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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. |
| 11 |
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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 |
| 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 |
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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, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include "applications/hydrodynamics/ApproximationModel.hpp" |
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#include "math/LU.hpp" |
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#include "math/DynamicRectMatrix.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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> |
#include "utils/PhysicalConstants.hpp" |
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#include "hydrodynamics/Sphere.hpp" |
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#include "hydrodynamics/Ellipsoid.hpp" |
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#include "applications/hydrodynamics/CompositeShape.hpp" |
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#include "math/LU.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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> |
namespace OpenMD { |
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/** |
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* Reference: |
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* Beatriz Carrasco and Jose Gracia de la Torre, Hydrodynamic Properties of Rigid Particles: |
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|
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Xiott += Cij; |
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Xiotr += U[i] * Cij; |
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< |
//Xiorr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I; |
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> |
// uncorrected here. Volume correction is added after we assemble Xiorr |
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Xiorr += -U[i] * Cij * U[j]; |
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} |
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} |
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+ |
|
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// add the volume correction |
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Xiorr += (6.0 * viscosity * volume) * I; |
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|
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const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs |
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Xiott *= convertConstant; |
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Xiotr *= convertConstant; |
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< |
Xiorr *= convertConstant; |
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> |
Xiott *= PhysicalConstants::viscoConvert; |
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> |
Xiotr *= PhysicalConstants::viscoConvert; |
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> |
Xiorr *= PhysicalConstants::viscoConvert; |
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|
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– |
|
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– |
|
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Mat3x3d tmp; |
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Mat3x3d tmpInv; |
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Vector3d tmpVec; |
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Dr6x6.getSubMatrix(0, 3, Drrt); |
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Dr6x6.getSubMatrix(3, 0, Drtr); |
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Dr6x6.getSubMatrix(3, 3, Drrr); |
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< |
RealType kt = OOPSEConstant::kB * temperature ; |
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> |
RealType kt = PhysicalConstants::kb * temperature ; // in kcal mol^-1 |
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Drtt *= kt; |
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Drrt *= kt; |
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Drtr *= kt; |
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Drrr *= kt; |
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< |
Xirtt *= OOPSEConstant::kb * temperature; |
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< |
Xirtr *= OOPSEConstant::kb * temperature; |
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< |
Xirrr *= OOPSEConstant::kb * temperature; |
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> |
//Xirtt *= PhysicalConstants::kb * temperature; |
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> |
//Xirtr *= PhysicalConstants::kb * temperature; |
| 213 |
> |
//Xirrr *= PhysicalConstants::kb * temperature; |
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|
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Mat6x6d Xi, D; |
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|
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|
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Xitt += Cij; |
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Xitr += U[i] * Cij; |
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< |
//Xirr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I; |
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> |
// uncorrected here. Volume correction is added after we assemble Xiorr |
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Xirr += -U[i] * Cij * U[j]; |
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} |
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} |
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+ |
// add the volume correction here: |
| 326 |
+ |
Xirr += (6.0 * viscosity * volume) * I; |
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|
|
| 328 |
< |
const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 329 |
< |
Xitt *= convertConstant; |
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< |
Xitr *= convertConstant; |
| 329 |
< |
Xirr *= convertConstant; |
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> |
Xitt *= PhysicalConstants::viscoConvert; |
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> |
Xitr *= PhysicalConstants::viscoConvert; |
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> |
Xirr *= PhysicalConstants::viscoConvert; |
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|
|
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< |
RealType kt = OOPSEConstant::kB * temperature; |
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> |
RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1 |
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|
|
| 334 |
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Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O |
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Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O |
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|
|
| 403 |
|
|
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//Xidtt in units of kcal*fs*mol^-1*Ang^-2 |
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< |
//Xid /= OOPSEConstant::energyConvert; |
| 406 |
< |
Xid *= OOPSEConstant::kb * temperature; |
| 405 |
> |
//Xid /= PhysicalConstants::energyConvert; |
| 406 |
> |
Xid *= PhysicalConstants::kb * temperature; |
| 407 |
|
|
| 408 |
|
Mat6x6d Xi, D; |
| 409 |
|
|
| 423 |
|
std::cout << "center of diffusion :" << std::endl; |
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std::cout << rod << std::endl; |
| 425 |
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std::cout << "diffusion tensor at center of diffusion " << std::endl; |
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< |
std::cout << "translation(A^2/fs) :" << std::endl; |
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> |
std::cout << "translation(A^2 / fs) :" << std::endl; |
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|
std::cout << Ddtt << std::endl; |
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< |
std::cout << "translation-rotation(A^3/fs):" << std::endl; |
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> |
std::cout << "translation-rotation(A / fs):" << std::endl; |
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|
std::cout << Ddtr << std::endl; |
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< |
std::cout << "rotation(A^4/fs):" << std::endl; |
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> |
std::cout << "rotation(fs^-1):" << std::endl; |
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|
std::cout << Ddrr << std::endl; |
| 432 |
|
|
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std::cout << "resistance tensor at center of diffusion " << std::endl; |
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Xid.getSubMatrix(3, 3, Xidrr); |
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|
| 445 |
|
std::cout << Xidtt << std::endl; |
| 446 |
< |
std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-3):" << std::endl; |
| 446 |
> |
std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-1):" << std::endl; |
| 447 |
|
std::cout << Xidrt << std::endl; |
| 448 |
< |
std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-3):" << std::endl; |
| 448 |
> |
std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-1):" << std::endl; |
| 449 |
|
std::cout << Xidtr << std::endl; |
| 450 |
< |
std::cout << "rotation(kcal*fs*mol^-1*Ang^-4):" << std::endl; |
| 450 |
> |
std::cout << "rotation(kcal*fs*mol^-1):" << std::endl; |
| 451 |
|
std::cout << Xidrr << std::endl; |
| 452 |
|
|
| 453 |
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return true; |
