applications/hydrodynamics/RoughShell.hpp

/*
 * 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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
#ifndef APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP
#define APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP

#include "applications/hydrodynamics/HydrodynamicsModel.hpp"

namespace oopse {
/**
 * @class Grid3d
 * A generic 3d grid class
 */
template<class Elem>
class Grid3D {
    public:
        Grid3D(unsigned int dim1, unsigned int dim2, unsigned int dim3) : dim1_(dim1), dim2_(dim2), dim3_(dim3) {
            data_.resize(dim1_*dim2_*dim3_);
        }
        Elem& operator ()(unsigned int i, unsigned int j, unsigned int k) {
            int index = isValidGrid(i, j , k);
            assert(index != -1);
            return data_[index];
        }

        const Elem& operator () (unsigned int i, unsigned int j, unsigned int k) const {
            int index = isValidGrid(i, j , k);
            assert(index != -1);
            return data_[index];
        }
        
        std::vector<Elem> getAllNeighbors(unsigned int i, unsigned int j, unsigned int k) {
            std::vector<Elem> result;
            int index;
            index = isValidGrid(i-1, j, k);
            if (index != -1)
                result.push_back(data_[index]);

            index = isValidGrid(i+1, j, k);
            if (index != -1)
                result.push_back(data_[index]);

            index = isValidGrid(i, j-1, k);
            if (index != -1)
                result.push_back(data_[index]);

            index = isValidGrid(i, j+1, k);
            if (index != -1)
                result.push_back(data_[index]);

            index = isValidGrid(i, j, k-1);
            if (index != -1)
                result.push_back(data_[index]);

            index = isValidGrid(i, j, k+1);
            if (index != -1)
                result.push_back(data_[index]);

            return result;
        }
    private:

        int isValidGrid(unsigned int i, unsigned int j, unsigned int k) {
            int index = i * dim2_*dim3_ + j * dim3_ + k;
            return index < data_.size() ? index : -1;
        };
        
        unsigned int dim1_;
        unsigned int dim2_;
        unsigned int dim3_;
        std::vector<Elem> data_;

};
    
    
class RoughShell : public HydrodynamicsModel {
    public:
        RoughShell(StuntDouble* sd, const DynamicProperty& extraParams);
    private:
        virtual bool createBeads(std::vector<BeadParam>& beads);
        StuntDoubleShape sdShape_;
        double sigma_;
};

}
#endif
Revision:	2623
Committed:	Wed Mar 15 15:51:44 2006 UTC (18 years, 5 months ago) by tim
File size:	4496 byte(s)
Log Message:	Adding RoughShell and BeadModel
#	User	Rev	Content
1	tim	2623	/*
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			* 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41			#ifndef APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP
42			#define APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP
43
44			#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
45
46			namespace oopse {
47			/**
48			* @class Grid3d
49			* A generic 3d grid class
50			*/
51			template<class Elem>
52			class Grid3D {
53			public:
54			Grid3D(unsigned int dim1, unsigned int dim2, unsigned int dim3) : dim1_(dim1), dim2_(dim2), dim3_(dim3) {
55			data_.resize(dim1_dim2_dim3_);
56			}
57			Elem& operator ()(unsigned int i, unsigned int j, unsigned int k) {
58			int index = isValidGrid(i, j , k);
59			assert(index != -1);
60			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
122			}
123			#endif