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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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#ifndef APPLICATION_HYDRODYNAMICS_MOLECULESHAPE_HPP |
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#define APPLICATION_HYDRODYNAMICS_MOLECULESHAPE_HPP |
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|
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#include "math/Vector3.hpp" |
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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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|
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/** @class Shape*/ |
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class Shape { |
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public: |
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virtual bool isInterior(Vector3d pos) = 0; |
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virtual std::pair<Vector3d, Vector3d> getBox() = 0; |
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virtual bool hasAnalyticalSolution() = 0; |
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//virtual Mat3x3d getTranslationalFriction() = 0; |
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//virtual Mat3x3d getRotationalFriction() = 0 ; |
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}; |
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|
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/** @class Spheric */ |
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class Spheric : public Shape { |
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public: |
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Spheric(Vector3d origin, double radius); |
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virtual bool isInterior(Vector3d pos); |
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virtual std::pair<Vector3d, Vector3d> getBox(); |
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virtual bool hasAnalyticalSolution() {return true;} |
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//virtual Mat3x3d getTranslationalFriction(); |
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//virtual Mat3x3d getRotationalFriction(); |
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|
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private: |
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Vector3d origin_; |
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double radius_; |
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}; |
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|
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/** @class Ellipsoid */ |
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class Ellipsoid : public Shape{ |
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public: |
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Ellipsoid(Vector3d origin, double radius, double ratio, Mat3x3d rotMat); |
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virtual bool isInterior(Vector3d pos); |
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virtual std::pair<Vector3d, Vector3d> getBox(); |
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virtual bool hasAnalyticalSolution() {return true;} |
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//virtual Mat3x3d getTranslationalFriction() { |
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// Mat3x3d Xirr; |
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//} |
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|
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//virtual Mat3x3d getFrictionCoff() { |
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|
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//} |
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|
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private: |
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|
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|
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/** |
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* calculate the ratio of friction coeffiction constant between ellipsoid and spheric |
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* with same volume. |
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* @param m |
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* @param n |
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* @note |
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* Reference: |
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* |
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* (1) Victor A. Bloomfield, On-Line Biophysics Textbook, Volume: Separations and Hydrodynamics |
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* Chapter 1,Survey of Biomolecular Hydrodynamics |
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* http://www.biophysics.org/education/vbloomfield.pdf |
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* (2) F. Perrin , J. Phys. Radium, [7] 5, 497-511, 1934 |
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* (3) F. Perrin, J. Phys. Radium, [7] 7, 1-11, 1936 |
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*/ |
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void calcFrictionRatio(double m, double n, double& Ft, double& Frm, double& Frn) { |
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double q = n/m; |
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if (q > 1.0) {//prolate |
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Ft = sqrt(1-q*q)/(pow(q, 2.0/3.0)*log((1 + sqrt(1-q*q))/q)); |
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Frm = 4*(1-q*q)/(3*(2 - 2*pow(q, 4.0/3.0)/Ft)); //not sure |
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Frn = 4*(1-q*q*q*q) /(3*q*q*(2*pow(q, -2.0/3.0)*(2-q*q)/Ft-2)); |
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} else {//oblate |
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Ft = sqrt(1-q*q)/(pow(q, 2.0/3.0)*atan(sqrt(q*q-1))); |
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Frm = 4*(1-q*q)/(3*(2 - 2*pow(q, 4.0/3.0)/Ft)); //not sure |
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Frn = 4*(1-q*q*q*q) /(3*q*q*(2*pow(q, -2.0/3.0)*(2-q*q)/Ft-2)); |
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} |
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} |
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Vector3d origin_; |
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double a_; |
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double b_; |
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Mat3x3d rotMat_; |
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}; |
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|
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/** @class StuntDoubleShape */ |
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class StuntDoubleShape { |
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public: |
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StuntDoubleShape(StuntDouble* sd); |
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~StuntDoubleShape(); |
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bool hasAnalyticalSolution(); |
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std::pair<Vector3d, Vector3d> getBox(); |
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bool isInterior(Vector3d pos); |
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private: |
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Shape* createShape(Atom* atom); |
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std::vector<Shape*> shapes_; |
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}; |
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|
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|
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class ShapeBuilder { |
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public: |
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|
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}; |
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|
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|
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} |
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|
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#endif |
