--- trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp 2006/02/22 20:35:16 891 +++ trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp 2006/03/15 20:58:47 900 @@ -43,6 +43,7 @@ #include "math/LU.hpp" #include "math/DynamicRectMatrix.hpp" #include "math/SquareMatrix3.hpp" +#include "utils/OOPSEConstant.hpp" namespace oopse { /** * Reference: @@ -50,16 +51,50 @@ namespace oopse { * Comparison of Different Modeling and Computational Procedures. * Biophysical Journal, 75(6), 3044, 1999 */ -bool HydrodynamicsModel::calcHydrodyanmicsProps(double eta) { + +HydrodynamicsModel::HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams) : sd_(sd){ + DynamicProperty::const_iterator iter; + + iter = extraParams.find("Viscosity"); + if (iter != extraParams.end()) { + boost::any param = iter->second; + viscosity_ = boost::any_cast(param); + }else { + std::cout << "HydrodynamicsModel Error\n" ; + } + + iter = extraParams.find("Temperature"); + if (iter != extraParams.end()) { + boost::any param = iter->second; + temperature_ = boost::any_cast(param); + }else { + std::cout << "HydrodynamicsModel Error\n" ; + } +} + +bool HydrodynamicsModel::calcHydrodyanmicsProps() { if (!createBeads(beads_)) { std::cout << "can not create beads" << std::endl; return false; } - + + //calcResistanceTensor(); + calcDiffusionTensor(); + return true; +} + +void HydrodynamicsModel::calcResistanceTensor() { +} + +void HydrodynamicsModel::calcDiffusionTensor() { int nbeads = beads_.size(); 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; @@ -69,11 +104,11 @@ bool HydrodynamicsModel::calcHydrodyanmicsProps(double double rij2 = rij * rij; double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2; Mat3x3d tmpMat; - tmpMat = outProduct(beads_[i].pos, beads_[j].pos) / rij2; - double constant = 8.0 * NumericConstant::PI * eta * rij; + 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 * eta * beads_[i].radius); + double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity_ * beads_[i].radius); Tij(0, 0) = constant; Tij(1, 1) = constant; Tij(2, 2) = constant; @@ -84,7 +119,7 @@ bool HydrodynamicsModel::calcHydrodyanmicsProps(double //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) { @@ -97,6 +132,13 @@ bool HydrodynamicsModel::calcHydrodyanmicsProps(double Mat3x3d Xitt; Mat3x3d Xirr; Mat3x3d Xitr; + + //calculate the total volume + + double 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); + } for (std::size_t i = 0; i < nbeads; ++i) { for (std::size_t j = 0; j < nbeads; ++j) { @@ -104,46 +146,63 @@ bool HydrodynamicsModel::calcHydrodyanmicsProps(double C.getSubMatrix(i*3, j*3, Cij); Xitt += Cij; - Xirr += U[i] * Cij; - Xitr += U[i] * Cij * U[j]; + Xitr += U[i] * Cij; + Xirr += -U[i] * Cij * U[j] + (6 * viscosity_ * volume) * I; } } - //invert Xi to get Diffusion Tensor at arbitrary origin O - RectMatrix Xi; - RectMatrix Do; - Xi.setSubMatrix(0, 0, Xitt); - Xi.setSubMatrix(0, 3, Xitr.transpose()); - Xi.setSubMatrix(3, 0, Xitr); - Xi.setSubMatrix(3, 3, Xitt); - invertMatrix(Xi, Do); + const double convertConstant = 6.023; //convert poise.angstrom to amu/fs + Xitt *= convertConstant; + Xitr *= convertConstant; + Xirr *= convertConstant; + double 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 - Do.getSubMatrix(0, 0 , Dott); - Do.getSubMatrix(3, 0, Dotr); - Do.getSubMatrix(3, 3, Dorr); + const static Mat3x3d zeroMat(0.0); + + Mat3x3d XittInv(0.0); + XittInv = Xitt.inverse(); + + Mat3x3d XirrInv; + XirrInv = Xirr.inverse(); + + Mat3x3d tmp; + Mat3x3d tmpInv; + tmp = Xitt - Xitr.transpose() * XirrInv * Xitr; + tmpInv = tmp.inverse(); + + Dott = kt*tmpInv; + Dotr = -kt*XirrInv * Xitr * tmpInv; + + tmp = Xirr - Xitr * XittInv * Xitr.transpose(); + tmpInv = tmp.inverse(); + + Dorr = kt * tmpInv; + //calculate center of diffusion - Mat3x3d tmpMat; - tmpMat(0, 0) = Dorr(1, 1) + Dorr(2, 2); - tmpMat(0, 1) = - Dorr(0, 1); - tmpMat(0, 2) = -Dorr(0, 2); - tmpMat(1, 0) = -Dorr(0, 1); - tmpMat(1, 1) = Dorr(0, 0) + Dorr(2, 2); - tmpMat(1, 2) = -Dorr(1, 2); - tmpMat(2, 0) = -Dorr(0, 2); - tmpMat(2, 1) = -Dorr(1, 2); - tmpMat(2, 2) = Dorr(1, 1) + Dorr(0, 0); + tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2); + tmp(0, 1) = - Dorr(0, 1); + tmp(0, 2) = -Dorr(0, 2); + tmp(1, 0) = -Dorr(0, 1); + tmp(1, 1) = Dorr(0, 0) + Dorr(2, 2); + tmp(1, 2) = -Dorr(1, 2); + tmp(2, 0) = -Dorr(0, 2); + tmp(2, 1) = -Dorr(1, 2); + tmp(2, 2) = Dorr(1, 1) + Dorr(0, 0); Vector3d tmpVec; tmpVec[0] = Dotr(1, 2) - Dotr(2, 1); tmpVec[1] = Dotr(2, 0) - Dotr(0, 2); tmpVec[2] = Dotr(0, 1) - Dotr(1, 0); - - Vector3d rod = tmpMat.inverse() * tmpVec; + tmpInv = tmp.inverse(); + + Vector3d rod = tmpInv * tmpVec; + //calculate Diffusion Tensor at center of diffusion Mat3x3d Uod; Uod.setupSkewMat(rod); @@ -155,21 +214,95 @@ bool HydrodynamicsModel::calcHydrodyanmicsProps(double Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr; Ddrr = Dorr; Ddtr = Dotr + Dorr * Uod; - + props_.diffCenter = rod; - props_.transDiff = Ddtt; - props_.transRotDiff = Ddtr; - props_.rotDiff = Ddrr; + props_.Ddtt = Ddtt; + props_.Ddtr = Ddtr; + props_.Ddrr = Ddrr; - return true; + 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; + invertMatrix(Dd, Xid); + + //Xidtt in units of kcal*fs*mol^-1*Ang^-2 + Xid *= OOPSEConstant::kb*temperature_; + + Xid.getSubMatrix(0, 0, props_.Xidtt); + Xid.getSubMatrix(0, 3, props_.Xidrt); + Xid.getSubMatrix(3, 0, props_.Xidtr); + Xid.getSubMatrix(3, 3, props_.Xidrr); + + + 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 << Ddtt << std::endl; + std::cout << "translation-rotation(A^3/fs):" << std::endl; + std::cout << Ddtr << std::endl; + std::cout << "rotation(A^4/fs):" << std::endl; + std::cout << Ddrr << std::endl; + + std::cout << "resistance tensor at center of diffusion " << std::endl; + std::cout << "translation(kcal*fs*mol^-1*Ang^-2) :" << std::endl; + std::cout << props_.Xidtt << std::endl; + std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-3):" << std::endl; + std::cout << props_.Xidrt << std::endl; + std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-3):" << std::endl; + std::cout << props_.Xidtr << std::endl; + std::cout << "rotation(kcal*fs*mol^-1*Ang^-4):" << std::endl; + std::cout << props_.Xidrr << std::endl; + + } void HydrodynamicsModel::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; + } } void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) { + os << sd_->getType() << "\t"; + os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\t"; + + os << props_.Ddtt(0, 0) << "\t" << props_.Ddtt(0, 1) << "\t" << props_.Ddtt(0, 2) << "\t" + << props_.Ddtt(1, 0) << "\t" << props_.Ddtt(1, 1) << "\t" << props_.Ddtt(1, 2) << "\t" + << props_.Ddtt(2, 0) << "\t" << props_.Ddtt(2, 1) << "\t" << props_.Ddtt(2, 2) << "\t"; + + os << props_.Ddtr(0, 0) << "\t" << props_.Ddtr(0, 1) << "\t" << props_.Ddtr(0, 2) << "\t" + << props_.Ddtr(1, 0) << "\t" << props_.Ddtr(1, 1) << "\t" << props_.Ddtr(1, 2) << "\t" + << props_.Ddtr(2, 0) << "\t" << props_.Ddtr(2, 1) << "\t" << props_.Ddtr(2, 2) << "\t"; + + os << props_.Ddrr(0, 0) << "\t" << props_.Ddrr(0, 1) << "\t" << props_.Ddrr(0, 2) << "\t" + << props_.Ddrr(1, 0) << "\t" << props_.Ddrr(1, 1) << "\t" << props_.Ddrr(1, 2) << "\t" + << props_.Ddrr(2, 0) << "\t" << props_.Ddrr(2, 1) << "\t" << props_.Ddrr(2, 2) <<"\t"; + + os << props_.Xidtt(0, 0) << "\t" << props_.Xidtt(0, 1) << "\t" << props_.Xidtt(0, 2) << "\t" + << props_.Xidtt(1, 0) << "\t" << props_.Xidtt(1, 1) << "\t" << props_.Xidtt(1, 2) << "\t" + << props_.Xidtt(2, 0) << "\t" << props_.Xidtt(2, 1) << "\t" << props_.Xidtt(2, 2) << "\t"; + + os << props_.Xidrt(0, 0) << "\t" << props_.Xidrt(0, 1) << "\t" << props_.Xidrt(0, 2) << "\t" + << props_.Xidrt(1, 0) << "\t" << props_.Xidrt(1, 1) << "\t" << props_.Xidrt(1, 2) << "\t" + << props_.Xidrt(2, 0) << "\t" << props_.Xidrt(2, 1) << "\t" << props_.Xidrt(2, 2) << "\t"; + + os << props_.Xidtr(0, 0) << "\t" << props_.Xidtr(0, 1) << "\t" << props_.Xidtr(0, 2) << "\t" + << props_.Xidtr(1, 0) << "\t" << props_.Xidtr(1, 1) << "\t" << props_.Xidtr(1, 2) << "\t" + << props_.Xidtr(2, 0) << "\t" << props_.Xidtr(2, 1) << "\t" << props_.Xidtr(2, 2) << "\t"; + + os << props_.Xidrr(0, 0) << "\t" << props_.Xidrr(0, 1) << "\t" << props_.Xidrr(0, 2) << "\t" + << props_.Xidrr(1, 0) << "\t" << props_.Xidrr(1, 1) << "\t" << props_.Xidrr(1, 2) << "\t" + << props_.Xidrr(2, 0) << "\t" << props_.Xidrr(2, 1) << "\t" << props_.Xidrr(2, 2) << std::endl; + } }