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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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void BaseAtomVisitor::visit(RigidBody* rb){ |
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//vector<Atom*> myAtoms; |
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//vector<Atom*>::iterator atomIter; |
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//myAtoms = rb->getAtoms(); |
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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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//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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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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//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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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 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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bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) { |
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std::vector<std::string>::iterator strIter; |
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|
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void SSDAtomVisitor::visit(DirectionalAtom* datom){ |
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for( strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); |
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++strIter ) |
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if (*strIter == atomType) |
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return true; |
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|
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vector<AtomInfo*> atoms; |
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return 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->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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|
|
149 |
< |
if(!haveAtomData){ |
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< |
atomData->setID("ATOMDATA"); |
151 |
< |
datom->addProperty(atomData); |
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< |
} |
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> |
atomData->addAtomInfo(atomInfo); |
150 |
|
|
151 |
< |
setVisited(datom); |
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> |
//oxygen |
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> |
//matVecMul3(rotTrans, ox, newVec); |
153 |
> |
newVec = rotTrans * ox; |
154 |
|
|
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atomInfo = new AtomInfo; |
156 |
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atomInfo->AtomType = "O"; |
157 |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
158 |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
159 |
+ |
atomInfo->pos[2] = pos[2] + newVec[2]; |
160 |
+ |
atomInfo->dipole[0] = 0.0; |
161 |
+ |
atomInfo->dipole[1] = 0.0; |
162 |
+ |
atomInfo->dipole[2] = 0.0; |
163 |
+ |
atomData->addAtomInfo(atomInfo); |
164 |
+ |
|
165 |
+ |
//hydrogen1 |
166 |
+ |
//matVecMul3(rotTrans, h1, newVec); |
167 |
+ |
newVec = rotTrans * h1; |
168 |
+ |
atomInfo = new AtomInfo; |
169 |
+ |
atomInfo->AtomType = "H"; |
170 |
+ |
atomInfo->pos[0] = pos[0] + newVec[0]; |
171 |
+ |
atomInfo->pos[1] = pos[1] + newVec[1]; |
172 |
+ |
atomInfo->pos[2] = pos[2] + newVec[2]; |
173 |
+ |
atomInfo->dipole[0] = 0.0; |
174 |
+ |
atomInfo->dipole[1] = 0.0; |
175 |
+ |
atomInfo->dipole[2] = 0.0; |
176 |
+ |
atomData->addAtomInfo(atomInfo); |
177 |
+ |
|
178 |
+ |
//hydrogen2 |
179 |
+ |
//matVecMul3(rotTrans, h2, newVec); |
180 |
+ |
newVec = rotTrans * h2; |
181 |
+ |
atomInfo = new AtomInfo; |
182 |
+ |
atomInfo->AtomType = "H"; |
183 |
+ |
atomInfo->pos[0] = pos[0] + newVec[0]; |
184 |
+ |
atomInfo->pos[1] = pos[1] + newVec[1]; |
185 |
+ |
atomInfo->pos[2] = pos[2] + newVec[2]; |
186 |
+ |
atomInfo->dipole[0] = 0.0; |
187 |
+ |
atomInfo->dipole[1] = 0.0; |
188 |
+ |
atomInfo->dipole[2] = 0.0; |
189 |
+ |
atomData->addAtomInfo(atomInfo); |
190 |
+ |
|
191 |
+ |
//add atom data into atom's property |
192 |
+ |
|
193 |
+ |
if (!haveAtomData) { |
194 |
+ |
atomData->setID("ATOMDATA"); |
195 |
+ |
datom->addProperty(atomData); |
196 |
+ |
} |
197 |
+ |
|
198 |
+ |
setVisited(datom); |
199 |
|
} |
200 |
|
|
201 |
< |
const string SSDAtomVisitor::toString(){ |
202 |
< |
char buffer[65535]; |
203 |
< |
string result; |
161 |
< |
|
162 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
163 |
< |
result += buffer; |
201 |
> |
const std::string SSDAtomVisitor::toString() { |
202 |
> |
char buffer[65535]; |
203 |
> |
std::string result; |
204 |
|
|
205 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
206 |
< |
result += buffer; |
205 |
> |
sprintf(buffer, |
206 |
> |
"------------------------------------------------------------------\n"); |
207 |
> |
result += buffer; |
208 |
|
|
209 |
< |
sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n"); |
210 |
< |
result += buffer; |
209 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
210 |
> |
result += buffer; |
211 |
|
|
212 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
213 |
< |
result += buffer; |
212 |
> |
sprintf(buffer, |
213 |
> |
"Visitor Description: Convert SSD into 4 different atoms\n"); |
214 |
> |
result += buffer; |
215 |
|
|
216 |
< |
return result; |
216 |
> |
sprintf(buffer, |
217 |
> |
"------------------------------------------------------------------\n"); |
218 |
> |
result += buffer; |
219 |
> |
|
220 |
> |
return result; |
221 |
|
} |
222 |
|
|
223 |
|
bool LinearAtomVisitor::isLinearAtom(const string& atomType){ |
355 |
|
|
356 |
|
//----------------------------------------------------------------------------// |
357 |
|
|
358 |
< |
void DefaultAtomVisitor::visit(Atom* atom){ |
359 |
< |
AtomData* atomData; |
360 |
< |
AtomInfo* atomInfo; |
361 |
< |
double pos[3]; |
358 |
> |
void DefaultAtomVisitor::visit(Atom *atom) { |
359 |
> |
AtomData *atomData; |
360 |
> |
AtomInfo *atomInfo; |
361 |
> |
Vector3d pos; |
362 |
|
|
363 |
< |
if(isVisited(atom)) |
364 |
< |
return; |
363 |
> |
if (isVisited(atom)) |
364 |
> |
return; |
365 |
|
|
366 |
< |
atomInfo =new AtomInfo; |
366 |
> |
atomInfo = new AtomInfo; |
367 |
|
|
368 |
< |
atomData = new AtomData; |
369 |
< |
atomData->setID("ATOMDATA"); |
324 |
< |
|
325 |
< |
atom->getPos(pos); |
326 |
< |
atomInfo->AtomType = atom->getType(); |
327 |
< |
atomInfo->pos[0] = pos[0]; |
328 |
< |
atomInfo->pos[1] = pos[1]; |
329 |
< |
atomInfo->pos[2] = pos[2]; |
330 |
< |
atomInfo->dipole[0] = 0.0; |
331 |
< |
atomInfo->dipole[1] = 0.0; |
332 |
< |
atomInfo->dipole[2] = 0.0; |
368 |
> |
atomData = new AtomData; |
369 |
> |
atomData->setID("ATOMDATA"); |
370 |
|
|
371 |
< |
|
372 |
< |
atomData->addAtomInfo(atomInfo); |
373 |
< |
|
374 |
< |
atom->addProperty(atomData); |
375 |
< |
|
376 |
< |
setVisited(atom); |
371 |
> |
pos = atom->getPos(); |
372 |
> |
atomInfo->AtomType = atom->getType(); |
373 |
> |
atomInfo->pos[0] = pos[0]; |
374 |
> |
atomInfo->pos[1] = pos[1]; |
375 |
> |
atomInfo->pos[2] = pos[2]; |
376 |
> |
atomInfo->dipole[0] = 0.0; |
377 |
> |
atomInfo->dipole[1] = 0.0; |
378 |
> |
atomInfo->dipole[2] = 0.0; |
379 |
> |
|
380 |
> |
atomData->addAtomInfo(atomInfo); |
381 |
> |
|
382 |
> |
atom->addProperty(atomData); |
383 |
> |
|
384 |
> |
setVisited(atom); |
385 |
|
} |
341 |
– |
void DefaultAtomVisitor::visit(DirectionalAtom* datom){ |
342 |
– |
AtomData* atomData; |
343 |
– |
AtomInfo* atomInfo; |
344 |
– |
double pos[3]; |
345 |
– |
double u[3]; |
386 |
|
|
387 |
< |
if(isVisited(datom)) |
388 |
< |
return; |
389 |
< |
|
390 |
< |
datom->getPos(pos); |
391 |
< |
datom->getU(u); |
387 |
> |
void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
388 |
> |
AtomData *atomData; |
389 |
> |
AtomInfo *atomInfo; |
390 |
> |
Vector3d pos; |
391 |
> |
Vector3d u; |
392 |
|
|
393 |
< |
atomData = new AtomData; |
394 |
< |
atomData->setID("ATOMDATA"); |
355 |
< |
atomInfo =new AtomInfo; |
356 |
< |
|
357 |
< |
atomInfo->AtomType = datom->getType(); |
358 |
< |
atomInfo->pos[0] = pos[0]; |
359 |
< |
atomInfo->pos[1] = pos[1]; |
360 |
< |
atomInfo->pos[2] = pos[2]; |
361 |
< |
atomInfo->dipole[0] = u[0]; |
362 |
< |
atomInfo->dipole[1] = u[1]; |
363 |
< |
atomInfo->dipole[2] = u[2]; |
393 |
> |
if (isVisited(datom)) |
394 |
> |
return; |
395 |
|
|
396 |
< |
atomData->addAtomInfo(atomInfo); |
396 |
> |
pos = datom->getPos(); |
397 |
> |
u = datom->getElectroFrame().getColumn(3); |
398 |
|
|
399 |
< |
datom->addProperty(atomData); |
399 |
> |
atomData = new AtomData; |
400 |
> |
atomData->setID("ATOMDATA"); |
401 |
> |
atomInfo = new AtomInfo; |
402 |
|
|
403 |
< |
setVisited(datom); |
404 |
< |
} |
403 |
> |
atomInfo->AtomType = datom->getType(); |
404 |
> |
atomInfo->pos[0] = pos[0]; |
405 |
> |
atomInfo->pos[1] = pos[1]; |
406 |
> |
atomInfo->pos[2] = pos[2]; |
407 |
> |
atomInfo->dipole[0] = u[0]; |
408 |
> |
atomInfo->dipole[1] = u[1]; |
409 |
> |
atomInfo->dipole[2] = u[2]; |
410 |
|
|
411 |
+ |
atomData->addAtomInfo(atomInfo); |
412 |
|
|
413 |
< |
const string DefaultAtomVisitor::toString(){ |
374 |
< |
char buffer[65535]; |
375 |
< |
string result; |
376 |
< |
|
377 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
378 |
< |
result += buffer; |
413 |
> |
datom->addProperty(atomData); |
414 |
|
|
415 |
< |
sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
416 |
< |
result += buffer; |
415 |
> |
setVisited(datom); |
416 |
> |
} |
417 |
|
|
418 |
< |
sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n"); |
419 |
< |
result += buffer; |
418 |
> |
const std::string DefaultAtomVisitor::toString() { |
419 |
> |
char buffer[65535]; |
420 |
> |
std::string result; |
421 |
|
|
422 |
< |
sprintf(buffer ,"------------------------------------------------------------------\n"); |
423 |
< |
result += buffer; |
422 |
> |
sprintf(buffer, |
423 |
> |
"------------------------------------------------------------------\n"); |
424 |
> |
result += buffer; |
425 |
|
|
426 |
< |
return result; |
427 |
< |
} |
426 |
> |
sprintf(buffer, "Visitor name: %s\n", visitorName.c_str()); |
427 |
> |
result += buffer; |
428 |
|
|
429 |
< |
}//namespace oopse |
429 |
> |
sprintf(buffer, |
430 |
> |
"Visitor Description: copy atom infomation into atom data\n"); |
431 |
> |
result += buffer; |
432 |
> |
|
433 |
> |
sprintf(buffer, |
434 |
> |
"------------------------------------------------------------------\n"); |
435 |
> |
result += buffer; |
436 |
> |
|
437 |
> |
return result; |
438 |
> |
} |
439 |
> |
} //namespace oopse |