| 38 |
|
* University of Notre Dame has been advised of the possibility of |
| 39 |
|
* such damages. |
| 40 |
|
*/ |
| 41 |
+ |
#include "applications/hydrodynamics/HydrodynamicsModel.hpp" |
| 42 |
+ |
#include "hydrodynamics/Shape.hpp" |
| 43 |
+ |
#include "hydrodynamics/Sphere.hpp" |
| 44 |
+ |
#include "hydrodynamics/Ellipsoid.hpp" |
| 45 |
+ |
#include "applications/hydrodynamics/CompositeShape.hpp" |
| 46 |
|
|
| 42 |
– |
#include "applications/hydrodynamics/HydrodynamicsModel.hpp" |
| 43 |
– |
#include "math/LU.hpp" |
| 44 |
– |
#include "math/DynamicRectMatrix.hpp" |
| 45 |
– |
#include "math/SquareMatrix3.hpp" |
| 47 |
|
namespace oopse { |
| 48 |
< |
/** |
| 49 |
< |
* Reference: |
| 50 |
< |
* Beatriz Carrasco and Jose Gracia de la Torre, Hydrodynamic Properties of Rigid Particles: |
| 51 |
< |
* Comparison of Different Modeling and Computational Procedures. |
| 52 |
< |
* Biophysical Journal, 75(6), 3044, 1999 |
| 53 |
< |
*/ |
| 53 |
< |
bool HydrodynamicsModel::calcHydrodyanmicsProps(double eta) { |
| 54 |
< |
if (!createBeads(beads_)) { |
| 55 |
< |
std::cout << "can not create beads" << std::endl; |
| 56 |
< |
return false; |
| 57 |
< |
} |
| 48 |
> |
|
| 49 |
> |
bool HydrodynamicsModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) { |
| 50 |
> |
return false; |
| 51 |
> |
} |
| 52 |
> |
|
| 53 |
> |
void HydrodynamicsModel::writeHydroProps(std::ostream& os) { |
| 54 |
|
|
| 59 |
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int nbeads = beads_.size(); |
| 60 |
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DynamicRectMatrix<double> B(3*nbeads, 3*nbeads); |
| 61 |
– |
DynamicRectMatrix<double> C(3*nbeads, 3*nbeads); |
| 62 |
– |
Mat3x3d I; |
| 63 |
– |
for (std::size_t i = 0; i < nbeads; ++i) { |
| 64 |
– |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 65 |
– |
Mat3x3d Tij; |
| 66 |
– |
if (i != j ) { |
| 67 |
– |
Vector3d Rij = beads_[i].pos - beads_[j].pos; |
| 68 |
– |
double rij = Rij.length(); |
| 69 |
– |
double rij2 = rij * rij; |
| 70 |
– |
double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2; |
| 71 |
– |
Mat3x3d tmpMat; |
| 72 |
– |
tmpMat = outProduct(beads_[i].pos, beads_[j].pos) / rij2; |
| 73 |
– |
double constant = 8.0 * NumericConstant::PI * eta * rij; |
| 74 |
– |
Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
| 75 |
– |
}else { |
| 76 |
– |
double constant = 1.0 / (6.0 * NumericConstant::PI * eta * beads_[i].radius); |
| 77 |
– |
Tij(0, 0) = constant; |
| 78 |
– |
Tij(1, 1) = constant; |
| 79 |
– |
Tij(2, 2) = constant; |
| 80 |
– |
} |
| 81 |
– |
B.setSubMatrix(i*3, j*3, Tij); |
| 82 |
– |
} |
| 83 |
– |
} |
| 84 |
– |
|
| 85 |
– |
//invert B Matrix |
| 86 |
– |
invertMatrix(B, C); |
| 55 |
|
|
| 56 |
< |
//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
| 89 |
< |
std::vector<Mat3x3d> U; |
| 90 |
< |
for (int i = 0; i < nbeads; ++i) { |
| 91 |
< |
Mat3x3d currU; |
| 92 |
< |
currU.setupSkewMat(beads_[i].pos); |
| 93 |
< |
U.push_back(currU); |
| 94 |
< |
} |
| 56 |
> |
os << sd_->getType() << "\t"; |
| 57 |
|
|
| 58 |
< |
//calculate Xi matrix at arbitrary origin O |
| 59 |
< |
Mat3x3d Xitt; |
| 98 |
< |
Mat3x3d Xirr; |
| 99 |
< |
Mat3x3d Xitr; |
| 100 |
< |
|
| 101 |
< |
for (std::size_t i = 0; i < nbeads; ++i) { |
| 102 |
< |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 103 |
< |
Mat3x3d Cij; |
| 104 |
< |
C.getSubMatrix(i*3, j*3, Cij); |
| 105 |
< |
|
| 106 |
< |
Xitt += Cij; |
| 107 |
< |
Xirr += U[i] * Cij; |
| 108 |
< |
Xitr += U[i] * Cij * U[j]; |
| 109 |
< |
} |
| 110 |
< |
} |
| 111 |
< |
|
| 112 |
< |
//invert Xi to get Diffusion Tensor at arbitrary origin O |
| 113 |
< |
RectMatrix<double, 6, 6> Xi; |
| 114 |
< |
RectMatrix<double, 6, 6> Do; |
| 115 |
< |
Xi.setSubMatrix(0, 0, Xitt); |
| 116 |
< |
Xi.setSubMatrix(0, 3, Xitr.transpose()); |
| 117 |
< |
Xi.setSubMatrix(3, 0, Xitr); |
| 118 |
< |
Xi.setSubMatrix(3, 3, Xitt); |
| 119 |
< |
invertMatrix(Xi, Do); |
| 120 |
< |
|
| 121 |
< |
Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O |
| 122 |
< |
Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O |
| 123 |
< |
Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O |
| 124 |
< |
Do.getSubMatrix(0, 0 , Dott); |
| 125 |
< |
Do.getSubMatrix(3, 0, Dotr); |
| 126 |
< |
Do.getSubMatrix(3, 3, Dorr); |
| 127 |
< |
|
| 128 |
< |
//calculate center of diffusion |
| 129 |
< |
Mat3x3d tmpMat; |
| 130 |
< |
tmpMat(0, 0) = Dorr(1, 1) + Dorr(2, 2); |
| 131 |
< |
tmpMat(0, 1) = - Dorr(0, 1); |
| 132 |
< |
tmpMat(0, 2) = -Dorr(0, 2); |
| 133 |
< |
tmpMat(1, 0) = -Dorr(0, 1); |
| 134 |
< |
tmpMat(1, 1) = Dorr(0, 0) + Dorr(2, 2); |
| 135 |
< |
tmpMat(1, 2) = -Dorr(1, 2); |
| 136 |
< |
tmpMat(2, 0) = -Dorr(0, 2); |
| 137 |
< |
tmpMat(2, 1) = -Dorr(1, 2); |
| 138 |
< |
tmpMat(2, 2) = Dorr(1, 1) + Dorr(0, 0); |
| 139 |
< |
|
| 140 |
< |
Vector3d tmpVec; |
| 141 |
< |
tmpVec[0] = Dotr(1, 2) - Dotr(2, 1); |
| 142 |
< |
tmpVec[1] = Dotr(2, 0) - Dotr(0, 2); |
| 143 |
< |
tmpVec[2] = Dotr(0, 1) - Dotr(1, 0); |
| 144 |
< |
|
| 145 |
< |
Vector3d rod = tmpMat.inverse() * tmpVec; |
| 146 |
< |
|
| 147 |
< |
//calculate Diffusion Tensor at center of diffusion |
| 148 |
< |
Mat3x3d Uod; |
| 149 |
< |
Uod.setupSkewMat(rod); |
| 58 |
> |
//center of resistance |
| 59 |
> |
os << cr_.center[0] << "\t" << cr_.center[1] << "\t" << cr_.center[2] << "\t"; |
| 60 |
|
|
| 61 |
< |
Mat3x3d Ddtt; //translational diffusion tensor at diffusion center |
| 62 |
< |
Mat3x3d Ddtr; //rotational diffusion tensor at diffusion center |
| 63 |
< |
Mat3x3d Ddrr; //translation-rotation couplingl diffusion tensor at diffusion tensor |
| 61 |
> |
//resistance tensor at center of resistance |
| 62 |
> |
//translation |
| 63 |
> |
os << cr_.Xi(0, 0) << "\t" << cr_.Xi(0, 1) << "\t" << cr_.Xi(0, 2) << "\t" |
| 64 |
> |
<< cr_.Xi(1, 0) << "\t" << cr_.Xi(1, 1) << "\t" << cr_.Xi(1, 2) << "\t" |
| 65 |
> |
<< cr_.Xi(2, 0) << "\t" << cr_.Xi(2, 1) << "\t" << cr_.Xi(2, 2) << "\t"; |
| 66 |
|
|
| 67 |
< |
Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr; |
| 68 |
< |
Ddrr = Dorr; |
| 69 |
< |
Ddtr = Dotr + Dorr * Uod; |
| 67 |
> |
//rotation-translation |
| 68 |
> |
os << cr_.Xi(0, 3) << "\t" << cr_.Xi(0, 4) << "\t" << cr_.Xi(0, 5) << "\t" |
| 69 |
> |
<< cr_.Xi(1, 3) << "\t" << cr_.Xi(1, 4) << "\t" << cr_.Xi(1, 5) << "\t" |
| 70 |
> |
<< cr_.Xi(2, 3) << "\t" << cr_.Xi(2, 4) << "\t" << cr_.Xi(2, 5) << "\t"; |
| 71 |
|
|
| 72 |
< |
props_.diffCenter = rod; |
| 73 |
< |
props_.transDiff = Ddtt; |
| 74 |
< |
props_.transRotDiff = Ddtr; |
| 75 |
< |
props_.rotDiff = Ddrr; |
| 76 |
< |
|
| 77 |
< |
return true; |
| 72 |
> |
//translation-rotation |
| 73 |
> |
os << cr_.Xi(3, 0) << "\t" << cr_.Xi(3, 1) << "\t" << cr_.Xi(3, 2) << "\t" |
| 74 |
> |
<< cr_.Xi(4, 0) << "\t" << cr_.Xi(4, 1) << "\t" << cr_.Xi(4, 2) << "\t" |
| 75 |
> |
<< cr_.Xi(5, 0) << "\t" << cr_.Xi(5, 1) << "\t" << cr_.Xi(5, 2) << "\t"; |
| 76 |
> |
|
| 77 |
> |
//rotation |
| 78 |
> |
os << cr_.Xi(3, 3) << "\t" << cr_.Xi(3, 4) << "\t" << cr_.Xi(3, 5) << "\t" |
| 79 |
> |
<< cr_.Xi(4, 3) << "\t" << cr_.Xi(4, 4) << "\t" << cr_.Xi(4, 5) << "\t" |
| 80 |
> |
<< cr_.Xi(5, 3) << "\t" << cr_.Xi(5, 4) << "\t" << cr_.Xi(5, 5) << "\t"; |
| 81 |
> |
|
| 82 |
> |
|
| 83 |
> |
//diffusion tensor at center of resistance |
| 84 |
> |
//translation |
| 85 |
> |
os << cr_.D(0, 0) << "\t" << cr_.D(0, 1) << "\t" << cr_.D(0, 2) << "\t" |
| 86 |
> |
<< cr_.D(1, 0) << "\t" << cr_.D(1, 1) << "\t" << cr_.D(1, 2) << "\t" |
| 87 |
> |
<< cr_.D(2, 0) << "\t" << cr_.D(2, 1) << "\t" << cr_.D(2, 2) << "\t"; |
| 88 |
> |
|
| 89 |
> |
//rotation-translation |
| 90 |
> |
os << cr_.D(0, 3) << "\t" << cr_.D(0, 4) << "\t" << cr_.D(0, 5) << "\t" |
| 91 |
> |
<< cr_.D(1, 3) << "\t" << cr_.D(1, 4) << "\t" << cr_.D(1, 5) << "\t" |
| 92 |
> |
<< cr_.D(2, 3) << "\t" << cr_.D(2, 4) << "\t" << cr_.D(2, 5) << "\t"; |
| 93 |
> |
|
| 94 |
> |
//translation-rotation |
| 95 |
> |
os << cr_.D(3, 0) << "\t" << cr_.D(3, 1) << "\t" << cr_.D(3, 2) << "\t" |
| 96 |
> |
<< cr_.D(4, 0) << "\t" << cr_.D(4, 1) << "\t" << cr_.D(4, 2) << "\t" |
| 97 |
> |
<< cr_.D(5, 0) << "\t" << cr_.D(5, 1) << "\t" << cr_.D(5, 2) << "\t"; |
| 98 |
> |
|
| 99 |
> |
//rotation |
| 100 |
> |
os << cr_.D(3, 3) << "\t" << cr_.D(3, 4) << "\t" << cr_.D(3, 5) << "\t" |
| 101 |
> |
<< cr_.D(4, 3) << "\t" << cr_.D(4, 4) << "\t" << cr_.D(4, 5) << "\t" |
| 102 |
> |
<< cr_.D(5, 3) << "\t" << cr_.D(5, 4) << "\t" << cr_.D(5, 5) << "\t"; |
| 103 |
> |
|
| 104 |
> |
//--------------------------------------------------------------------- |
| 105 |
> |
|
| 106 |
> |
//center of diffusion |
| 107 |
> |
os << cd_.center[0] << "\t" << cd_.center[1] << "\t" << cd_.center[2] << "\t"; |
| 108 |
> |
|
| 109 |
> |
//resistance tensor at center of diffusion |
| 110 |
> |
//translation |
| 111 |
> |
os << cd_.Xi(0, 0) << "\t" << cd_.Xi(0, 1) << "\t" << cd_.Xi(0, 2) << "\t" |
| 112 |
> |
<< cd_.Xi(1, 0) << "\t" << cd_.Xi(1, 1) << "\t" << cd_.Xi(1, 2) << "\t" |
| 113 |
> |
<< cd_.Xi(2, 0) << "\t" << cd_.Xi(2, 1) << "\t" << cd_.Xi(2, 2) << "\t"; |
| 114 |
> |
|
| 115 |
> |
//rotation-translation |
| 116 |
> |
os << cd_.Xi(0, 3) << "\t" << cd_.Xi(0, 4) << "\t" << cd_.Xi(0, 5) << "\t" |
| 117 |
> |
<< cd_.Xi(1, 3) << "\t" << cd_.Xi(1, 4) << "\t" << cd_.Xi(1, 5) << "\t" |
| 118 |
> |
<< cd_.Xi(2, 3) << "\t" << cd_.Xi(2, 4) << "\t" << cd_.Xi(2, 5) << "\t"; |
| 119 |
> |
|
| 120 |
> |
//translation-rotation |
| 121 |
> |
os << cd_.Xi(3, 0) << "\t" << cd_.Xi(3, 1) << "\t" << cd_.Xi(3, 2) << "\t" |
| 122 |
> |
<< cd_.Xi(4, 0) << "\t" << cd_.Xi(4, 1) << "\t" << cd_.Xi(4, 2) << "\t" |
| 123 |
> |
<< cd_.Xi(5, 0) << "\t" << cd_.Xi(5, 1) << "\t" << cd_.Xi(5, 2) << "\t"; |
| 124 |
> |
|
| 125 |
> |
//rotation |
| 126 |
> |
os << cd_.Xi(3, 3) << "\t" << cd_.Xi(3, 4) << "\t" << cd_.Xi(3, 5) << "\t" |
| 127 |
> |
<< cd_.Xi(4, 3) << "\t" << cd_.Xi(4, 4) << "\t" << cd_.Xi(4, 5) << "\t" |
| 128 |
> |
<< cd_.Xi(5, 3) << "\t" << cd_.Xi(5, 4) << "\t" << cd_.Xi(5, 5) << "\t"; |
| 129 |
> |
|
| 130 |
> |
|
| 131 |
> |
//diffusion tensor at center of diffusion |
| 132 |
> |
//translation |
| 133 |
> |
os << cd_.D(0, 0) << "\t" << cd_.D(0, 1) << "\t" << cd_.D(0, 2) << "\t" |
| 134 |
> |
<< cd_.D(1, 0) << "\t" << cd_.D(1, 1) << "\t" << cd_.D(1, 2) << "\t" |
| 135 |
> |
<< cd_.D(2, 0) << "\t" << cd_.D(2, 1) << "\t" << cd_.D(2, 2) << "\t"; |
| 136 |
> |
|
| 137 |
> |
//rotation-translation |
| 138 |
> |
os << cd_.D(0, 3) << "\t" << cd_.D(0, 4) << "\t" << cd_.D(0, 5) << "\t" |
| 139 |
> |
<< cd_.D(1, 3) << "\t" << cd_.D(1, 4) << "\t" << cd_.D(1, 5) << "\t" |
| 140 |
> |
<< cd_.D(2, 3) << "\t" << cd_.D(2, 4) << "\t" << cd_.D(2, 5) << "\t"; |
| 141 |
> |
|
| 142 |
> |
//translation-rotation |
| 143 |
> |
os << cd_.D(3, 0) << "\t" << cd_.D(3, 1) << "\t" << cd_.D(3, 2) << "\t" |
| 144 |
> |
<< cd_.D(4, 0) << "\t" << cd_.D(4, 1) << "\t" << cd_.D(4, 2) << "\t" |
| 145 |
> |
<< cd_.D(5, 0) << "\t" << cd_.D(5, 1) << "\t" << cd_.D(5, 2) << "\t"; |
| 146 |
> |
|
| 147 |
> |
//rotation |
| 148 |
> |
os << cd_.D(3, 3) << "\t" << cd_.D(3, 4) << "\t" << cd_.D(3, 5) << "\t" |
| 149 |
> |
<< cd_.D(4, 3) << "\t" << cd_.D(4, 4) << "\t" << cd_.D(4, 5) << "\t" |
| 150 |
> |
<< cd_.D(5, 3) << "\t" << cd_.D(5, 4) << "\t" << cd_.D(5, 5) << "\n"; |
| 151 |
> |
|
| 152 |
> |
} |
| 153 |
> |
|
| 154 |
|
} |
| 166 |
– |
|
| 167 |
– |
void HydrodynamicsModel::writeBeads(std::ostream& os) { |
| 168 |
– |
|
| 169 |
– |
} |
| 170 |
– |
|
| 171 |
– |
void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) { |
| 172 |
– |
|
| 173 |
– |
} |
| 174 |
– |
|
| 175 |
– |
} |
