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Comparing trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp (file contents):
Revision 893 by tim, Fri Feb 24 21:17:05 2006 UTC vs.
Revision 972 by gezelter, Wed May 24 18:31:12 2006 UTC

# Line 38 | Line 38
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"
46 #include "utils/OOPSEConstant.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 < */
54 <
55 < HydrodynamicsModel::HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams) : sd_(sd){
56 <    DynamicProperty::const_iterator iter;
57 <
58 <    iter = extraParams.find("Viscosity");
59 <    if (iter != extraParams.end()) {
60 <        boost::any param = iter->second;
61 <        viscosity_ = boost::any_cast<double>(param);
62 <    }else {
63 <        std::cout << "HydrodynamicsModel Error\n" ;
64 <    }
65 <
66 <    iter = extraParams.find("Temperature");
67 <    if (iter != extraParams.end()) {
68 <        boost::any param = iter->second;
69 <        temperature_ = boost::any_cast<double>(param);
70 <    }else {
71 <        std::cout << "HydrodynamicsModel Error\n" ;
72 <    }    
73 < }
74 <
75 < bool HydrodynamicsModel::calcHydrodyanmicsProps() {
76 <    if (!createBeads(beads_)) {
77 <        std::cout << "can not create beads" << std::endl;
78 <        return false;
79 <    }
48 >  
49 >  bool HydrodynamicsModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) {
50 >    return false;
51 >  }
52 >  
53 >  void HydrodynamicsModel::writeHydroProps(std::ostream& os) {
54      
81    int nbeads = beads_.size();
82    DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
83    DynamicRectMatrix<double> C(3*nbeads, 3*nbeads);
84    Mat3x3d I;
85    I(0, 0) = 1.0;
86    I(1, 1) = 1.0;
87    I(2, 2) = 1.0;
55      
56 <    for (std::size_t i = 0; i < nbeads; ++i) {
90 <        for (std::size_t j = 0; j < nbeads; ++j) {
91 <            Mat3x3d Tij;
92 <            if (i != j ) {
93 <                Vector3d Rij = beads_[i].pos - beads_[j].pos;
94 <                double rij = Rij.length();
95 <                double rij2 = rij * rij;
96 <                double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2;                
97 <                Mat3x3d tmpMat;
98 <                tmpMat = outProduct(Rij, Rij) / rij2;
99 <                double constant = 8.0 * NumericConstant::PI * viscosity_ * rij;
100 <                Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant;
101 <            }else {
102 <                double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity_ * beads_[i].radius);
103 <                Tij(0, 0) = constant;
104 <                Tij(1, 1) = constant;
105 <                Tij(2, 2) = constant;
106 <            }
107 <            B.setSubMatrix(i*3, j*3, Tij);
108 <            std::cout << Tij << std::endl;
109 <        }
110 <    }
111 <
112 <    std::cout << "B=\n"
113 <                  << B << std::endl;
114 <    //invert B Matrix
115 <    invertMatrix(B, C);
116 <
117 <    std::cout << "C=\n"
118 <                  << C << std::endl;
119 <
120 <    //prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0)
121 <    std::vector<Mat3x3d> U;
122 <    for (int i = 0; i < nbeads; ++i) {
123 <        Mat3x3d currU;
124 <        currU.setupSkewMat(beads_[i].pos);
125 <        U.push_back(currU);
126 <    }
56 >    os << sd_->getType() << "\t";
57      
58 <    //calculate Xi matrix at arbitrary origin O
59 <    Mat3x3d Xitt;
130 <    Mat3x3d Xirr;
131 <    Mat3x3d Xitr;
132 <
133 <    //calculate the total volume
134 <
135 <    double volume = 0.0;
136 <    for (std::vector<BeadParam>::iterator iter = beads_.begin(); iter != beads_.end(); ++iter) {
137 <        volume = 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3);
138 <    }
139 <        
140 <    for (std::size_t i = 0; i < nbeads; ++i) {
141 <        for (std::size_t j = 0; j < nbeads; ++j) {
142 <            Mat3x3d Cij;
143 <            C.getSubMatrix(i*3, j*3, Cij);
144 <            
145 <            Xitt += Cij;
146 <            Xitr += U[i] * Cij;
147 <            Xirr += -U[i] * Cij * U[j];            
148 <            //Xirr += -U[i] * Cij * U[j] + (0.166*6 * viscosity_ * volume) * I;            
149 <        }
150 <    }
151 <
152 <    //invert Xi to get Diffusion Tensor at arbitrary origin O
153 <    RectMatrix<double, 6, 6> Xi;    
154 <    RectMatrix<double, 6, 6> Do;
155 <    Xi.setSubMatrix(0, 0, Xitt);
156 <    Xi.setSubMatrix(0, 3, Xitr.transpose());
157 <    Xi.setSubMatrix(3, 0, Xitr);
158 <    Xi.setSubMatrix(3, 3, Xirr);
159 <    //invertMatrix(Xi, Do);
160 <    double kt = OOPSEConstant::kB * temperature_ * 1.66E-2;
161 <    //Do *= kt;    
162 <
163 <
164 <    Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O
165 <    Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O
166 <    Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O
167 <
168 <    const static Mat3x3d zeroMat(0.0);
58 >    //center of resistance
59 >    os << cr_.center[0] <<  "\t" << cr_.center[1] <<  "\t" << cr_.center[2] <<  "\t";
60      
61 <    Mat3x3d XittInv(0.0);
62 <    XittInv = Xitt.inverse();
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 <    //Xirr may not be inverted,if it one of the diagonal element is zero, for example
68 <    //( a11 a12 0)
69 <    //( a21 a22 0)
70 <    //( 0    0    0)
177 <    Mat3x3d XirrInv;
178 <    XirrInv = Xirr.inverse();
179 <
180 <    Mat3x3d tmp;
181 <    Mat3x3d tmpInv;
182 <    tmp = Xitt - Xitr.transpose() * XirrInv * Xitr;
183 <    tmpInv = tmp.inverse();
184 <
185 <    Dott = kt * tmpInv;
186 <    Dotr = -kt*XirrInv * Xitr * tmpInv* 1.0E8;
187 <
188 <    tmp = Xirr - Xitr * XittInv * Xitr.transpose();    
189 <    tmpInv = tmp.inverse();
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 <    Dorr = kt * tmpInv*1.0E16;
73 <
74 <    //Do.getSubMatrix(0, 0 , Dott);
75 <    //Do.getSubMatrix(3, 0, Dotr);
195 <    //Do.getSubMatrix(3, 3, Dorr);
196 <
197 <    //calculate center of diffusion
198 <    tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2);
199 <    tmp(0, 1) = - Dorr(0, 1);
200 <    tmp(0, 2) = -Dorr(0, 2);
201 <    tmp(1, 0) = -Dorr(0, 1);
202 <    tmp(1, 1) = Dorr(0, 0)  + Dorr(2, 2);
203 <    tmp(1, 2) = -Dorr(1, 2);
204 <    tmp(2, 0) = -Dorr(0, 2);
205 <    tmp(2, 1) = -Dorr(1, 2);
206 <    tmp(2, 2) = Dorr(1, 1) + Dorr(0, 0);
207 <
208 <    Vector3d tmpVec;
209 <    tmpVec[0] = Dotr(1, 2) - Dotr(2, 1);
210 <    tmpVec[1] = Dotr(2, 0) - Dotr(0, 2);
211 <    tmpVec[2] = Dotr(0, 1) - Dotr(1, 0);
212 <
213 <    tmpInv = tmp.inverse();
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 <    Vector3d rod = tmpInv * tmpVec;
78 <
79 <    //calculate Diffusion Tensor at center of diffusion
80 <    Mat3x3d Uod;
219 <    Uod.setupSkewMat(rod);
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      
221    Mat3x3d Ddtt; //translational diffusion tensor at diffusion center
222    Mat3x3d Ddtr; //rotational diffusion tensor at diffusion center
223    Mat3x3d Ddrr; //translation-rotation couplingl diffusion tensor at diffusion tensor
82      
83 <    Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr;
84 <    Ddrr = Dorr;
85 <    Ddtr = Dotr + Dorr * Uod;
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 <    props_.diffCenter = rod;
90 <    props_.transDiff = Ddtt;
91 <    props_.transRotDiff = Ddtr;
92 <    props_.rotDiff = Ddrr;
233 <
234 <    return true;    
235 < }
236 <
237 < void HydrodynamicsModel::writeBeads(std::ostream& os) {
238 <    std::vector<BeadParam>::iterator iter;
239 <    os << beads_.size() << std::endl;
240 <    os << "Generated by Hydro" << std::endl;
241 <    for (iter = beads_.begin(); iter != beads_.end(); ++iter) {
242 <        os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl;
243 <    }
244 <
245 < }
246 <
247 < void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) {
248 <    os << "//viscosity = " << viscosity_ << std::endl;
249 <    os << "//temperature = " << temperature_<< std::endl;
250 <    std::vector<BeadParam>::iterator iter;
251 <    os << sd_->getType() << "\n";
252 <
253 <    os << "//diffusion center" << std::endl;
254 <    os << props_.diffCenter << std::endl;
255 <
256 <    os << "//translational diffusion tensor" << std::endl;
257 <    os << props_.transDiff << std::endl;
258 <
259 <    os << "//translation-rotation coupling diffusion tensor" << std::endl;
260 <    os << props_.transRotDiff << std::endl;
261 <
262 <    os << "//rotational diffusion tensor" << std::endl;
263 <    os << props_.rotDiff << std::endl;
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 <    /*
95 <    os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\n"
96 <
97 <    os << props_.transDiff(0, 0) << "\t" << props_.transDiff(0, 1) << "\t" << props_.transDiff(0, 2) << "\t"
269 <        << props_.transDiff(1, 0) << "\t" << props_.transDiff(1, 1) << "\t" << props_.transDiff(1, 2) << "\t"
270 <        << props_.transDiff(2, 0) << "\t" << props_.transDiff(2, 1) << "\t" << props_.transDiff(2, 2) << "\n";
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 <    os << props_.transRotDiff(0, 0) << "\t" << props_.transRotDiff(0, 1) << "\t" << props_.transRotDiff(0, 2) << "\t"
100 <        << props_.transRotDiff(1, 0) << "\t" << props_.transRotDiff(1, 1) << "\t" << props_.transRotDiff(1, 2) << "\t"
101 <        << props_.transRotDiff(2, 0) << "\t" << props_.transRotDiff(2, 1) << "\t" << props_.transRotDiff(2, 2) << "\t"
102 <
103 <    os << props_.rotDiff(0, 0) << "\t" << props_.rotDiff(0, 1) << "\t" << props_.rotDiff(0, 2) << "\t"
104 <        << props_.rotDiff(1, 0) << "\t" << props_.rotDiff(1, 1) << "\t" << props_.rotDiff(1, 2) << "\t"
105 <        << props_.rotDiff(2, 0) << "\t" << props_.rotDiff(2, 1) << "\t" << props_.rotDiff(2, 2) << ";"
106 <        << std::endl;
107 <    */
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   }
282
283 }

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