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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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//----------------------------------------------------------------------------// |
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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]; |
183 |
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|
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if(isVisited(atom)) |
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return; |
186 |
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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; |
200 |
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|
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|
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atomData->addAtomInfo(atomInfo); |
203 |
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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]; |
212 |
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double u[3]; |
213 |
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|
214 |
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if(isVisited(datom)) |
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return; |
216 |
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|
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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]; |
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atomInfo->dipole[2] = u[2]; |
231 |
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|
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atomData->addAtomInfo(atomInfo); |
233 |
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|
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datom->addProperty(atomData); |
235 |
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|
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setVisited(datom); |
237 |
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} |
238 |
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|
239 |
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|
240 |
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const string DefaultAtomVisitor::toString(){ |
241 |
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char buffer[65535]; |
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string result; |
243 |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
245 |
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result += buffer; |
246 |
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|
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
249 |
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|
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sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n"); |
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result += buffer; |
252 |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
254 |
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result += buffer; |
255 |
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|
256 |
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return result; |
257 |
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} |
258 |
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|
259 |
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}//namespace oopse |
1 |
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#include <cstring> |
2 |
> |
#include "visitors/AtomVisitor.hpp" |
3 |
> |
#include "primitives/DirectionalAtom.hpp" |
4 |
> |
#include "math/MatVec3.h" |
5 |
> |
#include "primitives/RigidBody.hpp" |
6 |
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|
7 |
> |
namespace oopse { |
8 |
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|
9 |
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void BaseAtomVisitor::visit(RigidBody* rb){ |
10 |
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//vector<Atom*> myAtoms; |
11 |
> |
//vector<Atom*>::iterator atomIter; |
12 |
> |
|
13 |
> |
//myAtoms = rb->getAtoms(); |
14 |
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|
15 |
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//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
16 |
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// (*atomIter)->accept(this); |
17 |
> |
} |
18 |
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|
19 |
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void BaseAtomVisitor::setVisited(Atom* atom){ |
20 |
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GenericData* data; |
21 |
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data = atom->getProperty("VISITED"); |
22 |
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|
23 |
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//if visited property is not existed, add it as new property |
24 |
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if(data == NULL){ |
25 |
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data = new GenericData(); |
26 |
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data->setID("VISITED"); |
27 |
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atom->addProperty(data); |
28 |
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} |
29 |
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} |
30 |
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|
31 |
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bool BaseAtomVisitor::isVisited(Atom* atom){ |
32 |
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GenericData* data; |
33 |
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data = atom->getProperty("VISITED"); |
34 |
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return data == NULL ? false : true; |
35 |
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} |
36 |
> |
|
37 |
> |
bool SSDAtomVisitor::isSSDAtom(const string& atomType){ |
38 |
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vector<string>::iterator strIter; |
39 |
> |
|
40 |
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for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter) |
41 |
> |
if(*strIter == atomType) |
42 |
> |
return true; |
43 |
> |
|
44 |
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return false; |
45 |
> |
} |
46 |
> |
|
47 |
> |
void SSDAtomVisitor::visit(DirectionalAtom* datom){ |
48 |
> |
|
49 |
> |
vector<AtomInfo*> atoms; |
50 |
> |
|
51 |
> |
//we need to convert SSD into 4 differnet atoms |
52 |
> |
//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass |
53 |
> |
//of the water with a dipole moment |
54 |
> |
Vector3d h1(0.0, -0.75695, 0.5206); |
55 |
> |
Vector3d h2(0.0, 0.75695, 0.5206); |
56 |
> |
Vector3d ox(0.0, 0.0, -0.0654); |
57 |
> |
Vector3d u(0, 0, 1); |
58 |
> |
double rotMatrix[3][3]; |
59 |
> |
double rotTrans[3][3]; |
60 |
> |
AtomInfo* atomInfo; |
61 |
> |
Vector3d pos; |
62 |
> |
Vector3d newVec; |
63 |
> |
Quat4d q; |
64 |
> |
AtomData* atomData; |
65 |
> |
GenericData* data; |
66 |
> |
bool haveAtomData; |
67 |
> |
|
68 |
> |
//if atom is not SSD atom, just skip it |
69 |
> |
if(!isSSDAtom(datom->getType())) |
70 |
> |
return; |
71 |
> |
|
72 |
> |
data = datom->getProperty("ATOMDATA"); |
73 |
> |
if(data != NULL){ |
74 |
> |
|
75 |
> |
atomData = dynamic_cast<AtomData*>(data); |
76 |
> |
if(atomData == NULL){ |
77 |
> |
cerr << "can not get Atom Data from " << datom->getType() << endl; |
78 |
> |
atomData = new AtomData; |
79 |
> |
haveAtomData = false; |
80 |
> |
} |
81 |
> |
else |
82 |
> |
haveAtomData = true; |
83 |
> |
} |
84 |
> |
else{ |
85 |
> |
atomData = new AtomData; |
86 |
> |
haveAtomData = false; |
87 |
> |
} |
88 |
> |
|
89 |
> |
|
90 |
> |
pos = datom->getPos(); |
91 |
> |
q = datom->getQ(); |
92 |
> |
datom->getA(rotMatrix); |
93 |
> |
|
94 |
> |
// We need A^T to convert from body-fixed to space-fixed: |
95 |
> |
transposeMat3(rotMatrix, rotTrans); |
96 |
> |
|
97 |
> |
//center of mass of the water molecule |
98 |
> |
matVecMul3(rotTrans, u, newVec); |
99 |
> |
atomInfo = new AtomInfo; |
100 |
> |
atomInfo->AtomType = "X"; |
101 |
> |
atomInfo->pos[0] = pos[0]; |
102 |
> |
atomInfo->pos[1] = pos[1]; |
103 |
> |
atomInfo->pos[2] = pos[2]; |
104 |
> |
atomInfo->dipole[0] = newVec[0]; |
105 |
> |
atomInfo->dipole[1] = newVec[1]; |
106 |
> |
atomInfo->dipole[2] = newVec[2]; |
107 |
> |
|
108 |
> |
atomData->addAtomInfo(atomInfo); |
109 |
> |
|
110 |
> |
//oxygen |
111 |
> |
matVecMul3(rotTrans, ox, newVec); |
112 |
> |
atomInfo = new AtomInfo; |
113 |
> |
atomInfo->AtomType = "O"; |
114 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
115 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
116 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
117 |
> |
atomInfo->dipole[0] = 0.0; |
118 |
> |
atomInfo->dipole[1] = 0.0; |
119 |
> |
atomInfo->dipole[2] = 0.0; |
120 |
> |
atomData->addAtomInfo(atomInfo); |
121 |
> |
|
122 |
> |
|
123 |
> |
//hydrogen1 |
124 |
> |
matVecMul3(rotTrans, h1, newVec); |
125 |
> |
atomInfo = new AtomInfo; |
126 |
> |
atomInfo->AtomType = "H"; |
127 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
128 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
129 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
130 |
> |
atomInfo->dipole[0] = 0.0; |
131 |
> |
atomInfo->dipole[1] = 0.0; |
132 |
> |
atomInfo->dipole[2] = 0.0; |
133 |
> |
atomData->addAtomInfo(atomInfo); |
134 |
> |
|
135 |
> |
//hydrogen2 |
136 |
> |
matVecMul3(rotTrans, h2, newVec); |
137 |
> |
atomInfo = new AtomInfo; |
138 |
> |
atomInfo->AtomType = "H"; |
139 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
140 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
141 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
142 |
> |
atomInfo->dipole[0] = 0.0; |
143 |
> |
atomInfo->dipole[1] = 0.0; |
144 |
> |
atomInfo->dipole[2] = 0.0; |
145 |
> |
atomData->addAtomInfo(atomInfo); |
146 |
> |
|
147 |
> |
//add atom data into atom's property |
148 |
> |
|
149 |
> |
if(!haveAtomData){ |
150 |
> |
atomData->setID("ATOMDATA"); |
151 |
> |
datom->addProperty(atomData); |
152 |
> |
} |
153 |
> |
|
154 |
> |
setVisited(datom); |
155 |
> |
|
156 |
> |
} |
157 |
> |
|
158 |
> |
const string SSDAtomVisitor::toString(){ |
159 |
> |
char buffer[65535]; |
160 |
> |
string result; |
161 |
> |
|
162 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
163 |
> |
result += buffer; |
164 |
> |
|
165 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
166 |
> |
result += buffer; |
167 |
> |
|
168 |
> |
sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n"); |
169 |
> |
result += buffer; |
170 |
> |
|
171 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
172 |
> |
result += buffer; |
173 |
> |
|
174 |
> |
return result; |
175 |
> |
} |
176 |
> |
|
177 |
> |
//----------------------------------------------------------------------------// |
178 |
> |
|
179 |
> |
void DefaultAtomVisitor::visit(Atom* atom){ |
180 |
> |
AtomData* atomData; |
181 |
> |
AtomInfo* atomInfo; |
182 |
> |
double pos[3]; |
183 |
> |
|
184 |
> |
if(isVisited(atom)) |
185 |
> |
return; |
186 |
> |
|
187 |
> |
atomInfo =new AtomInfo; |
188 |
> |
|
189 |
> |
atomData = new AtomData; |
190 |
> |
atomData->setID("ATOMDATA"); |
191 |
> |
|
192 |
> |
pos = atom->getPos(); |
193 |
> |
atomInfo->AtomType = atom->getType(); |
194 |
> |
atomInfo->pos[0] = pos[0]; |
195 |
> |
atomInfo->pos[1] = pos[1]; |
196 |
> |
atomInfo->pos[2] = pos[2]; |
197 |
> |
atomInfo->dipole[0] = 0.0; |
198 |
> |
atomInfo->dipole[1] = 0.0; |
199 |
> |
atomInfo->dipole[2] = 0.0; |
200 |
> |
|
201 |
> |
|
202 |
> |
atomData->addAtomInfo(atomInfo); |
203 |
> |
|
204 |
> |
atom->addProperty(atomData); |
205 |
> |
|
206 |
> |
setVisited(atom); |
207 |
> |
} |
208 |
> |
void DefaultAtomVisitor::visit(DirectionalAtom* datom){ |
209 |
> |
AtomData* atomData; |
210 |
> |
AtomInfo* atomInfo; |
211 |
> |
double pos[3]; |
212 |
> |
double u[3]; |
213 |
> |
|
214 |
> |
if(isVisited(datom)) |
215 |
> |
return; |
216 |
> |
|
217 |
> |
pos = datom->getPos(); |
218 |
> |
u = datom->getU(); |
219 |
> |
|
220 |
> |
atomData = new AtomData; |
221 |
> |
atomData->setID("ATOMDATA"); |
222 |
> |
atomInfo =new AtomInfo; |
223 |
> |
|
224 |
> |
atomInfo->AtomType = datom->getType(); |
225 |
> |
atomInfo->pos[0] = pos[0]; |
226 |
> |
atomInfo->pos[1] = pos[1]; |
227 |
> |
atomInfo->pos[2] = pos[2]; |
228 |
> |
atomInfo->dipole[0] = u[0]; |
229 |
> |
atomInfo->dipole[1] = u[1]; |
230 |
> |
atomInfo->dipole[2] = u[2]; |
231 |
> |
|
232 |
> |
atomData->addAtomInfo(atomInfo); |
233 |
> |
|
234 |
> |
datom->addProperty(atomData); |
235 |
> |
|
236 |
> |
setVisited(datom); |
237 |
> |
} |
238 |
> |
|
239 |
> |
|
240 |
> |
const string DefaultAtomVisitor::toString(){ |
241 |
> |
char buffer[65535]; |
242 |
> |
string result; |
243 |
> |
|
244 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
245 |
> |
result += buffer; |
246 |
> |
|
247 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
248 |
> |
result += buffer; |
249 |
> |
|
250 |
> |
sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n"); |
251 |
> |
result += buffer; |
252 |
> |
|
253 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
254 |
> |
result += buffer; |
255 |
> |
|
256 |
> |
return result; |
257 |
> |
} |
258 |
> |
|
259 |
> |
}//namespace oopse |