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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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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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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 "primitives/RigidBody.hpp" |
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|
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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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|
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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->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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} |
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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->getPropertyByName("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 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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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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Vector3d h1(0.0, -0.75695, 0.5206); |
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Vector3d h2(0.0, 0.75695, 0.5206); |
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Vector3d ox(0.0, 0.0, -0.0654); |
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Vector3d u(0, 0, 1); |
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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 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->getPropertyByName("ATOMDATA"); |
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|
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if (data != NULL) { |
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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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} 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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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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//transposeMat3(rotMatrix, rotTrans); |
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rotTrans = rotMatrix.transpose(); |
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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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newVec = rotTrans * u; |
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|
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atomInfo = new AtomInfo; |
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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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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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newVec = rotTrans * ox; |
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|
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atomInfo = new AtomInfo; |
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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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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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//hydrogen1 |
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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->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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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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newVec = rotTrans * h2; |
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atomInfo = new AtomInfo; |
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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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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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const std::string SSDAtomVisitor::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, |
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"------------------------------------------------------------------\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, |
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"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, |
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"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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return result; |
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} |
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|
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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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|
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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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|
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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->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 = "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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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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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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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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//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 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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|
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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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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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return result; |
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} |
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|
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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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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: |
| 391 |
rotTrans = rotMatrix.transpose(); |
| 392 |
|
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newVec = rotTrans * c1; |
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atomInfo = new AtomInfo; |
| 395 |
atomInfo->atomTypeName = "K"; |
| 396 |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 397 |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 398 |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 399 |
atomInfo->dipole[0] = 0.0; |
| 400 |
atomInfo->dipole[1] = 0.0; |
| 401 |
atomInfo->dipole[2] = 0.0; |
| 402 |
atomData->addAtomInfo(atomInfo); |
| 403 |
|
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newVec = rotTrans * c2; |
| 405 |
atomInfo = new AtomInfo; |
| 406 |
atomInfo->atomTypeName = "K"; |
| 407 |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 408 |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 409 |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 410 |
atomInfo->dipole[0] = 0.0; |
| 411 |
atomInfo->dipole[1] = 0.0; |
| 412 |
atomInfo->dipole[2] = 0.0; |
| 413 |
atomData->addAtomInfo(atomInfo); |
| 414 |
|
| 415 |
newVec = rotTrans * c3; |
| 416 |
atomInfo = new AtomInfo; |
| 417 |
atomInfo->atomTypeName = "K"; |
| 418 |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 419 |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 420 |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 421 |
atomInfo->dipole[0] = 0.0; |
| 422 |
atomInfo->dipole[1] = 0.0; |
| 423 |
atomInfo->dipole[2] = 0.0; |
| 424 |
atomData->addAtomInfo(atomInfo); |
| 425 |
|
| 426 |
newVec = rotTrans * c4; |
| 427 |
atomInfo = new AtomInfo; |
| 428 |
atomInfo->atomTypeName = "K"; |
| 429 |
atomInfo->pos[0] = pos[0] + newVec[0]; |
| 430 |
atomInfo->pos[1] = pos[1] + newVec[1]; |
| 431 |
atomInfo->pos[2] = pos[2] + newVec[2]; |
| 432 |
atomInfo->dipole[0] = 0.0; |
| 433 |
atomInfo->dipole[1] = 0.0; |
| 434 |
atomInfo->dipole[2] = 0.0; |
| 435 |
atomData->addAtomInfo(atomInfo); |
| 436 |
|
| 437 |
//add atom data into atom's property |
| 438 |
|
| 439 |
if(!haveAtomData){ |
| 440 |
atomData->setID("ATOMDATA"); |
| 441 |
datom->addProperty(atomData); |
| 442 |
} |
| 443 |
|
| 444 |
setVisited(datom); |
| 445 |
|
| 446 |
} |
| 447 |
|
| 448 |
const std::string GBLipidAtomVisitor::toString(){ |
| 449 |
char buffer[65535]; |
| 450 |
std::string result; |
| 451 |
|
| 452 |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 453 |
result += buffer; |
| 454 |
|
| 455 |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
| 456 |
result += buffer; |
| 457 |
|
| 458 |
sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n"); |
| 459 |
result += buffer; |
| 460 |
|
| 461 |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
| 462 |
result += buffer; |
| 463 |
|
| 464 |
return result; |
| 465 |
} |
| 466 |
|
| 467 |
//----------------------------------------------------------------------------// |
| 468 |
|
| 469 |
void DefaultAtomVisitor::visit(Atom *atom) { |
| 470 |
AtomData *atomData; |
| 471 |
AtomInfo *atomInfo; |
| 472 |
Vector3d pos; |
| 473 |
|
| 474 |
if (isVisited(atom)) |
| 475 |
return; |
| 476 |
|
| 477 |
atomInfo = new AtomInfo; |
| 478 |
|
| 479 |
atomData = new AtomData; |
| 480 |
atomData->setID("ATOMDATA"); |
| 481 |
|
| 482 |
pos = atom->getPos(); |
| 483 |
atomInfo->atomTypeName = atom->getType(); |
| 484 |
atomInfo->pos[0] = pos[0]; |
| 485 |
atomInfo->pos[1] = pos[1]; |
| 486 |
atomInfo->pos[2] = pos[2]; |
| 487 |
atomInfo->dipole[0] = 0.0; |
| 488 |
atomInfo->dipole[1] = 0.0; |
| 489 |
atomInfo->dipole[2] = 0.0; |
| 490 |
|
| 491 |
atomData->addAtomInfo(atomInfo); |
| 492 |
|
| 493 |
atom->addProperty(atomData); |
| 494 |
|
| 495 |
setVisited(atom); |
| 496 |
} |
| 497 |
|
| 498 |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
| 499 |
AtomData *atomData; |
| 500 |
AtomInfo *atomInfo; |
| 501 |
Vector3d pos; |
| 502 |
Vector3d u; |
| 503 |
|
| 504 |
if (isVisited(datom)) |
| 505 |
return; |
| 506 |
|
| 507 |
pos = datom->getPos(); |
| 508 |
u = datom->getElectroFrame().getColumn(2); |
| 509 |
|
| 510 |
atomData = new AtomData; |
| 511 |
atomData->setID("ATOMDATA"); |
| 512 |
atomInfo = new AtomInfo; |
| 513 |
|
| 514 |
atomInfo->atomTypeName = datom->getType(); |
| 515 |
atomInfo->pos[0] = pos[0]; |
| 516 |
atomInfo->pos[1] = pos[1]; |
| 517 |
atomInfo->pos[2] = pos[2]; |
| 518 |
atomInfo->dipole[0] = u[0]; |
| 519 |
atomInfo->dipole[1] = u[1]; |
| 520 |
atomInfo->dipole[2] = u[2]; |
| 521 |
|
| 522 |
atomData->addAtomInfo(atomInfo); |
| 523 |
|
| 524 |
datom->addProperty(atomData); |
| 525 |
|
| 526 |
setVisited(datom); |
| 527 |
} |
| 528 |
|
| 529 |
const std::string DefaultAtomVisitor::toString() { |
| 530 |
char buffer[65535]; |
| 531 |
std::string result; |
| 532 |
|
| 533 |
sprintf(buffer, |
| 534 |
"------------------------------------------------------------------\n"); |
| 535 |
result += buffer; |
| 536 |
|
| 537 |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
| 538 |
result += buffer; |
| 539 |
|
| 540 |
sprintf(buffer, |
| 541 |
"Visitor Description: copy atom infomation into atom data\n"); |
| 542 |
result += buffer; |
| 543 |
|
| 544 |
sprintf(buffer, |
| 545 |
"------------------------------------------------------------------\n"); |
| 546 |
result += buffer; |
| 547 |
|
| 548 |
return result; |
| 549 |
} |
| 550 |
} //namespace oopse |
