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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 "math/MatVec3.h" |
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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::vector<std::string>::iterator strIter; |
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|
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for( strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); |
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++strIter ) |
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if (*strIter == atomType) |
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return true; |
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|
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return false; |
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} |
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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->AtomType = "X"; |
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atomInfo->pos[0] = pos[0]; |
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atomInfo->pos[1] = pos[1]; |
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atomInfo->pos[2] = pos[2]; |
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atomInfo->dipole[0] = newVec[0]; |
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atomInfo->dipole[1] = newVec[1]; |
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atomInfo->dipole[2] = newVec[2]; |
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|
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atomData->addAtomInfo(atomInfo); |
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|
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//oxygen |
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//matVecMul3(rotTrans, ox, newVec); |
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newVec = rotTrans * ox; |
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|
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "O"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
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|
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//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->AtomType = "H"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
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|
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//hydrogen2 |
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//matVecMul3(rotTrans, h2, newVec); |
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newVec = rotTrans * h2; |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "H"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
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|
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//add atom data into atom's property |
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|
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if (!haveAtomData) { |
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atomData->setID("ATOMDATA"); |
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datom->addProperty(atomData); |
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} |
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|
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setVisited(datom); |
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} |
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|
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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 string& atomType){ |
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vector<string>::iterator strIter; |
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|
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for(strIter = linearAtomType.begin(); strIter != linearAtomType.end(); |
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++strIter) |
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if(*strIter == atomType) |
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return true; |
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|
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return false; |
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} |
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|
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void LinearAtomVisitor::visit(DirectionalAtom* datom){ |
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|
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vector<AtomInfo*> atoms; |
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|
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//we need to convert linear into 4 different atoms |
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double c1[3] = {0.0, 0.0, -1.8}; |
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double c2[3] = {0.0, 0.0, -0.6}; |
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double c3[3] = {0.0, 0.0, 0.6}; |
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double c4[3] = {0.0, 0.0, 1.8}; |
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double rotMatrix[3][3]; |
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double rotTrans[3][3]; |
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AtomInfo* atomInfo; |
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double pos[3]; |
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double newVec[3]; |
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double q[4]; |
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AtomData* atomData; |
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GenericData* data; |
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bool haveAtomData; |
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|
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//if atom is not SSD atom, just skip it |
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if(!isLinearAtom(datom->getType())) |
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return; |
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|
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data = datom->getProperty("ATOMDATA"); |
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if(data != NULL){ |
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|
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atomData = dynamic_cast<AtomData*>(data); |
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if(atomData == NULL){ |
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cerr << "can not get Atom Data from " << datom->getType() << endl; |
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atomData = new AtomData; |
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haveAtomData = false; |
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} |
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else |
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haveAtomData = true; |
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} |
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else{ |
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atomData = new AtomData; |
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haveAtomData = false; |
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} |
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|
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|
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datom->getPos(pos); |
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datom->getQ(q); |
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datom->getA(rotMatrix); |
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|
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// We need A^T to convert from body-fixed to space-fixed: |
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transposeMat3(rotMatrix, rotTrans); |
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|
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matVecMul3(rotTrans, c1, newVec); |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
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|
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matVecMul3(rotTrans, c2, newVec); |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
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|
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matVecMul3(rotTrans, c3, newVec); |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
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|
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matVecMul3(rotTrans, c4, newVec); |
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atomInfo = new AtomInfo; |
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atomInfo->AtomType = "C"; |
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atomInfo->pos[0] = pos[0] + newVec[0]; |
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atomInfo->pos[1] = pos[1] + newVec[1]; |
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atomInfo->pos[2] = pos[2] + newVec[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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atomData->addAtomInfo(atomInfo); |
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|
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//add atom data into atom's property |
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|
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if(!haveAtomData){ |
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atomData->setID("ATOMDATA"); |
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datom->addProperty(atomData); |
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} |
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|
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setVisited(datom); |
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|
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} |
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|
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const string LinearAtomVisitor::toString(){ |
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char buffer[65535]; |
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string result; |
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|
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sprintf(buffer ,"------------------------------------------------------------------\n"); |
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result += buffer; |
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|
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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|
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sprintf(buffer , "Visitor Description: Convert 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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//----------------------------------------------------------------------------// |
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|
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void DefaultAtomVisitor::visit(Atom *atom) { |
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AtomData *atomData; |
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AtomInfo *atomInfo; |
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Vector3d pos; |
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|
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if (isVisited(atom)) |
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return; |
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|
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atomInfo = new AtomInfo; |
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|
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atomData = new AtomData; |
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atomData->setID("ATOMDATA"); |
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|
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pos = atom->getPos(); |
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atomInfo->AtomType = atom->getType(); |
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atomInfo->pos[0] = pos[0]; |
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atomInfo->pos[1] = pos[1]; |
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atomInfo->pos[2] = pos[2]; |
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atomInfo->dipole[0] = 0.0; |
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atomInfo->dipole[1] = 0.0; |
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atomInfo->dipole[2] = 0.0; |
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|
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atomData->addAtomInfo(atomInfo); |
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|
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atom->addProperty(atomData); |
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|
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setVisited(atom); |
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} |
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|
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void DefaultAtomVisitor::visit(DirectionalAtom *datom) { |
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AtomData *atomData; |
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AtomInfo *atomInfo; |
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Vector3d pos; |
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Vector3d u; |
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|
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if (isVisited(datom)) |
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return; |
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|
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pos = datom->getPos(); |
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u = datom->getElectroFrame().getColumn(3); |
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|
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atomData = new AtomData; |
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atomData->setID("ATOMDATA"); |
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atomInfo = new AtomInfo; |
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|
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atomInfo->AtomType = datom->getType(); |
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atomInfo->pos[0] = pos[0]; |
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atomInfo->pos[1] = pos[1]; |
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atomInfo->pos[2] = pos[2]; |
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atomInfo->dipole[0] = u[0]; |
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atomInfo->dipole[1] = u[1]; |
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atomInfo->dipole[2] = u[2]; |
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|
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atomData->addAtomInfo(atomInfo); |
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|
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datom->addProperty(atomData); |
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|
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setVisited(datom); |
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} |
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|
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const std::string DefaultAtomVisitor::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: copy atom infomation into atom data\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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} //namespace oopse |
