| 39 |
|
* such damages. |
| 40 |
|
*/ |
| 41 |
|
#include "applications/hydrodynamics/AnalyticalModel.hpp" |
| 42 |
< |
#include "applications/hydrodynamics/Spheric.hpp" |
| 43 |
< |
#include "applications/hydrodynamics/Ellipsoid.hpp" |
| 42 |
> |
#include "hydrodynamics/Sphere.hpp" |
| 43 |
> |
#include "hydrodynamics/Ellipsoid.hpp" |
| 44 |
|
#include "applications/hydrodynamics/CompositeShape.hpp" |
| 45 |
|
#include "math/LU.hpp" |
| 46 |
|
namespace oopse { |
| 47 |
< |
bool AnalyticalModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) { |
| 48 |
< |
|
| 49 |
< |
double radius = spheric->getRadius(); |
| 50 |
< |
HydroProps props; |
| 51 |
< |
props.center =V3Zero; |
| 52 |
< |
double Xitt = 6.0 * NumericConstant::PI * viscosity * radius; |
| 53 |
< |
double Xirr = 8.0 * NumericConstant::PI * viscosity * radius * radius * radius; |
| 54 |
< |
props.Xi(0, 0) = Xitt; |
| 55 |
< |
props.Xi(1, 1) = Xitt; |
| 56 |
< |
props.Xi(2, 2) = Xitt; |
| 57 |
< |
props.Xi(3, 3) = Xirr; |
| 58 |
< |
props.Xi(4, 4) = Xirr; |
| 59 |
< |
props.Xi(5, 5) = Xirr; |
| 47 |
> |
|
| 48 |
> |
bool AnalyticalModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) { |
| 49 |
|
|
| 50 |
< |
const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 51 |
< |
props.Xi *= convertConstant; |
| 52 |
< |
Mat6x6d XiCopy = props.Xi; |
| 53 |
< |
invertMatrix(XiCopy, props.D); |
| 54 |
< |
double kt = OOPSEConstant::kB * temperature; |
| 55 |
< |
props.D *= kt; |
| 56 |
< |
props.Xi *= OOPSEConstant::kb * temperature; |
| 57 |
< |
|
| 58 |
< |
setCR(props); |
| 59 |
< |
setCD(props); |
| 60 |
< |
|
| 61 |
< |
return true; |
| 50 |
> |
HydroProp* props; |
| 51 |
> |
Sphere* sphere = dynamic_cast<Sphere*>(shape); |
| 52 |
> |
if (sphere != NULL) { |
| 53 |
> |
props = sphere->getHydroProp(viscosity, temperature); |
| 54 |
> |
setCR(props); |
| 55 |
> |
setCD(props); |
| 56 |
> |
return true; |
| 57 |
> |
} else { |
| 58 |
> |
Ellipsoid* ellipsoid = dynamic_cast<Ellipsoid*>(shape); |
| 59 |
> |
if (ellipsoid != NULL) { |
| 60 |
> |
props = ellipsoid->getHydroProp(viscosity, temperature); |
| 61 |
> |
setCR(props); |
| 62 |
> |
setCD(props); |
| 63 |
> |
return true; |
| 64 |
> |
} else { |
| 65 |
> |
CompositeShape* composite = dynamic_cast<CompositeShape*>(shape); |
| 66 |
> |
if (composite != NULL) { |
| 67 |
> |
// props = composite->getHydroProp(viscosity, temperature); |
| 68 |
> |
// setCR(props); |
| 69 |
> |
// setCD(props); |
| 70 |
> |
// return true; |
| 71 |
> |
return false; |
| 72 |
> |
} else { |
| 73 |
> |
sprintf( painCave.errMsg, |
| 74 |
> |
"Could not figure out what kind of shape this is!\n"); |
| 75 |
> |
painCave.severity = OOPSE_ERROR; |
| 76 |
> |
painCave.isFatal = 1; |
| 77 |
> |
simError(); |
| 78 |
> |
return false; |
| 79 |
> |
} |
| 80 |
> |
} |
| 81 |
> |
} |
| 82 |
> |
} |
| 83 |
|
|
| 84 |
+ |
void AnalyticalModel::writeBeads(std::ostream& os) { |
| 85 |
+ |
os << "1\n"; |
| 86 |
+ |
os << "Generated by Hydro\n"; |
| 87 |
+ |
Vector3d pos = sd_->getPos(); |
| 88 |
+ |
os << sd_->getType() << "\t" << pos[0] << "\t" << pos[1] << "\t" << pos[2] << std::endl; |
| 89 |
+ |
} |
| 90 |
|
} |
| 75 |
– |
|
| 76 |
– |
/** |
| 77 |
– |
* calculate the ratio of friction coeffiction constant between ellipsoid and spheric |
| 78 |
– |
* with same volume. |
| 79 |
– |
* @param m |
| 80 |
– |
* @param n |
| 81 |
– |
* @note |
| 82 |
– |
* Reference: |
| 83 |
– |
* |
| 84 |
– |
* (1) Victor A. Bloomfield, On-Line Biophysics Textbook, Volume: Separations and Hydrodynamics |
| 85 |
– |
* Chapter 1,Survey of Biomolecular Hydrodynamics |
| 86 |
– |
* http://www.biophysics.org/education/vbloomfield.pdf |
| 87 |
– |
* (2) F. Perrin , J. Phys. Radium, [7] 5, 497-511, 1934 |
| 88 |
– |
* (3) F. Perrin, J. Phys. Radium, [7] 7, 1-11, 1936 |
| 89 |
– |
*/ |
| 90 |
– |
bool AnalyticalModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) { |
| 91 |
– |
double ft; |
| 92 |
– |
double fra; |
| 93 |
– |
double frb; |
| 94 |
– |
double a = ellipsoid->getA(); |
| 95 |
– |
double b = ellipsoid->getB(); |
| 96 |
– |
double q = a/b; //? |
| 97 |
– |
if (q > 1.0) {//prolate |
| 98 |
– |
ft = sqrt(1-q*q)/(pow(q, 2.0/3.0)*log((1 + sqrt(1-q*q))/q)); |
| 99 |
– |
fra = 4*(1-q*q)/(3*(2 - 2*pow(q, 4.0/3.0)/ft)); //not sure |
| 100 |
– |
frb = 4*(1-q*q*q*q) /(3*q*q*(2*pow(q, -2.0/3.0)*(2-q*q)/ft-2)); |
| 101 |
– |
} else {//oblate |
| 102 |
– |
ft = sqrt(1-q*q)/(pow(q, 2.0/3.0)*atan(sqrt(q*q-1))); |
| 103 |
– |
fra = 4*(1-q*q)/(3*(2 - 2*pow(q, 4.0/3.0)/ft)); //not sure |
| 104 |
– |
frb = 4*(1-q*q*q*q) /(3*q*q*(2*pow(q, -2.0/3.0)*(2-q*q)/ft-2)); |
| 105 |
– |
} |
| 106 |
– |
|
| 107 |
– |
double radius = pow(a*a*b, 1.0/3.0); |
| 108 |
– |
HydroProps props; |
| 109 |
– |
double Xitt = 6.0 * NumericConstant::PI * viscosity * radius; |
| 110 |
– |
double Xirr = 8.0 * NumericConstant::PI * viscosity * radius * radius * radius; |
| 111 |
– |
props.Xi(0, 0) = Xitt; |
| 112 |
– |
props.Xi(1, 1) = Xitt; |
| 113 |
– |
props.Xi(2, 2) = Xitt; |
| 114 |
– |
props.Xi(3, 3) = Xirr; |
| 115 |
– |
props.Xi(4, 4) = Xirr; |
| 116 |
– |
props.Xi(5, 5) = Xirr; |
| 117 |
– |
|
| 118 |
– |
const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
| 119 |
– |
props.Xi *= convertConstant; |
| 120 |
– |
props.Xi(0,0) *= ft; |
| 121 |
– |
props.Xi(1,1) *= ft; |
| 122 |
– |
props.Xi(2,2) *= ft; |
| 123 |
– |
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; |
| 137 |
– |
} |
| 138 |
– |
|
| 139 |
– |
bool AnalyticalModel::calcHydroProps(CompositeShape* compositexShape, double viscosity, double temperature) { |
| 140 |
– |
return false; |
| 141 |
– |
} |
| 142 |
– |
|
| 143 |
– |
|
| 144 |
– |
|
| 145 |
– |
} |
