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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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|
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#include "hydrodynamics/HydroProp.hpp" |
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#include "utils/StringTokenizer.hpp" |
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#include "math/CholeskyDecomposition.hpp" |
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|
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namespace OpenMD { |
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|
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HydroProp::HydroProp(){ |
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hasCOR = false; |
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hasXi = false; |
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} |
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|
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HydroProp::HydroProp(Vector3d cor, Mat6x6d Xi, Mat6x6d D) : cor_(cor), |
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Xi_(Xi), D_(D), |
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hasCOR(true), |
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hasXi(true) { |
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} |
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|
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HydroProp::HydroProp(const std::string &frictionLine) { |
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|
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StringTokenizer tokenizer(frictionLine); |
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if (tokenizer.countTokens() >= 40) { |
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name_ = tokenizer.nextToken(); |
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cor_[0] = tokenizer.nextTokenAsDouble(); |
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cor_[1] = tokenizer.nextTokenAsDouble(); |
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cor_[2] = tokenizer.nextTokenAsDouble(); |
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|
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Xitt_(0,0) = tokenizer.nextTokenAsDouble(); |
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Xitt_(0,1) = tokenizer.nextTokenAsDouble(); |
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Xitt_(0,2) = tokenizer.nextTokenAsDouble(); |
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Xitt_(1,0) = tokenizer.nextTokenAsDouble(); |
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Xitt_(1,1) = tokenizer.nextTokenAsDouble(); |
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Xitt_(1,2) = tokenizer.nextTokenAsDouble(); |
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Xitt_(2,0) = tokenizer.nextTokenAsDouble(); |
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Xitt_(2,1) = tokenizer.nextTokenAsDouble(); |
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Xitt_(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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Xirt_(0,0) = tokenizer.nextTokenAsDouble(); |
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Xirt_(0,1) = tokenizer.nextTokenAsDouble(); |
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Xirt_(0,2) = tokenizer.nextTokenAsDouble(); |
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Xirt_(1,0) = tokenizer.nextTokenAsDouble(); |
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Xirt_(1,1) = tokenizer.nextTokenAsDouble(); |
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Xirt_(1,2) = tokenizer.nextTokenAsDouble(); |
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Xirt_(2,0) = tokenizer.nextTokenAsDouble(); |
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Xirt_(2,1) = tokenizer.nextTokenAsDouble(); |
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Xirt_(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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Xitr_(0,0) = tokenizer.nextTokenAsDouble(); |
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Xitr_(0,1) = tokenizer.nextTokenAsDouble(); |
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Xitr_(0,2) = tokenizer.nextTokenAsDouble(); |
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Xitr_(1,0) = tokenizer.nextTokenAsDouble(); |
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Xitr_(1,1) = tokenizer.nextTokenAsDouble(); |
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Xitr_(1,2) = tokenizer.nextTokenAsDouble(); |
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Xitr_(2,0) = tokenizer.nextTokenAsDouble(); |
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Xitr_(2,1) = tokenizer.nextTokenAsDouble(); |
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Xitr_(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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Xirr_(0,0) = tokenizer.nextTokenAsDouble(); |
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Xirr_(0,1) = tokenizer.nextTokenAsDouble(); |
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Xirr_(0,2) = tokenizer.nextTokenAsDouble(); |
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Xirr_(1,0) = tokenizer.nextTokenAsDouble(); |
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Xirr_(1,1) = tokenizer.nextTokenAsDouble(); |
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Xirr_(1,2) = tokenizer.nextTokenAsDouble(); |
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Xirr_(2,0) = tokenizer.nextTokenAsDouble(); |
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Xirr_(2,1) = tokenizer.nextTokenAsDouble(); |
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Xirr_(2,2) = tokenizer.nextTokenAsDouble(); |
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|
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Xi_.setSubMatrix(0, 0, Xitt_); |
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Xi_.setSubMatrix(0, 3, Xirt_); |
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Xi_.setSubMatrix(3, 0, Xitr_); |
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Xi_.setSubMatrix(3, 3, Xirr_); |
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|
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CholeskyDecomposition(Xi_, S_); |
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|
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} |
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} |
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|
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void HydroProp::complete() { |
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|
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if (hasXi) { |
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for (int i1 = 0; i1 < 3; i1++) { |
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for (int j1 = 0; j1 < 3; j1++) { |
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Xitt_(i1,j1) = Xi_(i1,j1); |
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Xirt_(i1,j1) = Xi_(i1,j1+3); |
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Xitr_(i1,j1) = Xi_(i1+3,j1); |
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Xirr_(i1,j1) = Xi_(i1+3,j1+3); |
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} |
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} |
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CholeskyDecomposition(Xi_, S_); |
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} |
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} |
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|
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} |
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|
