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root/group/trunk/OOPSE-4/src/applications/hydrodynamics/HydrodynamicsModel.cpp
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Comparing trunk/OOPSE-4/src/applications/hydrodynamics/HydrodynamicsModel.cpp (file contents):
Revision 2597 by tim, Thu Feb 23 23:16:43 2006 UTC vs.
Revision 2634 by tim, Fri Mar 17 23:20:35 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 "applications/hydrodynamics/Spheric.hpp"
43 + #include "applications/hydrodynamics/Ellipsoid.hpp"
44 + #include "applications/hydrodynamics/CompositeShape.hpp"
45  
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"
46   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 – */
47  
48 < HydrodynamicsModel::HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams) : sd_(sd){
49 <    DynamicProperty::const_iterator iter;
48 > bool HydrodynamicsModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) {
49 >    return false;
50 > }
51  
52 <    iter = extraParams.find("Viscosity");
53 <    if (iter != extraParams.end()) {
54 <        boost::any param = iter->second;
61 <        viscosity_ = boost::any_cast<double>(param);
62 <    }else {
63 <        std::cout << "HydrodynamicsModel Error\n" ;
64 <    }
52 > bool HydrodynamicsModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) {
53 >    return false;
54 > }
55  
56 <    iter = extraParams.find("Temperature");
57 <    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 <    }    
56 > bool HydrodynamicsModel::calcHydroProps(CompositeShape* compositexShape, double viscosity, double temperature) {
57 >    return false;
58   }
59 <
60 < bool HydrodynamicsModel::calcHydrodyanmicsProps() {
61 <    if (!createBeads(beads_)) {
77 <        std::cout << "can not create beads" << std::endl;
78 <        return false;
79 <    }
59 >
60 > void HydrodynamicsModel::writeHydroProps(std::ostream& os) {
61 >
62      
63 <    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;
63 >    os << sd_->getType() << "\t";
64      
65 <    for (std::size_t i = 0; i < nbeads; ++i) {
66 <        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(beads_[i].pos, beads_[j].pos) / 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 <        }
109 <    }
65 >    //center of resistance
66 >    os << cr_.center[0] <<  "\t" << cr_.center[1] <<  "\t" << cr_.center[2] <<  "\t";
67  
68 <    //invert B Matrix
69 <    invertMatrix(B, C);
70 <    //prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0)
71 <    std::vector<Mat3x3d> U;
72 <    for (int i = 0; i < nbeads; ++i) {
116 <        Mat3x3d currU;
117 <        currU.setupSkewMat(beads_[i].pos);
118 <        U.push_back(currU);
119 <    }
120 <    
121 <    //calculate Xi matrix at arbitrary origin O
122 <    Mat3x3d Xitt;
123 <    Mat3x3d Xirr;
124 <    Mat3x3d Xitr;
125 <        
126 <    for (std::size_t i = 0; i < nbeads; ++i) {
127 <        for (std::size_t j = 0; j < nbeads; ++j) {
128 <            Mat3x3d Cij;
129 <            C.getSubMatrix(i*3, j*3, Cij);
130 <            
131 <            Xitt += Cij;
132 <            Xirr += U[i] * Cij;
133 <            Xitr += U[i] * Cij * U[j];            
134 <        }
135 <    }
68 >    //resistance tensor at center of resistance
69 >    //translation
70 >    os << cr_.Xi(0, 0) <<  "\t" << cr_.Xi(0, 1) <<  "\t" << cr_.Xi(0, 2) <<  "\t"
71 >        << cr_.Xi(1, 0) <<  "\t" << cr_.Xi(1, 1) <<  "\t" << cr_.Xi(1, 2) <<  "\t"
72 >        << cr_.Xi(2, 0) <<  "\t" << cr_.Xi(2, 1) <<  "\t" << cr_.Xi(2, 2) <<  "\t";
73  
74 <    //invert Xi to get Diffusion Tensor at arbitrary origin O
75 <    RectMatrix<double, 6, 6> Xi;    
76 <    RectMatrix<double, 6, 6> Do;
77 <    Xi.setSubMatrix(0, 0, Xitt);
141 <    Xi.setSubMatrix(0, 3, Xitr.transpose());
142 <    Xi.setSubMatrix(3, 0, Xitr);
143 <    Xi.setSubMatrix(3, 3, Xirr);
144 <    //invertMatrix(Xi, Do);
145 <    double kt = OOPSEConstant::kB * temperature_ * 1.66E-2;
146 <    //Do *= kt;    
74 >    //rotation-translation
75 >    os << cr_.Xi(0, 3) <<  "\t" << cr_.Xi(0, 4) <<  "\t" << cr_.Xi(0, 5) <<  "\t"
76 >        << cr_.Xi(1, 3) <<  "\t" << cr_.Xi(1, 4) <<  "\t" << cr_.Xi(1, 5) <<  "\t"
77 >        << cr_.Xi(2, 3) <<  "\t" << cr_.Xi(2, 4) <<  "\t" << cr_.Xi(2, 5) <<  "\t";
78  
79 +    //translation-rotation
80 +    os << cr_.Xi(3, 0) <<  "\t" << cr_.Xi(3, 1) <<  "\t" << cr_.Xi(3, 2) <<  "\t"
81 +        << cr_.Xi(4, 0) <<  "\t" << cr_.Xi(4, 1) <<  "\t" << cr_.Xi(4, 2) <<  "\t"
82 +        << cr_.Xi(5, 0) <<  "\t" << cr_.Xi(5, 1) <<  "\t" << cr_.Xi(5, 2) <<  "\t";
83  
84 <    Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O
85 <    Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O
86 <    Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O
84 >    //rotation
85 >    os << cr_.Xi(3, 3) <<  "\t" << cr_.Xi(3, 4) <<  "\t" << cr_.Xi(3, 5) <<  "\t"
86 >        << cr_.Xi(4, 3) <<  "\t" << cr_.Xi(4, 4) <<  "\t" << cr_.Xi(4, 5) <<  "\t"
87 >        << cr_.Xi(5, 3) <<  "\t" << cr_.Xi(5, 4) <<  "\t" << cr_.Xi(5, 5) <<  "\t";
88  
153 –    Mat3x3d XirrInv(0.0);
154 –    Mat3x3d XirrCopy;
155 –    XirrCopy = Xirr;
156 –    
157 –    Mat3x3d XittInv(0.0);
158 –    Mat3x3d XittCopy;
159 –    XittCopy = Xitt;
160 –    invertMatrix(XittCopy, XittInv);
89  
90 <    Mat3x3d tmp;
91 <    Mat3x3d tmpInv;
92 <    tmp = Xitt - Xitr.transpose() * XirrInv * Xitr;
90 >    //diffusion tensor at center of resistance
91 >    //translation
92 >    os << cr_.D(0, 0) <<  "\t" << cr_.D(0, 1) <<  "\t" << cr_.D(0, 2) <<  "\t"
93 >        << cr_.D(1, 0) <<  "\t" << cr_.D(1, 1) <<  "\t" << cr_.D(1, 2) <<  "\t"
94 >        << cr_.D(2, 0) <<  "\t" << cr_.D(2, 1) <<  "\t" << cr_.D(2, 2) <<  "\t";
95  
96 <    const static Mat3x3d zeroMat(0.0);
97 <    if (!invertMatrix(tmp, tmpInv)) {
98 <        tmpInv = zeroMat;
99 <    }
96 >    //rotation-translation
97 >    os << cr_.D(0, 3) <<  "\t" << cr_.D(0, 4) <<  "\t" << cr_.D(0, 5) <<  "\t"
98 >        << cr_.D(1, 3) <<  "\t" << cr_.D(1, 4) <<  "\t" << cr_.D(1, 5) <<  "\t"
99 >        << cr_.D(2, 3) <<  "\t" << cr_.D(2, 4) <<  "\t" << cr_.D(2, 5) <<  "\t";
100  
101 <    Dott = kt * tmpInv;
102 <    Dotr = -kt*XirrInv * Xitr * tmpInv;
101 >    //translation-rotation
102 >    os << cr_.D(3, 0) <<  "\t" << cr_.D(3, 1) <<  "\t" << cr_.D(3, 2) <<  "\t"
103 >        << cr_.D(4, 0) <<  "\t" << cr_.D(4, 1) <<  "\t" << cr_.D(4, 2) <<  "\t"
104 >        << cr_.D(5, 0) <<  "\t" << cr_.D(5, 1) <<  "\t" << cr_.D(5, 2) <<  "\t";
105  
106 <    tmp = Xirr - Xitr * XittInv * Xitr.transpose();
107 <    
108 <    if(!invertMatrix(tmp, tmpInv)) {
109 <        tmpInv = zeroMat;
110 <    }
111 <    Dorr = kt * tmpInv;
106 >    //rotation
107 >    os << cr_.D(3, 3) <<  "\t" << cr_.D(3, 4) <<  "\t" << cr_.D(3, 5) <<  "\t"
108 >        << cr_.D(4, 3) <<  "\t" << cr_.D(4, 4) <<  "\t" << cr_.D(4, 5) <<  "\t"
109 >        << cr_.D(5, 3) <<  "\t" << cr_.D(5, 4) <<  "\t" << cr_.D(5, 5) <<  "\t";
110 >        
111 >    //---------------------------------------------------------------------
112  
113 <    //Do.getSubMatrix(0, 0 , Dott);
114 <    //Do.getSubMatrix(3, 0, Dotr);
183 <    //Do.getSubMatrix(3, 3, Dorr);
113 >    //center of diffusion
114 >    os << cd_.center[0] <<  "\t" << cd_.center[1] <<  "\t" << cd_.center[2] <<  "\t";
115  
116 <    //calculate center of diffusion
117 <    tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2);
118 <    tmp(0, 1) = - Dorr(0, 1);
119 <    tmp(0, 2) = -Dorr(0, 2);
120 <    tmp(1, 0) = -Dorr(0, 1);
190 <    tmp(1, 1) = Dorr(0, 0)  + Dorr(2, 2);
191 <    tmp(1, 2) = -Dorr(1, 2);
192 <    tmp(2, 0) = -Dorr(0, 2);
193 <    tmp(2, 1) = -Dorr(1, 2);
194 <    tmp(2, 2) = Dorr(1, 1) + Dorr(0, 0);
116 >    //resistance tensor at center of diffusion
117 >    //translation
118 >    os << cd_.Xi(0, 0) <<  "\t" << cd_.Xi(0, 1) <<  "\t" << cd_.Xi(0, 2) <<  "\t"
119 >        << cd_.Xi(1, 0) <<  "\t" << cd_.Xi(1, 1) <<  "\t" << cd_.Xi(1, 2) <<  "\t"
120 >        << cd_.Xi(2, 0) <<  "\t" << cd_.Xi(2, 1) <<  "\t" << cd_.Xi(2, 2) <<  "\t";
121  
122 <    Vector3d tmpVec;
123 <    tmpVec[0] = Dotr(1, 2) - Dotr(2, 1);
124 <    tmpVec[1] = Dotr(2, 0) - Dotr(0, 2);
125 <    tmpVec[2] = Dotr(0, 1) - Dotr(1, 0);
122 >    //rotation-translation
123 >    os << cd_.Xi(0, 3) <<  "\t" << cd_.Xi(0, 4) <<  "\t" << cd_.Xi(0, 5) <<  "\t"
124 >        << cd_.Xi(1, 3) <<  "\t" << cd_.Xi(1, 4) <<  "\t" << cd_.Xi(1, 5) <<  "\t"
125 >        << cd_.Xi(2, 3) <<  "\t" << cd_.Xi(2, 4) <<  "\t" << cd_.Xi(2, 5) <<  "\t";
126  
127 <    if(!invertMatrix(tmp, tmpInv)) {
128 <        tmpInv = zeroMat;
129 <    }
130 <    
205 <    Vector3d rod = tmpInv * tmpVec;
127 >    //translation-rotation
128 >    os << cd_.Xi(3, 0) <<  "\t" << cd_.Xi(3, 1) <<  "\t" << cd_.Xi(3, 2) <<  "\t"
129 >        << cd_.Xi(4, 0) <<  "\t" << cd_.Xi(4, 1) <<  "\t" << cd_.Xi(4, 2) <<  "\t"
130 >        << cd_.Xi(5, 0) <<  "\t" << cd_.Xi(5, 1) <<  "\t" << cd_.Xi(5, 2) <<  "\t";
131  
132 <    //calculate Diffusion Tensor at center of diffusion
133 <    Mat3x3d Uod;
134 <    Uod.setupSkewMat(rod);
135 <    
211 <    Mat3x3d Ddtt; //translational diffusion tensor at diffusion center
212 <    Mat3x3d Ddtr; //rotational diffusion tensor at diffusion center
213 <    Mat3x3d Ddrr; //translation-rotation couplingl diffusion tensor at diffusion tensor
214 <    
215 <    Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr;
216 <    Ddrr = Dorr;
217 <    Ddtr = Dotr + Dorr * Uod;
218 <    
219 <    props_.diffCenter = rod;
220 <    props_.transDiff = Ddtt;
221 <    props_.transRotDiff = Ddtr;
222 <    props_.rotDiff = Ddrr;
132 >    //rotation
133 >    os << cd_.Xi(3, 3) <<  "\t" << cd_.Xi(3, 4) <<  "\t" << cd_.Xi(3, 5) <<  "\t"
134 >        << cd_.Xi(4, 3) <<  "\t" << cd_.Xi(4, 4) <<  "\t" << cd_.Xi(4, 5) <<  "\t"
135 >        << cd_.Xi(5, 3) <<  "\t" << cd_.Xi(5, 4) <<  "\t" << cd_.Xi(5, 5) <<  "\t";
136  
224 –    return true;    
225 – }
137  
138 < void HydrodynamicsModel::writeBeads(std::ostream& os) {
139 <    std::vector<BeadParam>::iterator iter;
140 <    os << beads_.size() << std::endl;
141 <    os << "Generated by Hydro" << std::endl;
142 <    for (iter = beads_.begin(); iter != beads_.end(); ++iter) {
232 <        os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl;
233 <    }
138 >    //diffusion tensor at center of diffusion
139 >    //translation
140 >    os << cd_.D(0, 0) <<  "\t" << cd_.D(0, 1) <<  "\t" << cd_.D(0, 2) <<  "\t"
141 >        << cd_.D(1, 0) <<  "\t" << cd_.D(1, 1) <<  "\t" << cd_.D(1, 2) <<  "\t"
142 >        << cd_.D(2, 0) <<  "\t" << cd_.D(2, 1) <<  "\t" << cd_.D(2, 2) <<  "\t";
143  
144 < }
144 >    //rotation-translation
145 >    os << cd_.D(0, 3) <<  "\t" << cd_.D(0, 4) <<  "\t" << cd_.D(0, 5) <<  "\t"
146 >        << cd_.D(1, 3) <<  "\t" << cd_.D(1, 4) <<  "\t" << cd_.D(1, 5) <<  "\t"
147 >        << cd_.D(2, 3) <<  "\t" << cd_.D(2, 4) <<  "\t" << cd_.D(2, 5) <<  "\t";
148  
149 < void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) {
150 <    os << "//viscosity = " << viscosity_ << std::endl;
151 <    os << "//temperature = " << temperature_<< std::endl;
152 <    std::vector<BeadParam>::iterator iter;
241 <    os << sd_->getType() << "\n";
149 >    //translation-rotation
150 >    os << cd_.D(3, 0) <<  "\t" << cd_.D(3, 1) <<  "\t" << cd_.D(3, 2) <<  "\t"
151 >        << cd_.D(4, 0) <<  "\t" << cd_.D(4, 1) <<  "\t" << cd_.D(4, 2) <<  "\t"
152 >        << cd_.D(5, 0) <<  "\t" << cd_.D(5, 1) <<  "\t" << cd_.D(5, 2) <<  "\t";
153  
154 <    os << "//diffusion center" << std::endl;
155 <    os << props_.diffCenter << std::endl;
154 >    //rotation
155 >    os << cd_.D(3, 3) <<  "\t" << cd_.D(3, 4) <<  "\t" << cd_.D(3, 5) <<  "\t"
156 >        << cd_.D(4, 3) <<  "\t" << cd_.D(4, 4) <<  "\t" << cd_.D(4, 5) <<  "\t"
157 >        << cd_.D(5, 3) <<  "\t" << cd_.D(5, 4) <<  "\t" << cd_.D(5, 5) <<  "\n";
158  
246 –    os << "//translational diffusion tensor" << std::endl;
247 –    os << props_.transDiff << std::endl;
159  
249 –    os << "//translational diffusion tensor" << std::endl;
250 –    os << props_.transRotDiff << std::endl;
251 –
252 –    os << "//rotational diffusion tensor" << std::endl;
253 –    os << props_.rotDiff << std::endl;
254 –    
255 –    /*
256 –    os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\n"
257 –
258 –    os << props_.transDiff(0, 0) << "\t" << props_.transDiff(0, 1) << "\t" << props_.transDiff(0, 2) << "\t"
259 –        << props_.transDiff(1, 0) << "\t" << props_.transDiff(1, 1) << "\t" << props_.transDiff(1, 2) << "\t"
260 –        << props_.transDiff(2, 0) << "\t" << props_.transDiff(2, 1) << "\t" << props_.transDiff(2, 2) << "\n";
261 –    
262 –    os << props_.transRotDiff(0, 0) << "\t" << props_.transRotDiff(0, 1) << "\t" << props_.transRotDiff(0, 2) << "\t"
263 –        << props_.transRotDiff(1, 0) << "\t" << props_.transRotDiff(1, 1) << "\t" << props_.transRotDiff(1, 2) << "\t"
264 –        << props_.transRotDiff(2, 0) << "\t" << props_.transRotDiff(2, 1) << "\t" << props_.transRotDiff(2, 2) << "\t"
265 –
266 –    os << props_.rotDiff(0, 0) << "\t" << props_.rotDiff(0, 1) << "\t" << props_.rotDiff(0, 2) << "\t"
267 –        << props_.rotDiff(1, 0) << "\t" << props_.rotDiff(1, 1) << "\t" << props_.rotDiff(1, 2) << "\t"
268 –        << props_.rotDiff(2, 0) << "\t" << props_.rotDiff(2, 1) << "\t" << props_.rotDiff(2, 2) << ";"
269 –        << std::endl;
270 –    */
160   }
161  
162   }

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