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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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} |
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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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|
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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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|
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return false; |
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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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void SSDAtomVisitor::visit(DirectionalAtom *datom) { |
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std::vector<AtomInfo *>atoms; |
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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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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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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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return result; |
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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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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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return strIter != linearAtomType.end() ? true : false; |
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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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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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vector<AtomInfo*> atoms; |
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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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//we need to convert linear into 4 different atoms |
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double c1[3] = {0.0, 0.0, -1.8}; |
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double c2[3] = {0.0, 0.0, -0.6}; |
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double c3[3] = {0.0, 0.0, 0.6}; |
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double c4[3] = {0.0, 0.0, 1.8}; |
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double rotMatrix[3][3]; |
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double rotTrans[3][3]; |
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AtomInfo* atomInfo; |
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double pos[3]; |
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double newVec[3]; |
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double q[4]; |
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AtomData* atomData; |
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GenericData* data; |
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bool haveAtomData; |
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|
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//if atom is not SSD atom, just skip it |
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if(!isLinearAtom(datom->getType())) |
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return; |
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|
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data = datom->getProperty("ATOMDATA"); |
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if(data != NULL){ |
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|
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atomData = dynamic_cast<AtomData*>(data); |
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if(atomData == NULL){ |
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cerr << "can not get Atom Data from " << datom->getType() << endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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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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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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datom->getPos(pos); |
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datom->getQ(q); |
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datom->getA(rotMatrix); |
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pos = datom->getPos(); |
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q = datom->getQ(); |
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rotMatrix = datom->getA(); |
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// We need A^T to convert from body-fixed to space-fixed: |
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transposeMat3(rotMatrix, rotTrans); |
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|
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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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// We need A^T to convert from body-fixed to space-fixed: |
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rotTrans = rotMatrix.transpose(); |
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matVecMul3(rotTrans, c2, newVec); |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
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newVec = rotTrans * c1; |
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atomInfo = new AtomInfo; |
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atomInfo->atomTypeName = "C"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
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|
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matVecMul3(rotTrans, c3, newVec); |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
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newVec = rotTrans * c2; |
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atomInfo = new AtomInfo; |
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atomInfo->atomTypeName = "C"; |
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> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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> |
atomData->addAtomInfo(atomInfo); |
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|
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< |
matVecMul3(rotTrans, c4, newVec); |
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< |
atomInfo = new AtomInfo; |
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< |
atomInfo->AtomType = "C"; |
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< |
atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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< |
atomInfo->pos[2] = pos[2] + newVec[2]; |
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< |
atomInfo->dipole[0] = 0.0; |
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< |
atomInfo->dipole[1] = 0.0; |
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< |
atomInfo->dipole[2] = 0.0; |
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< |
atomData->addAtomInfo(atomInfo); |
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> |
newVec = rotTrans * c3; |
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> |
atomInfo = new AtomInfo; |
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> |
atomInfo->atomTypeName = "C"; |
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> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
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> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
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> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
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> |
atomInfo->dipole[0] = 0.0; |
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> |
atomInfo->dipole[1] = 0.0; |
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> |
atomInfo->dipole[2] = 0.0; |
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> |
atomData->addAtomInfo(atomInfo); |
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|
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< |
//add atom data into atom's property |
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> |
newVec = rotTrans * c4; |
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> |
atomInfo = new AtomInfo; |
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> |
atomInfo->atomTypeName = "C"; |
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> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
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> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
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> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
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> |
atomInfo->dipole[0] = 0.0; |
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> |
atomInfo->dipole[1] = 0.0; |
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> |
atomInfo->dipole[2] = 0.0; |
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> |
atomData->addAtomInfo(atomInfo); |
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|
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< |
if(!haveAtomData){ |
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< |
atomData->setID("ATOMDATA"); |
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< |
datom->addProperty(atomData); |
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< |
} |
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> |
//add atom data into atom's property |
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|
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< |
setVisited(datom); |
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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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< |
const string LinearAtomVisitor::toString(){ |
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> |
const std::string LinearAtomVisitor::toString(){ |
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char buffer[65535]; |
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< |
string result; |
| 325 |
> |
std::string result; |
| 326 |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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atomData->setID("ATOMDATA"); |
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|
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pos = atom->getPos(); |
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< |
atomInfo->AtomType = atom->getType(); |
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> |
atomInfo->atomTypeName = atom->getType(); |
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> |
printf("setting a type to %s\n", atom->getType().c_str()); |
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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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return; |
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pos = datom->getPos(); |
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< |
u = datom->getElectroFrame().getColumn(3); |
| 384 |
> |
u = datom->getElectroFrame().getColumn(2); |
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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->atomTypeName = 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]; |
