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

Comparing trunk/src/applications/hydrodynamics/RoughShell.hpp (file contents):
Revision 898 by tim, Wed Mar 15 15:51:44 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_ROUGHSHELL_HPP
43		#define APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP
44
45	<	#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
45	>	#include "applications/hydrodynamics/ApproximationModel.hpp"
46	>	#include "applications/hydrodynamics/CompositeShape.hpp"
47	>	#include "utils/Grid3d.hpp"
48
49	<	namespace oopse {
50	<	/**
51	<	* @class Grid3d
52	<	* A generic 3d grid class
53	<	*/
54	<	template<class Elem>
55	<	class Grid3D {
56	<	public:
57	<	Grid3D(unsigned int dim1, unsigned int dim2, unsigned int dim3) : dim1_(dim1), dim2_(dim2), dim3_(dim3) {
58	<	data_.resize(dim1_*dim2_*dim3_);
59	<	}
60	<	Elem& operator ()(unsigned int i, unsigned int j, unsigned int k) {
61	<	int index = isValidGrid(i, j , k);
62	<	assert(index != -1);
63	<	return data_[index];
61	<	}
62	<
63	<	const Elem& operator () (unsigned int i, unsigned int j, unsigned int k) const {
64	<	int index = isValidGrid(i, j , k);
65	<	assert(index != -1);
66	<	return data_[index];
67	<	}
68	<
69	<	std::vector<Elem> getAllNeighbors(unsigned int i, unsigned int j, unsigned int k) {
70	<	std::vector<Elem> result;
71	<	int index;
72	<	index = isValidGrid(i-1, j, k);
73	<	if (index != -1)
74	<	result.push_back(data_[index]);
75	<
76	<	index = isValidGrid(i+1, j, k);
77	<	if (index != -1)
78	<	result.push_back(data_[index]);
79	<
80	<	index = isValidGrid(i, j-1, k);
81	<	if (index != -1)
82	<	result.push_back(data_[index]);
83	<
84	<	index = isValidGrid(i, j+1, k);
85	<	if (index != -1)
86	<	result.push_back(data_[index]);
87	<
88	<	index = isValidGrid(i, j, k-1);
89	<	if (index != -1)
90	<	result.push_back(data_[index]);
91	<
92	<	index = isValidGrid(i, j, k+1);
93	<	if (index != -1)
94	<	result.push_back(data_[index]);
95	<
96	<	return result;
97	<	}
98	<	private:
99	<
100	<	int isValidGrid(unsigned int i, unsigned int j, unsigned int k) {
101	<	int index = i * dim2_*dim3_ + j * dim3_ + k;
102	<	return index < data_.size() ? index : -1;
103	<	};
104	<
105	<	unsigned int dim1_;
106	<	unsigned int dim2_;
107	<	unsigned int dim3_;
108	<	std::vector<Elem> data_;
109	<
110	<	};
111	<
112	<
113	<	class RoughShell : public HydrodynamicsModel {
114	<	public:
115	<	RoughShell(StuntDouble* sd, const DynamicProperty& extraParams);
116	<	private:
117	<	virtual bool createBeads(std::vector<BeadParam>& beads);
118	<	StuntDoubleShape sdShape_;
119	<	double sigma_;
120	<	};
121	<
49	>	namespace OpenMD {
50	>
51	>	class RoughShell : public ApproximationModel {
52	>	public:
53	>	RoughShell(StuntDouble* sd, SimInfo* info);
54	>	virtual ~RoughShell() { delete shape_;}
55	>	void setSigma(RealType sigma) {sigma_ = sigma;}
56	>	RealType getSigma() {return sigma_;}
57	>	private:
58	>	virtual bool createBeads(vector<BeadParam>& beads);
59	>	//StuntDoubleShape sdShape_;
60	>	RealType sigma_;
61	>	Shape* shape_;
62	>	};
63	>
64		}
65		#endif

Comparing trunk/src/applications/hydrodynamics/RoughShell.hpp (property svn:keywords):
Revision 898 by tim, Wed Mar 15 15:51:44 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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