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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
#include "hydrodynamics/Shape.hpp"
#include "hydrodynamics/Sphere.hpp"
#include "hydrodynamics/Ellipsoid.hpp"
#include "applications/hydrodynamics/CompositeShape.hpp"

namespace OpenMD {
  
  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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	7144 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	tim	891	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	891	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	891	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	891	*/
42	tim	906	#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
43	gezelter	972	#include "hydrodynamics/Shape.hpp"
44			#include "hydrodynamics/Sphere.hpp"
45			#include "hydrodynamics/Ellipsoid.hpp"
46	tim	906	#include "applications/hydrodynamics/CompositeShape.hpp"
47	tim	891
48	gezelter	1390	namespace OpenMD {
49	gezelter	972
50			bool HydrodynamicsModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) {
51	tim	906	return false;
52	gezelter	972	}
53
54			void HydrodynamicsModel::writeHydroProps(std::ostream& os) {
55	gezelter	981
56			Vector3d center;
57			Mat6x6d Xi, D;
58	tim	895
59	tim	906	os << sd_->getType() << "\t";
60	tim	895
61	tim	906	//center of resistance
62	gezelter	981
63			center = cr_->getCOR();
64
65			os << center[0] << "\t" << center[1] << "\t" << center[2] << "\t";
66	gezelter	972
67	tim	906	//resistance tensor at center of resistance
68			//translation
69	gezelter	981
70			Xi = cr_->getXi();
71
72			os << Xi(0, 0) << "\t" << Xi(0, 1) << "\t" << Xi(0, 2) << "\t"
73			<< Xi(1, 0) << "\t" << Xi(1, 1) << "\t" << Xi(1, 2) << "\t"
74			<< Xi(2, 0) << "\t" << Xi(2, 1) << "\t" << Xi(2, 2) << "\t";
75	gezelter	972
76	tim	906	//rotation-translation
77	gezelter	981	os << Xi(0, 3) << "\t" << Xi(0, 4) << "\t" << Xi(0, 5) << "\t"
78			<< Xi(1, 3) << "\t" << Xi(1, 4) << "\t" << Xi(1, 5) << "\t"
79			<< Xi(2, 3) << "\t" << Xi(2, 4) << "\t" << Xi(2, 5) << "\t";
80	gezelter	972
81	tim	906	//translation-rotation
82	gezelter	981	os << Xi(3, 0) << "\t" << Xi(3, 1) << "\t" << Xi(3, 2) << "\t"
83			<< Xi(4, 0) << "\t" << Xi(4, 1) << "\t" << Xi(4, 2) << "\t"
84			<< Xi(5, 0) << "\t" << Xi(5, 1) << "\t" << Xi(5, 2) << "\t";
85	gezelter	972
86	tim	906	//rotation
87	gezelter	981	os << Xi(3, 3) << "\t" << Xi(3, 4) << "\t" << Xi(3, 5) << "\t"
88			<< Xi(4, 3) << "\t" << Xi(4, 4) << "\t" << Xi(4, 5) << "\t"
89			<< Xi(5, 3) << "\t" << Xi(5, 4) << "\t" << Xi(5, 5) << "\t";
90	gezelter	972
91
92	tim	906	//diffusion tensor at center of resistance
93			//translation
94	gezelter	981
95			D = cr_->getD();
96
97			os << D(0, 0) << "\t" << D(0, 1) << "\t" << D(0, 2) << "\t"
98			<< D(1, 0) << "\t" << D(1, 1) << "\t" << D(1, 2) << "\t"
99			<< D(2, 0) << "\t" << D(2, 1) << "\t" << D(2, 2) << "\t";
100	gezelter	972
101	tim	906	//rotation-translation
102	gezelter	981	os << D(0, 3) << "\t" << D(0, 4) << "\t" << D(0, 5) << "\t"
103			<< D(1, 3) << "\t" << D(1, 4) << "\t" << D(1, 5) << "\t"
104			<< D(2, 3) << "\t" << D(2, 4) << "\t" << D(2, 5) << "\t";
105	gezelter	972
106	tim	906	//translation-rotation
107	gezelter	981	os << D(3, 0) << "\t" << D(3, 1) << "\t" << D(3, 2) << "\t"
108			<< D(4, 0) << "\t" << D(4, 1) << "\t" << D(4, 2) << "\t"
109			<< D(5, 0) << "\t" << D(5, 1) << "\t" << D(5, 2) << "\t";
110	gezelter	972
111	tim	906	//rotation
112	gezelter	981	os << D(3, 3) << "\t" << D(3, 4) << "\t" << D(3, 5) << "\t"
113			<< D(4, 3) << "\t" << D(4, 4) << "\t" << D(4, 5) << "\t"
114			<< D(5, 3) << "\t" << D(5, 4) << "\t" << D(5, 5) << "\t";
115	gezelter	972
116	tim	906	//---------------------------------------------------------------------
117	gezelter	972
118	tim	906	//center of diffusion
119	gezelter	981
120			center = cd_->getCOR();
121
122			os << center[0] << "\t" << center[1] << "\t" << center[2] << "\t";
123	gezelter	972
124	tim	906	//resistance tensor at center of diffusion
125			//translation
126	gezelter	981
127			Xi = cd_->getXi();
128
129			os << Xi(0, 0) << "\t" << Xi(0, 1) << "\t" << Xi(0, 2) << "\t"
130			<< Xi(1, 0) << "\t" << Xi(1, 1) << "\t" << Xi(1, 2) << "\t"
131			<< Xi(2, 0) << "\t" << Xi(2, 1) << "\t" << Xi(2, 2) << "\t";
132	gezelter	972
133	tim	906	//rotation-translation
134	gezelter	981	os << Xi(0, 3) << "\t" << Xi(0, 4) << "\t" << Xi(0, 5) << "\t"
135			<< Xi(1, 3) << "\t" << Xi(1, 4) << "\t" << Xi(1, 5) << "\t"
136			<< Xi(2, 3) << "\t" << Xi(2, 4) << "\t" << Xi(2, 5) << "\t";
137	gezelter	972
138	tim	906	//translation-rotation
139	gezelter	981	os << Xi(3, 0) << "\t" << Xi(3, 1) << "\t" << Xi(3, 2) << "\t"
140			<< Xi(4, 0) << "\t" << Xi(4, 1) << "\t" << Xi(4, 2) << "\t"
141			<< Xi(5, 0) << "\t" << Xi(5, 1) << "\t" << Xi(5, 2) << "\t";
142	gezelter	972
143	tim	906	//rotation
144	gezelter	981	os << Xi(3, 3) << "\t" << Xi(3, 4) << "\t" << Xi(3, 5) << "\t"
145			<< Xi(4, 3) << "\t" << Xi(4, 4) << "\t" << Xi(4, 5) << "\t"
146			<< Xi(5, 3) << "\t" << Xi(5, 4) << "\t" << Xi(5, 5) << "\t";
147	gezelter	972
148
149	tim	906	//diffusion tensor at center of diffusion
150			//translation
151	gezelter	981
152			D = cd_->getD();
153
154			os << D(0, 0) << "\t" << D(0, 1) << "\t" << D(0, 2) << "\t"
155			<< D(1, 0) << "\t" << D(1, 1) << "\t" << D(1, 2) << "\t"
156			<< D(2, 0) << "\t" << D(2, 1) << "\t" << D(2, 2) << "\t";
157	gezelter	972
158	tim	906	//rotation-translation
159	gezelter	981	os << D(0, 3) << "\t" << D(0, 4) << "\t" << D(0, 5) << "\t"
160			<< D(1, 3) << "\t" << D(1, 4) << "\t" << D(1, 5) << "\t"
161			<< D(2, 3) << "\t" << D(2, 4) << "\t" << D(2, 5) << "\t";
162	gezelter	972
163	tim	906	//translation-rotation
164	gezelter	981	os << D(3, 0) << "\t" << D(3, 1) << "\t" << D(3, 2) << "\t"
165			<< D(4, 0) << "\t" << D(4, 1) << "\t" << D(4, 2) << "\t"
166			<< D(5, 0) << "\t" << D(5, 1) << "\t" << D(5, 2) << "\t";
167	gezelter	972
168	tim	906	//rotation
169	gezelter	981	os << D(3, 3) << "\t" << D(3, 4) << "\t" << D(3, 5) << "\t"
170			<< D(4, 3) << "\t" << D(4, 4) << "\t" << D(4, 5) << "\t"
171			<< D(5, 3) << "\t" << D(5, 4) << "\t" << D(5, 5) << "\n";
172	gezelter	972
173			}
174
175	tim	891	}