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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, 234107 (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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#include "applications/hydrodynamics/ShapeBuilder.hpp" |
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#include "hydrodynamics/Sphere.hpp" |
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#include "hydrodynamics/Ellipsoid.hpp" |
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#include "applications/hydrodynamics/CompositeShape.hpp" |
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#include "types/LennardJonesAdapter.hpp" |
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#include "types/GayBerneAdapter.hpp" |
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|
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namespace OpenMD { |
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|
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Shape* ShapeBuilder::createShape(StuntDouble* sd) { |
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Shape* currShape = NULL; |
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if (sd->isDirectionalAtom()) { |
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currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd)); |
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} else if (sd->isAtom()) { |
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currShape = internalCreateShape(static_cast<Atom*>(sd)); |
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} else if (sd->isRigidBody()) { |
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currShape = internalCreateShape(static_cast<RigidBody*>(sd)); |
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} |
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return currShape; |
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} |
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|
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Shape* ShapeBuilder::internalCreateShape(Atom* atom) { |
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AtomType* atomType = atom->getAtomType(); |
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Shape* currShape = NULL; |
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LennardJonesAdapter lja = LennardJonesAdapter(atomType); |
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if (lja.isLennardJones()){ |
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currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0); |
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} else { |
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int obanum = etab.GetAtomicNum((atom->getType()).c_str()); |
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if (obanum != 0) { |
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currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum)); |
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} else { |
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sprintf( painCave.errMsg, |
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"Could not find atom type in default element.txt\n"); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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return currShape; |
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} |
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|
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Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) { |
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AtomType* atomType = datom->getAtomType(); |
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Shape* currShape = NULL; |
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LennardJonesAdapter lja = LennardJonesAdapter(atomType); |
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GayBerneAdapter gba = GayBerneAdapter(atomType); |
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if (gba.isGayBerne()) { |
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currShape = new Ellipsoid(datom->getPos(), gba.getL()/2.0, |
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gba.getD()/2.0, datom->getA()); |
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} else if (lja.isLennardJones()) { |
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currShape = new Sphere(datom->getPos(), lja.getSigma()/2.0); |
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} else { |
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int obanum = etab.GetAtomicNum((datom->getType()).c_str()); |
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if (obanum != 0) { |
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currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum)); |
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} else { |
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sprintf( painCave.errMsg, |
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"Could not find atom type in default element.txt\n"); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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return currShape; |
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} |
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|
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Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) { |
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|
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std::vector<Atom*>::iterator ai; |
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CompositeShape* compositeShape = new CompositeShape; |
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Atom* atom; |
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for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) { |
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Shape* currShape = NULL; |
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if (atom->isDirectionalAtom()){ |
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currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom)); |
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}else if (atom->isAtom()){ |
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currShape = internalCreateShape(static_cast<Atom*>(atom)); |
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} |
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if (currShape != NULL) |
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compositeShape->addShape(currShape); |
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} |
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|
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return compositeShape; |
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} |
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} |
