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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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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#include "types/MultipoleAdapter.hpp" |
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#include "types/GayBerneAdapter.hpp" |
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|
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namespace OpenMD { |
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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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//------------------------------------------------------------------------// |
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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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Vector3d vel; |
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Vector3d frc; |
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Vector3d u; |
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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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vel = atom->getVel(); |
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frc = atom->getFrc(); |
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atomInfo->atomTypeName = 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->vel[0] = vel[0]; |
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atomInfo->vel[1] = vel[1]; |
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atomInfo->vel[2] = vel[2]; |
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atomInfo->hasVelocity = true; |
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atomInfo->frc[0] = frc[0]; |
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atomInfo->frc[1] = frc[1]; |
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atomInfo->frc[2] = frc[2]; |
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atomInfo->hasForce = true; |
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atomInfo->vec[0] = 0.0; |
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atomInfo->vec[1] = 0.0; |
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atomInfo->vec[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 vel; |
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Vector3d frc; |
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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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vel = datom->getVel(); |
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frc = datom->getFrc(); |
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|
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GayBerneAdapter gba = GayBerneAdapter(datom->getAtomType()); |
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MultipoleAdapter ma = MultipoleAdapter(datom->getAtomType()); |
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|
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if (gba.isGayBerne()) { |
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u = datom->getA().transpose()*V3Z; |
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} else if (ma.isDipole()) { |
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u = datom->getDipole(); |
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} else if (ma.isQuadrupole()) { |
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//u = datom->getQuadrupole().getColumn(2); |
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u = datom->getA().transpose()*V3Z; |
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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->atomTypeName = 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->vel[0] = vel[0]; |
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atomInfo->vel[1] = vel[1]; |
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atomInfo->vel[2] = vel[2]; |
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atomInfo->hasVelocity = true; |
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atomInfo->frc[0] = frc[0]; |
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atomInfo->frc[1] = frc[1]; |
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atomInfo->frc[2] = frc[2]; |
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atomInfo->hasForce = true; |
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atomInfo->vec[0] = u[0]; |
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atomInfo->vec[1] = u[1]; |
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atomInfo->vec[2] = u[2]; |
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atomInfo->hasVector = true; |
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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 OpenMD |
