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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 "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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#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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< |
void BaseAtomVisitor::visit(RigidBody* rb){ |
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//vector<Atom*> myAtoms; |
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//vector<Atom*>::iterator atomIter; |
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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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//myAtoms = rb->getAtoms(); |
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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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//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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|
|
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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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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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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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//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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void SSDAtomVisitor::visit(DirectionalAtom* datom){ |
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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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vector<AtomInfo*> atoms; |
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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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//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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void SSDAtomVisitor::visit(DirectionalAtom *datom) { |
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std::vector<AtomInfo*>atoms; |
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|
|
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data = datom->getProperty("ATOMDATA"); |
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if(data != NULL){ |
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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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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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//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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// 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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data = datom->getPropertyByName("ATOMDATA"); |
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|
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atomData->addAtomInfo(atomInfo); |
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if (data != NULL) { |
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atomData = dynamic_cast<AtomData *>(data); |
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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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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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< |
//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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> |
// 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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< |
//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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//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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< |
//add atom data into atom's property |
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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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< |
if(!haveAtomData){ |
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< |
atomData->setID("ATOMDATA"); |
149 |
< |
datom->addProperty(atomData); |
150 |
< |
} |
143 |
> |
atomData->addAtomInfo(atomInfo); |
144 |
|
|
145 |
< |
setVisited(datom); |
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> |
//oxygen |
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> |
//matVecMul3(rotTrans, ox, newVec); |
147 |
> |
newVec = rotTrans * ox; |
148 |
|
|
149 |
< |
} |
149 |
> |
atomInfo = new AtomInfo; |
150 |
> |
atomInfo->atomTypeName = "O"; |
151 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
152 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
153 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
154 |
> |
atomInfo->dipole[0] = 0.0; |
155 |
> |
atomInfo->dipole[1] = 0.0; |
156 |
> |
atomInfo->dipole[2] = 0.0; |
157 |
> |
atomData->addAtomInfo(atomInfo); |
158 |
|
|
159 |
< |
const string SSDAtomVisitor::toString(){ |
160 |
< |
char buffer[65535]; |
161 |
< |
string result; |
162 |
< |
|
163 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
164 |
< |
result += buffer; |
159 |
> |
//hydrogen1 |
160 |
> |
//matVecMul3(rotTrans, h1, newVec); |
161 |
> |
newVec = rotTrans * h1; |
162 |
> |
atomInfo = new AtomInfo; |
163 |
> |
atomInfo->atomTypeName = "H"; |
164 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
165 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
166 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
167 |
> |
atomInfo->dipole[0] = 0.0; |
168 |
> |
atomInfo->dipole[1] = 0.0; |
169 |
> |
atomInfo->dipole[2] = 0.0; |
170 |
> |
atomData->addAtomInfo(atomInfo); |
171 |
|
|
172 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
173 |
< |
result += buffer; |
172 |
> |
//hydrogen2 |
173 |
> |
//matVecMul3(rotTrans, h2, newVec); |
174 |
> |
newVec = rotTrans * h2; |
175 |
> |
atomInfo = new AtomInfo; |
176 |
> |
atomInfo->atomTypeName = "H"; |
177 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
178 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
179 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
180 |
> |
atomInfo->dipole[0] = 0.0; |
181 |
> |
atomInfo->dipole[1] = 0.0; |
182 |
> |
atomInfo->dipole[2] = 0.0; |
183 |
> |
atomData->addAtomInfo(atomInfo); |
184 |
|
|
185 |
< |
sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n"); |
167 |
< |
result += buffer; |
185 |
> |
//add atom data into atom's property |
186 |
|
|
187 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
188 |
< |
result += buffer; |
187 |
> |
if (!haveAtomData) { |
188 |
> |
atomData->setID("ATOMDATA"); |
189 |
> |
datom->addProperty(atomData); |
190 |
> |
} |
191 |
|
|
192 |
< |
return result; |
193 |
< |
} |
192 |
> |
setVisited(datom); |
193 |
> |
} |
194 |
|
|
195 |
< |
//----------------------------------------------------------------------------// |
195 |
> |
const std::string SSDAtomVisitor::toString() { |
196 |
> |
char buffer[65535]; |
197 |
> |
std::string result; |
198 |
|
|
199 |
< |
void DefaultAtomVisitor::visit(Atom* atom){ |
200 |
< |
AtomData* atomData; |
201 |
< |
AtomInfo* atomInfo; |
180 |
< |
double pos[3]; |
199 |
> |
sprintf(buffer, |
200 |
> |
"------------------------------------------------------------------\n"); |
201 |
> |
result += buffer; |
202 |
|
|
203 |
< |
if(isVisited(atom)) |
204 |
< |
return; |
203 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
204 |
> |
result += buffer; |
205 |
|
|
206 |
< |
atomInfo =new AtomInfo; |
206 |
> |
sprintf(buffer, |
207 |
> |
"Visitor Description: Convert SSD into 4 different atoms\n"); |
208 |
> |
result += buffer; |
209 |
|
|
210 |
< |
atomData = new AtomData; |
211 |
< |
atomData->setID("ATOMDATA"); |
212 |
< |
|
190 |
< |
atom->getPos(pos); |
191 |
< |
atomInfo->AtomType = atom->getType(); |
192 |
< |
atomInfo->pos[0] = pos[0]; |
193 |
< |
atomInfo->pos[1] = pos[1]; |
194 |
< |
atomInfo->pos[2] = pos[2]; |
195 |
< |
atomInfo->dipole[0] = 0.0; |
196 |
< |
atomInfo->dipole[1] = 0.0; |
197 |
< |
atomInfo->dipole[2] = 0.0; |
210 |
> |
sprintf(buffer, |
211 |
> |
"------------------------------------------------------------------\n"); |
212 |
> |
result += buffer; |
213 |
|
|
214 |
+ |
return result; |
215 |
+ |
} |
216 |
|
|
217 |
< |
atomData->addAtomInfo(atomInfo); |
218 |
< |
|
219 |
< |
atom->addProperty(atomData); |
217 |
> |
bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){ |
218 |
> |
std::set<std::string>::iterator strIter; |
219 |
> |
strIter = linearAtomType.find(atomType); |
220 |
|
|
221 |
< |
setVisited(atom); |
222 |
< |
} |
206 |
< |
void DefaultAtomVisitor::visit(DirectionalAtom* datom){ |
207 |
< |
AtomData* atomData; |
208 |
< |
AtomInfo* atomInfo; |
209 |
< |
double pos[3]; |
210 |
< |
double u[3]; |
221 |
> |
return strIter != linearAtomType.end() ? true : false; |
222 |
> |
} |
223 |
|
|
224 |
< |
if(isVisited(datom)) |
225 |
< |
return; |
224 |
> |
void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
225 |
> |
std::vector<AtomInfo*> atoms; |
226 |
> |
//we need to convert linear into 4 different atoms |
227 |
> |
Vector3d c1(0.0, 0.0, -1.8); |
228 |
> |
Vector3d c2(0.0, 0.0, -0.6); |
229 |
> |
Vector3d c3(0.0, 0.0, 0.6); |
230 |
> |
Vector3d c4(0.0, 0.0, 1.8); |
231 |
> |
RotMat3x3d rotMatrix; |
232 |
> |
RotMat3x3d rotTrans; |
233 |
> |
AtomInfo* atomInfo; |
234 |
> |
Vector3d pos; |
235 |
> |
Vector3d newVec; |
236 |
> |
Quat4d q; |
237 |
> |
AtomData* atomData; |
238 |
> |
GenericData* data; |
239 |
> |
bool haveAtomData; |
240 |
> |
|
241 |
> |
//if atom is not SSD atom, just skip it |
242 |
> |
if(!isLinearAtom(datom->getType())) |
243 |
> |
return; |
244 |
> |
|
245 |
> |
data = datom->getPropertyByName("ATOMDATA"); |
246 |
> |
if(data != NULL){ |
247 |
> |
atomData = dynamic_cast<AtomData*>(data); |
248 |
> |
if(atomData == NULL){ |
249 |
> |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
250 |
> |
atomData = new AtomData; |
251 |
> |
haveAtomData = false; |
252 |
> |
} else { |
253 |
> |
haveAtomData = true; |
254 |
> |
} |
255 |
> |
} else { |
256 |
> |
atomData = new AtomData; |
257 |
> |
haveAtomData = false; |
258 |
> |
} |
259 |
> |
|
260 |
|
|
261 |
< |
datom->getPos(pos); |
262 |
< |
datom->getU(u); |
261 |
> |
pos = datom->getPos(); |
262 |
> |
q = datom->getQ(); |
263 |
> |
rotMatrix = datom->getA(); |
264 |
|
|
265 |
< |
atomData = new AtomData; |
266 |
< |
atomData->setID("ATOMDATA"); |
267 |
< |
atomInfo =new AtomInfo; |
265 |
> |
// We need A^T to convert from body-fixed to space-fixed: |
266 |
> |
rotTrans = rotMatrix.transpose(); |
267 |
> |
|
268 |
> |
newVec = rotTrans * c1; |
269 |
> |
atomInfo = new AtomInfo; |
270 |
> |
atomInfo->atomTypeName = "C"; |
271 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
272 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
273 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
274 |
> |
atomInfo->dipole[0] = 0.0; |
275 |
> |
atomInfo->dipole[1] = 0.0; |
276 |
> |
atomInfo->dipole[2] = 0.0; |
277 |
> |
atomData->addAtomInfo(atomInfo); |
278 |
> |
|
279 |
> |
newVec = rotTrans * c2; |
280 |
> |
atomInfo = new AtomInfo; |
281 |
> |
atomInfo->atomTypeName = "C"; |
282 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
283 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
284 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
285 |
> |
atomInfo->dipole[0] = 0.0; |
286 |
> |
atomInfo->dipole[1] = 0.0; |
287 |
> |
atomInfo->dipole[2] = 0.0; |
288 |
> |
atomData->addAtomInfo(atomInfo); |
289 |
> |
|
290 |
> |
newVec = rotTrans * c3; |
291 |
> |
atomInfo = new AtomInfo; |
292 |
> |
atomInfo->atomTypeName = "C"; |
293 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
294 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
295 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
296 |
> |
atomInfo->dipole[0] = 0.0; |
297 |
> |
atomInfo->dipole[1] = 0.0; |
298 |
> |
atomInfo->dipole[2] = 0.0; |
299 |
> |
atomData->addAtomInfo(atomInfo); |
300 |
> |
|
301 |
> |
newVec = rotTrans * c4; |
302 |
> |
atomInfo = new AtomInfo; |
303 |
> |
atomInfo->atomTypeName = "C"; |
304 |
> |
atomInfo->pos[0] = pos[0] + newVec[0]; |
305 |
> |
atomInfo->pos[1] = pos[1] + newVec[1]; |
306 |
> |
atomInfo->pos[2] = pos[2] + newVec[2]; |
307 |
> |
atomInfo->dipole[0] = 0.0; |
308 |
> |
atomInfo->dipole[1] = 0.0; |
309 |
> |
atomInfo->dipole[2] = 0.0; |
310 |
> |
atomData->addAtomInfo(atomInfo); |
311 |
> |
|
312 |
> |
//add atom data into atom's property |
313 |
> |
|
314 |
> |
if(!haveAtomData){ |
315 |
> |
atomData->setID("ATOMDATA"); |
316 |
> |
datom->addProperty(atomData); |
317 |
> |
} |
318 |
> |
|
319 |
> |
setVisited(datom); |
320 |
> |
|
321 |
> |
} |
322 |
> |
|
323 |
> |
const std::string LinearAtomVisitor::toString(){ |
324 |
> |
char buffer[65535]; |
325 |
> |
std::string result; |
326 |
|
|
327 |
< |
atomInfo->AtomType = datom->getType(); |
328 |
< |
atomInfo->pos[0] = pos[0]; |
224 |
< |
atomInfo->pos[1] = pos[1]; |
225 |
< |
atomInfo->pos[2] = pos[2]; |
226 |
< |
atomInfo->dipole[0] = u[0]; |
227 |
< |
atomInfo->dipole[1] = u[1]; |
228 |
< |
atomInfo->dipole[2] = u[2]; |
327 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
328 |
> |
result += buffer; |
329 |
|
|
330 |
< |
atomData->addAtomInfo(atomInfo); |
330 |
> |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
331 |
> |
result += buffer; |
332 |
|
|
333 |
< |
datom->addProperty(atomData); |
333 |
> |
sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n"); |
334 |
> |
result += buffer; |
335 |
|
|
336 |
< |
setVisited(datom); |
337 |
< |
} |
336 |
> |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
337 |
> |
result += buffer; |
338 |
|
|
339 |
+ |
return result; |
340 |
+ |
} |
341 |
|
|
342 |
< |
const string DefaultAtomVisitor::toString(){ |
343 |
< |
char buffer[65535]; |
344 |
< |
string result; |
342 |
> |
bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){ |
343 |
> |
std::set<std::string>::iterator strIter; |
344 |
> |
strIter = GBLipidAtomType.find(atomType); |
345 |
> |
|
346 |
> |
return strIter != GBLipidAtomType.end() ? true : false; |
347 |
> |
} |
348 |
> |
|
349 |
> |
void GBLipidAtomVisitor::visit(DirectionalAtom* datom){ |
350 |
> |
std::vector<AtomInfo*> atoms; |
351 |
> |
//we need to convert linear into 4 different atoms |
352 |
> |
Vector3d c1(0.0, 0.0, -6.25); |
353 |
> |
Vector3d c2(0.0, 0.0, -2.1); |
354 |
> |
Vector3d c3(0.0, 0.0, 2.1); |
355 |
> |
Vector3d c4(0.0, 0.0, 6.25); |
356 |
> |
RotMat3x3d rotMatrix; |
357 |
> |
RotMat3x3d rotTrans; |
358 |
> |
AtomInfo* atomInfo; |
359 |
> |
Vector3d pos; |
360 |
> |
Vector3d newVec; |
361 |
> |
Quat4d q; |
362 |
> |
AtomData* atomData; |
363 |
> |
GenericData* data; |
364 |
> |
bool haveAtomData; |
365 |
> |
|
366 |
> |
//if atom is not GBlipid atom, just skip it |
367 |
> |
if(!isGBLipidAtom(datom->getType())) |
368 |
> |
return; |
369 |
> |
|
370 |
> |
data = datom->getPropertyByName("ATOMDATA"); |
371 |
> |
if(data != NULL){ |
372 |
> |
atomData = dynamic_cast<AtomData*>(data); |
373 |
> |
if(atomData == NULL){ |
374 |
> |
std::cerr << "can not get Atom Data from " << datom->getType() << std::endl; |
375 |
> |
atomData = new AtomData; |
376 |
> |
haveAtomData = false; |
377 |
> |
} else { |
378 |
> |
haveAtomData = true; |
379 |
> |
} |
380 |
> |
} else { |
381 |
> |
atomData = new AtomData; |
382 |
> |
haveAtomData = false; |
383 |
> |
} |
384 |
> |
|
385 |
|
|
386 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
387 |
< |
result += buffer; |
386 |
> |
pos = datom->getPos(); |
387 |
> |
q = datom->getQ(); |
388 |
> |
rotMatrix = datom->getA(); |
389 |
|
|
390 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
391 |
< |
result += buffer; |
390 |
> |
// We need A^T to convert from body-fixed to space-fixed: |
391 |
> |
rotTrans = rotMatrix.transpose(); |
392 |
|
|
393 |
< |
sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n"); |
394 |
< |
result += buffer; |
393 |
> |
newVec = rotTrans * c1; |
394 |
> |
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 |
|
|
404 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
405 |
< |
result += buffer; |
404 |
> |
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 |
< |
return result; |
416 |
< |
} |
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 |