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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 <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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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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std::vector<std::string>::iterator strIter; |
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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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for( strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); |
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++strIter ) |
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if (*strIter == atomType) |
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return true; |
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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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return false; |
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} |
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|
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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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//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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|
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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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newVec = rotTrans * u; |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "X"; |
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atomInfo->atomTypeName = "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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newVec = rotTrans * ox; |
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|
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "O"; |
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atomInfo->atomTypeName = "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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//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->atomTypeName = "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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//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->atomTypeName = "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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//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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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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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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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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|
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void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
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return strIter != linearAtomType.end() ? true : false; |
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} |
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|
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vector<AtomInfo*> atoms; |
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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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//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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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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Vector3d c2(0.0, 0.0, -0.6); |
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Vector3d c3(0.0, 0.0, 0.6); |
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Vector3d c4(0.0, 0.0, 1.8); |
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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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AtomType* atomType; |
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//if atom is not SSD atom, just skip it |
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if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne()) |
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return; |
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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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//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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|
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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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if (gayBerneData != NULL) { |
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> |
GayBerneParam gayBerneParam = gayBerneData->getData(); |
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|
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matVecMul3(rotTrans, c2, newVec); |
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atomInfo = new AtomInfo; |
| 259 |
< |
atomInfo->AtomType = "C"; |
| 260 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 261 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 262 |
< |
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; |
| 265 |
< |
atomInfo->dipole[2] = 0.0; |
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< |
atomData->addAtomInfo(atomInfo); |
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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; |
| 259 |
> |
c1[2] = -halfLen; |
| 260 |
> |
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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matVecMul3(rotTrans, c3, newVec); |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
| 307 |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
| 308 |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
| 309 |
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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); |
| 277 |
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atomInfo = new AtomInfo; |
| 278 |
< |
atomInfo->AtomType = "C"; |
| 279 |
< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 280 |
< |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 281 |
< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 282 |
< |
atomInfo->dipole[0] = 0.0; |
| 283 |
< |
atomInfo->dipole[1] = 0.0; |
| 284 |
< |
atomInfo->dipole[2] = 0.0; |
| 285 |
< |
atomData->addAtomInfo(atomInfo); |
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> |
data = datom->getPropertyByName("ATOMDATA"); |
| 277 |
> |
if(data != NULL){ |
| 278 |
> |
atomData = dynamic_cast<AtomData*>(data); |
| 279 |
> |
if(atomData == NULL){ |
| 280 |
> |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 281 |
> |
atomData = new AtomData; |
| 282 |
> |
haveAtomData = false; |
| 283 |
> |
} else { |
| 284 |
> |
haveAtomData = true; |
| 285 |
> |
} |
| 286 |
> |
} else { |
| 287 |
> |
atomData = new AtomData; |
| 288 |
> |
haveAtomData = false; |
| 289 |
> |
} |
| 290 |
> |
|
| 291 |
> |
|
| 292 |
> |
pos = datom->getPos(); |
| 293 |
> |
q = datom->getQ(); |
| 294 |
> |
rotMatrix = datom->getA(); |
| 295 |
|
|
| 296 |
< |
//add atom data into atom's property |
| 296 |
> |
// We need A^T to convert from body-fixed to space-fixed: |
| 297 |
> |
rotTrans = rotMatrix.transpose(); |
| 298 |
|
|
| 299 |
< |
if(!haveAtomData){ |
| 300 |
< |
atomData->setID("ATOMDATA"); |
| 301 |
< |
datom->addProperty(atomData); |
| 299 |
> |
newVec = rotTrans * c1; |
| 300 |
> |
atomInfo = new AtomInfo; |
| 301 |
> |
atomInfo->atomTypeName = "C"; |
| 302 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 303 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 304 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 305 |
> |
atomInfo->dipole[0] = 0.0; |
| 306 |
> |
atomInfo->dipole[1] = 0.0; |
| 307 |
> |
atomInfo->dipole[2] = 0.0; |
| 308 |
> |
atomData->addAtomInfo(atomInfo); |
| 309 |
> |
|
| 310 |
> |
newVec = rotTrans * c2; |
| 311 |
> |
atomInfo = new AtomInfo; |
| 312 |
> |
atomInfo->atomTypeName = "C"; |
| 313 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 314 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 315 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 316 |
> |
atomInfo->dipole[0] = 0.0; |
| 317 |
> |
atomInfo->dipole[1] = 0.0; |
| 318 |
> |
atomInfo->dipole[2] = 0.0; |
| 319 |
> |
atomData->addAtomInfo(atomInfo); |
| 320 |
> |
|
| 321 |
> |
newVec = rotTrans * c3; |
| 322 |
> |
atomInfo = new AtomInfo; |
| 323 |
> |
atomInfo->atomTypeName = "C"; |
| 324 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 325 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 326 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 327 |
> |
atomInfo->dipole[0] = 0.0; |
| 328 |
> |
atomInfo->dipole[1] = 0.0; |
| 329 |
> |
atomInfo->dipole[2] = 0.0; |
| 330 |
> |
atomData->addAtomInfo(atomInfo); |
| 331 |
> |
|
| 332 |
> |
newVec = rotTrans * c4; |
| 333 |
> |
atomInfo = new AtomInfo; |
| 334 |
> |
atomInfo->atomTypeName = "C"; |
| 335 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 336 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 337 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 338 |
> |
atomInfo->dipole[0] = 0.0; |
| 339 |
> |
atomInfo->dipole[1] = 0.0; |
| 340 |
> |
atomInfo->dipole[2] = 0.0; |
| 341 |
> |
atomData->addAtomInfo(atomInfo); |
| 342 |
> |
|
| 343 |
> |
//add atom data into atom's property |
| 344 |
> |
|
| 345 |
> |
if(!haveAtomData){ |
| 346 |
> |
atomData->setID("ATOMDATA"); |
| 347 |
> |
datom->addProperty(atomData); |
| 348 |
> |
} |
| 349 |
> |
|
| 350 |
> |
setVisited(datom); |
| 351 |
> |
|
| 352 |
|
} |
| 353 |
|
|
| 354 |
< |
setVisited(datom); |
| 354 |
> |
const std::string LinearAtomVisitor::toString(){ |
| 355 |
> |
char buffer[65535]; |
| 356 |
> |
std::string result; |
| 357 |
> |
|
| 358 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 359 |
> |
result += buffer; |
| 360 |
|
|
| 361 |
< |
} |
| 361 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 362 |
> |
result += buffer; |
| 363 |
|
|
| 364 |
< |
const string LinearAtomVisitor::toString(){ |
| 365 |
< |
char buffer[65535]; |
| 366 |
< |
string result; |
| 364 |
> |
sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
| 365 |
> |
result += buffer; |
| 366 |
> |
|
| 367 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 368 |
> |
result += buffer; |
| 369 |
> |
|
| 370 |
> |
return result; |
| 371 |
> |
} |
| 372 |
> |
|
| 373 |
> |
bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){ |
| 374 |
> |
std::set<std::string>::iterator strIter; |
| 375 |
> |
strIter = GBLipidAtomType.find(atomType); |
| 376 |
> |
|
| 377 |
> |
return strIter != GBLipidAtomType.end() ? true : false; |
| 378 |
> |
} |
| 379 |
> |
|
| 380 |
> |
void GBLipidAtomVisitor::visit(DirectionalAtom* datom){ |
| 381 |
> |
std::vector<AtomInfo*> atoms; |
| 382 |
> |
//we need to convert linear into 4 different atoms |
| 383 |
> |
Vector3d c1(0.0, 0.0, -6.25); |
| 384 |
> |
Vector3d c2(0.0, 0.0, -2.1); |
| 385 |
> |
Vector3d c3(0.0, 0.0, 2.1); |
| 386 |
> |
Vector3d c4(0.0, 0.0, 6.25); |
| 387 |
> |
RotMat3x3d rotMatrix; |
| 388 |
> |
RotMat3x3d rotTrans; |
| 389 |
> |
AtomInfo* atomInfo; |
| 390 |
> |
Vector3d pos; |
| 391 |
> |
Vector3d newVec; |
| 392 |
> |
Quat4d q; |
| 393 |
> |
AtomData* atomData; |
| 394 |
> |
GenericData* data; |
| 395 |
> |
bool haveAtomData; |
| 396 |
> |
|
| 397 |
> |
//if atom is not GBlipid atom, just skip it |
| 398 |
> |
if(!isGBLipidAtom(datom->getType())) |
| 399 |
> |
return; |
| 400 |
> |
|
| 401 |
> |
data = datom->getPropertyByName("ATOMDATA"); |
| 402 |
> |
if(data != NULL){ |
| 403 |
> |
atomData = dynamic_cast<AtomData*>(data); |
| 404 |
> |
if(atomData == NULL){ |
| 405 |
> |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
| 406 |
> |
atomData = new AtomData; |
| 407 |
> |
haveAtomData = false; |
| 408 |
> |
} else { |
| 409 |
> |
haveAtomData = true; |
| 410 |
> |
} |
| 411 |
> |
} else { |
| 412 |
> |
atomData = new AtomData; |
| 413 |
> |
haveAtomData = false; |
| 414 |
> |
} |
| 415 |
> |
|
| 416 |
|
|
| 417 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 418 |
< |
result += buffer; |
| 417 |
> |
pos = datom->getPos(); |
| 418 |
> |
q = datom->getQ(); |
| 419 |
> |
rotMatrix = datom->getA(); |
| 420 |
|
|
| 421 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 422 |
< |
result += buffer; |
| 421 |
> |
// We need A^T to convert from body-fixed to space-fixed: |
| 422 |
> |
rotTrans = rotMatrix.transpose(); |
| 423 |
|
|
| 424 |
< |
sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
| 425 |
< |
result += buffer; |
| 424 |
> |
newVec = rotTrans * c1; |
| 425 |
> |
atomInfo = new AtomInfo; |
| 426 |
> |
atomInfo->atomTypeName = "K"; |
| 427 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 428 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 429 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 430 |
> |
atomInfo->dipole[0] = 0.0; |
| 431 |
> |
atomInfo->dipole[1] = 0.0; |
| 432 |
> |
atomInfo->dipole[2] = 0.0; |
| 433 |
> |
atomData->addAtomInfo(atomInfo); |
| 434 |
|
|
| 435 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 436 |
< |
result += buffer; |
| 435 |
> |
newVec = rotTrans * c2; |
| 436 |
> |
atomInfo = new AtomInfo; |
| 437 |
> |
atomInfo->atomTypeName = "K"; |
| 438 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 439 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 440 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 441 |
> |
atomInfo->dipole[0] = 0.0; |
| 442 |
> |
atomInfo->dipole[1] = 0.0; |
| 443 |
> |
atomInfo->dipole[2] = 0.0; |
| 444 |
> |
atomData->addAtomInfo(atomInfo); |
| 445 |
|
|
| 446 |
< |
return result; |
| 447 |
< |
} |
| 446 |
> |
newVec = rotTrans * c3; |
| 447 |
> |
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 |
< |
//----------------------------------------------------------------------------// |
| 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 |
> |
atomInfo->dipole[2] = 0.0; |
| 466 |
> |
atomData->addAtomInfo(atomInfo); |
| 467 |
|
|
| 468 |
< |
void DefaultAtomVisitor::visit(Atom *atom) { |
| 468 |
> |
//add atom data into atom's property |
| 469 |
> |
|
| 470 |
> |
if(!haveAtomData){ |
| 471 |
> |
atomData->setID("ATOMDATA"); |
| 472 |
> |
datom->addProperty(atomData); |
| 473 |
> |
} |
| 474 |
> |
|
| 475 |
> |
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 |
> |
|
| 495 |
> |
return result; |
| 496 |
> |
} |
| 497 |
> |
|
| 498 |
> |
//----------------------------------------------------------------------------// |
| 499 |
> |
|
| 500 |
> |
void DefaultAtomVisitor::visit(Atom *atom) { |
| 501 |
|
AtomData *atomData; |
| 502 |
|
AtomInfo *atomInfo; |
| 503 |
|
Vector3d pos; |
| 504 |
|
|
| 505 |
|
if (isVisited(atom)) |
| 506 |
< |
return; |
| 506 |
> |
return; |
| 507 |
|
|
| 508 |
|
atomInfo = new AtomInfo; |
| 509 |
|
|
| 511 |
|
atomData->setID("ATOMDATA"); |
| 512 |
|
|
| 513 |
|
pos = atom->getPos(); |
| 514 |
< |
atomInfo->AtomType = atom->getType(); |
| 514 |
> |
atomInfo->atomTypeName = atom->getType(); |
| 515 |
|
atomInfo->pos[0] = pos[0]; |
| 516 |
|
atomInfo->pos[1] = pos[1]; |
| 517 |
|
atomInfo->pos[2] = pos[2]; |
| 524 |
|
atom->addProperty(atomData); |
| 525 |
|
|
| 526 |
|
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(3); |
| 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; |
| 547 |
|
|
| 548 |
< |
atomInfo->AtomType = datom->getType(); |
| 548 |
> |
atomInfo->atomTypeName = datom->getType(); |
| 549 |
|
atomInfo->pos[0] = pos[0]; |
| 550 |
|
atomInfo->pos[1] = pos[1]; |
| 551 |
|
atomInfo->pos[2] = pos[2]; |
| 558 |
|
datom->addProperty(atomData); |
| 559 |
|
|
| 560 |
|
setVisited(datom); |
| 561 |
< |
} |
| 561 |
> |
} |
| 562 |
|
|
| 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 |
