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tim |
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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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tim |
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#include "applications/hydrodynamics/HydrodynamicsModel.hpp" |
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gezelter |
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#include "hydrodynamics/Shape.hpp" |
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#include "hydrodynamics/Sphere.hpp" |
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#include "hydrodynamics/Ellipsoid.hpp" |
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tim |
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#include "applications/hydrodynamics/CompositeShape.hpp" |
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tim |
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namespace oopse { |
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gezelter |
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bool HydrodynamicsModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) { |
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tim |
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return false; |
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gezelter |
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} |
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void HydrodynamicsModel::writeHydroProps(std::ostream& os) { |
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tim |
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gezelter |
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tim |
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os << sd_->getType() << "\t"; |
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tim |
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|
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tim |
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//center of resistance |
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os << cr_.center[0] << "\t" << cr_.center[1] << "\t" << cr_.center[2] << "\t"; |
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gezelter |
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|
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tim |
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//resistance tensor at center of resistance |
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//translation |
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os << cr_.Xi(0, 0) << "\t" << cr_.Xi(0, 1) << "\t" << cr_.Xi(0, 2) << "\t" |
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gezelter |
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<< cr_.Xi(1, 0) << "\t" << cr_.Xi(1, 1) << "\t" << cr_.Xi(1, 2) << "\t" |
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<< cr_.Xi(2, 0) << "\t" << cr_.Xi(2, 1) << "\t" << cr_.Xi(2, 2) << "\t"; |
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tim |
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//rotation-translation |
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os << cr_.Xi(0, 3) << "\t" << cr_.Xi(0, 4) << "\t" << cr_.Xi(0, 5) << "\t" |
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gezelter |
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<< cr_.Xi(1, 3) << "\t" << cr_.Xi(1, 4) << "\t" << cr_.Xi(1, 5) << "\t" |
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<< cr_.Xi(2, 3) << "\t" << cr_.Xi(2, 4) << "\t" << cr_.Xi(2, 5) << "\t"; |
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tim |
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//translation-rotation |
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os << cr_.Xi(3, 0) << "\t" << cr_.Xi(3, 1) << "\t" << cr_.Xi(3, 2) << "\t" |
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gezelter |
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<< cr_.Xi(4, 0) << "\t" << cr_.Xi(4, 1) << "\t" << cr_.Xi(4, 2) << "\t" |
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<< cr_.Xi(5, 0) << "\t" << cr_.Xi(5, 1) << "\t" << cr_.Xi(5, 2) << "\t"; |
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tim |
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//rotation |
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os << cr_.Xi(3, 3) << "\t" << cr_.Xi(3, 4) << "\t" << cr_.Xi(3, 5) << "\t" |
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gezelter |
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<< cr_.Xi(4, 3) << "\t" << cr_.Xi(4, 4) << "\t" << cr_.Xi(4, 5) << "\t" |
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<< cr_.Xi(5, 3) << "\t" << cr_.Xi(5, 4) << "\t" << cr_.Xi(5, 5) << "\t"; |
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tim |
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//diffusion tensor at center of resistance |
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//translation |
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os << cr_.D(0, 0) << "\t" << cr_.D(0, 1) << "\t" << cr_.D(0, 2) << "\t" |
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gezelter |
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<< cr_.D(1, 0) << "\t" << cr_.D(1, 1) << "\t" << cr_.D(1, 2) << "\t" |
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<< cr_.D(2, 0) << "\t" << cr_.D(2, 1) << "\t" << cr_.D(2, 2) << "\t"; |
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tim |
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//rotation-translation |
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os << cr_.D(0, 3) << "\t" << cr_.D(0, 4) << "\t" << cr_.D(0, 5) << "\t" |
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gezelter |
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<< cr_.D(1, 3) << "\t" << cr_.D(1, 4) << "\t" << cr_.D(1, 5) << "\t" |
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<< cr_.D(2, 3) << "\t" << cr_.D(2, 4) << "\t" << cr_.D(2, 5) << "\t"; |
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tim |
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//translation-rotation |
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os << cr_.D(3, 0) << "\t" << cr_.D(3, 1) << "\t" << cr_.D(3, 2) << "\t" |
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gezelter |
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<< cr_.D(4, 0) << "\t" << cr_.D(4, 1) << "\t" << cr_.D(4, 2) << "\t" |
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<< cr_.D(5, 0) << "\t" << cr_.D(5, 1) << "\t" << cr_.D(5, 2) << "\t"; |
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tim |
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//rotation |
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os << cr_.D(3, 3) << "\t" << cr_.D(3, 4) << "\t" << cr_.D(3, 5) << "\t" |
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gezelter |
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<< cr_.D(4, 3) << "\t" << cr_.D(4, 4) << "\t" << cr_.D(4, 5) << "\t" |
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<< cr_.D(5, 3) << "\t" << cr_.D(5, 4) << "\t" << cr_.D(5, 5) << "\t"; |
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tim |
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//--------------------------------------------------------------------- |
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gezelter |
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|
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tim |
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//center of diffusion |
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os << cd_.center[0] << "\t" << cd_.center[1] << "\t" << cd_.center[2] << "\t"; |
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gezelter |
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tim |
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//resistance tensor at center of diffusion |
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//translation |
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os << cd_.Xi(0, 0) << "\t" << cd_.Xi(0, 1) << "\t" << cd_.Xi(0, 2) << "\t" |
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gezelter |
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<< cd_.Xi(1, 0) << "\t" << cd_.Xi(1, 1) << "\t" << cd_.Xi(1, 2) << "\t" |
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<< cd_.Xi(2, 0) << "\t" << cd_.Xi(2, 1) << "\t" << cd_.Xi(2, 2) << "\t"; |
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tim |
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//rotation-translation |
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os << cd_.Xi(0, 3) << "\t" << cd_.Xi(0, 4) << "\t" << cd_.Xi(0, 5) << "\t" |
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gezelter |
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<< cd_.Xi(1, 3) << "\t" << cd_.Xi(1, 4) << "\t" << cd_.Xi(1, 5) << "\t" |
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<< cd_.Xi(2, 3) << "\t" << cd_.Xi(2, 4) << "\t" << cd_.Xi(2, 5) << "\t"; |
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tim |
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//translation-rotation |
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os << cd_.Xi(3, 0) << "\t" << cd_.Xi(3, 1) << "\t" << cd_.Xi(3, 2) << "\t" |
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gezelter |
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<< cd_.Xi(4, 0) << "\t" << cd_.Xi(4, 1) << "\t" << cd_.Xi(4, 2) << "\t" |
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<< cd_.Xi(5, 0) << "\t" << cd_.Xi(5, 1) << "\t" << cd_.Xi(5, 2) << "\t"; |
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tim |
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//rotation |
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os << cd_.Xi(3, 3) << "\t" << cd_.Xi(3, 4) << "\t" << cd_.Xi(3, 5) << "\t" |
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gezelter |
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<< cd_.Xi(4, 3) << "\t" << cd_.Xi(4, 4) << "\t" << cd_.Xi(4, 5) << "\t" |
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<< cd_.Xi(5, 3) << "\t" << cd_.Xi(5, 4) << "\t" << cd_.Xi(5, 5) << "\t"; |
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tim |
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//diffusion tensor at center of diffusion |
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//translation |
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os << cd_.D(0, 0) << "\t" << cd_.D(0, 1) << "\t" << cd_.D(0, 2) << "\t" |
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gezelter |
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<< cd_.D(1, 0) << "\t" << cd_.D(1, 1) << "\t" << cd_.D(1, 2) << "\t" |
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<< cd_.D(2, 0) << "\t" << cd_.D(2, 1) << "\t" << cd_.D(2, 2) << "\t"; |
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tim |
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//rotation-translation |
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os << cd_.D(0, 3) << "\t" << cd_.D(0, 4) << "\t" << cd_.D(0, 5) << "\t" |
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gezelter |
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<< cd_.D(1, 3) << "\t" << cd_.D(1, 4) << "\t" << cd_.D(1, 5) << "\t" |
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<< cd_.D(2, 3) << "\t" << cd_.D(2, 4) << "\t" << cd_.D(2, 5) << "\t"; |
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tim |
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//translation-rotation |
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os << cd_.D(3, 0) << "\t" << cd_.D(3, 1) << "\t" << cd_.D(3, 2) << "\t" |
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gezelter |
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<< cd_.D(4, 0) << "\t" << cd_.D(4, 1) << "\t" << cd_.D(4, 2) << "\t" |
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<< cd_.D(5, 0) << "\t" << cd_.D(5, 1) << "\t" << cd_.D(5, 2) << "\t"; |
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tim |
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//rotation |
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os << cd_.D(3, 3) << "\t" << cd_.D(3, 4) << "\t" << cd_.D(3, 5) << "\t" |
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gezelter |
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<< cd_.D(4, 3) << "\t" << cd_.D(4, 4) << "\t" << cd_.D(4, 5) << "\t" |
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<< cd_.D(5, 3) << "\t" << cd_.D(5, 4) << "\t" << cd_.D(5, 5) << "\n"; |
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} |
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tim |
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} |
