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* such damages. |
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*/ |
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#include "applications/hydrodynamics/AnalyticalModel.hpp" |
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< |
#include "applications/hydrodynamics/Spheric.hpp" |
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< |
#include "applications/hydrodynamics/Ellipsoid.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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namespace oopse { |
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< |
bool AnalyticalModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) { |
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< |
|
| 49 |
< |
double radius = spheric->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; |
| 47 |
> |
|
| 48 |
> |
bool AnalyticalModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) { |
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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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/** |
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* calculate the ratio of friction coeffiction constant between ellipsoid and spheric |
| 78 |
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* with same volume. |
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* @param m |
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* @param n |
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* @note |
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* Reference: |
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– |
* |
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* (1) Victor A. Bloomfield, On-Line Biophysics Textbook, Volume: Separations and Hydrodynamics |
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– |
* Chapter 1,Survey of Biomolecular Hydrodynamics |
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* http://www.biophysics.org/education/vbloomfield.pdf |
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– |
* (2) F. Perrin , J. Phys. Radium, [7] 5, 497-511, 1934 |
| 88 |
– |
* (3) F. Perrin, J. Phys. Radium, [7] 7, 1-11, 1936 |
| 89 |
– |
*/ |
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– |
bool AnalyticalModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) { |
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– |
double ft; |
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– |
double fra; |
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– |
double frb; |
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– |
double a = ellipsoid->getA(); |
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– |
double b = ellipsoid->getB(); |
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– |
double q = a/b; //? |
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– |
if (q > 1.0) {//prolate |
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ft = sqrt(1-q*q)/(pow(q, 2.0/3.0)*log((1 + sqrt(1-q*q))/q)); |
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– |
fra = 4*(1-q*q)/(3*(2 - 2*pow(q, 4.0/3.0)/ft)); //not sure |
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frb = 4*(1-q*q*q*q) /(3*q*q*(2*pow(q, -2.0/3.0)*(2-q*q)/ft-2)); |
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} else {//oblate |
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ft = sqrt(1-q*q)/(pow(q, 2.0/3.0)*atan(sqrt(q*q-1))); |
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fra = 4*(1-q*q)/(3*(2 - 2*pow(q, 4.0/3.0)/ft)); //not sure |
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frb = 4*(1-q*q*q*q) /(3*q*q*(2*pow(q, -2.0/3.0)*(2-q*q)/ft-2)); |
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} |
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– |
|
| 107 |
– |
double radius = pow(a*a*b, 1.0/3.0); |
| 50 |
|
HydroProps props; |
| 51 |
< |
double Xitt = 6.0 * NumericConstant::PI * viscosity * radius; |
| 52 |
< |
double Xirr = 8.0 * NumericConstant::PI * viscosity * radius * radius * radius; |
| 53 |
< |
props.Xi(0, 0) = Xitt; |
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< |
props.Xi(1, 1) = Xitt; |
| 55 |
< |
props.Xi(2, 2) = Xitt; |
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< |
props.Xi(3, 3) = Xirr; |
| 57 |
< |
props.Xi(4, 4) = Xirr; |
| 58 |
< |
props.Xi(5, 5) = Xirr; |
| 51 |
> |
Sphere* sphere = dynamic_cast<Sphere*>(shape); |
| 52 |
> |
if (sphere != NULL) { |
| 53 |
> |
props = sphere->getHydroProps(viscosity, temperature); |
| 54 |
> |
setCR(props); |
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> |
setCD(props); |
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> |
return true; |
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> |
} else { |
| 58 |
> |
Ellipsoid* ellipsoid = dynamic_cast<Ellipsoid*>(shape); |
| 59 |
> |
if (ellipsoid != NULL) { |
| 60 |
> |
props = ellipsoid->getHydroProps(viscosity, temperature); |
| 61 |
> |
setCR(props); |
| 62 |
> |
setCD(props); |
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> |
return true; |
| 64 |
> |
} else { |
| 65 |
> |
CompositeShape* composite = dynamic_cast<CompositeShape*>(shape); |
| 66 |
> |
if (composite != NULL) { |
| 67 |
> |
return false; |
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> |
} else { |
| 69 |
> |
sprintf( painCave.errMsg, |
| 70 |
> |
"Could not figure out what kind of shape this is!\n"); |
| 71 |
> |
painCave.severity = OOPSE_ERROR; |
| 72 |
> |
painCave.isFatal = 1; |
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> |
simError(); |
| 74 |
> |
return false; |
| 75 |
> |
} |
| 76 |
> |
} |
| 77 |
> |
} |
| 78 |
> |
} |
| 79 |
|
|
| 80 |
< |
const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 81 |
< |
props.Xi *= convertConstant; |
| 82 |
< |
props.Xi(0,0) *= ft; |
| 83 |
< |
props.Xi(1,1) *= ft; |
| 84 |
< |
props.Xi(2,2) *= ft; |
| 85 |
< |
props.Xi(3,3) *= fra; |
| 124 |
< |
props.Xi(4,4) *= fra; |
| 125 |
< |
props.Xi(5,5) *= frb; |
| 126 |
< |
|
| 127 |
< |
Mat6x6d XiCopy = props.Xi; |
| 128 |
< |
XiCopy /= OOPSEConstant::kb * temperature; |
| 129 |
< |
invertMatrix(XiCopy, props.D); |
| 130 |
< |
double kt = OOPSEConstant::kB * temperature; |
| 131 |
< |
props.D *= kt; |
| 132 |
< |
|
| 133 |
< |
setCR(props); |
| 134 |
< |
setCD(props); |
| 135 |
< |
|
| 136 |
< |
return true; |
| 80 |
> |
void AnalyticalModel::writeBeads(std::ostream& os) { |
| 81 |
> |
os << "1\n"; |
| 82 |
> |
os << "Generated by Hydro\n"; |
| 83 |
> |
Vector3d pos = sd_->getPos(); |
| 84 |
> |
os << sd_->getType() << "\t" << pos[0] << "\t" << pos[1] << "\t" << pos[2] << std::endl; |
| 85 |
> |
} |
| 86 |
|
} |
| 138 |
– |
|
| 139 |
– |
bool AnalyticalModel::calcHydroProps(CompositeShape* compositexShape, double viscosity, double temperature) { |
| 140 |
– |
return false; |
| 141 |
– |
} |
| 142 |
– |
|
| 143 |
– |
|
| 144 |
– |
|
| 145 |
– |
} |
