ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp (file contents):
Revision 906 by tim, Fri Mar 17 23:20:35 2006 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 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, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41		#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
42	<	#include "applications/hydrodynamics/Spheric.hpp"
43	<	#include "applications/hydrodynamics/Ellipsoid.hpp"
42	>	#include "hydrodynamics/Shape.hpp"
43	>	#include "hydrodynamics/Sphere.hpp"
44	>	#include "hydrodynamics/Ellipsoid.hpp"
45		#include "applications/hydrodynamics/CompositeShape.hpp"
46
47	<	namespace oopse {
48	<
49	<	bool HydrodynamicsModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) {
47	>	namespace OpenMD {
48	>
49	>	bool HydrodynamicsModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) {
50		return false;
51	<	}
51	>	}
52	>
53	>	void HydrodynamicsModel::writeHydroProps(std::ostream& os) {
54
55	<	bool HydrodynamicsModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) {
56	<	return false;
54	<	}
55	<
56	<	bool HydrodynamicsModel::calcHydroProps(CompositeShape* compositexShape, double viscosity, double temperature) {
57	<	return false;
58	<	}
59	<
60	<	void HydrodynamicsModel::writeHydroProps(std::ostream& os) {
61	<
55	>	Vector3d center;
56	>	Mat6x6d Xi, D;
57
58		os << sd_->getType() << "\t";
59
60		//center of resistance
66	–	os << cr_.center[0] <<  "\t" << cr_.center[1] <<  "\t" << cr_.center[2] <<  "\t";
61
62	+	center = cr_->getCOR();
63	+
64	+	os << center[0] <<  "\t" << center[1] <<  "\t" << center[2] <<  "\t";
65	+
66		//resistance tensor at center of resistance
67		//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";
68
69	<	//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";
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	+
75	+	//rotation-translation
76	+	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	+
80		//translation-rotation
81	<	os << cr_.Xi(3, 0) <<  "\t" << cr_.Xi(3, 1) <<  "\t" << cr_.Xi(3, 2) <<  "\t"
82	<	<< cr_.Xi(4, 0) <<  "\t" << cr_.Xi(4, 1) <<  "\t" << cr_.Xi(4, 2) <<  "\t"
83	<	<< cr_.Xi(5, 0) <<  "\t" << cr_.Xi(5, 1) <<  "\t" << cr_.Xi(5, 2) <<  "\t";
84	<
81	>	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	>
85		//rotation
86	<	os << cr_.Xi(3, 3) <<  "\t" << cr_.Xi(3, 4) <<  "\t" << cr_.Xi(3, 5) <<  "\t"
87	<	<< cr_.Xi(4, 3) <<  "\t" << cr_.Xi(4, 4) <<  "\t" << cr_.Xi(4, 5) <<  "\t"
88	<	<< cr_.Xi(5, 3) <<  "\t" << cr_.Xi(5, 4) <<  "\t" << cr_.Xi(5, 5) <<  "\t";
89	<
90	<
86	>	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	>
90	>
91		//diffusion tensor at center of resistance
92		//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";
93
94	<	//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";
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	+
100	+	//rotation-translation
101	+	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	+
105		//translation-rotation
106	<	os << cr_.D(3, 0) <<  "\t" << cr_.D(3, 1) <<  "\t" << cr_.D(3, 2) <<  "\t"
107	<	<< cr_.D(4, 0) <<  "\t" << cr_.D(4, 1) <<  "\t" << cr_.D(4, 2) <<  "\t"
108	<	<< cr_.D(5, 0) <<  "\t" << cr_.D(5, 1) <<  "\t" << cr_.D(5, 2) <<  "\t";
109	<
106	>	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	>
110		//rotation
111	<	os << cr_.D(3, 3) <<  "\t" << cr_.D(3, 4) <<  "\t" << cr_.D(3, 5) <<  "\t"
112	<	<< cr_.D(4, 3) <<  "\t" << cr_.D(4, 4) <<  "\t" << cr_.D(4, 5) <<  "\t"
113	<	<< cr_.D(5, 3) <<  "\t" << cr_.D(5, 4) <<  "\t" << cr_.D(5, 5) <<  "\t";
114	<
111	>	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	>
115		//---------------------------------------------------------------------
116	<
116	>
117		//center of diffusion
114	–	os << cd_.center[0] <<  "\t" << cd_.center[1] <<  "\t" << cd_.center[2] <<  "\t";
118
119	+	center = cd_->getCOR();
120	+
121	+	os << center[0] <<  "\t" << center[1] <<  "\t" << center[2] <<  "\t";
122	+
123		//resistance tensor at center of diffusion
124		//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";
125
126	<	//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	>	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	+
132	+	//rotation-translation
133	+	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	+
137		//translation-rotation
138	<	os << cd_.Xi(3, 0) <<  "\t" << cd_.Xi(3, 1) <<  "\t" << cd_.Xi(3, 2) <<  "\t"
139	<	<< cd_.Xi(4, 0) <<  "\t" << cd_.Xi(4, 1) <<  "\t" << cd_.Xi(4, 2) <<  "\t"
140	<	<< cd_.Xi(5, 0) <<  "\t" << cd_.Xi(5, 1) <<  "\t" << cd_.Xi(5, 2) <<  "\t";
141	<
138	>	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	>
142		//rotation
143	<	os << cd_.Xi(3, 3) <<  "\t" << cd_.Xi(3, 4) <<  "\t" << cd_.Xi(3, 5) <<  "\t"
144	<	<< cd_.Xi(4, 3) <<  "\t" << cd_.Xi(4, 4) <<  "\t" << cd_.Xi(4, 5) <<  "\t"
145	<	<< cd_.Xi(5, 3) <<  "\t" << cd_.Xi(5, 4) <<  "\t" << cd_.Xi(5, 5) <<  "\t";
146	<
147	<
143	>	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	>
147	>
148		//diffusion tensor at center of diffusion
149		//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";
150
151	<	//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";
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	+
157	+	//rotation-translation
158	+	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	+
162		//translation-rotation
163	<	os << cd_.D(3, 0) <<  "\t" << cd_.D(3, 1) <<  "\t" << cd_.D(3, 2) <<  "\t"
164	<	<< cd_.D(4, 0) <<  "\t" << cd_.D(4, 1) <<  "\t" << cd_.D(4, 2) <<  "\t"
165	<	<< cd_.D(5, 0) <<  "\t" << cd_.D(5, 1) <<  "\t" << cd_.D(5, 2) <<  "\t";
166	<
163	>	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	>
167		//rotation
168	<	os << cd_.D(3, 3) <<  "\t" << cd_.D(3, 4) <<  "\t" << cd_.D(3, 5) <<  "\t"
169	<	<< cd_.D(4, 3) <<  "\t" << cd_.D(4, 4) <<  "\t" << cd_.D(4, 5) <<  "\t"
170	<	<< cd_.D(5, 3) <<  "\t" << cd_.D(5, 4) <<  "\t" << cd_.D(5, 5) <<  "\n";
171	<
172	<
168	>	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	>
172	>	}
173	>
174		}
161	–
162	–	}

Comparing trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp (property svn:keywords):
Revision 906 by tim, Fri Mar 17 23:20:35 2006 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines