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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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< |
#include "hydrodynamics/AnalyticalModel.hpp" |
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> |
#include "applications/hydrodynamics/AnalyticalModel.hpp" |
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#include "hydrodynamics/Sphere.hpp" |
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#include "hydrodynamics/Ellipsoid.hpp" |
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#include "hydrodynamics/CompositeShape.hpp" |
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#include "applications/hydrodynamics/CompositeShape.hpp" |
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#include "math/LU.hpp" |
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namespace oopse { |
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|
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bool AnalyticalModel::calcHydroProps(Sphere* sphere, double viscosity, double temperature) { |
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> |
bool AnalyticalModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) { |
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|
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double radius = sphere->getRadius(); |
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HydroProps props; |
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props.center =V3Zero; |
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double Xitt = 6.0 * NumericConstant::PI * viscosity * radius; |
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double Xirr = 8.0 * NumericConstant::PI * viscosity * radius * radius * radius; |
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props.Xi(0, 0) = Xitt; |
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props.Xi(1, 1) = Xitt; |
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props.Xi(2, 2) = Xitt; |
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props.Xi(3, 3) = Xirr; |
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props.Xi(4, 4) = Xirr; |
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props.Xi(5, 5) = Xirr; |
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|
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const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
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props.Xi *= convertConstant; |
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Mat6x6d XiCopy = props.Xi; |
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invertMatrix(XiCopy, props.D); |
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double kt = OOPSEConstant::kB * temperature; |
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props.D *= kt; |
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props.Xi *= OOPSEConstant::kb * temperature; |
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|
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setCR(props); |
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setCD(props); |
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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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* Reference: |
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* (2) F. Perrin , J. Phys. Radium, [7] 5, 497-511, 1934 |
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* (3) F. Perrin, J. Phys. Radium, [7] 7, 1-11, 1936 |
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*/ |
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bool AnalyticalModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) { |
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|
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double rMajor = ellipsoid->getRMajor(); |
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double rMinor = ellipsoid->getRMinor(); |
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|
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double a = rMinor; |
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double b = rMajor; |
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double a2 = a * a; |
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double b2 = b* b; |
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|
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double p = a /b; |
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double S; |
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if (p > 1.0) { //prolate |
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S = 2.0/sqrt(a2 - b2) * log((a + sqrt(a2-b2))/b); |
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} else { //oblate |
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S = 2.0/sqrt(b2 - a2) * atan(sqrt(b2-a2)/a); |
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} |
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|
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double P = 1.0/(a2 - b2) * (S - 2.0/a); |
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double Q = 0.5/(a2-b2) * (2.0*a/b2 - S); |
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|
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double transMinor = 16.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-b2)*S -2.0*a); |
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double transMajor = 32.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-3.0*b2)*S +2.0*a); |
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double rotMinor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2 - b2) * b2 /(2.0*a -b2*S); |
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double rotMajor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2*a2 - b2*b2)/((2.0*a2-b2)*S-2.0*a); |
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|
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|
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HydroProps props; |
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|
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props.Xi(0,0) = transMajor; |
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props.Xi(1,1) = transMajor; |
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props.Xi(2,2) = transMinor; |
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props.Xi(3,3) = rotMajor; |
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props.Xi(4,4) = rotMajor; |
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props.Xi(5,5) = rotMinor; |
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|
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const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
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< |
props.Xi *= convertConstant; |
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|
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Mat6x6d XiCopy = props.Xi; |
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invertMatrix(XiCopy, props.D); |
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double kt = OOPSEConstant::kB * temperature; |
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props.D *= kt; |
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props.Xi *= OOPSEConstant::kb * temperature; |
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|
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setCR(props); |
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setCD(props); |
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|
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return true; |
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> |
Sphere* sphere = dynamic_cast<Sphere*>(shape); |
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> |
if (sphere != NULL) { |
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> |
props = sphere->getHydroProps(viscosity, temperature); |
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> |
setCR(props); |
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> |
setCD(props); |
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> |
return true; |
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> |
} else { |
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> |
Ellipsoid* ellipsoid = dynamic_cast<Ellipsoid*>(shape); |
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> |
if (ellipsoid != NULL) { |
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> |
props = ellipsoid->getHydroProps(viscosity, temperature); |
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> |
setCR(props); |
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> |
setCD(props); |
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> |
return true; |
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> |
} else { |
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> |
CompositeShape* composite = dynamic_cast<CompositeShape*>(shape); |
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> |
if (composite != NULL) { |
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> |
return false; |
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> |
} else { |
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> |
sprintf( painCave.errMsg, |
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> |
"Could not figure out what kind of shape this is!\n"); |
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> |
painCave.severity = OOPSE_ERROR; |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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> |
return false; |
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> |
} |
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> |
} |
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> |
} |
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} |
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< |
|
| 132 |
< |
bool AnalyticalModel::calcHydroProps(CompositeShape* compositeShape, double viscosity, double temperature) { |
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< |
return false; |
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< |
} |
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< |
|
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> |
|
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|
void AnalyticalModel::writeBeads(std::ostream& os) { |
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os << "1\n"; |
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os << "Generated by Hydro\n"; |
