--- trunk/src/applications/hydrodynamics/ApproximationModel.cpp 2006/03/29 18:09:26 921 +++ trunk/src/applications/hydrodynamics/ApproximationModel.cpp 2008/01/16 20:19:28 1208 @@ -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" @@ -57,116 +57,109 @@ 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; + HydroProp* cr = new HydroProp(); + HydroProp* cd = new HydroProp(); calcHydroPropsAtCR(beads_, viscosity, temperature, cr); calcHydroPropsAtCD(beads_, viscosity, temperature, cd); setCR(cr); 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, HydroProp* 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; - } + for (std::size_t j = 0; j < nbeads; ++j) { + Mat3x3d Cij; + C.getSubMatrix(i*3, j*3, Cij); + + Xiott += Cij; + Xiotr += U[i] * Cij; + // uncorrected here. Volume correction is added after we assemble Xiorr + Xiorr += -U[i] * Cij * U[j]; + } } - const double convertConstant = 6.023; //convert poise.angstrom to amu/fs + // add the volume correction + Xiorr += (6.0 * viscosity * volume) * I; + + const RealType convertConstant = 1.439326479e4; //converts Poise angstroms + // to kcal fs mol^-1 Angstrom^-1 + Xiott *= convertConstant; Xiotr *= convertConstant; Xiorr *= convertConstant; - - Mat3x3d tmp; Mat3x3d tmpInv; Vector3d tmpVec; @@ -196,8 +189,8 @@ 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()); @@ -213,25 +206,32 @@ 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 ; // in kcal mol^-1 Drtt *= kt; Drrt *= kt; Drtr *= kt; Drrr *= kt; - Xirtt *= OOPSEConstant::kb * temperature; - Xirtr *= OOPSEConstant::kb * temperature; - Xirrr *= OOPSEConstant::kb * temperature; + //Xirtt *= OOPSEConstant::kb * temperature; + //Xirtr *= OOPSEConstant::kb * temperature; + //Xirrr *= OOPSEConstant::kb * temperature; + Mat6x6d Xi, D; - cr.center = ror; - cr.Xi.setSubMatrix(0, 0, Xirtt); - cr.Xi.setSubMatrix(0, 3, Xirtr); - cr.Xi.setSubMatrix(3, 0, Xirtr); - cr.Xi.setSubMatrix(3, 3, Xirrr); - cr.D.setSubMatrix(0, 0, Drtt); - cr.D.setSubMatrix(0, 3, Drrt); - cr.D.setSubMatrix(3, 0, Drtr); - cr.D.setSubMatrix(3, 3, Drrr); + cr->setCOR(ror); + + Xi.setSubMatrix(0, 0, Xirtt); + Xi.setSubMatrix(0, 3, Xirtr); + Xi.setSubMatrix(3, 0, Xirtr); + Xi.setSubMatrix(3, 3, Xirrr); + + cr->setXi(Xi); + + D.setSubMatrix(0, 0, Drtt); + D.setSubMatrix(0, 3, Drrt); + D.setSubMatrix(3, 0, Drtr); + D.setSubMatrix(3, 3, Drrr); + + cr->setD(D); std::cout << "-----------------------------------------\n"; std::cout << "center of resistance :" << std::endl; @@ -256,48 +256,50 @@ 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, HydroProp* cd) { + 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 @@ -307,33 +309,37 @@ 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; - Xirr += -U[i] * Cij * U[j] + (6 * viscosity * volume) * I; - } + Xitt += Cij; + Xitr += U[i] * Cij; + // uncorrected here. Volume correction is added after we assemble Xiorr + Xirr += -U[i] * Cij * U[j]; + } } - - const double convertConstant = 6.023; //convert poise.angstrom to amu/fs + // add the volume correction here: + Xirr += (6.0 * viscosity * volume) * I; + + const RealType convertConstant = 1.439326479e4; //converts Poise angstroms + // to kcal fs mol^-1 Angstrom^-1 Xitt *= convertConstant; Xitr *= convertConstant; Xirr *= convertConstant; - - double kt = OOPSEConstant::kB * temperature; - + + RealType kt = OOPSEConstant::kb * temperature; // in kcal mol^-1 + 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); @@ -387,12 +393,12 @@ 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; @@ -404,23 +410,29 @@ bool ApproximationModel::calcHydroPropsAtCD(std::vecto //Xid /= OOPSEConstant::energyConvert; Xid *= OOPSEConstant::kb * temperature; - cr.center = rod; - cr.D.setSubMatrix(0, 0, Ddtt); - cr.D.setSubMatrix(0, 3, Ddtr); - cr.D.setSubMatrix(3, 0, Ddtr); - cr.D.setSubMatrix(3, 3, Ddrr); - cr.Xi = Xid; + Mat6x6d Xi, D; + cd->setCOR(rod); + + cd->setXi(Xid); + + D.setSubMatrix(0, 0, Ddtt); + D.setSubMatrix(0, 3, Ddtr); + D.setSubMatrix(3, 0, Ddtr); + D.setSubMatrix(3, 3, Ddrr); + + cd->setD(D); + std::cout << "viscosity = " << viscosity << std::endl; std::cout << "temperature = " << temperature << std::endl; std::cout << "center of diffusion :" << std::endl; std::cout << rod << std::endl; std::cout << "diffusion tensor at center of diffusion " << std::endl; - std::cout << "translation(A^2/fs) :" << std::endl; + std::cout << "translation(A^2 / fs) :" << std::endl; std::cout << Ddtt << std::endl; - std::cout << "translation-rotation(A^3/fs):" << std::endl; + std::cout << "translation-rotation(A / fs):" << std::endl; std::cout << Ddtr << std::endl; - std::cout << "rotation(A^4/fs):" << std::endl; + std::cout << "rotation(fs^-1):" << std::endl; std::cout << Ddrr << std::endl; std::cout << "resistance tensor at center of diffusion " << std::endl; @@ -436,28 +448,24 @@ bool ApproximationModel::calcHydroPropsAtCD(std::vecto Xid.getSubMatrix(3, 3, Xidrr); std::cout << Xidtt << std::endl; - std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-3):" << std::endl; + std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-1):" << std::endl; std::cout << Xidrt << std::endl; - std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-3):" << std::endl; + std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-1):" << std::endl; std::cout << Xidtr << std::endl; - std::cout << "rotation(kcal*fs*mol^-1*Ang^-4):" << std::endl; + std::cout << "rotation(kcal*fs*mol^-1):" << std::endl; 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; } - + + } } - - - -}