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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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* @file MoleculeCreator.hpp |
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* @author tlin |
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* @date 11/04/2004 |
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* @time 13:51am |
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* @version 1.0 |
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*/ |
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#ifndef BRAINS_MOLECULECREATOR_HPP |
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#define BRAINS_MOLECULECREATOR_HPP |
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#include "brains/SimInfo.hpp" |
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#include "types/AtomStamp.hpp" |
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#include "types/BondStamp.hpp" |
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#include "types/BendStamp.hpp" |
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#include "types/CutoffGroupStamp.hpp" |
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#include "types/RigidBodyStamp.hpp" |
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#include "types/TorsionStamp.hpp" |
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#include "types/InversionStamp.hpp" |
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#include "primitives/Molecule.hpp" |
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namespace OpenMD { |
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/** |
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* @class MoleculeCreator MoleculeCreator.hpp "brains/MoleculeCreator.hpp" |
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* @brief |
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*/ |
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class MoleculeCreator { |
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public: |
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virtual Molecule* createMolecule(ForceField* ff, MoleculeStamp *molStamp, |
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int stampId, int globalIndex, |
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LocalIndexManager* localIndexMan); |
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protected: |
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/** Create an atom by its stamp */ |
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virtual Atom* createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp, |
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LocalIndexManager* localIndexMan); |
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virtual RigidBody* createRigidBody(MoleculeStamp *molStamp, Molecule* mol, |
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RigidBodyStamp* rbStamp, |
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LocalIndexManager* localIndexMan); |
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virtual Bond* createBond(ForceField* ff, Molecule* mol, BondStamp* stamp); |
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virtual Bend* createBend(ForceField* ff, Molecule* mol, BendStamp* stamp); |
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virtual Torsion* createTorsion(ForceField* ff, Molecule* mol, |
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TorsionStamp* stamp); |
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virtual Inversion* createInversion(ForceField* ff, Molecule* mol, |
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InversionStamp* stamp); |
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virtual CutoffGroup* createCutoffGroup(Molecule* mol, |
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CutoffGroupStamp* stamp, |
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LocalIndexManager* localIndexMan); |
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virtual CutoffGroup* createCutoffGroup(Molecule * mol, Atom* atom, |
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LocalIndexManager* localIndexMan); |
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virtual void createConstraintPair(Molecule* mol); |
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virtual void createConstraintElem(Molecule* mol); |
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}; |
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} |
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#endif //BRAINS_MOLECULECREATOR_HPP |
