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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
#ifndef APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP
#define APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP

#include "applications/hydrodynamics/ApproximationModel.hpp"
#include "applications/hydrodynamics/CompositeShape.hpp"
namespace OpenMD {
  /**
   * @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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 10 months ago) by chuckv
File size:	4523 byte(s)
Log Message:	Creating busticated version of OpenMD
#	User	Rev	Content
1	tim	898	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	898	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	898	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1390	*
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	tim	898	*/
41			#ifndef APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP
42			#define APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP
43
44	tim	906	#include "applications/hydrodynamics/ApproximationModel.hpp"
45			#include "applications/hydrodynamics/CompositeShape.hpp"
46	gezelter	1390	namespace OpenMD {
47	gezelter	972	/**
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	tim	898
63	gezelter	972	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	tim	898
69	gezelter	972	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	tim	898	}
127			#endif