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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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* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* 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 |
< |
* 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 |
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< |
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 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 |
| 13 |
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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 |
| 34 |
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* 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). |
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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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bool ApproximationModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) { |
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|
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bool ret = true; |
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HydroProp* cr; |
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HydroProp* cd; |
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> |
HydroProp* cr = new HydroProp(); |
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> |
HydroProp* cd = new HydroProp(); |
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calcHydroPropsAtCR(beads_, viscosity, temperature, cr); |
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//calcHydroPropsAtCD(beads_, viscosity, temperature, cd); |
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> |
calcHydroPropsAtCD(beads_, viscosity, temperature, cd); |
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setCR(cr); |
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setCD(cd); |
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– |
|
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return true; |
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} |
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|
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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; |
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> |
//Xirrr *= PhysicalConstants::kb * temperature; |
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|
|
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Mat6x6d Xi, D; |
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|
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|
return true; |
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} |
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|
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< |
bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProp* cr) { |
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> |
bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProp* cd) { |
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|
|
| 259 |
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int nbeads = beads.size(); |
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DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads); |
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|
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Xitt += Cij; |
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Xitr += U[i] * Cij; |
| 321 |
< |
//Xirr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I; |
| 321 |
> |
// uncorrected here. Volume correction is added after we assemble Xiorr |
| 322 |
|
Xirr += -U[i] * Cij * U[j]; |
| 323 |
|
} |
| 324 |
|
} |
| 325 |
+ |
// add the volume correction here: |
| 326 |
+ |
Xirr += (6.0 * viscosity * volume) * I; |
| 327 |
|
|
| 328 |
< |
const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 329 |
< |
Xitt *= convertConstant; |
| 330 |
< |
Xitr *= convertConstant; |
| 330 |
< |
Xirr *= convertConstant; |
| 328 |
> |
Xitt *= PhysicalConstants::viscoConvert; |
| 329 |
> |
Xitr *= PhysicalConstants::viscoConvert; |
| 330 |
> |
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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|
|
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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 |
| 402 |
|
|
| 403 |
|
|
| 404 |
|
//Xidtt in units of kcal*fs*mol^-1*Ang^-2 |
| 405 |
< |
//Xid /= OOPSEConstant::energyConvert; |
| 406 |
< |
Xid *= OOPSEConstant::kb * temperature; |
| 405 |
> |
//Xid /= PhysicalConstants::energyConvert; |
| 406 |
> |
Xid *= PhysicalConstants::kb * temperature; |
| 407 |
|
|
| 408 |
|
Mat6x6d Xi, D; |
| 409 |
|
|
| 410 |
< |
cr->setCOR(rod); |
| 410 |
> |
cd->setCOR(rod); |
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|
|
| 412 |
< |
cr->setXi(Xid); |
| 412 |
> |
cd->setXi(Xid); |
| 413 |
|
|
| 414 |
|
D.setSubMatrix(0, 0, Ddtt); |
| 415 |
|
D.setSubMatrix(0, 3, Ddtr); |
| 416 |
|
D.setSubMatrix(3, 0, Ddtr); |
| 417 |
|
D.setSubMatrix(3, 3, Ddrr); |
| 418 |
|
|
| 419 |
< |
cr->setD(D); |
| 419 |
> |
cd->setD(D); |
| 420 |
|
|
| 421 |
|
std::cout << "viscosity = " << viscosity << std::endl; |
| 422 |
|
std::cout << "temperature = " << temperature << std::endl; |
| 423 |
|
std::cout << "center of diffusion :" << std::endl; |
| 424 |
|
std::cout << rod << std::endl; |
| 425 |
|
std::cout << "diffusion tensor at center of diffusion " << std::endl; |
| 426 |
< |
std::cout << "translation(A^2/fs) :" << std::endl; |
| 426 |
> |
std::cout << "translation(A^2 / fs) :" << std::endl; |
| 427 |
|
std::cout << Ddtt << std::endl; |
| 428 |
< |
std::cout << "translation-rotation(A^3/fs):" << std::endl; |
| 428 |
> |
std::cout << "translation-rotation(A / fs):" << std::endl; |
| 429 |
|
std::cout << Ddtr << std::endl; |
| 430 |
< |
std::cout << "rotation(A^4/fs):" << std::endl; |
| 430 |
> |
std::cout << "rotation(fs^-1):" << std::endl; |
| 431 |
|
std::cout << Ddrr << std::endl; |
| 432 |
|
|
| 433 |
|
std::cout << "resistance tensor at center of diffusion " << std::endl; |
| 443 |
|
Xid.getSubMatrix(3, 3, Xidrr); |
| 444 |
|
|
| 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 |
|
return true; |
