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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 |
| 12 |
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* the article in which the program was described (Matthew |
| 13 |
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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 |
| 15 |
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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. |
| 11 |
|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 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 |
| 14 |
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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 |
| 30 |
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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 |
| 33 |
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* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
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+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#ifndef HYDRODYNAMICS_ELLIPSOID_HPP |
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#define HYDRODYNAMICS_ELLIPSOID_HPP |
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#include "hydrodynamics/Shape.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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/** @class Ellipsoid */ |
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> |
/** @class Ellipsoid |
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* |
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* An ellipsoid in OpenMD is restricted to having two equal |
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* equatorial semi-axes. OpenMD treats the "special" axis as the |
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> |
* z-coordinate in the body fixed reference frame. That is: |
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> |
* |
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> |
* z^2 / a^2 + (x^2 + y^2) / b^2 = 1 |
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> |
* |
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> |
* If a >= b, the ellipsoid is a prolate spheroid, and if a < b, |
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> |
* the ellipsoid is oblate. Ellipsoids are specified in the constructor |
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> |
* using an axial length (a), and a equatorial length (b). A Vector3d |
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> |
* can be used to position the center of the ellipsoid, and a rotation |
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* matrix can also be used to orient the ellipsoid to a preferred lab-fixed |
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* coordinate frame. |
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*/ |
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class Ellipsoid : public Shape{ |
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public: |
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< |
Ellipsoid(Vector3d origin, RealType rMajor, RealType rMinor, Mat3x3d rotMat); |
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> |
Ellipsoid(Vector3d origin, RealType rAxial, RealType rEquatorial, Mat3x3d rotMat); |
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virtual bool isInterior(Vector3d pos); |
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virtual std::pair<Vector3d, Vector3d> getBoundingBox(); |
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virtual bool hasAnalyticalSolution() {return true;} |
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|
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virtual HydroProps getHydroProps(RealType viscosity, RealType temperature); |
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> |
virtual HydroProp* getHydroProp(RealType viscosity, RealType temperature); |
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|
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< |
|
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> |
RealType getRAxial() {return rAxial_;} |
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> |
RealType getREquatorial() {return rEquatorial_;} |
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RealType getRMajor() {return rMajor_;} |
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RealType getRMinor() {return rMinor_;} |
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|
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private: |
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|
|
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Vector3d origin_; |
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+ |
RealType rAxial_; |
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+ |
RealType rEquatorial_; |
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RealType rMajor_; |
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RealType rMinor_; |
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|
Mat3x3d rotMat_; |
