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#ifndef __MOLOCATOR_H__ |
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#define __MOLOCATOR_H__ |
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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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#ifndef APPLICATIONS_SIMPLEBUILDER_MOLOCATOR_HPP |
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#define APPLICATIONS_SIMPLEBUILDER_MOLOCATOR_HPP |
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#include <vector> |
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#include "primitives/Atom.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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#include "types/MoleculeStamp.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "math/Vector3.hpp" |
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#include "UseTheForce/ForceFields.hpp" |
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using namespace std; |
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#include "UseTheForce/ForceField.hpp" |
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namespace oopse { |
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//convert lattice vector to rotation matrix |
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void latVec2RotMat(const Vector3d& lv, double rotMat[3][3]); |
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double getAtomMass(const std::string& at, ForceField* myFF); |
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double getMolMass(MoleculeStamp *molStamp, ForceField *myFF); |
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RotMat3x3d latVec2RotMat(const Vector3d& lv); |
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class MoLocator{ |
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public: |
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MoLocator( MoleculeStamp* theStamp, ForceFields* theFF); |
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public: |
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MoLocator( MoleculeStamp* theStamp, ForceField* theFF); |
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void placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol); |
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private: |
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void calcRef( void ); |
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MoleculeStamp* myStamp; |
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void placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol); |
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ForceField* myFF; |
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std::vector<Vector3d> refCoords; |
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int nIntegrableObjects; |
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private: |
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void calcRefCoords( void ); |
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MoleculeStamp* myStamp; |
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ForceFields* myFF; |
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vector<Vector3d> refCoords; |
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int nIntegrableObjects; |
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}; |
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} |
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#endif |
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