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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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#ifndef HYDRODYNAMICS_HYDROPROP_HPP |
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#define HYDRODYNAMICS_HYDROPROP_HPP |
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#include "math/Vector3.hpp" |
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#include "math/SquareMatrix3.hpp" |
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namespace OpenMD { |
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|
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/** |
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* @class HydroProp HydroProp.hpp "hydrodynamics/HydroProp.hpp" |
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* Container for information about the hydrodynamic behavior of objects |
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* undergoing Langevin dynamics. |
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* @note the units for the center of resistance (a location) are in Angstroms |
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* |
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* @note the units of Xi, the resistance tensor are: |
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* Xitt (Translation-translation) : kcal fs mol^-1 Angstroms^-2 |
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* Xirt (Rotation-translation) : kcal fs mol^-1 Angstroms^-1 radians^-1 |
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* Xitr (Translation-rotation) : kcal fs mol^-1 Angstroms^-1 radians^-1 |
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* Xirr (Rotation-rotation) : kcal fs mol^-1 radians^-2 |
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* |
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* @note the units of D, the diffusion tensor are: |
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* Dtt (Translation-translation) : Angstroms^2 fs^-1 |
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* Drt (Rotation-translation) : Angstroms fs^-1 |
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* Dtr (Translation-rotation) : Angstroms fs^-1 |
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* Drr (Rotation-rotation) : fs^-1 |
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* |
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* @note after setting the value of Xi manually, the complete() function |
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* should be called to perform the Cholesky Decomposition. |
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*/ |
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class HydroProp { |
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|
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public: |
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HydroProp(); |
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HydroProp(Vector3d cor, Mat6x6d Xi, Mat6x6d D); |
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HydroProp(const std::string &frictionLine); |
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~HydroProp() { } ; |
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void complete(); |
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void setCOR(Vector3d cor) {cor_ = cor; hasCOR = true;} |
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void setXi(Mat6x6d Xi) {Xi_ = Xi; hasXi = true;} |
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void setD(Mat6x6d D) {D_ = D;} |
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void setName(std::string name) {name_ = name;} |
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|
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Vector3d getCOR() {return cor_;} |
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Mat3x3d getXitt() {return Xitt_;} |
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Mat3x3d getXitr() {return Xitr_;} |
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Mat3x3d getXirt() {return Xirt_;} |
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Mat3x3d getXirr() {return Xirr_;} |
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Mat6x6d getS() {return S_;} |
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Mat6x6d getD() {return D_;} |
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Mat6x6d getXi() {return Xi_;} |
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std::string getName() {return name_;} |
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|
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private: |
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|
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std::string name_; |
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Vector3d cor_; |
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Mat6x6d Xi_; |
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Mat6x6d D_; |
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Mat3x3d Xitt_; |
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Mat3x3d Xirt_; //Xirrt == Xirtr |
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Mat3x3d Xitr_; |
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Mat3x3d Xirr_; |
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Mat6x6d S_; |
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bool hasCOR; |
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bool hasXi; |
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|
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}; |
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} |
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|
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#endif |
