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

Comparing trunk/src/applications/hydrodynamics/HydrodynamicsModel.hpp (file contents):
Revision 892 by tim, Thu Feb 23 23:16:43 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		#ifndef APPLICATION_HYDRODYNAMICS_HYDRODYNAMICSMODEL_HPP
43		#define APPLICATION_HYDRODYNAMICS_HYDRODYNAMICSMODEL_HPP
#	Line 46 | Line 47
47		#include "math/SquareMatrix3.hpp"
48		#include "math/DynamicRectMatrix.hpp"
49		#include "primitives/Molecule.hpp"
50	<	#include "applications/hydrodynamics/StuntDoubleShape.hpp"
51	<	#include "utils/any.hpp"
51	<	namespace oopse {
52	<	struct HydrodynamicProps {
53	<	Vector3d diffCenter;
54	<	Mat3x3d transDiff;
55	<	Mat3x3d rotDiff;
56	<	Mat3x3d transRotDiff;
57	<	};
50	>	#include "hydrodynamics/HydroProp.hpp"
51	>	#include "utils/PhysicalConstants.hpp"
52
53	<	struct BeadParam {
53	>	namespace OpenMD {
54	>
55	>	struct BeadParam {
56		std::string atomName;
57		Vector3d pos;
58	<	double radius;
59	<	};
58	>	RealType radius;
59	>	};
60	>
61	>	class Shape;
62	>	class Sphere;
63	>	class Ellipsoid;
64	>	class CompositeShape;
65	>
66	>	class HydrodynamicsModel {
67	>	public:
68	>	HydrodynamicsModel(StuntDouble* sd, SimInfo* info) : sd_(sd), info_(info) {}
69	>	virtual ~HydrodynamicsModel() {}
70
71	<	typedef std::map<std::string, boost::any> DynamicProperty;
72	<
73	<	class HydrodynamicsModel {
74	<	public:
75	<	HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams);
76	<	bool calcHydrodyanmicsProps();
77	<
78	<	Vector3d getDiffCenter();
79	<	Mat3x3d getTransDiff();
80	<	Mat3x3d getRotDiff();
81	<	Mat3x3d getTransRotDiff();
82	<	void writeBeads(std::ostream& os);
83	<	void writeDiffCenterAndDiffTensor(std::ostream& os);
84	<	protected:
85	<	StuntDouble* sd_;
86	<	private:
87	<	virtual bool createBeads(std::vector<BeadParam>& beads) = 0;
88	<
89	<
90	<	HydrodynamicProps props_;
85	<	std::vector<BeadParam> beads_;
86	<	double viscosity_;
87	<	double temperature_;
88	<
89	<	};
90	<
91	<
71	>	virtual bool calcHydroProps(Shape* shape, RealType viscosity, RealType temperature);
72	>
73	>	virtual void init() {};
74	>	virtual void writeBeads(std::ostream& os) = 0;
75	>	void writeHydroProps(std::ostream& os);
76	>	HydroProp* getHydroPropsAtCR() {return cr_;}
77	>	HydroProp* getHydroPropsAtCD() {return cd_;}
78	>
79	>	void setCR(HydroProp* cr) {cr_ = cr;}
80	>	void setCD(HydroProp* cd) {cd_ = cd;}
81	>	std::string getStuntDoubleName() { return sd_->getType();}
82	>	protected:
83	>	StuntDouble* sd_;
84	>	SimInfo* info_;
85	>	private:
86	>	HydroProp* cr_;
87	>	HydroProp* cd_;
88	>	std::vector<BeadParam> beads_;
89	>	};
90	>
91		}
92
93		#endif

Comparing trunk/src/applications/hydrodynamics/HydrodynamicsModel.hpp (property svn:keywords):
Revision 892 by tim, Thu Feb 23 23:16:43 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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