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 "hydrodynamics/AnalyticalModel.hpp"
#include "hydrodynamics/Sphere.hpp"
#include "hydrodynamics/Ellipsoid.hpp"
#include "hydrodynamics/CompositeShape.hpp"
#include "math/LU.hpp"
namespace oopse {
  
  bool AnalyticalModel::calcHydroProps(Sphere* sphere, double viscosity, double temperature) {
    
    double radius = sphere->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;    
}

  /**
   * Reference:
   * (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 rMajor = ellipsoid->getRMajor();
    double rMinor = ellipsoid->getRMinor();
    
    double a = rMinor;
    double b = rMajor;
    double a2 = a * a;
    double b2 = b* b;
    
    double p = a /b;
    double S;
    if (p > 1.0) { //prolate
      S = 2.0/sqrt(a2 - b2) * log((a + sqrt(a2-b2))/b);
    } else { //oblate
      S = 2.0/sqrt(b2 - a2) * atan(sqrt(b2-a2)/a);
    }
    
    double P = 1.0/(a2 - b2) * (S - 2.0/a);
    double Q = 0.5/(a2-b2) * (2.0*a/b2 - S);
    
    double transMinor = 16.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-b2)*S -2.0*a);
    double transMajor = 32.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-3.0*b2)*S +2.0*a);
    double rotMinor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2 - b2) * b2 /(2.0*a -b2*S);
    double rotMajor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2*a2 - b2*b2)/((2.0*a2-b2)*S-2.0*a);
    
    
    HydroProps props;
    
    props.Xi(0,0) = transMajor;
    props.Xi(1,1) = transMajor;
    props.Xi(2,2) = transMinor;
    props.Xi(3,3) = rotMajor;
    props.Xi(4,4) = rotMajor;
    props.Xi(5,5) = rotMinor;
    
    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;
  }
  
  bool AnalyticalModel::calcHydroProps(CompositeShape* compositeShape, double viscosity, double temperature) {
    return false;
  }
  
  void AnalyticalModel::writeBeads(std::ostream& os) {
    os << "1\n";
    os << "Generated by Hydro\n";
    Vector3d pos = sd_->getPos();
    os << sd_->getType() << "\t" << pos[0] << "\t" << pos[1] << "\t" << pos[2] << std::endl;
  }   
}
Revision:	2752
Committed:	Tue May 16 02:06:37 2006 UTC (18 years, 3 months ago) by gezelter
File size:	5280 byte(s)
Log Message:	* empty log message *
#	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	gezelter	2752	#include "hydrodynamics/AnalyticalModel.hpp"
42			#include "hydrodynamics/Sphere.hpp"
43			#include "hydrodynamics/Ellipsoid.hpp"
44			#include "hydrodynamics/CompositeShape.hpp"
45	tim	2634	#include "math/LU.hpp"
46			namespace oopse {
47	gezelter	2752
48			bool AnalyticalModel::calcHydroProps(Sphere* sphere, double viscosity, double temperature) {
49
50			double radius = sphere->getRadius();
51	tim	2634	HydroProps props;
52			props.center =V3Zero;
53			double Xitt = 6.0 * NumericConstant::PI * viscosity * radius;
54			double Xirr = 8.0 * NumericConstant::PI * viscosity * radius * radius * radius;
55			props.Xi(0, 0) = Xitt;
56			props.Xi(1, 1) = Xitt;
57			props.Xi(2, 2) = Xitt;
58			props.Xi(3, 3) = Xirr;
59			props.Xi(4, 4) = Xirr;
60			props.Xi(5, 5) = Xirr;
61
62			const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
63			props.Xi *= convertConstant;
64			Mat6x6d XiCopy = props.Xi;
65			invertMatrix(XiCopy, props.D);
66			double kt = OOPSEConstant::kB * temperature;
67			props.D *= kt;
68			props.Xi = OOPSEConstant::kb temperature;
69	gezelter	2752
70	tim	2634	setCR(props);
71			setCD(props);
72
73	gezelter	2752	return true;
74	tim	2634	}
75
76	gezelter	2752	/**
77			* Reference:
78			* (2) F. Perrin , J. Phys. Radium, [7] 5, 497-511, 1934
79			* (3) F. Perrin, J. Phys. Radium, [7] 7, 1-11, 1936
80			*/
81			bool AnalyticalModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) {
82
83	tim	2644	double rMajor = ellipsoid->getRMajor();
84			double rMinor = ellipsoid->getRMinor();
85	gezelter	2752
86	tim	2644	double a = rMinor;
87			double b = rMajor;
88			double a2 = a * a;
89			double b2 = b* b;
90
91			double p = a /b;
92			double S;
93			if (p > 1.0) { //prolate
94	gezelter	2752	S = 2.0/sqrt(a2 - b2) * log((a + sqrt(a2-b2))/b);
95	tim	2646	} else { //oblate
96	gezelter	2752	S = 2.0/sqrt(b2 - a2) * atan(sqrt(b2-a2)/a);
97	tim	2634	}
98	gezelter	2752
99	tim	2644	double P = 1.0/(a2 - b2) * (S - 2.0/a);
100			double Q = 0.5/(a2-b2) * (2.0*a/b2 - S);
101	gezelter	2752
102	tim	2644	double transMinor = 16.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0a2-b2)S -2.0*a);
103			double transMajor = 32.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0a2-3.0b2)S +2.0a);
104			double rotMinor = 32.0/3.0 * NumericConstant::PI * viscosity (a2 - b2) b2 /(2.0a -b2S);
105			double rotMajor = 32.0/3.0 * NumericConstant::PI * viscosity (a2a2 - b2b2)/((2.0a2-b2)S-2.0a);
106
107	gezelter	2752
108	tim	2634	HydroProps props;
109	gezelter	2752
110	tim	2644	props.Xi(0,0) = transMajor;
111			props.Xi(1,1) = transMajor;
112			props.Xi(2,2) = transMinor;
113			props.Xi(3,3) = rotMajor;
114			props.Xi(4,4) = rotMajor;
115			props.Xi(5,5) = rotMinor;
116	tim	2634
117			const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
118			props.Xi *= convertConstant;
119
120			Mat6x6d XiCopy = props.Xi;
121			invertMatrix(XiCopy, props.D);
122			double kt = OOPSEConstant::kB * temperature;
123			props.D *= kt;
124	tim	2644	props.Xi = OOPSEConstant::kb temperature;
125
126	tim	2634	setCR(props);
127			setCD(props);
128	gezelter	2752
129	tim	2634	return true;
130	gezelter	2752	}
131
132			bool AnalyticalModel::calcHydroProps(CompositeShape* compositeShape, double viscosity, double temperature) {
133	tim	2634	return false;
134	gezelter	2752	}
135
136			void AnalyticalModel::writeBeads(std::ostream& os) {
137	tim	2665	os << "1\n";
138			os << "Generated by Hydro\n";
139			Vector3d pos = sd_->getPos();
140			os << sd_->getType() << "\t" << pos[0] << "\t" << pos[1] << "\t" << pos[2] << std::endl;
141	gezelter	2752	}
142	tim	2665	}