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Comparing trunk/src/selection/NameFinder.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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   #include "selection/NameFinder.hpp"
42   #include "utils/wildcards.hpp"
43   #include "utils/StringTokenizer.hpp"
44   #include "primitives/Molecule.hpp"
45   #include "utils/StringUtils.hpp"
46 < namespace oopse {
46 > namespace OpenMD {
47  
48    TreeNode::~TreeNode(){
49      std::map<std::string, TreeNode*>::iterator i;
# Line 127 | Line 127 | namespace oopse {
127      return node;
128    }
129  
130 <  OOPSEBitSet NameFinder::match(const std::string& name){
131 <    OOPSEBitSet bs(nStuntDouble_);
130 >  OpenMDBitSet NameFinder::match(const std::string& name){
131 >    OpenMDBitSet bs(nStuntDouble_);
132    
133      StringTokenizer tokenizer(name, ".");
134  
# Line 173 | Line 173 | namespace oopse {
173      return bs;
174    }
175  
176 <  void NameFinder::matchMolecule(const std::string& molName, OOPSEBitSet& bs) {
176 >  void NameFinder::matchMolecule(const std::string& molName, OpenMDBitSet& bs) {
177      std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
178      std::vector<TreeNode*>::iterator i;
179      for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
# Line 181 | Line 181 | namespace oopse {
181      }    
182    }
183  
184 <  void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OOPSEBitSet& bs){
184 >  void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OpenMDBitSet& bs){
185      std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
186      std::vector<TreeNode*>::iterator i;
187      for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
# Line 194 | Line 194 | namespace oopse {
194  
195    }
196  
197 <  void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OOPSEBitSet& bs){
197 >  void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& bs){
198      std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName);            
199      std::vector<TreeNode*>::iterator i;
200      for( i = molNodes.begin(); i != molNodes.end(); ++i ) {
# Line 229 | Line 229 | namespace oopse {
229    }
230  
231  
232 <  void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OOPSEBitSet& bs){
232 >  void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs){
233  
234      std::map<std::string, TreeNode*>::iterator foundIter;
235      SimInfo::MoleculeIterator mi;

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