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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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> |
* 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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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 oopse { |
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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(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;} |
