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 (19 years, 1 month ago) by tim
File size:	5439 byte(s)
Log Message:	refactor Hydrodynamics module.
#	Content
1	/*
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	}