[ViewVC] Diff of: group/trunk/OOPSE-4/src/applications/hydrodynamics/HydrodynamicsModel.cpp

Comparing trunk/OOPSE-4/src/applications/hydrodynamics/HydrodynamicsModel.cpp (file contents):
Revision 2596 by tim, Wed Feb 22 20:35:16 2006 UTC vs.
Revision 2611 by tim, Mon Mar 13 22:42:40 2006 UTC

+#include "math/LU.hpp"
+#include "math/DynamicRectMatrix.hpp"
+#include "math/SquareMatrix3.hpp"
-+
+#include "utils/OOPSEConstant.hpp"
+namespace oopse {
+/**
+ * Reference:
+ * 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<double>(param);
->
+    }else {
->
+        std::cout << "HydrodynamicsModel Error\n" ;
->
+    }
->
->
+    iter = extraParams.find("Temperature");
->
+    if (iter != extraParams.end()) {
->
+        boost::any param = iter->second;
->
+        temperature_ = boost::any_cast<double>(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();
-+
+/*
+    int nbeads = beads_.size();
+    DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
+    DynamicRectMatrix<double> 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;
+                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;
+            B.setSubMatrix(i*3, j*3, Tij);
-+
+            std::cout << Tij << std::endl;
-+
+    std::cout << "B=\n"
-+
+                  << B << std::endl;
+    //invert B Matrix
+    invertMatrix(B, C);
-<
->
->
+    std::cout << "C=\n"
->
+                  << C << std::endl;
->
+    //prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0)
+    std::vector<Mat3x3d> U;
+    for (int i = 0; i < nbeads; ++i) {
+    Mat3x3d Xitt;
+    Mat3x3d Xirr;
+    Mat3x3d Xitr;
-+
-+
+    //calculate the total volume
-+
-+
+    double volume = 0.0;
-+
+    for (std::vector<BeadParam>::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) {
+            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];
->
+            Xirr += -U[i] * Cij * U[j] + (0.166*6 * viscosity_ * volume) * I;
+    Xi.setSubMatrix(0, 0, Xitt);
+    Xi.setSubMatrix(0, 3, Xitr.transpose());
+    Xi.setSubMatrix(3, 0, Xitr);
-<
+    Xi.setSubMatrix(3, 3, Xitt);
-<
+    invertMatrix(Xi, Do);
->
+    Xi.setSubMatrix(3, 3, Xirr);
->
+    //invertMatrix(Xi, Do);
->
+    double kt = OOPSEConstant::kB * temperature_ * 1.66E-2;
->
+    //Do *= kt;
-+
+    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();
-+
-+
+    //Xirr may not be inverted,if it one of the diagonal element is zero, for example
-+
+    //( a11 a12 0)
-+
+    //( a21 a22 0)
-+
+    //( 0    0    0)
-+
+    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* 1.0E8;
-+
-+
+    tmp = Xirr - Xitr * XittInv * Xitr.transpose();
-+
+    tmpInv = tmp.inverse();
-+
-+
+    Dorr = kt * tmpInv*1.0E16;
-+
-+
+    //Do.getSubMatrix(0, 0 , Dott);
-+
+    //Do.getSubMatrix(3, 0, Dotr);
-+
+    //Do.getSubMatrix(3, 3, Dorr);
-+
+    //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);
+    props_.transDiff = Ddtt;
+    props_.transRotDiff = Ddtr;
+    props_.rotDiff = Ddrr;
-<
->
+*/
+    return true;
-+
+}
-+
-+
+void HydrodynamicsModel::calcResistanceTensor() {
-+
-+
+    int nbeads = beads_.size();
-+
+    DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
-+
+    DynamicRectMatrix<double> 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_[i].radius*beads_[i].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);
-+
+        }
-+
+    }
-+
-+
-+
+    //invert B Matrix
-+
+    invertMatrix(B, C);
-+
-+
+    //prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0)
-+
+    std::vector<Mat3x3d> U;
-+
+    for (int i = 0; i < nbeads; ++i) {
-+
+        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;
-+
+    for (std::vector<BeadParam>::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) {
-+
+            Mat3x3d Cij;
-+
+            C.getSubMatrix(i*3, j*3, Cij);
-+
-+
+            Xiott += Cij;
-+
+            Xiotr += U[i] * Cij;
-+
+            //Xiorr += -U[i] * Cij * U[j];
-+
+            Xiorr += -U[i] * Cij * U[j] + (6 * viscosity_ * volume) * I;
-+
+        }
-+
+    }
-+
-+
+    Mat3x3d tmp;
-+
+    Mat3x3d tmpInv;
-+
+    Vector3d tmpVec;
-+
+    tmp(0, 0) = Xiott(1, 1) + Xiott(2, 2);
-+
+    tmp(0, 1) = - Xiott(0, 1);
-+
+    tmp(0, 2) = -Xiott(0, 2);
-+
+    tmp(1, 0) = -Xiott(0, 1);
-+
+    tmp(1, 1) = Xiott(0, 0)  + Xiott(2, 2);
-+
+    tmp(1, 2) = -Xiott(1, 2);
-+
+    tmp(2, 0) = -Xiott(0, 2);
-+
+    tmp(2, 1) = -Xiott(1, 2);
-+
+    tmp(2, 2) = Xiott(1, 1) + Xiott(0, 0);
-+
+    tmpVec[0] = Xiotr(2, 1) - Xiotr(1, 2);
-+
+    tmpVec[1] = Xiotr(0, 2) - Xiotr(2, 0);
-+
+    tmpVec[2] = Xiotr(1, 0) - Xiotr(0, 1);
-+
+    tmpInv = tmp.inverse();
-+
+    Vector3d ror = tmpInv * tmpVec; //center of resistance
-+
+    Mat3x3d Uor;
-+
+    Uor.setupSkewMat(ror);
-+
-+
+    Mat3x3d Xirtt;
-+
+    Mat3x3d Xirrr;
-+
+    Mat3x3d Xirtr;
-+
-+
+    Xirtt = Xiott;
-+
+    Xirtr = (Xiotr - Uor * Xiott) * 1E-8;
-+
+    Xirrr = Xiorr - Uor * Xiott * Uor + Xiotr * Uor - Uor * Xiotr.transpose() * 1E-16;
-+
+/*
-+
+    SquareMatrix<double,6> Xir6x6;
-+
+    SquareMatrix<double,6> Dr6x6;
-+
-+
+    Xir6x6.setSubMatrix(0, 0, Xirtt);
-+
+    Xir6x6.setSubMatrix(0, 3, Xirtr.transpose());
-+
+    Xir6x6.setSubMatrix(3, 0, Xirtr);
-+
+    Xir6x6.setSubMatrix(3, 3, Xirrr);
-+
-+
+    invertMatrix(Xir6x6, Dr6x6);
-+
+    Mat3x3d Drtt;
-+
+    Mat3x3d Drtr;
-+
+    Mat3x3d Drrr;
-+
+    Dr6x6.getSubMatrix(0, 0, Drtt);
-+
+    Dr6x6.getSubMatrix(3, 0, Drtr);
-+
+    Dr6x6.getSubMatrix(3, 3, Drrr);
-+
+    double kt = OOPSEConstant::kB * temperature_ * 1.66E-2;
-+
+    Drtt *= kt;
-+
+    Drtr *= kt*1E8;
-+
+    Drrr *= kt*1E16;
-+
+*/
-+
-+
+    const static Mat3x3d zeroMat(0.0);
-+
-+
-+
-+
+    Mat3x3d XirttInv(0.0);
-+
+    XirttInv = Xirtt.inverse();
-+
-+
+    //Xirr may not be inverted,if it one of the diagonal element is zero, for example
-+
+    //( a11 a12 0)
-+
+    //( a21 a22 0)
-+
+    //( 0    0    0)
-+
+    Mat3x3d XirrrInv;
-+
+    XirrrInv = Xirrr.inverse();
-+
+    tmp = Xirtt - Xirtr.transpose() * XirrrInv * Xirtr;
-+
+    tmpInv = tmp.inverse();
-+
-+
+    Mat3x3d Drtt;
-+
+    Mat3x3d Drtr;
-+
+    Mat3x3d Drrr;
-+
+    double kt = OOPSEConstant::kB * temperature_ * 1.66E-2;
-+
+    Drtt = kt * tmpInv;
-+
+    Drtr = -kt*XirrrInv * Xirtr * tmpInv* 1.0E8;
-+
-+
+    tmp = Xirrr - Xirtr * XirttInv * Xirtr.transpose();
-+
+    tmpInv = tmp.inverse();
-+
-+
+    Drrr = kt * tmpInv*1.0E16;
-+
-+
+    std::cout << "-----------------------------------------\n";
-+
+    std::cout << "center of resistance :" << std::endl;
-+
+    std::cout << ror << std::endl;
-+
+    std::cout << "resistant tensor at center of resistance" << std::endl;
-+
+    std::cout << "translation:" << std::endl;
-+
+    std::cout << Xirtt << std::endl;
-+
+    std::cout << "translation-rotation:" << std::endl;
-+
+    std::cout << Xirtr << std::endl;
-+
+    std::cout << "rotation:" << std::endl;
-+
+    std::cout << Xirrr << std::endl;
-+
+    std::cout << "diffusion tensor at center of resistance" << std::endl;
-+
+    std::cout << "translation:" << std::endl;
-+
+    std::cout << Drtt << std::endl;
-+
+    std::cout << "translation-rotation:" << std::endl;
-+
+    std::cout << Drtr << std::endl;
-+
+    std::cout << "rotation:" << std::endl;
-+
+    std::cout << Drrr << std::endl;
-+
+    std::cout << "-----------------------------------------\n";
-+
-+
+void HydrodynamicsModel::calcDiffusionTensor() {
-+
+    int nbeads = beads_.size();
-+
+    DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
-+
+    DynamicRectMatrix<double> 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_[i].radius*beads_[i].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);
-+
+        }
-+
+    }
-+
-+
+    //invert B Matrix
-+
+    invertMatrix(B, C);
-+
-+
+    //prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0)
-+
+    std::vector<Mat3x3d> U;
-+
+    for (int i = 0; i < nbeads; ++i) {
-+
+        Mat3x3d currU;
-+
+        currU.setupSkewMat(beads_[i].pos);
-+
+        U.push_back(currU);
-+
+    }
-+
-+
+    //calculate Xi matrix at arbitrary origin O
-+
+    Mat3x3d Xitt;
-+
+    Mat3x3d Xirr;
-+
+    Mat3x3d Xitr;
-+
-+
+    //calculate the total volume
-+
-+
+    double volume = 0.0;
-+
+    for (std::vector<BeadParam>::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) {
-+
+            Mat3x3d Cij;
-+
+            C.getSubMatrix(i*3, j*3, Cij);
-+
-+
+            Xitt += Cij;
-+
+            Xitr += U[i] * Cij;
-+
+            //Xirr += -U[i] * Cij * U[j];
-+
+            Xirr += -U[i] * Cij * U[j] + (6 * viscosity_ * volume) * I;
-+
+        }
-+
+    }
-+
-+
+    //invert Xi to get Diffusion Tensor at arbitrary origin O
-+
+    RectMatrix<double, 6, 6> Xi;
-+
+    RectMatrix<double, 6, 6> Do;
-+
+    Xi.setSubMatrix(0, 0, Xitt);
-+
+    Xi.setSubMatrix(0, 3, Xitr.transpose());
-+
+    Xi.setSubMatrix(3, 0, Xitr);
-+
+    Xi.setSubMatrix(3, 3, Xirr);
-+
+    //invertMatrix(Xi, Do);
-+
+    //double kt = OOPSEConstant::kB * temperature_ * 1.66E-2;
-+
-+
+    //1 poise = 0.1 N.S/m^2 = 1.661E-3 amu/ (Angstrom*fs)
-+
+    double kt = OOPSEConstant::kB * temperature_ * 1.66E-3;
-+
-+
+    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);
-+
+    XittInv = Xitt.inverse();
-+
-+
+    //Xirr may not be inverted,if it one of the diagonal element is zero, for example
-+
+    //( a11 a12 0)
-+
+    //( a21 a22 0)
-+
+    //( 0    0    0)
-+
+    Mat3x3d XirrInv;
-+
+    XirrInv = Xirr.inverse();
-+
-+
+    Mat3x3d tmp;
-+
+    Mat3x3d tmpInv;
-+
+    tmp = Xitt - Xitr.transpose() * XirrInv * Xitr;
-+
+    tmpInv = tmp.inverse();
-+
-+
+    //Dott = kt * tmpInv; //unit in A^2/fs
-+
+    Dott = tmpInv;
-+
+    //Dotr = -kt*XirrInv * Xitr * tmpInv*1E8;
-+
+    //Dotr = -kt*XirrInv * Xitr * tmpInv;
-+
+    Dotr = -XirrInv* Xitr * tmpInv;
-+
-+
+    tmp = Xirr - Xitr * XittInv * Xitr.transpose();
-+
+    tmpInv = tmp.inverse();
-+
-+
+    //Dorr = kt * tmpInv*1E16;
-+
+    //Dorr = kt * tmpInv;
-+
+    Dorr = tmpInv;
-+
+    //calculate center of diffusion
-+
+    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);
-+
-+
+    tmpInv = tmp.inverse();
-+
-+
+    Vector3d rod = tmpInv * tmpVec;
-+
-+
+    //calculate Diffusion Tensor at center of diffusion
-+
+    Mat3x3d Uod;
-+
+    Uod.setupSkewMat(rod);
-+
-+
+    Mat3x3d Ddtt; //translational diffusion tensor at diffusion center
-+
+    Mat3x3d Ddtr; //rotational diffusion tensor at diffusion center
-+
+    Mat3x3d Ddrr; //translation-rotation couplingl diffusion tensor at diffusion tensor
-+
-+
+    Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr;
-+
+    Ddrr = Dorr;
-+
+    Ddtr = Dotr + Dorr * Uod;
-+
-+
+    props_.diffCenter = rod;
-+
+    props_.Ddtt = Ddtt;
-+
+    props_.Ddtr = Ddtr;
-+
+    props_.Ddrr = Ddrr;
-+
-+
+    SquareMatrix<double, 6> Dd;
-+
+    Dd.setSubMatrix(0, 0, Ddtt);
-+
+    Dd.setSubMatrix(0, 3, Ddtr.transpose());
-+
+    Dd.setSubMatrix(3, 0, Ddtr);
-+
+    Dd.setSubMatrix(3, 3, Ddrr);
-+
+    SquareMatrix<double, 6> Xid;
-+
+    invertMatrix(Dd, Xid);
-+
-+
+    Ddtt *= kt;
-+
+    Ddtr *= kt;
-+
+    Ddrr *= kt;
-+
+    Xid /= 1.66E-3;
-+
-+
+    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:" << std::endl;
-+
+    std::cout << Ddtt << std::endl;
-+
+    std::cout << "translation-rotation:" << std::endl;
-+
+    std::cout << Ddtr << std::endl;
-+
+    std::cout << "rotation:" << std::endl;
-+
+    std::cout << Ddrr << std::endl;
-+
+    */
-+
-+
+}
-+
+void HydrodynamicsModel::writeBeads(std::ostream& os) {
-+
+    std::vector<BeadParam>::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;
-+

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+Removed lines
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Comparing trunk/OOPSE-4/src/applications/hydrodynamics/HydrodynamicsModel.cpp (file contents): Revision 2596 by tim, Wed Feb 22 20:35:16 2006 UTC vs. Revision 2611 by tim, Mon Mar 13 22:42:40 2006 UTC

Diff Legend

Comparing trunk/OOPSE-4/src/applications/hydrodynamics/HydrodynamicsModel.cpp (file contents):
Revision 2596 by tim, Wed Feb 22 20:35:16 2006 UTC vs.
Revision 2611 by tim, Mon Mar 13 22:42:40 2006 UTC