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 "hydrodynamics/Shape.hpp"
#include "hydrodynamics/Sphere.hpp"
#include "hydrodynamics/Ellipsoid.hpp"
#include "applications/hydrodynamics/CompositeShape.hpp"

namespace oopse {
  
  bool HydrodynamicsModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) {
    return false;
  }
  
  void HydrodynamicsModel::writeHydroProps(std::ostream& os) {

    Vector3d center;
    Mat6x6d Xi, D;
    
    os << sd_->getType() << "\t";
    
    //center of resistance

    center = cr_->getCOR();

    os << center[0] <<  "\t" << center[1] <<  "\t" << center[2] <<  "\t"; 
    
    //resistance tensor at center of resistance
    //translation

    Xi = cr_->getXi();

    os << Xi(0, 0) <<  "\t" << Xi(0, 1) <<  "\t" << Xi(0, 2) <<  "\t" 
       << Xi(1, 0) <<  "\t" << Xi(1, 1) <<  "\t" << Xi(1, 2) <<  "\t" 
       << Xi(2, 0) <<  "\t" << Xi(2, 1) <<  "\t" << Xi(2, 2) <<  "\t"; 
    
    //rotation-translation
    os << Xi(0, 3) <<  "\t" << Xi(0, 4) <<  "\t" << Xi(0, 5) <<  "\t" 
       << Xi(1, 3) <<  "\t" << Xi(1, 4) <<  "\t" << Xi(1, 5) <<  "\t" 
       << Xi(2, 3) <<  "\t" << Xi(2, 4) <<  "\t" << Xi(2, 5) <<  "\t";
    
    //translation-rotation
    os << Xi(3, 0) <<  "\t" << Xi(3, 1) <<  "\t" << Xi(3, 2) <<  "\t" 
       << Xi(4, 0) <<  "\t" << Xi(4, 1) <<  "\t" << Xi(4, 2) <<  "\t" 
       << Xi(5, 0) <<  "\t" << Xi(5, 1) <<  "\t" << Xi(5, 2) <<  "\t"; 
    
    //rotation
    os << Xi(3, 3) <<  "\t" << Xi(3, 4) <<  "\t" << Xi(3, 5) <<  "\t" 
       << Xi(4, 3) <<  "\t" << Xi(4, 4) <<  "\t" << Xi(4, 5) <<  "\t" 
       << Xi(5, 3) <<  "\t" << Xi(5, 4) <<  "\t" << Xi(5, 5) <<  "\t"; 
    
    
    //diffusion tensor at center of resistance
    //translation

    D = cr_->getD();

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

    center = cd_->getCOR();

    os << center[0] <<  "\t" << center[1] <<  "\t" << center[2] <<  "\t"; 
    
    //resistance tensor at center of diffusion
    //translation

    Xi = cd_->getXi();

    os << Xi(0, 0) <<  "\t" << Xi(0, 1) <<  "\t" << Xi(0, 2) <<  "\t" 
       << Xi(1, 0) <<  "\t" << Xi(1, 1) <<  "\t" << Xi(1, 2) <<  "\t" 
       << Xi(2, 0) <<  "\t" << Xi(2, 1) <<  "\t" << Xi(2, 2) <<  "\t"; 
    
    //rotation-translation
    os << Xi(0, 3) <<  "\t" << Xi(0, 4) <<  "\t" << Xi(0, 5) <<  "\t" 
       << Xi(1, 3) <<  "\t" << Xi(1, 4) <<  "\t" << Xi(1, 5) <<  "\t" 
       << Xi(2, 3) <<  "\t" << Xi(2, 4) <<  "\t" << Xi(2, 5) <<  "\t"; 
    
    //translation-rotation
    os << Xi(3, 0) <<  "\t" << Xi(3, 1) <<  "\t" << Xi(3, 2) <<  "\t" 
       << Xi(4, 0) <<  "\t" << Xi(4, 1) <<  "\t" << Xi(4, 2) <<  "\t" 
       << Xi(5, 0) <<  "\t" << Xi(5, 1) <<  "\t" << Xi(5, 2) <<  "\t"; 
    
    //rotation
    os << Xi(3, 3) <<  "\t" << Xi(3, 4) <<  "\t" << Xi(3, 5) <<  "\t" 
       << Xi(4, 3) <<  "\t" << Xi(4, 4) <<  "\t" << Xi(4, 5) <<  "\t" 
       << Xi(5, 3) <<  "\t" << Xi(5, 4) <<  "\t" << Xi(5, 5) <<  "\t"; 
    
    
    //diffusion tensor at center of diffusion
    //translation

    D = cd_->getD();

    os << D(0, 0) <<  "\t" << D(0, 1) <<  "\t" << D(0, 2) <<  "\t" 
       << D(1, 0) <<  "\t" << D(1, 1) <<  "\t" << D(1, 2) <<  "\t" 
       << D(2, 0) <<  "\t" << D(2, 1) <<  "\t" << D(2, 2) <<  "\t"; 
    
    //rotation-translation
    os << D(0, 3) <<  "\t" << D(0, 4) <<  "\t" << D(0, 5) <<  "\t" 
       << D(1, 3) <<  "\t" << D(1, 4) <<  "\t" << D(1, 5) <<  "\t" 
       << D(2, 3) <<  "\t" << D(2, 4) <<  "\t" << D(2, 5) <<  "\t"; 
    
    //translation-rotation
    os << D(3, 0) <<  "\t" << D(3, 1) <<  "\t" << D(3, 2) <<  "\t" 
       << D(4, 0) <<  "\t" << D(4, 1) <<  "\t" << D(4, 2) <<  "\t" 
       << D(5, 0) <<  "\t" << D(5, 1) <<  "\t" << D(5, 2) <<  "\t"; 
    
    //rotation
    os << D(3, 3) <<  "\t" << D(3, 4) <<  "\t" << D(3, 5) <<  "\t" 
       << D(4, 3) <<  "\t" << D(4, 4) <<  "\t" << D(4, 5) <<  "\t" 
       << D(5, 3) <<  "\t" << D(5, 4) <<  "\t" << D(5, 5) <<  "\n";    
    
  }
  
}
Revision:	2787
Committed:	Mon Jun 5 18:24:45 2006 UTC (18 years, 3 months ago) by gezelter
File size:	7036 byte(s)
Log Message:	Massive changes for GB code with multiple ellipsoid types (a la Cleaver's paper). Also, changes in hydrodynamics code to make HydroProp a somewhat smarter class (rather than just a struct).
#	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	gezelter	2768	#include "hydrodynamics/Shape.hpp"
43			#include "hydrodynamics/Sphere.hpp"
44			#include "hydrodynamics/Ellipsoid.hpp"
45	tim	2634	#include "applications/hydrodynamics/CompositeShape.hpp"
46	tim	2596
47			namespace oopse {
48	gezelter	2768
49			bool HydrodynamicsModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) {
50	tim	2634	return false;
51	gezelter	2768	}
52
53			void HydrodynamicsModel::writeHydroProps(std::ostream& os) {
54	gezelter	2787
55			Vector3d center;
56			Mat6x6d Xi, D;
57	tim	2611
58	tim	2634	os << sd_->getType() << "\t";
59	tim	2611
60	tim	2634	//center of resistance
61	gezelter	2787
62			center = cr_->getCOR();
63
64			os << center[0] << "\t" << center[1] << "\t" << center[2] << "\t";
65	gezelter	2768
66	tim	2634	//resistance tensor at center of resistance
67			//translation
68	gezelter	2787
69			Xi = cr_->getXi();
70
71			os << Xi(0, 0) << "\t" << Xi(0, 1) << "\t" << Xi(0, 2) << "\t"
72			<< Xi(1, 0) << "\t" << Xi(1, 1) << "\t" << Xi(1, 2) << "\t"
73			<< Xi(2, 0) << "\t" << Xi(2, 1) << "\t" << Xi(2, 2) << "\t";
74	gezelter	2768
75	tim	2634	//rotation-translation
76	gezelter	2787	os << Xi(0, 3) << "\t" << Xi(0, 4) << "\t" << Xi(0, 5) << "\t"
77			<< Xi(1, 3) << "\t" << Xi(1, 4) << "\t" << Xi(1, 5) << "\t"
78			<< Xi(2, 3) << "\t" << Xi(2, 4) << "\t" << Xi(2, 5) << "\t";
79	gezelter	2768
80	tim	2634	//translation-rotation
81	gezelter	2787	os << Xi(3, 0) << "\t" << Xi(3, 1) << "\t" << Xi(3, 2) << "\t"
82			<< Xi(4, 0) << "\t" << Xi(4, 1) << "\t" << Xi(4, 2) << "\t"
83			<< Xi(5, 0) << "\t" << Xi(5, 1) << "\t" << Xi(5, 2) << "\t";
84	gezelter	2768
85	tim	2634	//rotation
86	gezelter	2787	os << Xi(3, 3) << "\t" << Xi(3, 4) << "\t" << Xi(3, 5) << "\t"
87			<< Xi(4, 3) << "\t" << Xi(4, 4) << "\t" << Xi(4, 5) << "\t"
88			<< Xi(5, 3) << "\t" << Xi(5, 4) << "\t" << Xi(5, 5) << "\t";
89	gezelter	2768
90
91	tim	2634	//diffusion tensor at center of resistance
92			//translation
93	gezelter	2787
94			D = cr_->getD();
95
96			os << D(0, 0) << "\t" << D(0, 1) << "\t" << D(0, 2) << "\t"
97			<< D(1, 0) << "\t" << D(1, 1) << "\t" << D(1, 2) << "\t"
98			<< D(2, 0) << "\t" << D(2, 1) << "\t" << D(2, 2) << "\t";
99	gezelter	2768
100	tim	2634	//rotation-translation
101	gezelter	2787	os << D(0, 3) << "\t" << D(0, 4) << "\t" << D(0, 5) << "\t"
102			<< D(1, 3) << "\t" << D(1, 4) << "\t" << D(1, 5) << "\t"
103			<< D(2, 3) << "\t" << D(2, 4) << "\t" << D(2, 5) << "\t";
104	gezelter	2768
105	tim	2634	//translation-rotation
106	gezelter	2787	os << D(3, 0) << "\t" << D(3, 1) << "\t" << D(3, 2) << "\t"
107			<< D(4, 0) << "\t" << D(4, 1) << "\t" << D(4, 2) << "\t"
108			<< D(5, 0) << "\t" << D(5, 1) << "\t" << D(5, 2) << "\t";
109	gezelter	2768
110	tim	2634	//rotation
111	gezelter	2787	os << D(3, 3) << "\t" << D(3, 4) << "\t" << D(3, 5) << "\t"
112			<< D(4, 3) << "\t" << D(4, 4) << "\t" << D(4, 5) << "\t"
113			<< D(5, 3) << "\t" << D(5, 4) << "\t" << D(5, 5) << "\t";
114	gezelter	2768
115	tim	2634	//---------------------------------------------------------------------
116	gezelter	2768
117	tim	2634	//center of diffusion
118	gezelter	2787
119			center = cd_->getCOR();
120
121			os << center[0] << "\t" << center[1] << "\t" << center[2] << "\t";
122	gezelter	2768
123	tim	2634	//resistance tensor at center of diffusion
124			//translation
125	gezelter	2787
126			Xi = cd_->getXi();
127
128			os << Xi(0, 0) << "\t" << Xi(0, 1) << "\t" << Xi(0, 2) << "\t"
129			<< Xi(1, 0) << "\t" << Xi(1, 1) << "\t" << Xi(1, 2) << "\t"
130			<< Xi(2, 0) << "\t" << Xi(2, 1) << "\t" << Xi(2, 2) << "\t";
131	gezelter	2768
132	tim	2634	//rotation-translation
133	gezelter	2787	os << Xi(0, 3) << "\t" << Xi(0, 4) << "\t" << Xi(0, 5) << "\t"
134			<< Xi(1, 3) << "\t" << Xi(1, 4) << "\t" << Xi(1, 5) << "\t"
135			<< Xi(2, 3) << "\t" << Xi(2, 4) << "\t" << Xi(2, 5) << "\t";
136	gezelter	2768
137	tim	2634	//translation-rotation
138	gezelter	2787	os << Xi(3, 0) << "\t" << Xi(3, 1) << "\t" << Xi(3, 2) << "\t"
139			<< Xi(4, 0) << "\t" << Xi(4, 1) << "\t" << Xi(4, 2) << "\t"
140			<< Xi(5, 0) << "\t" << Xi(5, 1) << "\t" << Xi(5, 2) << "\t";
141	gezelter	2768
142	tim	2634	//rotation
143	gezelter	2787	os << Xi(3, 3) << "\t" << Xi(3, 4) << "\t" << Xi(3, 5) << "\t"
144			<< Xi(4, 3) << "\t" << Xi(4, 4) << "\t" << Xi(4, 5) << "\t"
145			<< Xi(5, 3) << "\t" << Xi(5, 4) << "\t" << Xi(5, 5) << "\t";
146	gezelter	2768
147
148	tim	2634	//diffusion tensor at center of diffusion
149			//translation
150	gezelter	2787
151			D = cd_->getD();
152
153			os << D(0, 0) << "\t" << D(0, 1) << "\t" << D(0, 2) << "\t"
154			<< D(1, 0) << "\t" << D(1, 1) << "\t" << D(1, 2) << "\t"
155			<< D(2, 0) << "\t" << D(2, 1) << "\t" << D(2, 2) << "\t";
156	gezelter	2768
157	tim	2634	//rotation-translation
158	gezelter	2787	os << D(0, 3) << "\t" << D(0, 4) << "\t" << D(0, 5) << "\t"
159			<< D(1, 3) << "\t" << D(1, 4) << "\t" << D(1, 5) << "\t"
160			<< D(2, 3) << "\t" << D(2, 4) << "\t" << D(2, 5) << "\t";
161	gezelter	2768
162	tim	2634	//translation-rotation
163	gezelter	2787	os << D(3, 0) << "\t" << D(3, 1) << "\t" << D(3, 2) << "\t"
164			<< D(4, 0) << "\t" << D(4, 1) << "\t" << D(4, 2) << "\t"
165			<< D(5, 0) << "\t" << D(5, 1) << "\t" << D(5, 2) << "\t";
166	gezelter	2768
167	tim	2634	//rotation
168	gezelter	2787	os << D(3, 3) << "\t" << D(3, 4) << "\t" << D(3, 5) << "\t"
169			<< D(4, 3) << "\t" << D(4, 4) << "\t" << D(4, 5) << "\t"
170			<< D(5, 3) << "\t" << D(5, 4) << "\t" << D(5, 5) << "\n";
171	gezelter	2768
172			}
173
174	tim	2596	}