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/ApproximationModel.hpp"
#include "applications/hydrodynamics/CompositeShape.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) const {
      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 ApproximationModel {
  public:
    RoughShell(StuntDouble* sd, SimInfo* info);
    virtual ~RoughShell() { delete shape_;}
    void setSigma(RealType sigma) {sigma_ = sigma;}
    RealType getSigma() {return sigma_;}
  private:
    virtual bool createBeads(std::vector<BeadParam>& beads);
    //StuntDoubleShape sdShape_;
    RealType sigma_;
    Shape* shape_;
  };
  
}
#endif
Revision:	2768
Committed:	Wed May 24 18:31:12 2006 UTC (18 years, 1 month ago) by gezelter
File size:	4481 byte(s)
Log Message:	fixes for Hydrodynamics
#	Content
1	/*
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/ApproximationModel.hpp"
45	#include "applications/hydrodynamics/CompositeShape.hpp"
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) const {
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 ApproximationModel {
114	public:
115	RoughShell(StuntDouble* sd, SimInfo* info);
116	virtual ~RoughShell() { delete shape_;}
117	void setSigma(RealType sigma) {sigma_ = sigma;}
118	RealType getSigma() {return sigma_;}
119	private:
120	virtual bool createBeads(std::vector<BeadParam>& beads);
121	//StuntDoubleShape sdShape_;
122	RealType sigma_;
123	Shape* shape_;
124	};
125
126	}
127	#endif