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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include "hydrodynamics/Sphere.hpp" |
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#include "utils/PhysicalConstants.hpp" |
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#include "math/LU.hpp" |
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|
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namespace OpenMD { |
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|
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Sphere::Sphere(Vector3d origin, RealType radius) : origin_(origin), radius_(radius){ |
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|
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} |
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|
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bool Sphere::isInterior(Vector3d pos) { |
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Vector3d r = pos - origin_; |
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|
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bool result; |
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if (r.length() < radius_) |
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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> Sphere::getBoundingBox() { |
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std::pair<Vector3d, Vector3d> boundary; |
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Vector3d r(radius_, radius_, radius_); |
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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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HydroProp* Sphere::getHydroProp(RealType viscosity, RealType temperature) { |
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|
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RealType Xitt = 6.0 * NumericConstant::PI * viscosity * radius_; |
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RealType Xirr = 8.0 * NumericConstant::PI * viscosity * radius_ * radius_ * radius_; |
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|
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Mat6x6d Xi, XiCopy, D; |
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|
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Xi(0, 0) = Xitt; |
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Xi(1, 1) = Xitt; |
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Xi(2, 2) = Xitt; |
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Xi(3, 3) = Xirr; |
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Xi(4, 4) = Xirr; |
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Xi(5, 5) = Xirr; |
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|
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Xi *= PhysicalConstants::viscoConvert; |
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XiCopy = Xi; |
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|
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invertMatrix(XiCopy, D); |
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RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1 |
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D *= kt; // now in angstroms^2 fs^-1 (at least for Trans-trans) |
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|
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HydroProp* hprop = new HydroProp(V3Zero, Xi, D); |
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|
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return hprop; |
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} |
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|
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} |
