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#include <cstring> |
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#include "AtomVisitor.hpp" |
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#include "DirectionalAtom.hpp" |
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#include "MatVec3.h" |
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#include "RigidBody.hpp" |
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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; |
| 173 |
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} |
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|
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//----------------------------------------------------------------------------// |
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|
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void DefaultAtomVisitor::visit(Atom* atom){ |
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AtomData* atomData; |
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AtomInfo* atomInfo; |
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double pos[3]; |
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|
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if(isVisited(atom)) |
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return; |
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|
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atomInfo =new AtomInfo; |
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|
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atomData = new AtomData; |
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atomData->setID("ATOMDATA"); |
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|
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atom->getPos(pos); |
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atomInfo->AtomType = atom->getType(); |
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atomInfo->pos[0] = pos[0]; |
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atomInfo->pos[1] = pos[1]; |
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atomInfo->pos[2] = pos[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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|
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|
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atomData->addAtomInfo(atomInfo); |
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|
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atom->addProperty(atomData); |
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|
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setVisited(atom); |
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} |
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void DefaultAtomVisitor::visit(DirectionalAtom* datom){ |
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AtomData* atomData; |
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AtomInfo* atomInfo; |
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double pos[3]; |
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double u[3]; |
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|
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if(isVisited(datom)) |
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return; |
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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]; |
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|
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atomData->addAtomInfo(atomInfo); |
| 231 |
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|
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datom->addProperty(atomData); |
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|
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setVisited(datom); |
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} |
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|
| 237 |
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|
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const string DefaultAtomVisitor::toString(){ |
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char buffer[65535]; |
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string result; |
| 241 |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 243 |
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result += buffer; |
| 244 |
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|
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
| 247 |
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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; |
| 250 |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 252 |
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result += buffer; |
| 253 |
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|
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return result; |
| 255 |
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} |
| 1 |
> |
#include <cstring> |
| 2 |
> |
#include "visitors/AtomVisitor.hpp" |
| 3 |
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#include "primitives/DirectionalAtom.hpp" |
| 4 |
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#include "math/MatVec3.h" |
| 5 |
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#include "primitives/RigidBody.hpp" |
| 6 |
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|
| 7 |
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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 |
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//vector<Atom*>::iterator atomIter; |
| 12 |
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|
| 13 |
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//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 |
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} |
| 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->getPropertyByName("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 |
> |
|
| 31 |
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bool BaseAtomVisitor::isVisited(Atom* atom){ |
| 32 |
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GenericData* data; |
| 33 |
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data = atom->getPropertyByName("VISITED"); |
| 34 |
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return data == NULL ? false : true; |
| 35 |
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} |
| 36 |
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|
| 37 |
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bool SSDAtomVisitor::isSSDAtom(const string& atomType){ |
| 38 |
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vector<string>::iterator strIter; |
| 39 |
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|
| 40 |
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for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter) |
| 41 |
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if(*strIter == atomType) |
| 42 |
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return true; |
| 43 |
> |
|
| 44 |
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return false; |
| 45 |
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} |
| 46 |
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|
| 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 |
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//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 |
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Vector3d ox(0.0, 0.0, -0.0654); |
| 57 |
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Vector3d u(0, 0, 1); |
| 58 |
> |
RotMat3x3d rotMatrix; |
| 59 |
> |
RotMat3x3d rotTrans; |
| 60 |
> |
AtomInfo* atomInfo; |
| 61 |
> |
Vector3d pos; |
| 62 |
> |
Vector3d newVec; |
| 63 |
> |
Quat4d q; |
| 64 |
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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 |
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return; |
| 71 |
> |
|
| 72 |
> |
data = datom->getPropertyByName("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 |
> |
rotMatrix= datom->getA(); |
| 93 |
> |
|
| 94 |
> |
// We need A^T to convert from body-fixed to space-fixed: |
| 95 |
> |
//transposeMat3(rotMatrix, rotTrans); |
| 96 |
> |
rotTrans = rotMatrix.transpose(); |
| 97 |
> |
|
| 98 |
> |
//center of mass of the water molecule |
| 99 |
> |
//matVecMul3(rotTrans, u, newVec); |
| 100 |
> |
newVec = rotTrans * u; |
| 101 |
> |
|
| 102 |
> |
atomInfo = new AtomInfo; |
| 103 |
> |
atomInfo->AtomType = "X"; |
| 104 |
> |
atomInfo->pos[0] = pos[0]; |
| 105 |
> |
atomInfo->pos[1] = pos[1]; |
| 106 |
> |
atomInfo->pos[2] = pos[2]; |
| 107 |
> |
atomInfo->dipole[0] = newVec[0]; |
| 108 |
> |
atomInfo->dipole[1] = newVec[1]; |
| 109 |
> |
atomInfo->dipole[2] = newVec[2]; |
| 110 |
> |
|
| 111 |
> |
atomData->addAtomInfo(atomInfo); |
| 112 |
> |
|
| 113 |
> |
//oxygen |
| 114 |
> |
//matVecMul3(rotTrans, ox, newVec); |
| 115 |
> |
newVec = rotTrans * ox; |
| 116 |
> |
|
| 117 |
> |
atomInfo = new AtomInfo; |
| 118 |
> |
atomInfo->AtomType = "O"; |
| 119 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 120 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 121 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 122 |
> |
atomInfo->dipole[0] = 0.0; |
| 123 |
> |
atomInfo->dipole[1] = 0.0; |
| 124 |
> |
atomInfo->dipole[2] = 0.0; |
| 125 |
> |
atomData->addAtomInfo(atomInfo); |
| 126 |
> |
|
| 127 |
> |
|
| 128 |
> |
//hydrogen1 |
| 129 |
> |
//matVecMul3(rotTrans, h1, newVec); |
| 130 |
> |
newVec = rotTrans * h1; |
| 131 |
> |
atomInfo = new AtomInfo; |
| 132 |
> |
atomInfo->AtomType = "H"; |
| 133 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 134 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 135 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 136 |
> |
atomInfo->dipole[0] = 0.0; |
| 137 |
> |
atomInfo->dipole[1] = 0.0; |
| 138 |
> |
atomInfo->dipole[2] = 0.0; |
| 139 |
> |
atomData->addAtomInfo(atomInfo); |
| 140 |
> |
|
| 141 |
> |
//hydrogen2 |
| 142 |
> |
//matVecMul3(rotTrans, h2, newVec); |
| 143 |
> |
newVec = rotTrans * h2; |
| 144 |
> |
atomInfo = new AtomInfo; |
| 145 |
> |
atomInfo->AtomType = "H"; |
| 146 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 147 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 148 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 149 |
> |
atomInfo->dipole[0] = 0.0; |
| 150 |
> |
atomInfo->dipole[1] = 0.0; |
| 151 |
> |
atomInfo->dipole[2] = 0.0; |
| 152 |
> |
atomData->addAtomInfo(atomInfo); |
| 153 |
> |
|
| 154 |
> |
//add atom data into atom's property |
| 155 |
> |
|
| 156 |
> |
if(!haveAtomData){ |
| 157 |
> |
atomData->setID("ATOMDATA"); |
| 158 |
> |
datom->addProperty(atomData); |
| 159 |
> |
} |
| 160 |
> |
|
| 161 |
> |
setVisited(datom); |
| 162 |
> |
|
| 163 |
> |
} |
| 164 |
> |
|
| 165 |
> |
const string SSDAtomVisitor::toString(){ |
| 166 |
> |
char buffer[65535]; |
| 167 |
> |
string result; |
| 168 |
> |
|
| 169 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 170 |
> |
result += buffer; |
| 171 |
> |
|
| 172 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 173 |
> |
result += buffer; |
| 174 |
> |
|
| 175 |
> |
sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n"); |
| 176 |
> |
result += buffer; |
| 177 |
> |
|
| 178 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 179 |
> |
result += buffer; |
| 180 |
> |
|
| 181 |
> |
return result; |
| 182 |
> |
} |
| 183 |
> |
|
| 184 |
> |
//----------------------------------------------------------------------------// |
| 185 |
> |
|
| 186 |
> |
void DefaultAtomVisitor::visit(Atom* atom){ |
| 187 |
> |
AtomData* atomData; |
| 188 |
> |
AtomInfo* atomInfo; |
| 189 |
> |
Vector3d pos; |
| 190 |
> |
|
| 191 |
> |
if(isVisited(atom)) |
| 192 |
> |
return; |
| 193 |
> |
|
| 194 |
> |
atomInfo =new AtomInfo; |
| 195 |
> |
|
| 196 |
> |
atomData = new AtomData; |
| 197 |
> |
atomData->setID("ATOMDATA"); |
| 198 |
> |
|
| 199 |
> |
pos = atom->getPos(); |
| 200 |
> |
atomInfo->AtomType = atom->getType(); |
| 201 |
> |
atomInfo->pos[0] = pos[0]; |
| 202 |
> |
atomInfo->pos[1] = pos[1]; |
| 203 |
> |
atomInfo->pos[2] = pos[2]; |
| 204 |
> |
atomInfo->dipole[0] = 0.0; |
| 205 |
> |
atomInfo->dipole[1] = 0.0; |
| 206 |
> |
atomInfo->dipole[2] = 0.0; |
| 207 |
> |
|
| 208 |
> |
|
| 209 |
> |
atomData->addAtomInfo(atomInfo); |
| 210 |
> |
|
| 211 |
> |
atom->addProperty(atomData); |
| 212 |
> |
|
| 213 |
> |
setVisited(atom); |
| 214 |
> |
} |
| 215 |
> |
void DefaultAtomVisitor::visit(DirectionalAtom* datom){ |
| 216 |
> |
AtomData* atomData; |
| 217 |
> |
AtomInfo* atomInfo; |
| 218 |
> |
Vector3d pos; |
| 219 |
> |
Vector3d u; |
| 220 |
> |
|
| 221 |
> |
if(isVisited(datom)) |
| 222 |
> |
return; |
| 223 |
> |
|
| 224 |
> |
pos = datom->getPos(); |
| 225 |
> |
u = datom->getUnitVector(); |
| 226 |
> |
|
| 227 |
> |
atomData = new AtomData; |
| 228 |
> |
atomData->setID("ATOMDATA"); |
| 229 |
> |
atomInfo =new AtomInfo; |
| 230 |
> |
|
| 231 |
> |
atomInfo->AtomType = datom->getType(); |
| 232 |
> |
atomInfo->pos[0] = pos[0]; |
| 233 |
> |
atomInfo->pos[1] = pos[1]; |
| 234 |
> |
atomInfo->pos[2] = pos[2]; |
| 235 |
> |
atomInfo->dipole[0] = u[0]; |
| 236 |
> |
atomInfo->dipole[1] = u[1]; |
| 237 |
> |
atomInfo->dipole[2] = u[2]; |
| 238 |
> |
|
| 239 |
> |
atomData->addAtomInfo(atomInfo); |
| 240 |
> |
|
| 241 |
> |
datom->addProperty(atomData); |
| 242 |
> |
|
| 243 |
> |
setVisited(datom); |
| 244 |
> |
} |
| 245 |
> |
|
| 246 |
> |
|
| 247 |
> |
const string DefaultAtomVisitor::toString(){ |
| 248 |
> |
char buffer[65535]; |
| 249 |
> |
string result; |
| 250 |
> |
|
| 251 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 252 |
> |
result += buffer; |
| 253 |
> |
|
| 254 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 255 |
> |
result += buffer; |
| 256 |
> |
|
| 257 |
> |
sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n"); |
| 258 |
> |
result += buffer; |
| 259 |
> |
|
| 260 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 261 |
> |
result += buffer; |
| 262 |
> |
|
| 263 |
> |
return result; |
| 264 |
> |
} |
| 265 |
> |
|
| 266 |
> |
}//namespace oopse |
