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Comparing:
trunk/src/selection/NameFinder.hpp (file contents), Revision 288 by tim, Fri Feb 4 22:39:26 2005 UTC vs.
branches/development/src/selection/NameFinder.hpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41   #ifndef SELECTION_NAMEFINDER_HPP
42   #define SELECTION_NAMEFINDER_HPP
# Line 44 | Line 44
44   #include <string>
45   #include <map>
46   #include "brains/SimInfo.hpp"
47 < #include "utils/BitSet.hpp"
48 < namespace oopse {
47 > #include "utils/OpenMDBitSet.hpp"
48 > namespace OpenMD {
49  
50 < class TreeNode{
51 <    public:
52 <        ~TreeNode();
53 <        std::string name;
54 <        BitSet bs;
55 <        std::map<std::string, TreeNode*> children;
56 < };
50 >  class TreeNode{
51 >  public:
52 >    ~TreeNode();
53 >    std::string name;
54 >    OpenMDBitSet bs;
55 >    std::map<std::string, TreeNode*> children;
56 >  };
57  
58 < class NameFinder{
59 <    public:
60 <        NameFinder(SimInfo* info);
61 <        ~NameFinder();
62 <        BitSet  match(const std::string& name);
58 >  class NameFinder{
59 >  public:
60 >    NameFinder(SimInfo* info);
61 >    ~NameFinder();
62 >    OpenMDBitSet  match(const std::string& name);
63  
64 <    private:
65 <        void loadNames();
66 <        void matchMolecule(const std::string& molName, BitSet& bs);
67 <        void matchStuntDouble(const std::string& molName, const std::string& sdName, BitSet& bs);
68 <        void matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& bs);
64 >  private:
65 >    void loadNames();
66 >    void matchMolecule(const std::string& molName, OpenMDBitSet& bs);
67 >    void matchStuntDouble(const std::string& molName, const std::string& sdName, OpenMDBitSet& bs);
68 >    void matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& bs);
69  
70 <        TreeNode* createNode(TreeNode* parent, const std::string& name);
71 <        std::vector<TreeNode*> getMatchedChildren(TreeNode* node, const std::string& name);
72 <        bool isMatched(const std::string& str, const std::string& wildcard);
70 >    void matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs);
71  
72 <        SimInfo* info_;
73 <        int nStuntDouble_;
74 <        TreeNode* root_;
77 < };
72 >    TreeNode* createNode(TreeNode* parent, const std::string& name);
73 >    std::vector<TreeNode*> getMatchedChildren(TreeNode* node, const std::string& name);
74 >    bool isMatched(const std::string& str, const std::string& wildcard);
75  
76 +    bool isInteger(const std::string str);
77  
78 +    SimInfo* info_;
79 +    int nStuntDouble_;
80 +    TreeNode* root_;
81 +  };
82 +
83 +
84   }
85   #endif

Comparing:
trunk/src/selection/NameFinder.hpp (property svn:keywords), Revision 288 by tim, Fri Feb 4 22:39:26 2005 UTC vs.
branches/development/src/selection/NameFinder.hpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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