applications/hydrodynamics/AnalyticalModel.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
#include "applications/hydrodynamics/AnalyticalModel.hpp"
#include "applications/hydrodynamics/Spheric.hpp"
#include "applications/hydrodynamics/Ellipsoid.hpp"
#include "applications/hydrodynamics/CompositeShape.hpp"
#include "math/LU.hpp"
namespace oopse {
bool AnalyticalModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) {

    double radius = spheric->getRadius(); 
    HydroProps props;
    props.center =V3Zero;
    double Xitt  = 6.0 * NumericConstant::PI * viscosity * radius;
    double Xirr = 8.0 * NumericConstant::PI * viscosity * radius * radius * radius;
    props.Xi(0, 0) = Xitt;
    props.Xi(1, 1) = Xitt;
    props.Xi(2, 2) = Xitt;
    props.Xi(3, 3) = Xirr;
    props.Xi(4, 4) = Xirr;
    props.Xi(5, 5) = Xirr;
    
    const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
    props.Xi *= convertConstant;
    Mat6x6d XiCopy = props.Xi;
    invertMatrix(XiCopy, props.D);
    double kt = OOPSEConstant::kB * temperature;
    props.D *= kt;
    props.Xi *= OOPSEConstant::kb * temperature;

    setCR(props);
    setCD(props);

    return true;
    
}

/**
 * calculate the ratio of friction coeffiction constant between ellipsoid and spheric 
 * with same volume.
 * @param m
 * @param n 
 * @note 
 * Reference:
 *
 * (1) Victor A. Bloomfield, On-Line Biophysics Textbook, Volume: Separations and Hydrodynamics
 * Chapter 1,Survey of Biomolecular Hydrodynamics
 * http://www.biophysics.org/education/vbloomfield.pdf 
 * (2) F. Perrin , J. Phys. Radium, [7] 5, 497-511, 1934
 * (3) F. Perrin, J. Phys. Radium, [7] 7, 1-11, 1936
 */        
bool AnalyticalModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) {
    double ft;
    double fra;
    double frb;
    double a = ellipsoid->getA();
    double b = ellipsoid->getB();
    double q = a/b; //?
    if (q > 1.0) {//prolate
        ft = sqrt(1-q*q)/(pow(q, 2.0/3.0)*log((1 + sqrt(1-q*q))/q));
        fra = 4*(1-q*q)/(3*(2 - 2*pow(q, 4.0/3.0)/ft)); //not sure
        frb = 4*(1-q*q*q*q) /(3*q*q*(2*pow(q, -2.0/3.0)*(2-q*q)/ft-2));
    } else {//oblate
        ft = sqrt(1-q*q)/(pow(q, 2.0/3.0)*atan(sqrt(q*q-1)));
        fra = 4*(1-q*q)/(3*(2 - 2*pow(q, 4.0/3.0)/ft)); //not sure
        frb = 4*(1-q*q*q*q) /(3*q*q*(2*pow(q, -2.0/3.0)*(2-q*q)/ft-2));
    }
                    
    double radius = pow(a*a*b, 1.0/3.0);
    HydroProps props;
    double Xitt  = 6.0 * NumericConstant::PI * viscosity * radius;
    double Xirr = 8.0 * NumericConstant::PI * viscosity * radius * radius * radius;
    props.Xi(0, 0) = Xitt;
    props.Xi(1, 1) = Xitt;
    props.Xi(2, 2) = Xitt;
    props.Xi(3, 3) = Xirr;
    props.Xi(4, 4) = Xirr;
    props.Xi(5, 5) = Xirr;
    
    const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
    props.Xi *= convertConstant;    
    props.Xi(0,0) *= ft;
    props.Xi(1,1) *= ft;
    props.Xi(2,2) *= ft;
    props.Xi(3,3) *= fra;
    props.Xi(4,4) *= fra;
    props.Xi(5,5) *= frb;
    
    Mat6x6d XiCopy = props.Xi;
    XiCopy /= OOPSEConstant::kb * temperature;
    invertMatrix(XiCopy, props.D);
    double kt = OOPSEConstant::kB * temperature;
    props.D *= kt;

    setCR(props);
    setCD(props);

    return true;
}

bool AnalyticalModel::calcHydroProps(CompositeShape* compositexShape, double viscosity, double temperature) {
    return false;
}
        

}
Revision:	2634
Committed:	Fri Mar 17 23:20:35 2006 UTC (18 years, 5 months ago) by tim
File size:	5439 byte(s)
Log Message:	refactor Hydrodynamics module.
#	User	Rev	Content
1	tim	2634	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41			#include "applications/hydrodynamics/AnalyticalModel.hpp"
42			#include "applications/hydrodynamics/Spheric.hpp"
43			#include "applications/hydrodynamics/Ellipsoid.hpp"
44			#include "applications/hydrodynamics/CompositeShape.hpp"
45			#include "math/LU.hpp"
46			namespace oopse {
47			bool AnalyticalModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) {
48
49			double radius = spheric->getRadius();
50			HydroProps props;
51			props.center =V3Zero;
52			double Xitt = 6.0 * NumericConstant::PI * viscosity * radius;
53			double Xirr = 8.0 * NumericConstant::PI * viscosity * radius * radius * radius;
54			props.Xi(0, 0) = Xitt;
55			props.Xi(1, 1) = Xitt;
56			props.Xi(2, 2) = Xitt;
57			props.Xi(3, 3) = Xirr;
58			props.Xi(4, 4) = Xirr;
59			props.Xi(5, 5) = Xirr;
60
61			const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
62			props.Xi *= convertConstant;
63			Mat6x6d XiCopy = props.Xi;
64			invertMatrix(XiCopy, props.D);
65			double kt = OOPSEConstant::kB * temperature;
66			props.D *= kt;
67			props.Xi = OOPSEConstant::kb temperature;
68
69			setCR(props);
70			setCD(props);
71
72			return true;
73
74			}
75
76			/**
77			* calculate the ratio of friction coeffiction constant between ellipsoid and spheric
78			* with same volume.
79			* @param m
80			* @param n
81			* @note
82			* Reference:
83			*
84			* (1) Victor A. Bloomfield, On-Line Biophysics Textbook, Volume: Separations and Hydrodynamics
85			* Chapter 1,Survey of Biomolecular Hydrodynamics
86			* http://www.biophysics.org/education/vbloomfield.pdf
87			* (2) F. Perrin , J. Phys. Radium, [7] 5, 497-511, 1934
88			* (3) F. Perrin, J. Phys. Radium, [7] 7, 1-11, 1936
89			*/
90			bool AnalyticalModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) {
91			double ft;
92			double fra;
93			double frb;
94			double a = ellipsoid->getA();
95			double b = ellipsoid->getB();
96			double q = a/b; //?
97			if (q > 1.0) {//prolate
98			ft = sqrt(1-qq)/(pow(q, 2.0/3.0)log((1 + sqrt(1-q*q))/q));
99			fra = 4(1-qq)/(3(2 - 2pow(q, 4.0/3.0)/ft)); //not sure
100			frb = 4(1-qqqq) /(3qq(2pow(q, -2.0/3.0)(2-qq)/ft-2));
101			} else {//oblate
102			ft = sqrt(1-qq)/(pow(q, 2.0/3.0)atan(sqrt(q*q-1)));
103			fra = 4(1-qq)/(3(2 - 2pow(q, 4.0/3.0)/ft)); //not sure
104			frb = 4(1-qqqq) /(3qq(2pow(q, -2.0/3.0)(2-qq)/ft-2));
105			}
106
107			double radius = pow(aab, 1.0/3.0);
108			HydroProps props;
109			double Xitt = 6.0 * NumericConstant::PI * viscosity * radius;
110			double Xirr = 8.0 * NumericConstant::PI * viscosity * radius * radius * radius;
111			props.Xi(0, 0) = Xitt;
112			props.Xi(1, 1) = Xitt;
113			props.Xi(2, 2) = Xitt;
114			props.Xi(3, 3) = Xirr;
115			props.Xi(4, 4) = Xirr;
116			props.Xi(5, 5) = Xirr;
117
118			const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
119			props.Xi *= convertConstant;
120			props.Xi(0,0) *= ft;
121			props.Xi(1,1) *= ft;
122			props.Xi(2,2) *= ft;
123			props.Xi(3,3) *= fra;
124			props.Xi(4,4) *= fra;
125			props.Xi(5,5) *= frb;
126
127			Mat6x6d XiCopy = props.Xi;
128			XiCopy /= OOPSEConstant::kb * temperature;
129			invertMatrix(XiCopy, props.D);
130			double kt = OOPSEConstant::kB * temperature;
131			props.D *= kt;
132
133			setCR(props);
134			setCD(props);
135
136			return true;
137			}
138
139			bool AnalyticalModel::calcHydroProps(CompositeShape* compositexShape, double viscosity, double temperature) {
140			return false;
141			}
142
143
144
145			}