| 5 |
|
* redistribute this software in source and binary code form, provided |
| 6 |
|
* that the following conditions are met: |
| 7 |
|
* |
| 8 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 9 |
< |
* publication of scientific results based in part on use of the |
| 10 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 11 |
< |
* the article in which the program was described (Matthew |
| 12 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 13 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 14 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 15 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 16 |
< |
* |
| 17 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 8 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 9 |
|
* notice, this list of conditions and the following disclaimer. |
| 10 |
|
* |
| 11 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 11 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 12 |
|
* notice, this list of conditions and the following disclaimer in the |
| 13 |
|
* documentation and/or other materials provided with the |
| 14 |
|
* distribution. |
| 28 |
|
* University of Notre Dame has been advised of the possibility of |
| 29 |
|
* such damages. |
| 30 |
|
* |
| 31 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 32 |
+ |
* research, please cite the appropriate papers when you publish your |
| 33 |
+ |
* work. Good starting points are: |
| 34 |
+ |
* |
| 35 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 36 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 37 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
|
* |
| 40 |
+ |
* |
| 41 |
|
* Triangle.hpp |
| 42 |
|
* |
| 43 |
< |
* Purpose: Provide basic triangle class for oopse. Hates Particle class. |
| 43 |
> |
* Purpose: Provide basic triangle class for OpenMD. Hates Particle class. |
| 44 |
|
* |
| 45 |
|
* Created by Charles F. Vardeman II on 29 July 2008. |
| 46 |
|
* @author Charles F. Vardeman II |
| 47 |
< |
* @version $Id: Triangle.hpp,v 1.3 2008-11-14 15:44:34 chuckv Exp $ |
| 47 |
> |
* @version $Id: Triangle.hpp,v 1.6 2009-11-25 20:02:01 gezelter Exp $ |
| 48 |
|
* |
| 49 |
|
*/ |
| 50 |
|
|
| 53 |
|
#define MATH_FACET_HPP |
| 54 |
|
|
| 55 |
|
#include "math/Vector3.hpp" |
| 56 |
+ |
#include "math/SquareMatrix3.hpp" |
| 57 |
|
#include "config.h" |
| 58 |
|
#include "primitives/StuntDouble.hpp" |
| 59 |
|
|
| 60 |
|
#include <vector> |
| 61 |
|
|
| 62 |
|
|
| 63 |
< |
namespace oopse { |
| 63 |
> |
namespace OpenMD { |
| 64 |
|
|
| 65 |
|
/** |
| 66 |
|
* @class Triangle |
| 67 |
|
* |
| 68 |
< |
* Triangle provides geometric data to oopse. Triangle includes |
| 68 |
> |
* Triangle provides geometric data to OpenMD. Triangle includes |
| 69 |
|
* information about the normal, centroid and the atoms |
| 70 |
|
* that belong to this triangle. |
| 71 |
|
*/ |
| 177 |
|
RealType t2 = -a1 + b1 + c1; |
| 178 |
|
RealType t3 = a1 - b1 + c1; |
| 179 |
|
RealType t4 = a1 + b1 - c1; |
| 180 |
+ |
RealType junk = t1*t2*t3*t4; |
| 181 |
|
return a1 * b1 * c1 / sqrt(t1 * t2 * t3 * t4); |
| 182 |
|
} |
| 183 |
|
|
| 184 |
+ |
Mat3x3d computeHydrodynamicTensor(RealType viscosity); |
| 185 |
|
|
| 186 |
|
|
| 187 |
|
private: |
| 188 |
+ |
Mat3x3d hydro_tensor(const Vector3d& ri, const Vector3d& rj0, const Vector3d& rj1, const Vector3d& rj2,RealType s, RealType viscosity); |
| 189 |
+ |
|
| 190 |
|
/* Local Indentity of vertex atoms in pos array*/ |
| 191 |
|
std::vector <StuntDouble*> vertexSD_; |
| 192 |
|
Vector3d normal_; |
| 206 |
|
|
| 207 |
|
|
| 208 |
|
|
| 209 |
< |
} //End Namespace oopse |
| 209 |
> |
} //end namespace OpenMD |
| 210 |
|
|
| 211 |
|
|
| 212 |
|
|
