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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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#ifndef APPLICATION_HYDRODYNAMICS_HYDRODYNAMICSMODEL_HPP |
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#define APPLICATION_HYDRODYNAMICS_HYDRODYNAMICSMODEL_HPP |
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#include <vector> |
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|
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#include "math/Vector3.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "math/DynamicRectMatrix.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "applications/hydrodynamics/StuntDoubleShape.hpp" |
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#include "utils/any.hpp" |
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namespace oopse { |
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struct HydrodynamicProps { |
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Vector3d diffCenter; |
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Mat3x3d Ddtt; |
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Mat3x3d Ddtr; |
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Mat3x3d Ddrr; |
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Mat3x3d Xidtt; |
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Mat3x3d Xidrt; |
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Mat3x3d Xidtr; |
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Mat3x3d Xidrr; |
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}; |
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|
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struct BeadParam { |
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std::string atomName; |
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Vector3d pos; |
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double radius; |
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}; |
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|
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typedef std::map<std::string, boost::any> DynamicProperty; |
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|
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class HydrodynamicsModel { |
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public: |
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HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams); |
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bool calcHydrodyanmicsProps(); |
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|
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Vector3d getDiffCenter(); |
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Mat3x3d getTransDiff(); |
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Mat3x3d getRotDiff(); |
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Mat3x3d getTransRotDiff(); |
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void writeBeads(std::ostream& os); |
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void writeDiffCenterAndDiffTensor(std::ostream& os); |
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protected: |
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StuntDouble* sd_; |
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private: |
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virtual bool createBeads(std::vector<BeadParam>& beads) = 0; |
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|
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void calcResistanceTensor(); |
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void calcDiffusionTensor(); |
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HydrodynamicProps props_; |
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std::vector<BeadParam> beads_; |
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double viscosity_; |
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double temperature_; |
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|
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}; |
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|
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|
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} |
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|
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#endif |
