if(data != NULL){ |
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|
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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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|
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|
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datom->getPos(pos); |
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datom->getQ(q); |
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datom->getA(rotMatrix); |
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|
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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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|
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matVecMul3(rotTrans, c1, newVec); |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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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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|
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matVecMul3(rotTrans, c2, newVec); |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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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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|
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matVecMul3(rotTrans, c3, newVec); |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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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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|
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matVecMul3(rotTrans, c4, newVec); |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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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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|
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//add atom data into atom's property |
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|
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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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|
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setVisited(datom); |
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|
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} |
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|
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const string LinearAtomVisitor::toString(){ |
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char buffer[65535]; |
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string result; |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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|
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sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
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result += buffer; |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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return result; |
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} |
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|
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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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double pos[3]; |
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|
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if(isVisited(atom)) |
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return; |
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|
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atomInfo =new AtomInfo; |
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|
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atomData = new AtomData; |
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atomData->setID("ATOMDATA"); |
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|
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atom->getPos(pos); |
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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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|
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|
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atomData->addAtomInfo(atomInfo); |
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|
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atom->addProperty(atomData); |
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|
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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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double pos[3]; |
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double u[3]; |
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|
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if(isVisited(datom)) |
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return; |
| 349 |
|
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datom->getPos(pos); |
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datom->getU(u); |
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|
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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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|
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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]; |
| 363 |
atomInfo->dipole[2] = u[2]; |
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|
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atomData->addAtomInfo(atomInfo); |
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|
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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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|
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|
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const string DefaultAtomVisitor::toString(){ |
| 374 |
char buffer[65535]; |
| 375 |
string result; |
| 376 |
|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 378 |
result += buffer; |
| 379 |
|
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 381 |
result += buffer; |
| 382 |
|
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sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n"); |
| 384 |
result += buffer; |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
| 388 |
|
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return result; |
| 390 |
} |
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|
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}//namespace oopse |
