applications/hydrodynamics/HydrodynamicsModel.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/HydrodynamicsModel.hpp"
#include "applications/hydrodynamics/Spheric.hpp"
#include "applications/hydrodynamics/Ellipsoid.hpp"
#include "applications/hydrodynamics/CompositeShape.hpp"

namespace oopse {

bool HydrodynamicsModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) {
    return false;
}

bool HydrodynamicsModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) {
    return false;
}

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

void HydrodynamicsModel::writeHydroProps(std::ostream& os) {

    
    os << sd_->getType() << "\t";
    
    //center of resistance
    os << cr_.center[0] <<  "\t" << cr_.center[1] <<  "\t" << cr_.center[2] <<  "\t"; 

    //resistance tensor at center of resistance
    //translation
    os << cr_.Xi(0, 0) <<  "\t" << cr_.Xi(0, 1) <<  "\t" << cr_.Xi(0, 2) <<  "\t" 
        << cr_.Xi(1, 0) <<  "\t" << cr_.Xi(1, 1) <<  "\t" << cr_.Xi(1, 2) <<  "\t" 
        << cr_.Xi(2, 0) <<  "\t" << cr_.Xi(2, 1) <<  "\t" << cr_.Xi(2, 2) <<  "\t"; 

    //rotation-translation
    os << cr_.Xi(0, 3) <<  "\t" << cr_.Xi(0, 4) <<  "\t" << cr_.Xi(0, 5) <<  "\t" 
        << cr_.Xi(1, 3) <<  "\t" << cr_.Xi(1, 4) <<  "\t" << cr_.Xi(1, 5) <<  "\t" 
        << cr_.Xi(2, 3) <<  "\t" << cr_.Xi(2, 4) <<  "\t" << cr_.Xi(2, 5) <<  "\t";

    //translation-rotation
    os << cr_.Xi(3, 0) <<  "\t" << cr_.Xi(3, 1) <<  "\t" << cr_.Xi(3, 2) <<  "\t" 
        << cr_.Xi(4, 0) <<  "\t" << cr_.Xi(4, 1) <<  "\t" << cr_.Xi(4, 2) <<  "\t" 
        << cr_.Xi(5, 0) <<  "\t" << cr_.Xi(5, 1) <<  "\t" << cr_.Xi(5, 2) <<  "\t"; 

    //rotation
    os << cr_.Xi(3, 3) <<  "\t" << cr_.Xi(3, 4) <<  "\t" << cr_.Xi(3, 5) <<  "\t" 
        << cr_.Xi(4, 3) <<  "\t" << cr_.Xi(4, 4) <<  "\t" << cr_.Xi(4, 5) <<  "\t" 
        << cr_.Xi(5, 3) <<  "\t" << cr_.Xi(5, 4) <<  "\t" << cr_.Xi(5, 5) <<  "\t"; 


    //diffusion tensor at center of resistance
    //translation
    os << cr_.D(0, 0) <<  "\t" << cr_.D(0, 1) <<  "\t" << cr_.D(0, 2) <<  "\t" 
        << cr_.D(1, 0) <<  "\t" << cr_.D(1, 1) <<  "\t" << cr_.D(1, 2) <<  "\t" 
        << cr_.D(2, 0) <<  "\t" << cr_.D(2, 1) <<  "\t" << cr_.D(2, 2) <<  "\t"; 

    //rotation-translation
    os << cr_.D(0, 3) <<  "\t" << cr_.D(0, 4) <<  "\t" << cr_.D(0, 5) <<  "\t" 
        << cr_.D(1, 3) <<  "\t" << cr_.D(1, 4) <<  "\t" << cr_.D(1, 5) <<  "\t" 
        << cr_.D(2, 3) <<  "\t" << cr_.D(2, 4) <<  "\t" << cr_.D(2, 5) <<  "\t"; 

    //translation-rotation
    os << cr_.D(3, 0) <<  "\t" << cr_.D(3, 1) <<  "\t" << cr_.D(3, 2) <<  "\t" 
        << cr_.D(4, 0) <<  "\t" << cr_.D(4, 1) <<  "\t" << cr_.D(4, 2) <<  "\t" 
        << cr_.D(5, 0) <<  "\t" << cr_.D(5, 1) <<  "\t" << cr_.D(5, 2) <<  "\t"; 

    //rotation
    os << cr_.D(3, 3) <<  "\t" << cr_.D(3, 4) <<  "\t" << cr_.D(3, 5) <<  "\t" 
        << cr_.D(4, 3) <<  "\t" << cr_.D(4, 4) <<  "\t" << cr_.D(4, 5) <<  "\t" 
        << cr_.D(5, 3) <<  "\t" << cr_.D(5, 4) <<  "\t" << cr_.D(5, 5) <<  "\t"; 
        
    //---------------------------------------------------------------------

    //center of diffusion
    os << cd_.center[0] <<  "\t" << cd_.center[1] <<  "\t" << cd_.center[2] <<  "\t"; 

    //resistance tensor at center of diffusion
    //translation
    os << cd_.Xi(0, 0) <<  "\t" << cd_.Xi(0, 1) <<  "\t" << cd_.Xi(0, 2) <<  "\t" 
        << cd_.Xi(1, 0) <<  "\t" << cd_.Xi(1, 1) <<  "\t" << cd_.Xi(1, 2) <<  "\t" 
        << cd_.Xi(2, 0) <<  "\t" << cd_.Xi(2, 1) <<  "\t" << cd_.Xi(2, 2) <<  "\t"; 

    //rotation-translation
    os << cd_.Xi(0, 3) <<  "\t" << cd_.Xi(0, 4) <<  "\t" << cd_.Xi(0, 5) <<  "\t" 
        << cd_.Xi(1, 3) <<  "\t" << cd_.Xi(1, 4) <<  "\t" << cd_.Xi(1, 5) <<  "\t" 
        << cd_.Xi(2, 3) <<  "\t" << cd_.Xi(2, 4) <<  "\t" << cd_.Xi(2, 5) <<  "\t"; 

    //translation-rotation
    os << cd_.Xi(3, 0) <<  "\t" << cd_.Xi(3, 1) <<  "\t" << cd_.Xi(3, 2) <<  "\t" 
        << cd_.Xi(4, 0) <<  "\t" << cd_.Xi(4, 1) <<  "\t" << cd_.Xi(4, 2) <<  "\t" 
        << cd_.Xi(5, 0) <<  "\t" << cd_.Xi(5, 1) <<  "\t" << cd_.Xi(5, 2) <<  "\t"; 

    //rotation
    os << cd_.Xi(3, 3) <<  "\t" << cd_.Xi(3, 4) <<  "\t" << cd_.Xi(3, 5) <<  "\t" 
        << cd_.Xi(4, 3) <<  "\t" << cd_.Xi(4, 4) <<  "\t" << cd_.Xi(4, 5) <<  "\t" 
        << cd_.Xi(5, 3) <<  "\t" << cd_.Xi(5, 4) <<  "\t" << cd_.Xi(5, 5) <<  "\t"; 


    //diffusion tensor at center of diffusion
    //translation
    os << cd_.D(0, 0) <<  "\t" << cd_.D(0, 1) <<  "\t" << cd_.D(0, 2) <<  "\t" 
        << cd_.D(1, 0) <<  "\t" << cd_.D(1, 1) <<  "\t" << cd_.D(1, 2) <<  "\t" 
        << cd_.D(2, 0) <<  "\t" << cd_.D(2, 1) <<  "\t" << cd_.D(2, 2) <<  "\t"; 

    //rotation-translation
    os << cd_.D(0, 3) <<  "\t" << cd_.D(0, 4) <<  "\t" << cd_.D(0, 5) <<  "\t" 
        << cd_.D(1, 3) <<  "\t" << cd_.D(1, 4) <<  "\t" << cd_.D(1, 5) <<  "\t" 
        << cd_.D(2, 3) <<  "\t" << cd_.D(2, 4) <<  "\t" << cd_.D(2, 5) <<  "\t"; 

    //translation-rotation
    os << cd_.D(3, 0) <<  "\t" << cd_.D(3, 1) <<  "\t" << cd_.D(3, 2) <<  "\t" 
        << cd_.D(4, 0) <<  "\t" << cd_.D(4, 1) <<  "\t" << cd_.D(4, 2) <<  "\t" 
        << cd_.D(5, 0) <<  "\t" << cd_.D(5, 1) <<  "\t" << cd_.D(5, 2) <<  "\t"; 

    //rotation
    os << cd_.D(3, 3) <<  "\t" << cd_.D(3, 4) <<  "\t" << cd_.D(3, 5) <<  "\t" 
        << cd_.D(4, 3) <<  "\t" << cd_.D(4, 4) <<  "\t" << cd_.D(4, 5) <<  "\t" 
        << cd_.D(5, 3) <<  "\t" << cd_.D(5, 4) <<  "\t" << cd_.D(5, 5) <<  "\n"; 


}

}
Revision:	2634
Committed:	Fri Mar 17 23:20:35 2006 UTC (18 years, 4 months ago) by tim
File size:	7629 byte(s)
Log Message:	refactor Hydrodynamics module.
#	User	Rev	Content
1	tim	2596	/*
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	tim	2634	#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
42			#include "applications/hydrodynamics/Spheric.hpp"
43			#include "applications/hydrodynamics/Ellipsoid.hpp"
44			#include "applications/hydrodynamics/CompositeShape.hpp"
45	tim	2596
46			namespace oopse {
47	tim	2597
48	tim	2634	bool HydrodynamicsModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) {
49			return false;
50	tim	2597	}
51	tim	2611
52	tim	2634	bool HydrodynamicsModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) {
53			return false;
54	tim	2596	}
55
56	tim	2634	bool HydrodynamicsModel::calcHydroProps(CompositeShape* compositexShape, double viscosity, double temperature) {
57			return false;
58	tim	2611	}
59
60	tim	2634	void HydrodynamicsModel::writeHydroProps(std::ostream& os) {
61	tim	2611
62
63	tim	2634	os << sd_->getType() << "\t";
64	tim	2611
65	tim	2634	//center of resistance
66			os << cr_.center[0] << "\t" << cr_.center[1] << "\t" << cr_.center[2] << "\t";
67	tim	2611
68	tim	2634	//resistance tensor at center of resistance
69			//translation
70			os << cr_.Xi(0, 0) << "\t" << cr_.Xi(0, 1) << "\t" << cr_.Xi(0, 2) << "\t"
71			<< cr_.Xi(1, 0) << "\t" << cr_.Xi(1, 1) << "\t" << cr_.Xi(1, 2) << "\t"
72			<< cr_.Xi(2, 0) << "\t" << cr_.Xi(2, 1) << "\t" << cr_.Xi(2, 2) << "\t";
73	tim	2611
74	tim	2634	//rotation-translation
75			os << cr_.Xi(0, 3) << "\t" << cr_.Xi(0, 4) << "\t" << cr_.Xi(0, 5) << "\t"
76			<< cr_.Xi(1, 3) << "\t" << cr_.Xi(1, 4) << "\t" << cr_.Xi(1, 5) << "\t"
77			<< cr_.Xi(2, 3) << "\t" << cr_.Xi(2, 4) << "\t" << cr_.Xi(2, 5) << "\t";
78	tim	2626
79	tim	2634	//translation-rotation
80			os << cr_.Xi(3, 0) << "\t" << cr_.Xi(3, 1) << "\t" << cr_.Xi(3, 2) << "\t"
81			<< cr_.Xi(4, 0) << "\t" << cr_.Xi(4, 1) << "\t" << cr_.Xi(4, 2) << "\t"
82			<< cr_.Xi(5, 0) << "\t" << cr_.Xi(5, 1) << "\t" << cr_.Xi(5, 2) << "\t";
83	tim	2611
84	tim	2634	//rotation
85			os << cr_.Xi(3, 3) << "\t" << cr_.Xi(3, 4) << "\t" << cr_.Xi(3, 5) << "\t"
86			<< cr_.Xi(4, 3) << "\t" << cr_.Xi(4, 4) << "\t" << cr_.Xi(4, 5) << "\t"
87			<< cr_.Xi(5, 3) << "\t" << cr_.Xi(5, 4) << "\t" << cr_.Xi(5, 5) << "\t";
88	tim	2611
89
90	tim	2634	//diffusion tensor at center of resistance
91			//translation
92			os << cr_.D(0, 0) << "\t" << cr_.D(0, 1) << "\t" << cr_.D(0, 2) << "\t"
93			<< cr_.D(1, 0) << "\t" << cr_.D(1, 1) << "\t" << cr_.D(1, 2) << "\t"
94			<< cr_.D(2, 0) << "\t" << cr_.D(2, 1) << "\t" << cr_.D(2, 2) << "\t";
95	tim	2611
96	tim	2634	//rotation-translation
97			os << cr_.D(0, 3) << "\t" << cr_.D(0, 4) << "\t" << cr_.D(0, 5) << "\t"
98			<< cr_.D(1, 3) << "\t" << cr_.D(1, 4) << "\t" << cr_.D(1, 5) << "\t"
99			<< cr_.D(2, 3) << "\t" << cr_.D(2, 4) << "\t" << cr_.D(2, 5) << "\t";
100	tim	2627
101	tim	2634	//translation-rotation
102			os << cr_.D(3, 0) << "\t" << cr_.D(3, 1) << "\t" << cr_.D(3, 2) << "\t"
103			<< cr_.D(4, 0) << "\t" << cr_.D(4, 1) << "\t" << cr_.D(4, 2) << "\t"
104			<< cr_.D(5, 0) << "\t" << cr_.D(5, 1) << "\t" << cr_.D(5, 2) << "\t";
105	tim	2632
106	tim	2634	//rotation
107			os << cr_.D(3, 3) << "\t" << cr_.D(3, 4) << "\t" << cr_.D(3, 5) << "\t"
108			<< cr_.D(4, 3) << "\t" << cr_.D(4, 4) << "\t" << cr_.D(4, 5) << "\t"
109			<< cr_.D(5, 3) << "\t" << cr_.D(5, 4) << "\t" << cr_.D(5, 5) << "\t";
110
111			//---------------------------------------------------------------------
112	tim	2632
113	tim	2634	//center of diffusion
114			os << cd_.center[0] << "\t" << cd_.center[1] << "\t" << cd_.center[2] << "\t";
115	tim	2611
116	tim	2634	//resistance tensor at center of diffusion
117			//translation
118			os << cd_.Xi(0, 0) << "\t" << cd_.Xi(0, 1) << "\t" << cd_.Xi(0, 2) << "\t"
119			<< cd_.Xi(1, 0) << "\t" << cd_.Xi(1, 1) << "\t" << cd_.Xi(1, 2) << "\t"
120			<< cd_.Xi(2, 0) << "\t" << cd_.Xi(2, 1) << "\t" << cd_.Xi(2, 2) << "\t";
121	tim	2626
122	tim	2634	//rotation-translation
123			os << cd_.Xi(0, 3) << "\t" << cd_.Xi(0, 4) << "\t" << cd_.Xi(0, 5) << "\t"
124			<< cd_.Xi(1, 3) << "\t" << cd_.Xi(1, 4) << "\t" << cd_.Xi(1, 5) << "\t"
125			<< cd_.Xi(2, 3) << "\t" << cd_.Xi(2, 4) << "\t" << cd_.Xi(2, 5) << "\t";
126	tim	2626
127	tim	2634	//translation-rotation
128			os << cd_.Xi(3, 0) << "\t" << cd_.Xi(3, 1) << "\t" << cd_.Xi(3, 2) << "\t"
129			<< cd_.Xi(4, 0) << "\t" << cd_.Xi(4, 1) << "\t" << cd_.Xi(4, 2) << "\t"
130			<< cd_.Xi(5, 0) << "\t" << cd_.Xi(5, 1) << "\t" << cd_.Xi(5, 2) << "\t";
131	tim	2611
132	tim	2634	//rotation
133			os << cd_.Xi(3, 3) << "\t" << cd_.Xi(3, 4) << "\t" << cd_.Xi(3, 5) << "\t"
134			<< cd_.Xi(4, 3) << "\t" << cd_.Xi(4, 4) << "\t" << cd_.Xi(4, 5) << "\t"
135			<< cd_.Xi(5, 3) << "\t" << cd_.Xi(5, 4) << "\t" << cd_.Xi(5, 5) << "\t";
136	tim	2596
137
138	tim	2634	//diffusion tensor at center of diffusion
139			//translation
140			os << cd_.D(0, 0) << "\t" << cd_.D(0, 1) << "\t" << cd_.D(0, 2) << "\t"
141			<< cd_.D(1, 0) << "\t" << cd_.D(1, 1) << "\t" << cd_.D(1, 2) << "\t"
142			<< cd_.D(2, 0) << "\t" << cd_.D(2, 1) << "\t" << cd_.D(2, 2) << "\t";
143	tim	2596
144	tim	2634	//rotation-translation
145			os << cd_.D(0, 3) << "\t" << cd_.D(0, 4) << "\t" << cd_.D(0, 5) << "\t"
146			<< cd_.D(1, 3) << "\t" << cd_.D(1, 4) << "\t" << cd_.D(1, 5) << "\t"
147			<< cd_.D(2, 3) << "\t" << cd_.D(2, 4) << "\t" << cd_.D(2, 5) << "\t";
148	tim	2597
149	tim	2634	//translation-rotation
150			os << cd_.D(3, 0) << "\t" << cd_.D(3, 1) << "\t" << cd_.D(3, 2) << "\t"
151			<< cd_.D(4, 0) << "\t" << cd_.D(4, 1) << "\t" << cd_.D(4, 2) << "\t"
152			<< cd_.D(5, 0) << "\t" << cd_.D(5, 1) << "\t" << cd_.D(5, 2) << "\t";
153	tim	2597
154	tim	2634	//rotation
155			os << cd_.D(3, 3) << "\t" << cd_.D(3, 4) << "\t" << cd_.D(3, 5) << "\t"
156			<< cd_.D(4, 3) << "\t" << cd_.D(4, 4) << "\t" << cd_.D(4, 5) << "\t"
157			<< cd_.D(5, 3) << "\t" << cd_.D(5, 4) << "\t" << cd_.D(5, 5) << "\n";
158	tim	2597
159	tim	2611
160	tim	2596	}
161
162			}