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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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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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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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//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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//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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void BaseAtomVisitor::setVisited(Atom *atom) { |
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GenericData *data; |
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data = atom->getPropertyByName("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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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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|
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bool BaseAtomVisitor::isVisited(Atom *atom) { |
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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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} |
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|
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bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) { |
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bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) { |
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std::set<std::string>::iterator strIter; |
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strIter = ssdAtomType.find(atomType); |
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return strIter != ssdAtomType.end() ? true : false; |
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} |
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} |
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|
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void SSDAtomVisitor::visit(DirectionalAtom *datom) { |
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void SSDAtomVisitor::visit(DirectionalAtom *datom) { |
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std::vector<AtomInfo*>atoms; |
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|
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//we need to convert SSD into 4 differnet atoms |
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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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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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atomData = dynamic_cast<AtomData *>(data); |
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|
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if (atomData == NULL) { |
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std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} else |
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haveAtomData = true; |
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if (atomData == NULL) { |
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std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} else |
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haveAtomData = true; |
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} else { |
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atomData = new AtomData; |
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haveAtomData = false; |
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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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//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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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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} |
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|
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const std::string SSDAtomVisitor::toString() { |
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const std::string SSDAtomVisitor::toString() { |
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char buffer[65535]; |
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std::string result; |
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result += buffer; |
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return result; |
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} |
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} |
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|
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bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){ |
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bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){ |
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std::set<std::string>::iterator strIter; |
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strIter = linearAtomType.find(atomType); |
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return strIter != linearAtomType.end() ? true : false; |
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} |
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} |
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|
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void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
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void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){ |
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linearAtomType.insert(atomType); |
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} |
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|
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void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
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std::vector<AtomInfo*> atoms; |
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//we need to convert linear into 4 different atoms |
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Vector3d c1(0.0, 0.0, -1.8); |
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AtomData* atomData; |
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GenericData* data; |
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bool haveAtomData; |
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AtomType* atomType; |
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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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if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne()) |
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return; |
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|
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//setup GayBerne type in fortran side |
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data = datom->getAtomType()->getPropertyByName("GayBerne"); |
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if (data != NULL) { |
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GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data); |
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if (gayBerneData != NULL) { |
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GayBerneParam gayBerneParam = gayBerneData->getData(); |
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|
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// double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0; |
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double halfLen = gayBerneParam.GB_l/2.0; |
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c1[2] = -halfLen; |
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c2[2] = -halfLen /2; |
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c3[2] = halfLen/2; |
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c4[2] = halfLen; |
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|
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} |
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|
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else { |
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sprintf( painCave.errMsg, |
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"Can not cast GenericData to GayBerneParam\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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|
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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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std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} else { |
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haveAtomData = true; |
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} |
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atomData = dynamic_cast<AtomData*>(data); |
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if(atomData == NULL){ |
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std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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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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atomData = new AtomData; |
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haveAtomData = false; |
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} |
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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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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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} |
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} |
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|
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const std::string LinearAtomVisitor::toString(){ |
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char buffer[65535]; |
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std::string result; |
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const std::string LinearAtomVisitor::toString(){ |
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char buffer[65535]; |
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std::string result; |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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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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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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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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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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return result; |
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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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bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){ |
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std::set<std::string>::iterator strIter; |
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strIter = GBLipidAtomType.find(atomType); |
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|
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void DefaultAtomVisitor::visit(Atom *atom) { |
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return strIter != GBLipidAtomType.end() ? true : false; |
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} |
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|
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void GBLipidAtomVisitor::visit(DirectionalAtom* datom){ |
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std::vector<AtomInfo*> atoms; |
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//we need to convert linear into 4 different atoms |
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Vector3d c1(0.0, 0.0, -6.25); |
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Vector3d c2(0.0, 0.0, -2.1); |
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Vector3d c3(0.0, 0.0, 2.1); |
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Vector3d c4(0.0, 0.0, 6.25); |
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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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|
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//if atom is not GBlipid atom, just skip it |
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if(!isGBLipidAtom(datom->getType())) |
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return; |
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|
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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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std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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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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pos = datom->getPos(); |
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q = datom->getQ(); |
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rotMatrix = datom->getA(); |
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|
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// We need A^T to convert from body-fixed to space-fixed: |
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rotTrans = rotMatrix.transpose(); |
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> |
|
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newVec = rotTrans * c1; |
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atomInfo = new AtomInfo; |
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> |
atomInfo->atomTypeName = "K"; |
| 427 |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
| 428 |
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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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newVec = rotTrans * c2; |
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atomInfo = new AtomInfo; |
| 437 |
> |
atomInfo->atomTypeName = "K"; |
| 438 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 439 |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
| 440 |
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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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> |
|
| 446 |
> |
newVec = rotTrans * c3; |
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atomInfo = new AtomInfo; |
| 448 |
> |
atomInfo->atomTypeName = "K"; |
| 449 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 450 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 451 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 452 |
> |
atomInfo->dipole[0] = 0.0; |
| 453 |
> |
atomInfo->dipole[1] = 0.0; |
| 454 |
> |
atomInfo->dipole[2] = 0.0; |
| 455 |
> |
atomData->addAtomInfo(atomInfo); |
| 456 |
> |
|
| 457 |
> |
newVec = rotTrans * c4; |
| 458 |
> |
atomInfo = new AtomInfo; |
| 459 |
> |
atomInfo->atomTypeName = "K"; |
| 460 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 461 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 462 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 463 |
> |
atomInfo->dipole[0] = 0.0; |
| 464 |
> |
atomInfo->dipole[1] = 0.0; |
| 465 |
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atomInfo->dipole[2] = 0.0; |
| 466 |
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atomData->addAtomInfo(atomInfo); |
| 467 |
> |
|
| 468 |
> |
//add atom data into atom's property |
| 469 |
> |
|
| 470 |
> |
if(!haveAtomData){ |
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atomData->setID("ATOMDATA"); |
| 472 |
> |
datom->addProperty(atomData); |
| 473 |
> |
} |
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> |
|
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> |
setVisited(datom); |
| 476 |
> |
|
| 477 |
> |
} |
| 478 |
> |
|
| 479 |
> |
const std::string GBLipidAtomVisitor::toString(){ |
| 480 |
> |
char buffer[65535]; |
| 481 |
> |
std::string result; |
| 482 |
> |
|
| 483 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 484 |
> |
result += buffer; |
| 485 |
> |
|
| 486 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 487 |
> |
result += buffer; |
| 488 |
> |
|
| 489 |
> |
sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n"); |
| 490 |
> |
result += buffer; |
| 491 |
> |
|
| 492 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 493 |
> |
result += buffer; |
| 494 |
> |
|
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> |
return result; |
| 496 |
> |
} |
| 497 |
> |
|
| 498 |
> |
//----------------------------------------------------------------------------// |
| 499 |
> |
|
| 500 |
> |
void DefaultAtomVisitor::visit(Atom *atom) { |
| 501 |
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AtomData *atomData; |
| 502 |
|
AtomInfo *atomInfo; |
| 503 |
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Vector3d pos; |
| 504 |
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|
| 505 |
|
if (isVisited(atom)) |
| 506 |
< |
return; |
| 506 |
> |
return; |
| 507 |
|
|
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atomInfo = new AtomInfo; |
| 509 |
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|
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atom->addProperty(atomData); |
| 525 |
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|
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setVisited(atom); |
| 527 |
< |
} |
| 527 |
> |
} |
| 528 |
|
|
| 529 |
< |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
| 529 |
> |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
| 530 |
|
AtomData *atomData; |
| 531 |
|
AtomInfo *atomInfo; |
| 532 |
|
Vector3d pos; |
| 533 |
|
Vector3d u; |
| 534 |
|
|
| 535 |
|
if (isVisited(datom)) |
| 536 |
< |
return; |
| 536 |
> |
return; |
| 537 |
|
|
| 538 |
|
pos = datom->getPos(); |
| 539 |
< |
u = datom->getElectroFrame().getColumn(2); |
| 540 |
< |
|
| 539 |
> |
if (datom->getAtomType()->isGayBerne()) { |
| 540 |
> |
u = datom->getA().transpose()*V3Z; |
| 541 |
> |
} else if (datom->getAtomType()->isMultipole()) { |
| 542 |
> |
u = datom->getElectroFrame().getColumn(2); |
| 543 |
> |
} |
| 544 |
|
atomData = new AtomData; |
| 545 |
|
atomData->setID("ATOMDATA"); |
| 546 |
|
atomInfo = new AtomInfo; |
| 558 |
|
datom->addProperty(atomData); |
| 559 |
|
|
| 560 |
|
setVisited(datom); |
| 561 |
< |
} |
| 561 |
> |
} |
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|
|
| 563 |
< |
const std::string DefaultAtomVisitor::toString() { |
| 563 |
> |
const std::string DefaultAtomVisitor::toString() { |
| 564 |
|
char buffer[65535]; |
| 565 |
|
std::string result; |
| 566 |
|
|
| 580 |
|
result += buffer; |
| 581 |
|
|
| 582 |
|
return result; |
| 583 |
< |
} |
| 583 |
> |
} |
| 584 |
|
} //namespace oopse |
