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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 "hydrodynamics/Ellipsoid.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "math/LU.hpp" |
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|
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namespace oopse { |
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|
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Ellipsoid::Ellipsoid(Vector3d origin, double rMajor, double rMinor,Mat3x3d rotMat) |
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: origin_(origin), rMajor_(rMajor), rMinor_(rMinor), rotMat_(rotMat) { |
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|
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} |
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bool Ellipsoid::isInterior(Vector3d pos) { |
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Vector3d r = pos - origin_; |
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Vector3d rbody = rotMat_ * r; |
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double xovera = rbody[0]/rMajor_; |
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double yovera = rbody[1]/rMajor_; |
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double zoverb = rbody[2]/rMinor_; |
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|
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bool result; |
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if (xovera*xovera + yovera*yovera + zoverb*zoverb < 1) |
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result = true; |
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else |
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result = false; |
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|
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return result; |
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} |
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|
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std::pair<Vector3d, Vector3d> Ellipsoid::getBoundingBox() { |
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|
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std::pair<Vector3d, Vector3d> boundary; |
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//make a cubic box |
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double rad = rMajor_ > rMinor_ ? rMajor_ : rMinor_; |
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Vector3d r(rad, rad, rad); |
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boundary.first = origin_ - r; |
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boundary.second = origin_ + r; |
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return boundary; |
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} |
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|
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HydroProps Ellipsoid::getHydroProps(double viscosity, double temperature) { |
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|
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double a = rMinor_; |
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double b = rMajor_; |
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double a2 = a * a; |
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double b2 = b* b; |
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|
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double p = a /b; |
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double S; |
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if (p > 1.0) { //prolate |
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S = 2.0/sqrt(a2 - b2) * log((a + sqrt(a2-b2))/b); |
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} else { //oblate |
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S = 2.0/sqrt(b2 - a2) * atan(sqrt(b2-a2)/a); |
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} |
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|
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double P = 1.0/(a2 - b2) * (S - 2.0/a); |
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double Q = 0.5/(a2-b2) * (2.0*a/b2 - S); |
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|
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double transMinor = 16.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-b2)*S -2.0*a); |
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double transMajor = 32.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-3.0*b2)*S +2.0*a); |
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double rotMinor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2 - b2) * b2 /(2.0*a -b2*S); |
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double rotMajor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2*a2 - b2*b2)/((2.0*a2-b2)*S-2.0*a); |
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|
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|
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HydroProps props; |
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|
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props.Xi(0,0) = transMajor; |
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props.Xi(1,1) = transMajor; |
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props.Xi(2,2) = transMinor; |
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props.Xi(3,3) = rotMajor; |
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props.Xi(4,4) = rotMajor; |
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props.Xi(5,5) = rotMinor; |
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|
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const double convertConstant = 6.023; //convert poise.angstrom to amu/fs |
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props.Xi *= convertConstant; |
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|
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Mat6x6d XiCopy = props.Xi; |
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invertMatrix(XiCopy, props.D); |
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double kt = OOPSEConstant::kB * temperature; |
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props.D *= kt; |
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props.Xi *= OOPSEConstant::kb * temperature; |
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|
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return props; |
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|
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} |
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} |
