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Comparing trunk/src/applications/hydrodynamics/ApproximationModel.cpp (file contents):
Revision 972 by gezelter, Wed May 24 18:31:12 2006 UTC vs.
Revision 1208 by xsun, Wed Jan 16 20:19:28 2008 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;
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);
81 –    
81      return true;    
82    }
83    
84 <  bool ApproximationModel::calcHydroPropsAtCR(std::vector<BeadParam>& beads, double viscosity, double temperature, HydroProps& cr) {
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;
# Line 97 | Line 96 | namespace oopse {
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;                
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 <              double constant = 8.0 * NumericConstant::PI * viscosity * rij;
105 <              Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant;
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);
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;
# Line 132 | Line 133 | namespace oopse {
133      
134      //calculate the total volume
135      
136 <    double volume = 0.0;
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);
139      }
# Line 144 | Line 145 | namespace oopse {
145          
146          Xiott += Cij;
147          Xiotr += U[i] * Cij;
148 <        //Xiorr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I;    
148 >        // uncorrected here.  Volume correction is added after we assemble Xiorr
149          Xiorr += -U[i] * Cij * U[j];
150        }
151      }
152 +
153 +    // add the volume correction
154 +    Xiorr += (6.0 * viscosity * volume) * I;    
155      
156 <    const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
156 >    const RealType convertConstant = 1.439326479e4; //converts Poise angstroms
157 >                                                    // to kcal fs mol^-1 Angstrom^-1
158 >
159      Xiott *= convertConstant;
160      Xiotr *= convertConstant;
161      Xiorr *= convertConstant;
162      
157 –    
158 –    
163      Mat3x3d tmp;
164      Mat3x3d tmpInv;
165      Vector3d tmpVec;
# Line 185 | Line 189 | namespace oopse {
189      Xirrr = Xiorr - Uor * Xiott * Uor + Xiotr * Uor - Uor * Xiotr.transpose();
190      
191  
192 <    SquareMatrix<double,6> Xir6x6;
193 <    SquareMatrix<double,6> Dr6x6;
192 >    SquareMatrix<RealType,6> Xir6x6;
193 >    SquareMatrix<RealType,6> Dr6x6;
194  
195      Xir6x6.setSubMatrix(0, 0, Xirtt);
196      Xir6x6.setSubMatrix(0, 3, Xirtr.transpose());
# Line 202 | Line 206 | namespace oopse {
206      Dr6x6.getSubMatrix(0, 3, Drrt);
207      Dr6x6.getSubMatrix(3, 0, Drtr);
208      Dr6x6.getSubMatrix(3, 3, Drrr);
209 <    double kt = OOPSEConstant::kB * temperature ;
209 >    RealType kt = OOPSEConstant::kb * temperature ; // in kcal mol^-1
210      Drtt *= kt;
211      Drrt *= kt;
212      Drtr *= kt;
213      Drrr *= kt;
214 <    Xirtt *= OOPSEConstant::kb * temperature;
215 <    Xirtr *= OOPSEConstant::kb * temperature;
216 <    Xirrr *= OOPSEConstant::kb * temperature;
214 >    //Xirtt *= OOPSEConstant::kb * temperature;
215 >    //Xirtr *= OOPSEConstant::kb * temperature;
216 >    //Xirrr *= OOPSEConstant::kb * temperature;
217      
218 +    Mat6x6d Xi, D;
219  
220 <    cr.center = ror;
221 <    cr.Xi.setSubMatrix(0, 0, Xirtt);
222 <    cr.Xi.setSubMatrix(0, 3, Xirtr);
223 <    cr.Xi.setSubMatrix(3, 0, Xirtr);
224 <    cr.Xi.setSubMatrix(3, 3, Xirrr);
225 <    cr.D.setSubMatrix(0, 0, Drtt);
226 <    cr.D.setSubMatrix(0, 3, Drrt);
227 <    cr.D.setSubMatrix(3, 0, Drtr);
228 <    cr.D.setSubMatrix(3, 3, Drrr);    
220 >    cr->setCOR(ror);
221 >
222 >    Xi.setSubMatrix(0, 0, Xirtt);
223 >    Xi.setSubMatrix(0, 3, Xirtr);
224 >    Xi.setSubMatrix(3, 0, Xirtr);
225 >    Xi.setSubMatrix(3, 3, Xirrr);
226 >
227 >    cr->setXi(Xi);
228 >
229 >    D.setSubMatrix(0, 0, Drtt);
230 >    D.setSubMatrix(0, 3, Drrt);
231 >    D.setSubMatrix(3, 0, Drtr);
232 >    D.setSubMatrix(3, 3, Drrr);    
233 >
234 >    cr->setD(D);
235      
236      std::cout << "-----------------------------------------\n";
237      std::cout << "center of resistance :" << std::endl;
# Line 246 | Line 257 | namespace oopse {
257      return true;
258   }
259    
260 <  bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, double viscosity, double temperature, HydroProps& cr) {
260 >  bool ApproximationModel::calcHydroPropsAtCD(std::vector<BeadParam>& beads, RealType viscosity, RealType temperature, HydroProp* cd) {
261      
262      int nbeads = beads.size();
263 <    DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
264 <    DynamicRectMatrix<double> C(3*nbeads, 3*nbeads);
263 >    DynamicRectMatrix<RealType> B(3*nbeads, 3*nbeads);
264 >    DynamicRectMatrix<RealType> C(3*nbeads, 3*nbeads);
265      Mat3x3d I;
266      I(0, 0) = 1.0;
267      I(1, 1) = 1.0;
# Line 261 | Line 272 | namespace oopse {
272          Mat3x3d Tij;
273          if (i != j ) {
274            Vector3d Rij = beads[i].pos - beads[j].pos;
275 <          double rij = Rij.length();
276 <          double rij2 = rij * rij;
277 <          double sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2;                
275 >          RealType rij = Rij.length();
276 >          RealType rij2 = rij * rij;
277 >          RealType sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2;                
278            Mat3x3d tmpMat;
279            tmpMat = outProduct(Rij, Rij) / rij2;
280 <          double constant = 8.0 * NumericConstant::PI * viscosity * rij;
281 <          Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant;
280 >          RealType constant = 8.0 * NumericConstant::PI * viscosity * rij;
281 >          RealType tmp1 = 1.0 + sumSigma2OverRij2/3.0;
282 >          RealType tmp2 = 1.0 - sumSigma2OverRij2;
283 >          Tij = (tmp1 * I + tmp2 * tmpMat ) / constant;
284          }else {
285 <          double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius);
285 >          RealType constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius);
286            Tij(0, 0) = constant;
287            Tij(1, 1) = constant;
288            Tij(2, 2) = constant;
# Line 296 | Line 309 | namespace oopse {
309  
310      //calculate the total volume
311  
312 <    double volume = 0.0;
312 >    RealType volume = 0.0;
313      for (std::vector<BeadParam>::iterator iter = beads.begin(); iter != beads.end(); ++iter) {
314        volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3);
315      }
# Line 308 | Line 321 | namespace oopse {
321              
322          Xitt += Cij;
323          Xitr += U[i] * Cij;
324 <            //Xirr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I;            
324 >        // uncorrected here.  Volume correction is added after we assemble Xiorr
325          Xirr += -U[i] * Cij * U[j];
326        }
327      }
328 +    // add the volume correction here:
329 +    Xirr += (6.0 * viscosity * volume) * I;    
330      
331 <    const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
331 >    const RealType convertConstant = 1.439326479e4; //converts Poise angstroms
332 >                                                    // to kcal fs mol^-1 Angstrom^-1
333      Xitt *= convertConstant;
334      Xitr *= convertConstant;
335      Xirr *= convertConstant;
336      
337 <    double kt = OOPSEConstant::kB * temperature;
337 >    RealType kt = OOPSEConstant::kb * temperature; // in kcal mol^-1
338      
339      Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O
340      Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O
# Line 377 | Line 393 | namespace oopse {
393      Ddrr = Dorr;
394      Ddtr = Dotr + Dorr * Uod;
395  
396 <    SquareMatrix<double, 6> Dd;
396 >    SquareMatrix<RealType, 6> Dd;
397      Dd.setSubMatrix(0, 0, Ddtt);
398      Dd.setSubMatrix(0, 3, Ddtr.transpose());
399      Dd.setSubMatrix(3, 0, Ddtr);
400      Dd.setSubMatrix(3, 3, Ddrr);    
401 <    SquareMatrix<double, 6> Xid;
401 >    SquareMatrix<RealType, 6> Xid;
402      Ddtt *= kt;
403      Ddtr *=kt;
404      Ddrr *= kt;
# Line 394 | Line 410 | namespace oopse {
410      //Xid /= OOPSEConstant::energyConvert;
411      Xid *= OOPSEConstant::kb * temperature;
412  
413 <    cr.center = rod;
398 <    cr.D.setSubMatrix(0, 0, Ddtt);
399 <    cr.D.setSubMatrix(0, 3, Ddtr);
400 <    cr.D.setSubMatrix(3, 0, Ddtr);
401 <    cr.D.setSubMatrix(3, 3, Ddrr);
402 <    cr.Xi = Xid;
413 >    Mat6x6d Xi, D;
414  
415 +    cd->setCOR(rod);
416 +
417 +    cd->setXi(Xid);
418 +
419 +    D.setSubMatrix(0, 0, Ddtt);
420 +    D.setSubMatrix(0, 3, Ddtr);
421 +    D.setSubMatrix(3, 0, Ddtr);
422 +    D.setSubMatrix(3, 3, Ddrr);
423 +
424 +    cd->setD(D);
425 +
426      std::cout << "viscosity = " << viscosity << std::endl;
427      std::cout << "temperature = " << temperature << std::endl;
428      std::cout << "center of diffusion :" << std::endl;
429      std::cout << rod << std::endl;
430      std::cout << "diffusion tensor at center of diffusion " << std::endl;
431 <    std::cout << "translation(A^2/fs) :" << std::endl;
431 >    std::cout << "translation(A^2 / fs) :" << std::endl;
432      std::cout << Ddtt << std::endl;
433 <    std::cout << "translation-rotation(A^3/fs):" << std::endl;
433 >    std::cout << "translation-rotation(A / fs):" << std::endl;
434      std::cout << Ddtr << std::endl;
435 <    std::cout << "rotation(A^4/fs):" << std::endl;
435 >    std::cout << "rotation(fs^-1):" << std::endl;
436      std::cout << Ddrr << std::endl;
437  
438      std::cout << "resistance tensor at center of diffusion " << std::endl;
# Line 426 | Line 448 | namespace oopse {
448      Xid.getSubMatrix(3, 3, Xidrr);
449  
450      std::cout << Xidtt << std::endl;
451 <    std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-3):" << std::endl;
451 >    std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-1):" << std::endl;
452      std::cout << Xidrt << std::endl;
453 <    std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-3):" << std::endl;
453 >    std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-1):" << std::endl;
454      std::cout << Xidtr << std::endl;
455 <    std::cout << "rotation(kcal*fs*mol^-1*Ang^-4):" << std::endl;
455 >    std::cout << "rotation(kcal*fs*mol^-1):" << std::endl;
456      std::cout << Xidrr << std::endl;
457  
458      return true;

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