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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 |
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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 |
| 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 |
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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, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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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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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 = new HydroProp(); |
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HydroProp* cd = new HydroProp(); |
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calcHydroPropsAtCR(beads_, viscosity, temperature, cr); |
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|
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bool ApproximationModel::calcHydroPropsAtCR(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProp* cr) { |
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|
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int nbeads = beads.size(); |
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> |
unsigned int nbeads = beads.size(); |
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DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads); |
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DynamicRectMatrix<RealType> C(3*nbeads, 3*nbeads); |
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Mat3x3d I; |
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|
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//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
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std::vector<Mat3x3d> U; |
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< |
for (int i = 0; i < nbeads; ++i) { |
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> |
for (unsigned int i = 0; i < nbeads; ++i) { |
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Mat3x3d currU; |
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currU.setupSkewMat(beads[i].pos); |
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U.push_back(currU); |
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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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> |
Xiorr += (RealType(6.0) * viscosity * volume) * I; |
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|
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< |
Xiott *= OOPSEConstant::viscoConvert; |
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< |
Xiotr *= OOPSEConstant::viscoConvert; |
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< |
Xiorr *= OOPSEConstant::viscoConvert; |
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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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Mat3x3d tmp; |
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Mat3x3d tmpInv; |
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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 ; // in kcal mol^-1 |
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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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|
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bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProp* cd) { |
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|
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< |
int nbeads = beads.size(); |
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> |
unsigned int nbeads = beads.size(); |
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DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads); |
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DynamicRectMatrix<RealType> C(3*nbeads, 3*nbeads); |
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Mat3x3d I; |
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|
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//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
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std::vector<Mat3x3d> U; |
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< |
for (int i = 0; i < nbeads; ++i) { |
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> |
for (unsigned int i = 0; i < nbeads; ++i) { |
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Mat3x3d currU; |
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currU.setupSkewMat(beads[i].pos); |
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U.push_back(currU); |
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} |
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} |
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// add the volume correction here: |
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< |
Xirr += (6.0 * viscosity * volume) * I; |
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> |
Xirr += (RealType(6.0) * viscosity * volume) * I; |
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|
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< |
Xitt *= OOPSEConstant::viscoConvert; |
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< |
Xitr *= OOPSEConstant::viscoConvert; |
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< |
Xirr *= OOPSEConstant::viscoConvert; |
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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; // in kcal mol^-1 |
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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 |
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|
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|
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//Xidtt in units of kcal*fs*mol^-1*Ang^-2 |
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< |
//Xid /= OOPSEConstant::energyConvert; |
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< |
Xid *= OOPSEConstant::kb * temperature; |
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> |
//Xid /= PhysicalConstants::energyConvert; |
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> |
Xid *= PhysicalConstants::kb * temperature; |
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|
|
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|
Mat6x6d Xi, D; |
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|
