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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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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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|
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void HydrodynamicsModel::calcDiffusionTensor() { |
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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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//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 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] + (6 * viscosity_ * volume) * I; |
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} |
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} |
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|
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const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
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Xitt *= convertConstant; |
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Xitr *= convertConstant; |
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Xirr *= convertConstant; |
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|
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double kt = OOPSEConstant::kB * temperature_; |
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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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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 = tmpInv; |
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Dotr = -XirrInv * Xitr * tmpInv; |
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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 = tmpInv; |
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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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SquareMatrix<double, 6> Dd; |
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Dd.setSubMatrix(0, 0, Ddtt); |
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Dd.setSubMatrix(0, 3, Ddtr.transpose()); |
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Dd.setSubMatrix(3, 0, Ddtr); |
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Dd.setSubMatrix(3, 3, Ddrr); |
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SquareMatrix<double, 6> Xid; |
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invertMatrix(Dd, Xid); |
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|
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Ddtt *= kt; |
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Ddtr *=kt; |
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Ddrr *= kt; |
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|
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//Xidtt in units of kcal*fs*mol^-1*Ang^-2 |
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Xid *= OOPSEConstant::kb*temperature_/kt; |
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|
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props_.diffCenter = rod; |
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props_.Ddtt = Ddtt; |
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props_.Ddtr = Ddtr; |
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props_.Ddrr = Ddrr; |
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Xid.getSubMatrix(0, 0, props_.Xidtt); |
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Xid.getSubMatrix(0, 3, props_.Xidrt); |
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Xid.getSubMatrix(3, 0, props_.Xidtr); |
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Xid.getSubMatrix(3, 3, props_.Xidrr); |
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|
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|
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std::cout << "viscosity = " << viscosity_ << std::endl; |
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std::cout << "temperature = " << temperature_ << std::endl; |
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std::cout << "center of diffusion :" << std::endl; |
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std::cout << rod << std::endl; |
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std::cout << "diffusion tensor at center of diffusion " << std::endl; |
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std::cout << "translation(A^2/fs) :" << std::endl; |
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std::cout << Ddtt << std::endl; |
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std::cout << "translation-rotation(A^3/fs):" << std::endl; |
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std::cout << Ddtr << std::endl; |
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std::cout << "rotation(A^4/fs):" << std::endl; |
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std::cout << Ddrr << std::endl; |
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|
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std::cout << "resistance tensor at center of diffusion " << std::endl; |
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std::cout << "translation(kcal*fs*mol^-1*Ang^-2) :" << std::endl; |
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std::cout << props_.Xidtt << std::endl; |
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std::cout << "rotation-translation (kcal*fs*mol^-1*Ang^-3):" << std::endl; |
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std::cout << props_.Xidrt << std::endl; |
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std::cout << "translation-rotation(kcal*fs*mol^-1*Ang^-3):" << std::endl; |
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std::cout << props_.Xidtr << std::endl; |
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std::cout << "rotation(kcal*fs*mol^-1*Ang^-4):" << std::endl; |
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std::cout << props_.Xidrr << std::endl; |
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|
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|
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} |
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|
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void HydrodynamicsModel::writeBeads(std::ostream& os) { |
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std::vector<BeadParam>::iterator iter; |
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os << beads_.size() << std::endl; |
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os << "Generated by Hydro" << std::endl; |
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for (iter = beads_.begin(); iter != beads_.end(); ++iter) { |
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os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl; |
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} |
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|
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} |
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|
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void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) { |
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|
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os << sd_->getType() << "\t"; |
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os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\t"; |
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|
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os << props_.Ddtt(0, 0) << "\t" << props_.Ddtt(0, 1) << "\t" << props_.Ddtt(0, 2) << "\t" |
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<< props_.Ddtt(1, 0) << "\t" << props_.Ddtt(1, 1) << "\t" << props_.Ddtt(1, 2) << "\t" |
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<< props_.Ddtt(2, 0) << "\t" << props_.Ddtt(2, 1) << "\t" << props_.Ddtt(2, 2) << "\t"; |
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|
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os << props_.Ddtr(0, 0) << "\t" << props_.Ddtr(0, 1) << "\t" << props_.Ddtr(0, 2) << "\t" |
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<< props_.Ddtr(1, 0) << "\t" << props_.Ddtr(1, 1) << "\t" << props_.Ddtr(1, 2) << "\t" |
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<< props_.Ddtr(2, 0) << "\t" << props_.Ddtr(2, 1) << "\t" << props_.Ddtr(2, 2) << "\t"; |
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|
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os << props_.Ddrr(0, 0) << "\t" << props_.Ddrr(0, 1) << "\t" << props_.Ddrr(0, 2) << "\t" |
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<< props_.Ddrr(1, 0) << "\t" << props_.Ddrr(1, 1) << "\t" << props_.Ddrr(1, 2) << "\t" |
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<< props_.Ddrr(2, 0) << "\t" << props_.Ddrr(2, 1) << "\t" << props_.Ddrr(2, 2) <<"\t"; |
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|
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os << props_.Xidtt(0, 0) << "\t" << props_.Xidtt(0, 1) << "\t" << props_.Xidtt(0, 2) << "\t" |
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<< props_.Xidtt(1, 0) << "\t" << props_.Xidtt(1, 1) << "\t" << props_.Xidtt(1, 2) << "\t" |
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<< props_.Xidtt(2, 0) << "\t" << props_.Xidtt(2, 1) << "\t" << props_.Xidtt(2, 2) << "\t"; |
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|
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os << props_.Xidrt(0, 0) << "\t" << props_.Xidrt(0, 1) << "\t" << props_.Xidrt(0, 2) << "\t" |
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<< props_.Xidrt(1, 0) << "\t" << props_.Xidrt(1, 1) << "\t" << props_.Xidrt(1, 2) << "\t" |
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<< props_.Xidrt(2, 0) << "\t" << props_.Xidrt(2, 1) << "\t" << props_.Xidrt(2, 2) << "\t"; |
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|
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os << props_.Xidtr(0, 0) << "\t" << props_.Xidtr(0, 1) << "\t" << props_.Xidtr(0, 2) << "\t" |
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<< props_.Xidtr(1, 0) << "\t" << props_.Xidtr(1, 1) << "\t" << props_.Xidtr(1, 2) << "\t" |
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<< props_.Xidtr(2, 0) << "\t" << props_.Xidtr(2, 1) << "\t" << props_.Xidtr(2, 2) << "\t"; |
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|
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os << props_.Xidrr(0, 0) << "\t" << props_.Xidrr(0, 1) << "\t" << props_.Xidrr(0, 2) << "\t" |
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<< props_.Xidrr(1, 0) << "\t" << props_.Xidrr(1, 1) << "\t" << props_.Xidrr(1, 2) << "\t" |
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<< props_.Xidrr(2, 0) << "\t" << props_.Xidrr(2, 1) << "\t" << props_.Xidrr(2, 2) << std::endl; |
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|
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} |
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|
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} |
