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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#include "applications/hydrodynamics/HydrodynamicsModel.hpp" |
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#include "math/LU.hpp" |
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#include "math/DynamicRectMatrix.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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namespace oopse { |
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/** |
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* Reference: |
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* Beatriz Carrasco and Jose Gracia de la Torre, Hydrodynamic Properties of Rigid Particles: |
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* Comparison of Different Modeling and Computational Procedures. |
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* Biophysical Journal, 75(6), 3044, 1999 |
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*/ |
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|
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HydrodynamicsModel::HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams) : sd_(sd){ |
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DynamicProperty::const_iterator iter; |
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|
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iter = extraParams.find("Viscosity"); |
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if (iter != extraParams.end()) { |
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boost::any param = iter->second; |
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viscosity_ = boost::any_cast<double>(param); |
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}else { |
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std::cout << "HydrodynamicsModel Error\n" ; |
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} |
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|
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iter = extraParams.find("Temperature"); |
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if (iter != extraParams.end()) { |
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boost::any param = iter->second; |
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temperature_ = boost::any_cast<double>(param); |
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}else { |
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std::cout << "HydrodynamicsModel Error\n" ; |
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} |
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} |
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|
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bool HydrodynamicsModel::calcHydrodyanmicsProps() { |
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if (!createBeads(beads_)) { |
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std::cout << "can not create beads" << std::endl; |
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return false; |
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} |
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|
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//calcResistanceTensor(); |
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calcDiffusionTensor(); |
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|
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/* |
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int nbeads = beads_.size(); |
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DynamicRectMatrix<double> B(3*nbeads, 3*nbeads); |
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DynamicRectMatrix<double> C(3*nbeads, 3*nbeads); |
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Mat3x3d I; |
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I(0, 0) = 1.0; |
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I(1, 1) = 1.0; |
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I(2, 2) = 1.0; |
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|
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for (std::size_t i = 0; i < nbeads; ++i) { |
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for (std::size_t j = 0; j < nbeads; ++j) { |
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Mat3x3d Tij; |
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if (i != j ) { |
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Vector3d Rij = beads_[i].pos - beads_[j].pos; |
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double rij = Rij.length(); |
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double rij2 = rij * rij; |
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double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2; |
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Mat3x3d tmpMat; |
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tmpMat = outProduct(Rij, Rij) / rij2; |
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double constant = 8.0 * NumericConstant::PI * viscosity_ * rij; |
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Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
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}else { |
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double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity_ * beads_[i].radius); |
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Tij(0, 0) = constant; |
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Tij(1, 1) = constant; |
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Tij(2, 2) = constant; |
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} |
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B.setSubMatrix(i*3, j*3, Tij); |
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std::cout << Tij << std::endl; |
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} |
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} |
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|
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std::cout << "B=\n" |
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<< B << std::endl; |
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//invert B Matrix |
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invertMatrix(B, C); |
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|
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std::cout << "C=\n" |
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<< C << std::endl; |
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|
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//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
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std::vector<Mat3x3d> U; |
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for (int i = 0; i < nbeads; ++i) { |
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Mat3x3d currU; |
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currU.setupSkewMat(beads_[i].pos); |
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U.push_back(currU); |
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} |
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|
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//calculate Xi matrix at arbitrary origin O |
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Mat3x3d Xitt; |
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Mat3x3d Xirr; |
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Mat3x3d Xitr; |
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|
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//calculate the total volume |
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|
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double volume = 0.0; |
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for (std::vector<BeadParam>::iterator iter = beads_.begin(); iter != beads_.end(); ++iter) { |
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volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
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} |
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|
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for (std::size_t i = 0; i < nbeads; ++i) { |
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for (std::size_t j = 0; j < nbeads; ++j) { |
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Mat3x3d Cij; |
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C.getSubMatrix(i*3, j*3, Cij); |
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|
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Xitt += Cij; |
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Xitr += U[i] * Cij; |
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//Xirr += -U[i] * Cij * U[j]; |
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Xirr += -U[i] * Cij * U[j] + (0.166*6 * viscosity_ * volume) * I; |
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} |
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} |
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|
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//invert Xi to get Diffusion Tensor at arbitrary origin O |
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RectMatrix<double, 6, 6> Xi; |
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RectMatrix<double, 6, 6> Do; |
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Xi.setSubMatrix(0, 0, Xitt); |
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Xi.setSubMatrix(0, 3, Xitr.transpose()); |
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Xi.setSubMatrix(3, 0, Xitr); |
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Xi.setSubMatrix(3, 3, Xirr); |
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//invertMatrix(Xi, Do); |
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double kt = OOPSEConstant::kB * temperature_ * 1.66E-2; |
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//Do *= kt; |
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|
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|
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Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O |
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Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O |
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Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O |
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|
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const static Mat3x3d zeroMat(0.0); |
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|
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Mat3x3d XittInv(0.0); |
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XittInv = Xitt.inverse(); |
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|
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//Xirr may not be inverted,if it one of the diagonal element is zero, for example |
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//( a11 a12 0) |
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//( a21 a22 0) |
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//( 0 0 0) |
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Mat3x3d XirrInv; |
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XirrInv = Xirr.inverse(); |
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|
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Mat3x3d tmp; |
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Mat3x3d tmpInv; |
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tmp = Xitt - Xitr.transpose() * XirrInv * Xitr; |
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tmpInv = tmp.inverse(); |
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|
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Dott = kt * tmpInv; |
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Dotr = -kt*XirrInv * Xitr * tmpInv* 1.0E8; |
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|
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tmp = Xirr - Xitr * XittInv * Xitr.transpose(); |
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tmpInv = tmp.inverse(); |
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|
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Dorr = kt * tmpInv*1.0E16; |
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|
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//Do.getSubMatrix(0, 0 , Dott); |
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//Do.getSubMatrix(3, 0, Dotr); |
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//Do.getSubMatrix(3, 3, Dorr); |
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|
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//calculate center of diffusion |
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tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2); |
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tmp(0, 1) = - Dorr(0, 1); |
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tmp(0, 2) = -Dorr(0, 2); |
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tmp(1, 0) = -Dorr(0, 1); |
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tmp(1, 1) = Dorr(0, 0) + Dorr(2, 2); |
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tmp(1, 2) = -Dorr(1, 2); |
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tmp(2, 0) = -Dorr(0, 2); |
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tmp(2, 1) = -Dorr(1, 2); |
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tmp(2, 2) = Dorr(1, 1) + Dorr(0, 0); |
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|
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Vector3d tmpVec; |
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tmpVec[0] = Dotr(1, 2) - Dotr(2, 1); |
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tmpVec[1] = Dotr(2, 0) - Dotr(0, 2); |
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tmpVec[2] = Dotr(0, 1) - Dotr(1, 0); |
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|
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tmpInv = tmp.inverse(); |
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|
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Vector3d rod = tmpInv * tmpVec; |
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|
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//calculate Diffusion Tensor at center of diffusion |
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Mat3x3d Uod; |
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Uod.setupSkewMat(rod); |
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|
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Mat3x3d Ddtt; //translational diffusion tensor at diffusion center |
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Mat3x3d Ddtr; //rotational diffusion tensor at diffusion center |
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Mat3x3d Ddrr; //translation-rotation couplingl diffusion tensor at diffusion tensor |
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|
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Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr; |
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Ddrr = Dorr; |
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Ddtr = Dotr + Dorr * Uod; |
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|
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props_.diffCenter = rod; |
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props_.transDiff = Ddtt; |
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props_.transRotDiff = Ddtr; |
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props_.rotDiff = Ddrr; |
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*/ |
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return true; |
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} |
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|
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void HydrodynamicsModel::calcResistanceTensor() { |
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|
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int nbeads = beads_.size(); |
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DynamicRectMatrix<double> B(3*nbeads, 3*nbeads); |
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DynamicRectMatrix<double> C(3*nbeads, 3*nbeads); |
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Mat3x3d I; |
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I(0, 0) = 1.0; |
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I(1, 1) = 1.0; |
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I(2, 2) = 1.0; |
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|
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for (std::size_t i = 0; i < nbeads; ++i) { |
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for (std::size_t j = 0; j < nbeads; ++j) { |
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Mat3x3d Tij; |
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if (i != j ) { |
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Vector3d Rij = beads_[i].pos - beads_[j].pos; |
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double rij = Rij.length(); |
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double rij2 = rij * rij; |
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double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2; |
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Mat3x3d tmpMat; |
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tmpMat = outProduct(Rij, Rij) / rij2; |
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double constant = 8.0 * NumericConstant::PI * viscosity_ * rij; |
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Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
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}else { |
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double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity_ * beads_[i].radius); |
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Tij(0, 0) = constant; |
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Tij(1, 1) = constant; |
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Tij(2, 2) = constant; |
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} |
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B.setSubMatrix(i*3, j*3, Tij); |
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} |
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} |
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|
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|
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//invert B Matrix |
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invertMatrix(B, C); |
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|
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//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
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std::vector<Mat3x3d> U; |
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for (int i = 0; i < nbeads; ++i) { |
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Mat3x3d currU; |
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currU.setupSkewMat(beads_[i].pos); |
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U.push_back(currU); |
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} |
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|
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//calculate Xi matrix at arbitrary origin O |
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Mat3x3d Xiott; |
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Mat3x3d Xiorr; |
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Mat3x3d Xiotr; |
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|
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//calculate the total volume |
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|
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double volume = 0.0; |
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for (std::vector<BeadParam>::iterator iter = beads_.begin(); iter != beads_.end(); ++iter) { |
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volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
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} |
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|
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for (std::size_t i = 0; i < nbeads; ++i) { |
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for (std::size_t j = 0; j < nbeads; ++j) { |
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Mat3x3d Cij; |
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C.getSubMatrix(i*3, j*3, Cij); |
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|
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Xiott += Cij; |
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Xiotr += U[i] * Cij; |
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//Xiorr += -U[i] * Cij * U[j]; |
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Xiorr += -U[i] * Cij * U[j] + (6 * viscosity_ * volume) * I; |
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} |
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} |
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|
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Mat3x3d tmp; |
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Mat3x3d tmpInv; |
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Vector3d tmpVec; |
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tmp(0, 0) = Xiott(1, 1) + Xiott(2, 2); |
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tmp(0, 1) = - Xiott(0, 1); |
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tmp(0, 2) = -Xiott(0, 2); |
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tmp(1, 0) = -Xiott(0, 1); |
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tmp(1, 1) = Xiott(0, 0) + Xiott(2, 2); |
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tmp(1, 2) = -Xiott(1, 2); |
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tmp(2, 0) = -Xiott(0, 2); |
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tmp(2, 1) = -Xiott(1, 2); |
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tmp(2, 2) = Xiott(1, 1) + Xiott(0, 0); |
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tmpVec[0] = Xiotr(2, 1) - Xiotr(1, 2); |
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tmpVec[1] = Xiotr(0, 2) - Xiotr(2, 0); |
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tmpVec[2] = Xiotr(1, 0) - Xiotr(0, 1); |
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tmpInv = tmp.inverse(); |
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Vector3d ror = tmpInv * tmpVec; //center of resistance |
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Mat3x3d Uor; |
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Uor.setupSkewMat(ror); |
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|
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Mat3x3d Xirtt; |
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Mat3x3d Xirrr; |
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Mat3x3d Xirtr; |
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|
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Xirtt = Xiott; |
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Xirtr = (Xiotr - Uor * Xiott) * 1E-8; |
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Xirrr = Xiorr - Uor * Xiott * Uor + Xiotr * Uor - Uor * Xiotr.transpose() * 1E-16; |
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/* |
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SquareMatrix<double,6> Xir6x6; |
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SquareMatrix<double,6> Dr6x6; |
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|
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Xir6x6.setSubMatrix(0, 0, Xirtt); |
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Xir6x6.setSubMatrix(0, 3, Xirtr.transpose()); |
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Xir6x6.setSubMatrix(3, 0, Xirtr); |
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Xir6x6.setSubMatrix(3, 3, Xirrr); |
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|
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invertMatrix(Xir6x6, Dr6x6); |
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Mat3x3d Drtt; |
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Mat3x3d Drtr; |
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Mat3x3d Drrr; |
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Dr6x6.getSubMatrix(0, 0, Drtt); |
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Dr6x6.getSubMatrix(3, 0, Drtr); |
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Dr6x6.getSubMatrix(3, 3, Drrr); |
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double kt = OOPSEConstant::kB * temperature_ * 1.66E-2; |
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Drtt *= kt; |
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Drtr *= kt*1E8; |
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Drrr *= kt*1E16; |
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*/ |
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|
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const static Mat3x3d zeroMat(0.0); |
| 359 |
|
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|
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|
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Mat3x3d XirttInv(0.0); |
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XirttInv = Xirtt.inverse(); |
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|
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//Xirr may not be inverted,if it one of the diagonal element is zero, for example |
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//( a11 a12 0) |
| 367 |
//( a21 a22 0) |
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//( 0 0 0) |
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Mat3x3d XirrrInv; |
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XirrrInv = Xirrr.inverse(); |
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tmp = Xirtt - Xirtr.transpose() * XirrrInv * Xirtr; |
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tmpInv = tmp.inverse(); |
| 373 |
|
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Mat3x3d Drtt; |
| 375 |
Mat3x3d Drtr; |
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Mat3x3d Drrr; |
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double kt = OOPSEConstant::kB * temperature_ * 1.66E-2; |
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Drtt = kt * tmpInv; |
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Drtr = -kt*XirrrInv * Xirtr * tmpInv* 1.0E8; |
| 380 |
|
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tmp = Xirrr - Xirtr * XirttInv * Xirtr.transpose(); |
| 382 |
tmpInv = tmp.inverse(); |
| 383 |
|
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Drrr = kt * tmpInv*1.0E16; |
| 385 |
|
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std::cout << "-----------------------------------------\n"; |
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std::cout << "center of resistance :" << std::endl; |
| 388 |
std::cout << ror << std::endl; |
| 389 |
std::cout << "resistant tensor at center of resistance" << std::endl; |
| 390 |
std::cout << "translation:" << std::endl; |
| 391 |
std::cout << Xirtt << std::endl; |
| 392 |
std::cout << "translation-rotation:" << std::endl; |
| 393 |
std::cout << Xirtr << std::endl; |
| 394 |
std::cout << "rotation:" << std::endl; |
| 395 |
std::cout << Xirrr << std::endl; |
| 396 |
std::cout << "diffusion tensor at center of resistance" << std::endl; |
| 397 |
std::cout << "translation:" << std::endl; |
| 398 |
std::cout << Drtt << std::endl; |
| 399 |
std::cout << "translation-rotation:" << std::endl; |
| 400 |
std::cout << Drtr << std::endl; |
| 401 |
std::cout << "rotation:" << std::endl; |
| 402 |
std::cout << Drrr << std::endl; |
| 403 |
std::cout << "-----------------------------------------\n"; |
| 404 |
|
| 405 |
} |
| 406 |
|
| 407 |
void HydrodynamicsModel::calcDiffusionTensor() { |
| 408 |
int nbeads = beads_.size(); |
| 409 |
DynamicRectMatrix<double> B(3*nbeads, 3*nbeads); |
| 410 |
DynamicRectMatrix<double> C(3*nbeads, 3*nbeads); |
| 411 |
Mat3x3d I; |
| 412 |
I(0, 0) = 1.0; |
| 413 |
I(1, 1) = 1.0; |
| 414 |
I(2, 2) = 1.0; |
| 415 |
|
| 416 |
for (std::size_t i = 0; i < nbeads; ++i) { |
| 417 |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 418 |
Mat3x3d Tij; |
| 419 |
if (i != j ) { |
| 420 |
Vector3d Rij = beads_[i].pos - beads_[j].pos; |
| 421 |
double rij = Rij.length(); |
| 422 |
double rij2 = rij * rij; |
| 423 |
double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2; |
| 424 |
Mat3x3d tmpMat; |
| 425 |
tmpMat = outProduct(Rij, Rij) / rij2; |
| 426 |
double constant = 8.0 * NumericConstant::PI * viscosity_ * rij; |
| 427 |
Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant; |
| 428 |
}else { |
| 429 |
double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity_ * beads_[i].radius); |
| 430 |
Tij(0, 0) = constant; |
| 431 |
Tij(1, 1) = constant; |
| 432 |
Tij(2, 2) = constant; |
| 433 |
} |
| 434 |
B.setSubMatrix(i*3, j*3, Tij); |
| 435 |
} |
| 436 |
} |
| 437 |
|
| 438 |
//invert B Matrix |
| 439 |
invertMatrix(B, C); |
| 440 |
|
| 441 |
//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0) |
| 442 |
std::vector<Mat3x3d> U; |
| 443 |
for (int i = 0; i < nbeads; ++i) { |
| 444 |
Mat3x3d currU; |
| 445 |
currU.setupSkewMat(beads_[i].pos); |
| 446 |
U.push_back(currU); |
| 447 |
} |
| 448 |
|
| 449 |
//calculate Xi matrix at arbitrary origin O |
| 450 |
Mat3x3d Xitt; |
| 451 |
Mat3x3d Xirr; |
| 452 |
Mat3x3d Xitr; |
| 453 |
|
| 454 |
//calculate the total volume |
| 455 |
|
| 456 |
double volume = 0.0; |
| 457 |
for (std::vector<BeadParam>::iterator iter = beads_.begin(); iter != beads_.end(); ++iter) { |
| 458 |
volume += 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3); |
| 459 |
} |
| 460 |
|
| 461 |
for (std::size_t i = 0; i < nbeads; ++i) { |
| 462 |
for (std::size_t j = 0; j < nbeads; ++j) { |
| 463 |
Mat3x3d Cij; |
| 464 |
C.getSubMatrix(i*3, j*3, Cij); |
| 465 |
|
| 466 |
Xitt += Cij; |
| 467 |
Xitr += U[i] * Cij; |
| 468 |
//Xirr += -U[i] * Cij * U[j]; |
| 469 |
Xirr += -U[i] * Cij * U[j] + (6 * viscosity_ * volume) * I; |
| 470 |
} |
| 471 |
} |
| 472 |
|
| 473 |
//invert Xi to get Diffusion Tensor at arbitrary origin O |
| 474 |
RectMatrix<double, 6, 6> Xi; |
| 475 |
RectMatrix<double, 6, 6> Do; |
| 476 |
Xi.setSubMatrix(0, 0, Xitt); |
| 477 |
Xi.setSubMatrix(0, 3, Xitr.transpose()); |
| 478 |
Xi.setSubMatrix(3, 0, Xitr); |
| 479 |
Xi.setSubMatrix(3, 3, Xirr); |
| 480 |
//invertMatrix(Xi, Do); |
| 481 |
//double kt = OOPSEConstant::kB * temperature_ * 1.66E-2; |
| 482 |
|
| 483 |
//1 poise = 0.1 N.S/m^2 = 1.661E-3 amu/ (Angstrom*fs) |
| 484 |
double kt = OOPSEConstant::kB * temperature_ * 1.66E-3; |
| 485 |
|
| 486 |
Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O |
| 487 |
Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O |
| 488 |
Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O |
| 489 |
|
| 490 |
const static Mat3x3d zeroMat(0.0); |
| 491 |
|
| 492 |
Mat3x3d XittInv(0.0); |
| 493 |
XittInv = Xitt.inverse(); |
| 494 |
|
| 495 |
//Xirr may not be inverted,if it one of the diagonal element is zero, for example |
| 496 |
//( a11 a12 0) |
| 497 |
//( a21 a22 0) |
| 498 |
//( 0 0 0) |
| 499 |
Mat3x3d XirrInv; |
| 500 |
XirrInv = Xirr.inverse(); |
| 501 |
|
| 502 |
Mat3x3d tmp; |
| 503 |
Mat3x3d tmpInv; |
| 504 |
tmp = Xitt - Xitr.transpose() * XirrInv * Xitr; |
| 505 |
tmpInv = tmp.inverse(); |
| 506 |
|
| 507 |
//Dott = kt * tmpInv; //unit in A^2/fs |
| 508 |
Dott = tmpInv; |
| 509 |
//Dotr = -kt*XirrInv * Xitr * tmpInv*1E8; |
| 510 |
//Dotr = -kt*XirrInv * Xitr * tmpInv; |
| 511 |
Dotr = -XirrInv* Xitr * tmpInv; |
| 512 |
|
| 513 |
tmp = Xirr - Xitr * XittInv * Xitr.transpose(); |
| 514 |
tmpInv = tmp.inverse(); |
| 515 |
|
| 516 |
//Dorr = kt * tmpInv*1E16; |
| 517 |
//Dorr = kt * tmpInv; |
| 518 |
Dorr = tmpInv; |
| 519 |
//calculate center of diffusion |
| 520 |
tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2); |
| 521 |
tmp(0, 1) = - Dorr(0, 1); |
| 522 |
tmp(0, 2) = -Dorr(0, 2); |
| 523 |
tmp(1, 0) = -Dorr(0, 1); |
| 524 |
tmp(1, 1) = Dorr(0, 0) + Dorr(2, 2); |
| 525 |
tmp(1, 2) = -Dorr(1, 2); |
| 526 |
tmp(2, 0) = -Dorr(0, 2); |
| 527 |
tmp(2, 1) = -Dorr(1, 2); |
| 528 |
tmp(2, 2) = Dorr(1, 1) + Dorr(0, 0); |
| 529 |
|
| 530 |
Vector3d tmpVec; |
| 531 |
tmpVec[0] = Dotr(1, 2) - Dotr(2, 1); |
| 532 |
tmpVec[1] = Dotr(2, 0) - Dotr(0, 2); |
| 533 |
tmpVec[2] = Dotr(0, 1) - Dotr(1, 0); |
| 534 |
|
| 535 |
tmpInv = tmp.inverse(); |
| 536 |
|
| 537 |
Vector3d rod = tmpInv * tmpVec; |
| 538 |
|
| 539 |
//calculate Diffusion Tensor at center of diffusion |
| 540 |
Mat3x3d Uod; |
| 541 |
Uod.setupSkewMat(rod); |
| 542 |
|
| 543 |
Mat3x3d Ddtt; //translational diffusion tensor at diffusion center |
| 544 |
Mat3x3d Ddtr; //rotational diffusion tensor at diffusion center |
| 545 |
Mat3x3d Ddrr; //translation-rotation couplingl diffusion tensor at diffusion tensor |
| 546 |
|
| 547 |
Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr; |
| 548 |
Ddrr = Dorr; |
| 549 |
Ddtr = Dotr + Dorr * Uod; |
| 550 |
|
| 551 |
props_.diffCenter = rod; |
| 552 |
props_.Ddtt = Ddtt; |
| 553 |
props_.Ddtr = Ddtr; |
| 554 |
props_.Ddrr = Ddrr; |
| 555 |
|
| 556 |
SquareMatrix<double, 6> Dd; |
| 557 |
Dd.setSubMatrix(0, 0, Ddtt); |
| 558 |
Dd.setSubMatrix(0, 3, Ddtr.transpose()); |
| 559 |
Dd.setSubMatrix(3, 0, Ddtr); |
| 560 |
Dd.setSubMatrix(3, 3, Ddrr); |
| 561 |
SquareMatrix<double, 6> Xid; |
| 562 |
invertMatrix(Dd, Xid); |
| 563 |
|
| 564 |
Ddtt *= kt; |
| 565 |
Ddtr *= kt; |
| 566 |
Ddrr *= kt; |
| 567 |
Xid /= 1.66E-3; |
| 568 |
|
| 569 |
Xid.getSubMatrix(0, 0, props_.Xidtt); |
| 570 |
Xid.getSubMatrix(0, 3, props_.Xidrt); |
| 571 |
Xid.getSubMatrix(3, 0, props_.Xidtr); |
| 572 |
Xid.getSubMatrix(3, 3, props_.Xidrr); |
| 573 |
|
| 574 |
/* |
| 575 |
std::cout << "center of diffusion :" << std::endl; |
| 576 |
std::cout << rod << std::endl; |
| 577 |
std::cout << "diffusion tensor at center of diffusion" << std::endl; |
| 578 |
std::cout << "translation:" << std::endl; |
| 579 |
std::cout << Ddtt << std::endl; |
| 580 |
std::cout << "translation-rotation:" << std::endl; |
| 581 |
std::cout << Ddtr << std::endl; |
| 582 |
std::cout << "rotation:" << std::endl; |
| 583 |
std::cout << Ddrr << std::endl; |
| 584 |
*/ |
| 585 |
|
| 586 |
} |
| 587 |
|
| 588 |
void HydrodynamicsModel::writeBeads(std::ostream& os) { |
| 589 |
std::vector<BeadParam>::iterator iter; |
| 590 |
os << beads_.size() << std::endl; |
| 591 |
os << "Generated by Hydro" << std::endl; |
| 592 |
for (iter = beads_.begin(); iter != beads_.end(); ++iter) { |
| 593 |
os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl; |
| 594 |
} |
| 595 |
|
| 596 |
} |
| 597 |
|
| 598 |
void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) { |
| 599 |
|
| 600 |
os << sd_->getType() << "\t"; |
| 601 |
os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\t"; |
| 602 |
|
| 603 |
os << props_.Ddtt(0, 0) << "\t" << props_.Ddtt(0, 1) << "\t" << props_.Ddtt(0, 2) << "\t" |
| 604 |
<< props_.Ddtt(1, 0) << "\t" << props_.Ddtt(1, 1) << "\t" << props_.Ddtt(1, 2) << "\t" |
| 605 |
<< props_.Ddtt(2, 0) << "\t" << props_.Ddtt(2, 1) << "\t" << props_.Ddtt(2, 2) << "\t"; |
| 606 |
|
| 607 |
os << props_.Ddtr(0, 0) << "\t" << props_.Ddtr(0, 1) << "\t" << props_.Ddtr(0, 2) << "\t" |
| 608 |
<< props_.Ddtr(1, 0) << "\t" << props_.Ddtr(1, 1) << "\t" << props_.Ddtr(1, 2) << "\t" |
| 609 |
<< props_.Ddtr(2, 0) << "\t" << props_.Ddtr(2, 1) << "\t" << props_.Ddtr(2, 2) << "\t"; |
| 610 |
|
| 611 |
os << props_.Ddrr(0, 0) << "\t" << props_.Ddrr(0, 1) << "\t" << props_.Ddrr(0, 2) << "\t" |
| 612 |
<< props_.Ddrr(1, 0) << "\t" << props_.Ddrr(1, 1) << "\t" << props_.Ddrr(1, 2) << "\t" |
| 613 |
<< props_.Ddrr(2, 0) << "\t" << props_.Ddrr(2, 1) << "\t" << props_.Ddrr(2, 2) <<"\t"; |
| 614 |
|
| 615 |
os << props_.Xidtt(0, 0) << "\t" << props_.Xidtt(0, 1) << "\t" << props_.Xidtt(0, 2) << "\t" |
| 616 |
<< props_.Xidtt(1, 0) << "\t" << props_.Xidtt(1, 1) << "\t" << props_.Xidtt(1, 2) << "\t" |
| 617 |
<< props_.Xidtt(2, 0) << "\t" << props_.Xidtt(2, 1) << "\t" << props_.Xidtt(2, 2) << "\t"; |
| 618 |
|
| 619 |
os << props_.Xidrt(0, 0) << "\t" << props_.Xidrt(0, 1) << "\t" << props_.Xidrt(0, 2) << "\t" |
| 620 |
<< props_.Xidrt(1, 0) << "\t" << props_.Xidrt(1, 1) << "\t" << props_.Xidrt(1, 2) << "\t" |
| 621 |
<< props_.Xidrt(2, 0) << "\t" << props_.Xidrt(2, 1) << "\t" << props_.Xidrt(2, 2) << "\t"; |
| 622 |
|
| 623 |
os << props_.Xidtr(0, 0) << "\t" << props_.Xidtr(0, 1) << "\t" << props_.Xidtr(0, 2) << "\t" |
| 624 |
<< props_.Xidtr(1, 0) << "\t" << props_.Xidtr(1, 1) << "\t" << props_.Xidtr(1, 2) << "\t" |
| 625 |
<< props_.Xidtr(2, 0) << "\t" << props_.Xidtr(2, 1) << "\t" << props_.Xidtr(2, 2) << "\t"; |
| 626 |
|
| 627 |
os << props_.Xidrr(0, 0) << "\t" << props_.Xidrr(0, 1) << "\t" << props_.Xidrr(0, 2) << "\t" |
| 628 |
<< props_.Xidrr(1, 0) << "\t" << props_.Xidrr(1, 1) << "\t" << props_.Xidrr(1, 2) << "\t" |
| 629 |
<< props_.Xidrr(2, 0) << "\t" << props_.Xidrr(2, 1) << "\t" << props_.Xidrr(2, 2) << std::endl; |
| 630 |
|
| 631 |
} |
| 632 |
|
| 633 |
} |
