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root/OpenMD/trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp

Comparing trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp (file contents):
Revision 972 by gezelter, Wed May 24 18:31:12 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
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	+	*
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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
43		#include "hydrodynamics/Shape.hpp"
#	Line 44 | Line 45
45		#include "hydrodynamics/Ellipsoid.hpp"
46		#include "applications/hydrodynamics/CompositeShape.hpp"
47
48	<	namespace oopse {
48	>	namespace OpenMD {
49
50		bool HydrodynamicsModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) {
51		return false;
52		}
53
54		void HydrodynamicsModel::writeHydroProps(std::ostream& os) {
55	+
56	+	Vector3d center;
57	+	Mat6x6d Xi, D;
58
55	–
59		os << sd_->getType() << "\t";
60
61		//center of resistance
62	<	os << cr_.center[0] <<  "\t" << cr_.center[1] <<  "\t" << cr_.center[2] <<  "\t";
62	>
63	>	center = cr_->getCOR();
64	>
65	>	os << center[0] <<  "\t" << center[1] <<  "\t" << center[2] <<  "\t";
66
67		//resistance tensor at center of resistance
68		//translation
69	<	os << cr_.Xi(0, 0) <<  "\t" << cr_.Xi(0, 1) <<  "\t" << cr_.Xi(0, 2) <<  "\t"
70	<	<< cr_.Xi(1, 0) <<  "\t" << cr_.Xi(1, 1) <<  "\t" << cr_.Xi(1, 2) <<  "\t"
71	<	<< cr_.Xi(2, 0) <<  "\t" << cr_.Xi(2, 1) <<  "\t" << cr_.Xi(2, 2) <<  "\t";
69	>
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
76		//rotation-translation
77	<	os << cr_.Xi(0, 3) <<  "\t" << cr_.Xi(0, 4) <<  "\t" << cr_.Xi(0, 5) <<  "\t"
78	<	<< cr_.Xi(1, 3) <<  "\t" << cr_.Xi(1, 4) <<  "\t" << cr_.Xi(1, 5) <<  "\t"
79	<	<< cr_.Xi(2, 3) <<  "\t" << cr_.Xi(2, 4) <<  "\t" << cr_.Xi(2, 5) <<  "\t";
77	>	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
81		//translation-rotation
82	<	os << cr_.Xi(3, 0) <<  "\t" << cr_.Xi(3, 1) <<  "\t" << cr_.Xi(3, 2) <<  "\t"
83	<	<< cr_.Xi(4, 0) <<  "\t" << cr_.Xi(4, 1) <<  "\t" << cr_.Xi(4, 2) <<  "\t"
84	<	<< cr_.Xi(5, 0) <<  "\t" << cr_.Xi(5, 1) <<  "\t" << cr_.Xi(5, 2) <<  "\t";
82	>	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
86		//rotation
87	<	os << cr_.Xi(3, 3) <<  "\t" << cr_.Xi(3, 4) <<  "\t" << cr_.Xi(3, 5) <<  "\t"
88	<	<< cr_.Xi(4, 3) <<  "\t" << cr_.Xi(4, 4) <<  "\t" << cr_.Xi(4, 5) <<  "\t"
89	<	<< cr_.Xi(5, 3) <<  "\t" << cr_.Xi(5, 4) <<  "\t" << cr_.Xi(5, 5) <<  "\t";
87	>	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
91
92		//diffusion tensor at center of resistance
93		//translation
94	<	os << cr_.D(0, 0) <<  "\t" << cr_.D(0, 1) <<  "\t" << cr_.D(0, 2) <<  "\t"
95	<	<< cr_.D(1, 0) <<  "\t" << cr_.D(1, 1) <<  "\t" << cr_.D(1, 2) <<  "\t"
96	<	<< cr_.D(2, 0) <<  "\t" << cr_.D(2, 1) <<  "\t" << cr_.D(2, 2) <<  "\t";
94	>
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
101		//rotation-translation
102	<	os << cr_.D(0, 3) <<  "\t" << cr_.D(0, 4) <<  "\t" << cr_.D(0, 5) <<  "\t"
103	<	<< cr_.D(1, 3) <<  "\t" << cr_.D(1, 4) <<  "\t" << cr_.D(1, 5) <<  "\t"
104	<	<< cr_.D(2, 3) <<  "\t" << cr_.D(2, 4) <<  "\t" << cr_.D(2, 5) <<  "\t";
102	>	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
106		//translation-rotation
107	<	os << cr_.D(3, 0) <<  "\t" << cr_.D(3, 1) <<  "\t" << cr_.D(3, 2) <<  "\t"
108	<	<< cr_.D(4, 0) <<  "\t" << cr_.D(4, 1) <<  "\t" << cr_.D(4, 2) <<  "\t"
109	<	<< cr_.D(5, 0) <<  "\t" << cr_.D(5, 1) <<  "\t" << cr_.D(5, 2) <<  "\t";
107	>	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
111		//rotation
112	<	os << cr_.D(3, 3) <<  "\t" << cr_.D(3, 4) <<  "\t" << cr_.D(3, 5) <<  "\t"
113	<	<< cr_.D(4, 3) <<  "\t" << cr_.D(4, 4) <<  "\t" << cr_.D(4, 5) <<  "\t"
114	<	<< cr_.D(5, 3) <<  "\t" << cr_.D(5, 4) <<  "\t" << cr_.D(5, 5) <<  "\t";
112	>	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
116		//---------------------------------------------------------------------
117
118		//center of diffusion
119	<	os << cd_.center[0] <<  "\t" << cd_.center[1] <<  "\t" << cd_.center[2] <<  "\t";
119	>
120	>	center = cd_->getCOR();
121	>
122	>	os << center[0] <<  "\t" << center[1] <<  "\t" << center[2] <<  "\t";
123
124		//resistance tensor at center of diffusion
125		//translation
126	<	os << cd_.Xi(0, 0) <<  "\t" << cd_.Xi(0, 1) <<  "\t" << cd_.Xi(0, 2) <<  "\t"
127	<	<< cd_.Xi(1, 0) <<  "\t" << cd_.Xi(1, 1) <<  "\t" << cd_.Xi(1, 2) <<  "\t"
128	<	<< cd_.Xi(2, 0) <<  "\t" << cd_.Xi(2, 1) <<  "\t" << cd_.Xi(2, 2) <<  "\t";
126	>
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
133		//rotation-translation
134	<	os << cd_.Xi(0, 3) <<  "\t" << cd_.Xi(0, 4) <<  "\t" << cd_.Xi(0, 5) <<  "\t"
135	<	<< cd_.Xi(1, 3) <<  "\t" << cd_.Xi(1, 4) <<  "\t" << cd_.Xi(1, 5) <<  "\t"
136	<	<< cd_.Xi(2, 3) <<  "\t" << cd_.Xi(2, 4) <<  "\t" << cd_.Xi(2, 5) <<  "\t";
134	>	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
138		//translation-rotation
139	<	os << cd_.Xi(3, 0) <<  "\t" << cd_.Xi(3, 1) <<  "\t" << cd_.Xi(3, 2) <<  "\t"
140	<	<< cd_.Xi(4, 0) <<  "\t" << cd_.Xi(4, 1) <<  "\t" << cd_.Xi(4, 2) <<  "\t"
141	<	<< cd_.Xi(5, 0) <<  "\t" << cd_.Xi(5, 1) <<  "\t" << cd_.Xi(5, 2) <<  "\t";
139	>	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
143		//rotation
144	<	os << cd_.Xi(3, 3) <<  "\t" << cd_.Xi(3, 4) <<  "\t" << cd_.Xi(3, 5) <<  "\t"
145	<	<< cd_.Xi(4, 3) <<  "\t" << cd_.Xi(4, 4) <<  "\t" << cd_.Xi(4, 5) <<  "\t"
146	<	<< cd_.Xi(5, 3) <<  "\t" << cd_.Xi(5, 4) <<  "\t" << cd_.Xi(5, 5) <<  "\t";
144	>	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
148
149		//diffusion tensor at center of diffusion
150		//translation
151	<	os << cd_.D(0, 0) <<  "\t" << cd_.D(0, 1) <<  "\t" << cd_.D(0, 2) <<  "\t"
152	<	<< cd_.D(1, 0) <<  "\t" << cd_.D(1, 1) <<  "\t" << cd_.D(1, 2) <<  "\t"
153	<	<< cd_.D(2, 0) <<  "\t" << cd_.D(2, 1) <<  "\t" << cd_.D(2, 2) <<  "\t";
151	>
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
158		//rotation-translation
159	<	os << cd_.D(0, 3) <<  "\t" << cd_.D(0, 4) <<  "\t" << cd_.D(0, 5) <<  "\t"
160	<	<< cd_.D(1, 3) <<  "\t" << cd_.D(1, 4) <<  "\t" << cd_.D(1, 5) <<  "\t"
161	<	<< cd_.D(2, 3) <<  "\t" << cd_.D(2, 4) <<  "\t" << cd_.D(2, 5) <<  "\t";
159	>	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
163		//translation-rotation
164	<	os << cd_.D(3, 0) <<  "\t" << cd_.D(3, 1) <<  "\t" << cd_.D(3, 2) <<  "\t"
165	<	<< cd_.D(4, 0) <<  "\t" << cd_.D(4, 1) <<  "\t" << cd_.D(4, 2) <<  "\t"
166	<	<< cd_.D(5, 0) <<  "\t" << cd_.D(5, 1) <<  "\t" << cd_.D(5, 2) <<  "\t";
164	>	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
168		//rotation
169	<	os << cd_.D(3, 3) <<  "\t" << cd_.D(3, 4) <<  "\t" << cd_.D(3, 5) <<  "\t"
170	<	<< cd_.D(4, 3) <<  "\t" << cd_.D(4, 4) <<  "\t" << cd_.D(4, 5) <<  "\t"
171	<	<< cd_.D(5, 3) <<  "\t" << cd_.D(5, 4) <<  "\t" << cd_.D(5, 5) <<  "\n";
169	>	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
173		}
174

Comparing trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp (property svn:keywords):
Revision 972 by gezelter, Wed May 24 18:31:12 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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