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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/HydrodynamicsModel.hpp" |
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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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#include "applications/hydrodynamics/CompositeShape.hpp" |
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|
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namespace OpenMD { |
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|
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bool HydrodynamicsModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) { |
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return false; |
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} |
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|
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void HydrodynamicsModel::writeHydroProps(std::ostream& os) { |
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|
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Vector3d center; |
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Mat6x6d Xi, D; |
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|
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os << sd_->getType() << "\t"; |
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|
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//center of resistance |
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|
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center = cr_->getCOR(); |
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|
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os << center[0] << "\t" << center[1] << "\t" << center[2] << "\t"; |
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|
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//resistance tensor at center of resistance |
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//translation |
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|
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Xi = cr_->getXi(); |
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|
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os << Xi(0, 0) << "\t" << Xi(0, 1) << "\t" << Xi(0, 2) << "\t" |
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<< Xi(1, 0) << "\t" << Xi(1, 1) << "\t" << Xi(1, 2) << "\t" |
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<< Xi(2, 0) << "\t" << Xi(2, 1) << "\t" << Xi(2, 2) << "\t"; |
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|
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//rotation-translation |
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os << Xi(0, 3) << "\t" << Xi(0, 4) << "\t" << Xi(0, 5) << "\t" |
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<< Xi(1, 3) << "\t" << Xi(1, 4) << "\t" << Xi(1, 5) << "\t" |
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<< Xi(2, 3) << "\t" << Xi(2, 4) << "\t" << Xi(2, 5) << "\t"; |
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|
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//translation-rotation |
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os << Xi(3, 0) << "\t" << Xi(3, 1) << "\t" << Xi(3, 2) << "\t" |
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<< Xi(4, 0) << "\t" << Xi(4, 1) << "\t" << Xi(4, 2) << "\t" |
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<< Xi(5, 0) << "\t" << Xi(5, 1) << "\t" << Xi(5, 2) << "\t"; |
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|
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//rotation |
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os << Xi(3, 3) << "\t" << Xi(3, 4) << "\t" << Xi(3, 5) << "\t" |
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<< Xi(4, 3) << "\t" << Xi(4, 4) << "\t" << Xi(4, 5) << "\t" |
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<< Xi(5, 3) << "\t" << Xi(5, 4) << "\t" << Xi(5, 5) << "\t"; |
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|
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|
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//diffusion tensor at center of resistance |
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//translation |
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|
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D = cr_->getD(); |
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|
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os << D(0, 0) << "\t" << D(0, 1) << "\t" << D(0, 2) << "\t" |
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<< D(1, 0) << "\t" << D(1, 1) << "\t" << D(1, 2) << "\t" |
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<< D(2, 0) << "\t" << D(2, 1) << "\t" << D(2, 2) << "\t"; |
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|
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//rotation-translation |
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os << D(0, 3) << "\t" << D(0, 4) << "\t" << D(0, 5) << "\t" |
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<< D(1, 3) << "\t" << D(1, 4) << "\t" << D(1, 5) << "\t" |
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<< D(2, 3) << "\t" << D(2, 4) << "\t" << D(2, 5) << "\t"; |
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|
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//translation-rotation |
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os << D(3, 0) << "\t" << D(3, 1) << "\t" << D(3, 2) << "\t" |
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<< D(4, 0) << "\t" << D(4, 1) << "\t" << D(4, 2) << "\t" |
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<< D(5, 0) << "\t" << D(5, 1) << "\t" << D(5, 2) << "\t"; |
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|
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//rotation |
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os << D(3, 3) << "\t" << D(3, 4) << "\t" << D(3, 5) << "\t" |
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<< D(4, 3) << "\t" << D(4, 4) << "\t" << D(4, 5) << "\t" |
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<< D(5, 3) << "\t" << D(5, 4) << "\t" << D(5, 5) << "\t"; |
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|
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//--------------------------------------------------------------------- |
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|
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//center of diffusion |
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|
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center = cd_->getCOR(); |
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|
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os << center[0] << "\t" << center[1] << "\t" << center[2] << "\t"; |
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|
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//resistance tensor at center of diffusion |
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//translation |
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|
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Xi = cd_->getXi(); |
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|
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os << Xi(0, 0) << "\t" << Xi(0, 1) << "\t" << Xi(0, 2) << "\t" |
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<< Xi(1, 0) << "\t" << Xi(1, 1) << "\t" << Xi(1, 2) << "\t" |
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<< Xi(2, 0) << "\t" << Xi(2, 1) << "\t" << Xi(2, 2) << "\t"; |
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|
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//rotation-translation |
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os << Xi(0, 3) << "\t" << Xi(0, 4) << "\t" << Xi(0, 5) << "\t" |
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<< Xi(1, 3) << "\t" << Xi(1, 4) << "\t" << Xi(1, 5) << "\t" |
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<< Xi(2, 3) << "\t" << Xi(2, 4) << "\t" << Xi(2, 5) << "\t"; |
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|
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//translation-rotation |
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os << Xi(3, 0) << "\t" << Xi(3, 1) << "\t" << Xi(3, 2) << "\t" |
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<< Xi(4, 0) << "\t" << Xi(4, 1) << "\t" << Xi(4, 2) << "\t" |
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<< Xi(5, 0) << "\t" << Xi(5, 1) << "\t" << Xi(5, 2) << "\t"; |
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|
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//rotation |
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os << Xi(3, 3) << "\t" << Xi(3, 4) << "\t" << Xi(3, 5) << "\t" |
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<< Xi(4, 3) << "\t" << Xi(4, 4) << "\t" << Xi(4, 5) << "\t" |
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<< Xi(5, 3) << "\t" << Xi(5, 4) << "\t" << Xi(5, 5) << "\t"; |
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|
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|
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//diffusion tensor at center of diffusion |
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//translation |
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|
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D = cd_->getD(); |
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|
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os << D(0, 0) << "\t" << D(0, 1) << "\t" << D(0, 2) << "\t" |
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<< D(1, 0) << "\t" << D(1, 1) << "\t" << D(1, 2) << "\t" |
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<< D(2, 0) << "\t" << D(2, 1) << "\t" << D(2, 2) << "\t"; |
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|
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//rotation-translation |
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os << D(0, 3) << "\t" << D(0, 4) << "\t" << D(0, 5) << "\t" |
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<< D(1, 3) << "\t" << D(1, 4) << "\t" << D(1, 5) << "\t" |
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<< D(2, 3) << "\t" << D(2, 4) << "\t" << D(2, 5) << "\t"; |
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|
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//translation-rotation |
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os << D(3, 0) << "\t" << D(3, 1) << "\t" << D(3, 2) << "\t" |
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<< D(4, 0) << "\t" << D(4, 1) << "\t" << D(4, 2) << "\t" |
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<< D(5, 0) << "\t" << D(5, 1) << "\t" << D(5, 2) << "\t"; |
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|
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//rotation |
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os << D(3, 3) << "\t" << D(3, 4) << "\t" << D(3, 5) << "\t" |
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<< D(4, 3) << "\t" << D(4, 4) << "\t" << D(4, 5) << "\t" |
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<< D(5, 3) << "\t" << D(5, 4) << "\t" << D(5, 5) << "\n"; |
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|
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} |
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|
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} |
