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Comparing trunk/src/applications/hydrodynamics/ApproximationModel.cpp (file contents):
Revision 954 by tim, Wed May 10 01:44:48 2006 UTC vs.
Revision 1177 by xsun, Tue Aug 14 17:40:33 2007 UTC

# Line 44 | Line 44
44   #include "math/DynamicRectMatrix.hpp"
45   #include "math/SquareMatrix3.hpp"
46   #include "utils/OOPSEConstant.hpp"
47 < #include "applications/hydrodynamics/Spheric.hpp"
48 < #include "applications/hydrodynamics/Ellipsoid.hpp"
47 > #include "hydrodynamics/Sphere.hpp"
48 > #include "hydrodynamics/Ellipsoid.hpp"
49   #include "applications/hydrodynamics/CompositeShape.hpp"
50   #include "math/LU.hpp"
51   #include "utils/simError.h"
# Line 57 | Line 57 | namespace oopse {
57   * Biophysical Journal, 75(6), 3044, 1999
58   */
59  
60 < ApproximationModel::ApproximationModel(StuntDouble* sd, SimInfo* info): HydrodynamicsModel(sd, info){
61 <
62 < }
63 <
64 < bool ApproximationModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) {
65 <    return internalCalcHydroProps(static_cast<Shape*>(spheric), viscosity, temperature);
66 < }
67 <
68 < bool ApproximationModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) {
69 <    return internalCalcHydroProps(static_cast<Shape*>(ellipsoid), viscosity, temperature);
70 < }
71 < bool ApproximationModel::calcHydroProps(CompositeShape* compositeShape, double viscosity, double temperature) {
72 <    return internalCalcHydroProps(static_cast<Shape*>(compositeShape), viscosity, temperature);
73 < }
74 <
75 < void ApproximationModel::init() {
60 >  ApproximationModel::ApproximationModel(StuntDouble* sd, SimInfo* info): HydrodynamicsModel(sd, info){    
61 >  }
62 >  
63 >  void ApproximationModel::init() {
64      if (!createBeads(beads_)) {
65        sprintf(painCave.errMsg, "ApproximationModel::init() : Can not create beads\n");
66        painCave.isFatal = 1;
67        simError();        
68      }
69 <
70 < }
71 <
72 < bool ApproximationModel::internalCalcHydroProps(Shape* shape, double viscosity, double temperature) {
73 <
69 >    
70 >  }
71 >  
72 >  bool ApproximationModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) {
73 >    
74      bool ret = true;
75 <    HydroProps cr;
76 <    HydroProps cd;
75 >    HydroProp* cr = new HydroProp();
76 >    HydroProp* cd = new HydroProp();
77      calcHydroPropsAtCR(beads_, viscosity, temperature, cr);
78 <    //calcHydroPropsAtCD(beads_, viscosity, temperature, cd);
78 >    calcHydroPropsAtCD(beads_, viscosity, temperature, cd);
79      setCR(cr);
80      setCD(cd);
93 –    
81      return true;    
82 < }
83 <
84 < bool ApproximationModel::calcHydroPropsAtCR(std::vector<BeadParam>& beads, double viscosity, double temperature, HydroProps& cr) {
85 <
82 >  }
83 >  
84 >  bool ApproximationModel::calcHydroPropsAtCR(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProp* cr) {
85 >    
86      int nbeads = beads.size();
87 <    DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
88 <    DynamicRectMatrix<double> C(3*nbeads, 3*nbeads);
87 >    DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads);
88 >    DynamicRectMatrix<RealType> C(3*nbeads, 3*nbeads);
89      Mat3x3d I;
90      I(0, 0) = 1.0;
91      I(1, 1) = 1.0;
92      I(2, 2) = 1.0;
93      
94      for (std::size_t i = 0; i < nbeads; ++i) {
95 <        for (std::size_t j = 0; j < nbeads; ++j) {
96 <            Mat3x3d Tij;
95 >      for (std::size_t j = 0; j < nbeads; ++j) {
96 >        Mat3x3d Tij;
97              if (i != j ) {
98 <                Vector3d Rij = beads[i].pos - beads[j].pos;
99 <                double rij = Rij.length();
100 <                double rij2 = rij * rij;
101 <                double sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2;                
102 <                Mat3x3d tmpMat;
103 <                tmpMat = outProduct(Rij, Rij) / rij2;
104 <                double constant = 8.0 * NumericConstant::PI * viscosity * rij;
105 <                Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant;
98 >              Vector3d Rij = beads[i].pos - beads[j].pos;
99 >              RealType rij = Rij.length();
100 >              RealType rij2 = rij * rij;
101 >              RealType sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2;                
102 >              Mat3x3d tmpMat;
103 >              tmpMat = outProduct(Rij, Rij) / rij2;
104 >              RealType constant = 8.0 * NumericConstant::PI * viscosity * rij;
105 >              RealType tmp1 = 1.0 + sumSigma2OverRij2/3.0;
106 >              RealType tmp2 = 1.0 - sumSigma2OverRij2;
107 >              Tij = (tmp1 * I + tmp2 * tmpMat ) / constant;
108              }else {
109 <                double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius);
110 <                Tij(0, 0) = constant;
111 <                Tij(1, 1) = constant;
112 <                Tij(2, 2) = constant;
109 >              RealType constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius);
110 >              Tij(0, 0) = constant;
111 >              Tij(1, 1) = constant;
112 >              Tij(2, 2) = constant;
113              }
114              B.setSubMatrix(i*3, j*3, Tij);
115 <        }
115 >      }
116      }
117 <
117 >    
118      //invert B Matrix
119      invertMatrix(B, C);
120      
121      //prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0)
122      std::vector<Mat3x3d> U;
123      for (int i = 0; i < nbeads; ++i) {
124 <        Mat3x3d currU;
125 <        currU.setupSkewMat(beads[i].pos);
126 <        U.push_back(currU);
124 >      Mat3x3d currU;
125 >      currU.setupSkewMat(beads[i].pos);
126 >      U.push_back(currU);
127      }
128      
129      //calculate Xi matrix at arbitrary origin O
130      Mat3x3d Xiott;
131      Mat3x3d Xiorr;
132      Mat3x3d Xiotr;
133 <
133 >    
134      //calculate the total volume
135 <
136 <    double volume = 0.0;
135 >    
136 >    RealType volume = 0.0;
137      for (std::vector<BeadParam>::iterator iter = beads.begin(); iter != beads.end(); ++iter) {
138 <        volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3);
138 >      volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3);
139      }
140 <        
140 >    
141      for (std::size_t i = 0; i < nbeads; ++i) {
142 <        for (std::size_t j = 0; j < nbeads; ++j) {
143 <            Mat3x3d Cij;
144 <            C.getSubMatrix(i*3, j*3, Cij);
145 <            
146 <            Xiott += Cij;
147 <            Xiotr += U[i] * Cij;
148 <            //Xiorr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I;    
149 <            Xiorr += -U[i] * Cij * U[j];
150 <        }
142 >      for (std::size_t j = 0; j < nbeads; ++j) {
143 >        Mat3x3d Cij;
144 >        C.getSubMatrix(i*3, j*3, Cij);
145 >        
146 >        Xiott += Cij;
147 >        Xiotr += U[i] * Cij;
148 >        //Xiorr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I;    
149 >        Xiorr += -U[i] * Cij * U[j];
150 >      }
151      }
152 <
153 <    const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
152 >    
153 >    const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs
154      Xiott *= convertConstant;
155      Xiotr *= convertConstant;
156      Xiorr *= convertConstant;
157      
169 –
158      
159 +    
160      Mat3x3d tmp;
161      Mat3x3d tmpInv;
162      Vector3d tmpVec;
# Line 197 | Line 186 | bool ApproximationModel::calcHydroPropsAtCR(std::vecto
186      Xirrr = Xiorr - Uor * Xiott * Uor + Xiotr * Uor - Uor * Xiotr.transpose();
187      
188  
189 <    SquareMatrix<double,6> Xir6x6;
190 <    SquareMatrix<double,6> Dr6x6;
189 >    SquareMatrix<RealType,6> Xir6x6;
190 >    SquareMatrix<RealType,6> Dr6x6;
191  
192      Xir6x6.setSubMatrix(0, 0, Xirtt);
193      Xir6x6.setSubMatrix(0, 3, Xirtr.transpose());
# Line 214 | Line 203 | bool ApproximationModel::calcHydroPropsAtCR(std::vecto
203      Dr6x6.getSubMatrix(0, 3, Drrt);
204      Dr6x6.getSubMatrix(3, 0, Drtr);
205      Dr6x6.getSubMatrix(3, 3, Drrr);
206 <    double kt = OOPSEConstant::kB * temperature ;
206 >    RealType kt = OOPSEConstant::kB * temperature ;
207      Drtt *= kt;
208      Drrt *= kt;
209      Drtr *= kt;
# Line 223 | Line 212 | bool ApproximationModel::calcHydroPropsAtCR(std::vecto
212      Xirtr *= OOPSEConstant::kb * temperature;
213      Xirrr *= OOPSEConstant::kb * temperature;
214      
215 +    Mat6x6d Xi, D;
216  
217 <    cr.center = ror;
218 <    cr.Xi.setSubMatrix(0, 0, Xirtt);
219 <    cr.Xi.setSubMatrix(0, 3, Xirtr);
220 <    cr.Xi.setSubMatrix(3, 0, Xirtr);
221 <    cr.Xi.setSubMatrix(3, 3, Xirrr);
222 <    cr.D.setSubMatrix(0, 0, Drtt);
223 <    cr.D.setSubMatrix(0, 3, Drrt);
224 <    cr.D.setSubMatrix(3, 0, Drtr);
225 <    cr.D.setSubMatrix(3, 3, Drrr);    
217 >    cr->setCOR(ror);
218 >
219 >    Xi.setSubMatrix(0, 0, Xirtt);
220 >    Xi.setSubMatrix(0, 3, Xirtr);
221 >    Xi.setSubMatrix(3, 0, Xirtr);
222 >    Xi.setSubMatrix(3, 3, Xirrr);
223 >
224 >    cr->setXi(Xi);
225 >
226 >    D.setSubMatrix(0, 0, Drtt);
227 >    D.setSubMatrix(0, 3, Drrt);
228 >    D.setSubMatrix(3, 0, Drtr);
229 >    D.setSubMatrix(3, 3, Drrr);    
230 >
231 >    cr->setD(D);
232      
233      std::cout << "-----------------------------------------\n";
234      std::cout << "center of resistance :" << std::endl;
# Line 257 | Line 253 | bool ApproximationModel::calcHydroPropsAtCR(std::vecto
253  
254      return true;
255   }
256 <
257 < bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, double viscosity, double temperature, HydroProps& cr) {
258 <
256 >  
257 >  bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProp* cd) {
258 >    
259      int nbeads = beads.size();
260 <    DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
261 <    DynamicRectMatrix<double> C(3*nbeads, 3*nbeads);
260 >    DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads);
261 >    DynamicRectMatrix<RealType> C(3*nbeads, 3*nbeads);
262      Mat3x3d I;
263      I(0, 0) = 1.0;
264      I(1, 1) = 1.0;
265      I(2, 2) = 1.0;
266      
267      for (std::size_t i = 0; i < nbeads; ++i) {
268 <        for (std::size_t j = 0; j < nbeads; ++j) {
269 <            Mat3x3d Tij;
270 <            if (i != j ) {
271 <                Vector3d Rij = beads[i].pos - beads[j].pos;
272 <                double rij = Rij.length();
273 <                double rij2 = rij * rij;
274 <                double sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2;                
275 <                Mat3x3d tmpMat;
276 <                tmpMat = outProduct(Rij, Rij) / rij2;
277 <                double constant = 8.0 * NumericConstant::PI * viscosity * rij;
278 <                Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant;
279 <            }else {
280 <                double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius);
281 <                Tij(0, 0) = constant;
282 <                Tij(1, 1) = constant;
283 <                Tij(2, 2) = constant;
284 <            }
285 <            B.setSubMatrix(i*3, j*3, Tij);
268 >      for (std::size_t j = 0; j < nbeads; ++j) {
269 >        Mat3x3d Tij;
270 >        if (i != j ) {
271 >          Vector3d Rij = beads[i].pos - beads[j].pos;
272 >          RealType rij = Rij.length();
273 >          RealType rij2 = rij * rij;
274 >          RealType sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2;                
275 >          Mat3x3d tmpMat;
276 >          tmpMat = outProduct(Rij, Rij) / rij2;
277 >          RealType constant = 8.0 * NumericConstant::PI * viscosity * rij;
278 >          RealType tmp1 = 1.0 + sumSigma2OverRij2/3.0;
279 >          RealType tmp2 = 1.0 - sumSigma2OverRij2;
280 >          Tij = (tmp1 * I + tmp2 * tmpMat ) / constant;
281 >        }else {
282 >          RealType constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius);
283 >          Tij(0, 0) = constant;
284 >          Tij(1, 1) = constant;
285 >          Tij(2, 2) = constant;
286          }
287 +        B.setSubMatrix(i*3, j*3, Tij);
288 +      }
289      }
290 <
290 >    
291      //invert B Matrix
292      invertMatrix(B, C);
293 <
293 >    
294      //prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0)
295      std::vector<Mat3x3d> U;
296      for (int i = 0; i < nbeads; ++i) {
297 <        Mat3x3d currU;
298 <        currU.setupSkewMat(beads[i].pos);
299 <        U.push_back(currU);
297 >      Mat3x3d currU;
298 >      currU.setupSkewMat(beads[i].pos);
299 >      U.push_back(currU);
300      }
301      
302      //calculate Xi matrix at arbitrary origin O
# Line 308 | Line 306 | bool ApproximationModel::calcHydroPropsAtCD(std::vecto
306  
307      //calculate the total volume
308  
309 <    double volume = 0.0;
309 >    RealType volume = 0.0;
310      for (std::vector<BeadParam>::iterator iter = beads.begin(); iter != beads.end(); ++iter) {
311 <        volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3);
311 >      volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3);
312      }
313 <        
313 >    
314      for (std::size_t i = 0; i < nbeads; ++i) {
315 <        for (std::size_t j = 0; j < nbeads; ++j) {
316 <            Mat3x3d Cij;
317 <            C.getSubMatrix(i*3, j*3, Cij);
315 >      for (std::size_t j = 0; j < nbeads; ++j) {
316 >        Mat3x3d Cij;
317 >        C.getSubMatrix(i*3, j*3, Cij);
318              
319 <            Xitt += Cij;
320 <            Xitr += U[i] * Cij;
319 >        Xitt += Cij;
320 >        Xitr += U[i] * Cij;
321              //Xirr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I;            
322 <            Xirr += -U[i] * Cij * U[j];
323 <        }
322 >        Xirr += -U[i] * Cij * U[j];
323 >      }
324      }
325 <
326 <    const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
325 >    
326 >    const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs
327      Xitt *= convertConstant;
328      Xitr *= convertConstant;
329      Xirr *= convertConstant;
330 <
331 <    double kt = OOPSEConstant::kB * temperature;
332 <
330 >    
331 >    RealType kt = OOPSEConstant::kB * temperature;
332 >    
333      Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O
334      Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O
335      Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O
336 <
336 >    
337      const static Mat3x3d zeroMat(0.0);
338      
339      Mat3x3d XittInv(0.0);
# Line 389 | Line 387 | bool ApproximationModel::calcHydroPropsAtCD(std::vecto
387      Ddrr = Dorr;
388      Ddtr = Dotr + Dorr * Uod;
389  
390 <    SquareMatrix<double, 6> Dd;
390 >    SquareMatrix<RealType, 6> Dd;
391      Dd.setSubMatrix(0, 0, Ddtt);
392      Dd.setSubMatrix(0, 3, Ddtr.transpose());
393      Dd.setSubMatrix(3, 0, Ddtr);
394      Dd.setSubMatrix(3, 3, Ddrr);    
395 <    SquareMatrix<double, 6> Xid;
395 >    SquareMatrix<RealType, 6> Xid;
396      Ddtt *= kt;
397      Ddtr *=kt;
398      Ddrr *= kt;
# Line 406 | Line 404 | bool ApproximationModel::calcHydroPropsAtCD(std::vecto
404      //Xid /= OOPSEConstant::energyConvert;
405      Xid *= OOPSEConstant::kb * temperature;
406  
407 <    cr.center = rod;
410 <    cr.D.setSubMatrix(0, 0, Ddtt);
411 <    cr.D.setSubMatrix(0, 3, Ddtr);
412 <    cr.D.setSubMatrix(3, 0, Ddtr);
413 <    cr.D.setSubMatrix(3, 3, Ddrr);
414 <    cr.Xi = Xid;
407 >    Mat6x6d Xi, D;
408  
409 +    cd->setCOR(rod);
410 +
411 +    cd->setXi(Xid);
412 +
413 +    D.setSubMatrix(0, 0, Ddtt);
414 +    D.setSubMatrix(0, 3, Ddtr);
415 +    D.setSubMatrix(3, 0, Ddtr);
416 +    D.setSubMatrix(3, 3, Ddrr);
417 +
418 +    cd->setD(D);
419 +
420      std::cout << "viscosity = " << viscosity << std::endl;
421      std::cout << "temperature = " << temperature << std::endl;
422      std::cout << "center of diffusion :" << std::endl;
# Line 446 | Line 450 | bool ApproximationModel::calcHydroPropsAtCD(std::vecto
450      std::cout << Xidrr << std::endl;
451  
452      return true;
453 <      
454 < }
453 >    
454 >  }
455  
456 <
453 < void ApproximationModel::writeBeads(std::ostream& os) {
456 >  void ApproximationModel::writeBeads(std::ostream& os) {
457      std::vector<BeadParam>::iterator iter;
458      os << beads_.size() << std::endl;
459      os << "Generated by Hydro" << std::endl;
460      for (iter = beads_.begin(); iter != beads_.end(); ++iter) {
461 <        os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl;
461 >      os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl;
462      }
463 <
463 >    
464 >  }    
465   }
462 –
463 –
464 –
465 – }

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