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root/group/trunk/OOPSE-4/src/applications/hydrodynamics/ApproximationModel.cpp
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Comparing trunk/OOPSE-4/src/applications/hydrodynamics/ApproximationModel.cpp (file contents):
Revision 2768 by gezelter, Wed May 24 18:31:12 2006 UTC vs.
Revision 2774 by tim, Thu May 25 17:02:00 2006 UTC

# Line 69 | Line 69 | namespace oopse {
69      
70    }
71    
72 <  bool ApproximationModel::calcHydroProps(Shape* shape, double viscosity, double temperature) {
72 >  bool ApproximationModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) {
73      
74      bool ret = true;
75      HydroProps cr;
# Line 82 | Line 82 | namespace oopse {
82      return true;    
83    }
84    
85 <  bool ApproximationModel::calcHydroPropsAtCR(std::vector<BeadParam>& beads, double viscosity, double temperature, HydroProps& cr) {
85 >  bool ApproximationModel::calcHydroPropsAtCR(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProps& cr) {
86      
87      int nbeads = beads.size();
88 <    DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
89 <    DynamicRectMatrix<double> C(3*nbeads, 3*nbeads);
88 >    DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads);
89 >    DynamicRectMatrix<RealType> C(3*nbeads, 3*nbeads);
90      Mat3x3d I;
91      I(0, 0) = 1.0;
92      I(1, 1) = 1.0;
# Line 97 | Line 97 | namespace oopse {
97          Mat3x3d Tij;
98              if (i != j ) {
99                Vector3d Rij = beads[i].pos - beads[j].pos;
100 <              double rij = Rij.length();
101 <              double rij2 = rij * rij;
102 <              double sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2;                
100 >              RealType rij = Rij.length();
101 >              RealType rij2 = rij * rij;
102 >              RealType sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2;                
103                Mat3x3d tmpMat;
104                tmpMat = outProduct(Rij, Rij) / rij2;
105 <              double constant = 8.0 * NumericConstant::PI * viscosity * rij;
106 <              Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant;
105 >              RealType constant = 8.0 * NumericConstant::PI * viscosity * rij;
106 >              RealType tmp1 = 1.0 + sumSigma2OverRij2/3.0;
107 >              RealType tmp2 = 1.0 - sumSigma2OverRij2;
108 >              Tij = (tmp1 * I + tmp2 * tmpMat ) / constant;
109              }else {
110 <              double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius);
110 >              RealType constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius);
111                Tij(0, 0) = constant;
112                Tij(1, 1) = constant;
113                Tij(2, 2) = constant;
# Line 132 | Line 134 | namespace oopse {
134      
135      //calculate the total volume
136      
137 <    double volume = 0.0;
137 >    RealType volume = 0.0;
138      for (std::vector<BeadParam>::iterator iter = beads.begin(); iter != beads.end(); ++iter) {
139        volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3);
140      }
# Line 149 | Line 151 | namespace oopse {
151        }
152      }
153      
154 <    const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
154 >    const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs
155      Xiott *= convertConstant;
156      Xiotr *= convertConstant;
157      Xiorr *= convertConstant;
# Line 185 | Line 187 | namespace oopse {
187      Xirrr = Xiorr - Uor * Xiott * Uor + Xiotr * Uor - Uor * Xiotr.transpose();
188      
189  
190 <    SquareMatrix<double,6> Xir6x6;
191 <    SquareMatrix<double,6> Dr6x6;
190 >    SquareMatrix<RealType,6> Xir6x6;
191 >    SquareMatrix<RealType,6> Dr6x6;
192  
193      Xir6x6.setSubMatrix(0, 0, Xirtt);
194      Xir6x6.setSubMatrix(0, 3, Xirtr.transpose());
# Line 202 | Line 204 | namespace oopse {
204      Dr6x6.getSubMatrix(0, 3, Drrt);
205      Dr6x6.getSubMatrix(3, 0, Drtr);
206      Dr6x6.getSubMatrix(3, 3, Drrr);
207 <    double kt = OOPSEConstant::kB * temperature ;
207 >    RealType kt = OOPSEConstant::kB * temperature ;
208      Drtt *= kt;
209      Drrt *= kt;
210      Drtr *= kt;
# Line 246 | Line 248 | namespace oopse {
248      return true;
249   }
250    
251 <  bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, double viscosity, double temperature, HydroProps& cr) {
251 >  bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProps& cr) {
252      
253      int nbeads = beads.size();
254 <    DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
255 <    DynamicRectMatrix<double> C(3*nbeads, 3*nbeads);
254 >    DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads);
255 >    DynamicRectMatrix<RealType> C(3*nbeads, 3*nbeads);
256      Mat3x3d I;
257      I(0, 0) = 1.0;
258      I(1, 1) = 1.0;
# Line 261 | Line 263 | namespace oopse {
263          Mat3x3d Tij;
264          if (i != j ) {
265            Vector3d Rij = beads[i].pos - beads[j].pos;
266 <          double rij = Rij.length();
267 <          double rij2 = rij * rij;
268 <          double sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2;                
266 >          RealType rij = Rij.length();
267 >          RealType rij2 = rij * rij;
268 >          RealType sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2;                
269            Mat3x3d tmpMat;
270            tmpMat = outProduct(Rij, Rij) / rij2;
271 <          double constant = 8.0 * NumericConstant::PI * viscosity * rij;
272 <          Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant;
271 >          RealType constant = 8.0 * NumericConstant::PI * viscosity * rij;
272 >          RealType tmp1 = 1.0 + sumSigma2OverRij2/3.0;
273 >          RealType tmp2 = 1.0 - sumSigma2OverRij2;
274 >          Tij = (tmp1 * I + tmp2 * tmpMat ) / constant;
275          }else {
276 <          double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius);
276 >          RealType constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius);
277            Tij(0, 0) = constant;
278            Tij(1, 1) = constant;
279            Tij(2, 2) = constant;
# Line 296 | Line 300 | namespace oopse {
300  
301      //calculate the total volume
302  
303 <    double volume = 0.0;
303 >    RealType volume = 0.0;
304      for (std::vector<BeadParam>::iterator iter = beads.begin(); iter != beads.end(); ++iter) {
305        volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3);
306      }
# Line 313 | Line 317 | namespace oopse {
317        }
318      }
319      
320 <    const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
320 >    const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs
321      Xitt *= convertConstant;
322      Xitr *= convertConstant;
323      Xirr *= convertConstant;
324      
325 <    double kt = OOPSEConstant::kB * temperature;
325 >    RealType kt = OOPSEConstant::kB * temperature;
326      
327      Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O
328      Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O
# Line 377 | Line 381 | namespace oopse {
381      Ddrr = Dorr;
382      Ddtr = Dotr + Dorr * Uod;
383  
384 <    SquareMatrix<double, 6> Dd;
384 >    SquareMatrix<RealType, 6> Dd;
385      Dd.setSubMatrix(0, 0, Ddtt);
386      Dd.setSubMatrix(0, 3, Ddtr.transpose());
387      Dd.setSubMatrix(3, 0, Ddtr);
388      Dd.setSubMatrix(3, 3, Ddrr);    
389 <    SquareMatrix<double, 6> Xid;
389 >    SquareMatrix<RealType, 6> Xid;
390      Ddtt *= kt;
391      Ddtr *=kt;
392      Ddrr *= kt;

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