| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#include "hydrodynamics/Sphere.hpp" |
| 43 |
< |
#include "utils/OOPSEConstant.hpp" |
| 43 |
> |
#include "utils/PhysicalConstants.hpp" |
| 44 |
|
#include "math/LU.hpp" |
| 45 |
|
|
| 46 |
< |
namespace oopse { |
| 46 |
> |
namespace OpenMD { |
| 47 |
|
|
| 48 |
< |
Sphere::Sphere(Vector3d origin, double radius) : origin_(origin), radius_(radius){ |
| 48 |
> |
Sphere::Sphere(Vector3d origin, RealType radius) : origin_(origin), radius_(radius){ |
| 49 |
|
|
| 50 |
|
} |
| 51 |
|
|
| 69 |
|
return boundary; |
| 70 |
|
} |
| 71 |
|
|
| 72 |
< |
HydroProps Sphere::getHydroProps(double viscosity, double temperature) { |
| 73 |
< |
HydroProps props; |
| 74 |
< |
props.center =V3Zero; |
| 75 |
< |
double Xitt = 6.0 * NumericConstant::PI * viscosity * radius_; |
| 76 |
< |
double Xirr = 8.0 * NumericConstant::PI * viscosity * radius_ * radius_ * radius_; |
| 77 |
< |
props.Xi(0, 0) = Xitt; |
| 78 |
< |
props.Xi(1, 1) = Xitt; |
| 79 |
< |
props.Xi(2, 2) = Xitt; |
| 80 |
< |
props.Xi(3, 3) = Xirr; |
| 81 |
< |
props.Xi(4, 4) = Xirr; |
| 82 |
< |
props.Xi(5, 5) = Xirr; |
| 72 |
> |
HydroProp* Sphere::getHydroProp(RealType viscosity, RealType temperature) { |
| 73 |
|
|
| 74 |
< |
const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 75 |
< |
props.Xi *= convertConstant; |
| 76 |
< |
Mat6x6d XiCopy = props.Xi; |
| 77 |
< |
invertMatrix(XiCopy, props.D); |
| 78 |
< |
double kt = OOPSEConstant::kB * temperature; |
| 79 |
< |
props.D *= kt; |
| 80 |
< |
props.Xi *= OOPSEConstant::kb * temperature; |
| 74 |
> |
RealType Xitt = 6.0 * NumericConstant::PI * viscosity * radius_; |
| 75 |
> |
RealType Xirr = 8.0 * NumericConstant::PI * viscosity * radius_ * radius_ * radius_; |
| 76 |
> |
|
| 77 |
> |
Mat6x6d Xi, XiCopy, D; |
| 78 |
> |
|
| 79 |
> |
Xi(0, 0) = Xitt; |
| 80 |
> |
Xi(1, 1) = Xitt; |
| 81 |
> |
Xi(2, 2) = Xitt; |
| 82 |
> |
Xi(3, 3) = Xirr; |
| 83 |
> |
Xi(4, 4) = Xirr; |
| 84 |
> |
Xi(5, 5) = Xirr; |
| 85 |
|
|
| 86 |
< |
return props; |
| 86 |
> |
Xi *= PhysicalConstants::viscoConvert; |
| 87 |
> |
XiCopy = Xi; |
| 88 |
> |
|
| 89 |
> |
invertMatrix(XiCopy, D); |
| 90 |
> |
RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1 |
| 91 |
> |
D *= kt; // now in angstroms^2 fs^-1 (at least for Trans-trans) |
| 92 |
> |
|
| 93 |
> |
HydroProp* hprop = new HydroProp(V3Zero, Xi, D); |
| 94 |
> |
|
| 95 |
> |
return hprop; |
| 96 |
|
} |
| 97 |
|
|
| 98 |
|
} |
