--- trunk/src/applications/hydrodynamics/ApproximationModel.cpp 2006/05/10 01:44:48 954 +++ trunk/src/applications/hydrodynamics/ApproximationModel.cpp 2006/05/25 17:02:00 978 @@ -44,8 +44,8 @@ #include "math/DynamicRectMatrix.hpp" #include "math/SquareMatrix3.hpp" #include "utils/OOPSEConstant.hpp" -#include "applications/hydrodynamics/Spheric.hpp" -#include "applications/hydrodynamics/Ellipsoid.hpp" +#include "hydrodynamics/Sphere.hpp" +#include "hydrodynamics/Ellipsoid.hpp" #include "applications/hydrodynamics/CompositeShape.hpp" #include "math/LU.hpp" #include "utils/simError.h" @@ -57,32 +57,20 @@ namespace oopse { * Biophysical Journal, 75(6), 3044, 1999 */ -ApproximationModel::ApproximationModel(StuntDouble* sd, SimInfo* info): HydrodynamicsModel(sd, info){ - -} - -bool ApproximationModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) { - return internalCalcHydroProps(static_cast(spheric), viscosity, temperature); -} - -bool ApproximationModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) { - return internalCalcHydroProps(static_cast(ellipsoid), viscosity, temperature); -} -bool ApproximationModel::calcHydroProps(CompositeShape* compositeShape, double viscosity, double temperature) { - return internalCalcHydroProps(static_cast(compositeShape), viscosity, temperature); -} - -void ApproximationModel::init() { + ApproximationModel::ApproximationModel(StuntDouble* sd, SimInfo* info): HydrodynamicsModel(sd, info){ + } + + void ApproximationModel::init() { if (!createBeads(beads_)) { sprintf(painCave.errMsg, "ApproximationModel::init() : Can not create beads\n"); painCave.isFatal = 1; simError(); } - -} - -bool ApproximationModel::internalCalcHydroProps(Shape* shape, double viscosity, double temperature) { - + + } + + bool ApproximationModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) { + bool ret = true; HydroProps cr; HydroProps cd; @@ -92,82 +80,84 @@ bool ApproximationModel::internalCalcHydroProps(Shape* setCD(cd); return true; -} - -bool ApproximationModel::calcHydroPropsAtCR(std::vector& beads, double viscosity, double temperature, HydroProps& cr) { - + } + + bool ApproximationModel::calcHydroPropsAtCR(std::vector& beads, RealType viscosity, RealType temperature, HydroProps& cr) { + int nbeads = beads.size(); - DynamicRectMatrix B(3*nbeads, 3*nbeads); - DynamicRectMatrix C(3*nbeads, 3*nbeads); + DynamicRectMatrix B(3*nbeads, 3*nbeads); + DynamicRectMatrix C(3*nbeads, 3*nbeads); Mat3x3d I; I(0, 0) = 1.0; I(1, 1) = 1.0; I(2, 2) = 1.0; for (std::size_t i = 0; i < nbeads; ++i) { - for (std::size_t j = 0; j < nbeads; ++j) { - Mat3x3d Tij; + for (std::size_t j = 0; j < nbeads; ++j) { + Mat3x3d Tij; if (i != j ) { - Vector3d Rij = beads[i].pos - beads[j].pos; - double rij = Rij.length(); - double rij2 = rij * rij; - double sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2; - Mat3x3d tmpMat; - tmpMat = outProduct(Rij, Rij) / rij2; - double constant = 8.0 * NumericConstant::PI * viscosity * rij; - Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; + Vector3d Rij = beads[i].pos - beads[j].pos; + RealType rij = Rij.length(); + RealType rij2 = rij * rij; + RealType sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2; + Mat3x3d tmpMat; + tmpMat = outProduct(Rij, Rij) / rij2; + RealType constant = 8.0 * NumericConstant::PI * viscosity * rij; + RealType tmp1 = 1.0 + sumSigma2OverRij2/3.0; + RealType tmp2 = 1.0 - sumSigma2OverRij2; + Tij = (tmp1 * I + tmp2 * tmpMat ) / constant; }else { - double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius); - Tij(0, 0) = constant; - Tij(1, 1) = constant; - Tij(2, 2) = constant; + RealType constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius); + Tij(0, 0) = constant; + Tij(1, 1) = constant; + Tij(2, 2) = constant; } B.setSubMatrix(i*3, j*3, Tij); - } + } } - + //invert B Matrix invertMatrix(B, C); //prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) std::vector U; for (int i = 0; i < nbeads; ++i) { - Mat3x3d currU; - currU.setupSkewMat(beads[i].pos); - U.push_back(currU); + Mat3x3d currU; + currU.setupSkewMat(beads[i].pos); + U.push_back(currU); } //calculate Xi matrix at arbitrary origin O Mat3x3d Xiott; Mat3x3d Xiorr; Mat3x3d Xiotr; - + //calculate the total volume - - double volume = 0.0; + + RealType volume = 0.0; for (std::vector::iterator iter = beads.begin(); iter != beads.end(); ++iter) { - volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); + volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); } - + for (std::size_t i = 0; i < nbeads; ++i) { - for (std::size_t j = 0; j < nbeads; ++j) { - Mat3x3d Cij; - C.getSubMatrix(i*3, j*3, Cij); - - Xiott += Cij; - Xiotr += U[i] * Cij; - //Xiorr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I; - Xiorr += -U[i] * Cij * U[j]; - } + for (std::size_t j = 0; j < nbeads; ++j) { + Mat3x3d Cij; + C.getSubMatrix(i*3, j*3, Cij); + + Xiott += Cij; + Xiotr += U[i] * Cij; + //Xiorr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I; + Xiorr += -U[i] * Cij * U[j]; + } } - - const double convertConstant = 6.023; //convert poise.angstrom to amu/fs + + const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs Xiott *= convertConstant; Xiotr *= convertConstant; Xiorr *= convertConstant; - + Mat3x3d tmp; Mat3x3d tmpInv; Vector3d tmpVec; @@ -197,8 +187,8 @@ bool ApproximationModel::calcHydroPropsAtCR(std::vecto Xirrr = Xiorr - Uor * Xiott * Uor + Xiotr * Uor - Uor * Xiotr.transpose(); - SquareMatrix Xir6x6; - SquareMatrix Dr6x6; + SquareMatrix Xir6x6; + SquareMatrix Dr6x6; Xir6x6.setSubMatrix(0, 0, Xirtt); Xir6x6.setSubMatrix(0, 3, Xirtr.transpose()); @@ -214,7 +204,7 @@ bool ApproximationModel::calcHydroPropsAtCR(std::vecto Dr6x6.getSubMatrix(0, 3, Drrt); Dr6x6.getSubMatrix(3, 0, Drtr); Dr6x6.getSubMatrix(3, 3, Drrr); - double kt = OOPSEConstant::kB * temperature ; + RealType kt = OOPSEConstant::kB * temperature ; Drtt *= kt; Drrt *= kt; Drtr *= kt; @@ -257,48 +247,50 @@ bool ApproximationModel::calcHydroPropsAtCR(std::vecto return true; } - -bool ApproximationModel::calcHydroPropsAtCD(std::vector& beads, double viscosity, double temperature, HydroProps& cr) { - + + bool ApproximationModel::calcHydroPropsAtCD(std::vector& beads, RealType viscosity, RealType temperature, HydroProps& cr) { + int nbeads = beads.size(); - DynamicRectMatrix B(3*nbeads, 3*nbeads); - DynamicRectMatrix C(3*nbeads, 3*nbeads); + DynamicRectMatrix B(3*nbeads, 3*nbeads); + DynamicRectMatrix C(3*nbeads, 3*nbeads); Mat3x3d I; I(0, 0) = 1.0; I(1, 1) = 1.0; I(2, 2) = 1.0; for (std::size_t i = 0; i < nbeads; ++i) { - for (std::size_t j = 0; j < nbeads; ++j) { - Mat3x3d Tij; - if (i != j ) { - Vector3d Rij = beads[i].pos - beads[j].pos; - double rij = Rij.length(); - double rij2 = rij * rij; - double sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2; - Mat3x3d tmpMat; - tmpMat = outProduct(Rij, Rij) / rij2; - double constant = 8.0 * NumericConstant::PI * viscosity * rij; - Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; - }else { - double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius); - Tij(0, 0) = constant; - Tij(1, 1) = constant; - Tij(2, 2) = constant; - } - B.setSubMatrix(i*3, j*3, Tij); + for (std::size_t j = 0; j < nbeads; ++j) { + Mat3x3d Tij; + if (i != j ) { + Vector3d Rij = beads[i].pos - beads[j].pos; + RealType rij = Rij.length(); + RealType rij2 = rij * rij; + RealType sumSigma2OverRij2 = ((beads[i].radius*beads[i].radius) + (beads[j].radius*beads[j].radius)) / rij2; + Mat3x3d tmpMat; + tmpMat = outProduct(Rij, Rij) / rij2; + RealType constant = 8.0 * NumericConstant::PI * viscosity * rij; + RealType tmp1 = 1.0 + sumSigma2OverRij2/3.0; + RealType tmp2 = 1.0 - sumSigma2OverRij2; + Tij = (tmp1 * I + tmp2 * tmpMat ) / constant; + }else { + RealType constant = 1.0 / (6.0 * NumericConstant::PI * viscosity * beads[i].radius); + Tij(0, 0) = constant; + Tij(1, 1) = constant; + Tij(2, 2) = constant; } + B.setSubMatrix(i*3, j*3, Tij); + } } - + //invert B Matrix invertMatrix(B, C); - + //prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) std::vector U; for (int i = 0; i < nbeads; ++i) { - Mat3x3d currU; - currU.setupSkewMat(beads[i].pos); - U.push_back(currU); + Mat3x3d currU; + currU.setupSkewMat(beads[i].pos); + U.push_back(currU); } //calculate Xi matrix at arbitrary origin O @@ -308,34 +300,34 @@ bool ApproximationModel::calcHydroPropsAtCD(std::vecto //calculate the total volume - double volume = 0.0; + RealType volume = 0.0; for (std::vector::iterator iter = beads.begin(); iter != beads.end(); ++iter) { - volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); + volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); } - + for (std::size_t i = 0; i < nbeads; ++i) { - for (std::size_t j = 0; j < nbeads; ++j) { - Mat3x3d Cij; - C.getSubMatrix(i*3, j*3, Cij); + for (std::size_t j = 0; j < nbeads; ++j) { + Mat3x3d Cij; + C.getSubMatrix(i*3, j*3, Cij); - Xitt += Cij; - Xitr += U[i] * Cij; + Xitt += Cij; + Xitr += U[i] * Cij; //Xirr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I; - Xirr += -U[i] * Cij * U[j]; - } + Xirr += -U[i] * Cij * U[j]; + } } - - const double convertConstant = 6.023; //convert poise.angstrom to amu/fs + + const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs Xitt *= convertConstant; Xitr *= convertConstant; Xirr *= convertConstant; - - double kt = OOPSEConstant::kB * temperature; - + + RealType kt = OOPSEConstant::kB * temperature; + Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O - + const static Mat3x3d zeroMat(0.0); Mat3x3d XittInv(0.0); @@ -389,12 +381,12 @@ bool ApproximationModel::calcHydroPropsAtCD(std::vecto Ddrr = Dorr; Ddtr = Dotr + Dorr * Uod; - SquareMatrix Dd; + SquareMatrix Dd; Dd.setSubMatrix(0, 0, Ddtt); Dd.setSubMatrix(0, 3, Ddtr.transpose()); Dd.setSubMatrix(3, 0, Ddtr); Dd.setSubMatrix(3, 3, Ddrr); - SquareMatrix Xid; + SquareMatrix Xid; Ddtt *= kt; Ddtr *=kt; Ddrr *= kt; @@ -446,20 +438,16 @@ bool ApproximationModel::calcHydroPropsAtCD(std::vecto std::cout << Xidrr << std::endl; return true; - -} + + } - -void ApproximationModel::writeBeads(std::ostream& os) { + void ApproximationModel::writeBeads(std::ostream& os) { std::vector::iterator iter; os << beads_.size() << std::endl; os << "Generated by Hydro" << std::endl; for (iter = beads_.begin(); iter != beads_.end(); ++iter) { - os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl; + os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl; } - + + } } - - - -}