--- trunk/src/applications/hydrodynamics/ShapeBuilder.cpp 2006/03/20 19:12:14 908 +++ trunk/src/applications/hydrodynamics/ShapeBuilder.cpp 2009/11/25 20:02:06 1390 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,100 +28,142 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). */ #include "applications/hydrodynamics/ShapeBuilder.hpp" -#include "applications/hydrodynamics/Spheric.hpp" -#include "applications/hydrodynamics/Ellipsoid.hpp" +#include "hydrodynamics/Sphere.hpp" +#include "hydrodynamics/Ellipsoid.hpp" #include "applications/hydrodynamics/CompositeShape.hpp" -namespace oopse { - -Shape* ShapeBuilder::createShape(StuntDouble* sd) { +namespace OpenMD { + + Shape* ShapeBuilder::createShape(StuntDouble* sd) { Shape* currShape = NULL; - if (sd->isDirectionalAtom()) { - currShape = internalCreateShape(static_cast(sd)); - } else if (sd->isAtom()) { - currShape = internalCreateShape(static_cast(sd)); - } else if (sd->isRigidBody()) { - currShape = internalCreateShape(static_cast(sd)); - } - - - - return currShape; - -} - -Shape* ShapeBuilder::internalCreateShape(Atom* atom) { + if (sd->isDirectionalAtom()) { + currShape = internalCreateShape(static_cast(sd)); + } else if (sd->isAtom()) { + currShape = internalCreateShape(static_cast(sd)); + } else if (sd->isRigidBody()) { + currShape = internalCreateShape(static_cast(sd)); + } + return currShape; + } + + Shape* ShapeBuilder::internalCreateShape(Atom* atom) { AtomType* atomType = atom->getAtomType(); Shape* currShape = NULL; if (atomType->isLennardJones()){ - GenericData* data = atomType->getPropertyByName("LennardJones"); - if (data != NULL) { - LJParamGenericData* ljData = dynamic_cast(data); - - if (ljData != NULL) { - LJParam ljParam = ljData->getData(); - currShape = new Spheric(atom->getPos(), ljParam.sigma/2.0); + GenericData* data = atomType->getPropertyByName("LennardJones"); + if (data != NULL) { + LJParamGenericData* ljData = dynamic_cast(data); + + if (ljData != NULL) { + LJParam ljParam = ljData->getData(); + currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0); } else { - sprintf( painCave.errMsg, - "Can not cast GenericData to LJParam\n"); - painCave.severity = OOPSE_ERROR; - painCave.isFatal = 1; - simError(); - } - } - + sprintf( painCave.errMsg, + "Can not cast GenericData to LJParam\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } + } else { + int obanum = etab.GetAtomicNum((atom->getType()).c_str()); + if (obanum != 0) { + currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum)); + } else { + sprintf( painCave.errMsg, + "Could not find atom type in default element.txt\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } } - return currShape; -} - -Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) { + } + + Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) { AtomType* atomType = datom->getAtomType(); Shape* currShape = NULL; if (atomType->isGayBerne()) { - DirectionalAtomType* dAtomType = dynamic_cast(atomType); - - GenericData* data = dAtomType->getPropertyByName("GayBerne"); - if (data != NULL) { - GayBerneParamGenericData* gayBerneData = dynamic_cast(data); - - if (gayBerneData != NULL) { - GayBerneParam gayBerneParam = gayBerneData->getData(); - currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_sigma/2.0, gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, datom->getA()); - } else { - sprintf( painCave.errMsg, - "Can not cast GenericData to GayBerneParam\n"); - painCave.severity = OOPSE_ERROR; - painCave.isFatal = 1; - simError(); - } + DirectionalAtomType* dAtomType = dynamic_cast(atomType); + + GenericData* data = dAtomType->getPropertyByName("GayBerne"); + if (data != NULL) { + GayBerneParamGenericData* gayBerneData = dynamic_cast(data); + + if (gayBerneData != NULL) { + GayBerneParam gayBerneParam = gayBerneData->getData(); + currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_l/2.0, + gayBerneParam.GB_d/2.0, datom->getA()); } else { - sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n"); - painCave.severity = OOPSE_ERROR; - painCave.isFatal = 1; - simError(); - } + sprintf( painCave.errMsg, + "Can not cast GenericData to GayBerneParam\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } else { + sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } else if (atomType->isLennardJones()) { + GenericData* data = atomType->getPropertyByName("LennardJones"); + if (data != NULL) { + LJParamGenericData* ljData = dynamic_cast(data); + + if (ljData != NULL) { + LJParam ljParam = ljData->getData(); + currShape = new Sphere(datom->getPos(), ljParam.sigma/2.0); + } else { + sprintf( painCave.errMsg, + "Can not cast GenericData to LJParam\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } else { + int obanum = etab.GetAtomicNum((datom->getType()).c_str()); + if (obanum != 0) { + currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum)); + } else { + sprintf( painCave.errMsg, + "Could not find atom type in default element.txt\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } } return currShape; -} -Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) { + } - std::vector::iterator ai; - CompositeShape* compositeShape = new CompositeShape; - Atom* atom; - for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { - Shape* currShape = NULL; - if (atom->isDirectionalAtom()){ - currShape = internalCreateShape(static_cast(atom)); - }else if (atom->isAtom()){ - currShape = internalCreateShape(static_cast(atom)); - } - if (currShape != NULL) - compositeShape->addShape(currShape); - } - - return compositeShape; + Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) { + + std::vector::iterator ai; + CompositeShape* compositeShape = new CompositeShape; + Atom* atom; + for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { + Shape* currShape = NULL; + if (atom->isDirectionalAtom()){ + currShape = internalCreateShape(static_cast(atom)); + }else if (atom->isAtom()){ + currShape = internalCreateShape(static_cast(atom)); + } + if (currShape != NULL) + compositeShape->addShape(currShape); + } + + return compositeShape; + } } - -}