| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
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* |
| 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 |
< |
* |
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* 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 |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
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* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
+ |
* |
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+ |
* 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). |
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*/ |
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#include "selection/NameFinder.hpp" |
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#include "utils/wildcards.hpp" |
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#include "utils/StringTokenizer.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/StringUtils.hpp" |
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
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TreeNode::~TreeNode(){ |
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std::map<std::string, TreeNode*>::iterator i; |
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return node; |
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} |
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|
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BitSet NameFinder::match(const std::string& name){ |
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BitSet bs(nStuntDouble_); |
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> |
OpenMDBitSet NameFinder::match(const std::string& name){ |
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> |
OpenMDBitSet bs(nStuntDouble_); |
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|
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StringTokenizer tokenizer(name, "."); |
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|
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return bs; |
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} |
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|
| 176 |
< |
void NameFinder::matchMolecule(const std::string& molName, BitSet& bs) { |
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> |
void NameFinder::matchMolecule(const std::string& molName, OpenMDBitSet& bs) { |
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std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
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std::vector<TreeNode*>::iterator i; |
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for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
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} |
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} |
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|
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< |
void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, BitSet& bs){ |
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> |
void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OpenMDBitSet& bs){ |
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std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
| 186 |
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std::vector<TreeNode*>::iterator i; |
| 187 |
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for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
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|
| 195 |
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} |
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|
|
| 197 |
< |
void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& bs){ |
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> |
void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& bs){ |
| 198 |
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std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
| 199 |
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std::vector<TreeNode*>::iterator i; |
| 200 |
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for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
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} |
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|
| 231 |
|
|
| 232 |
< |
void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, BitSet& bs){ |
| 232 |
> |
void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs){ |
| 233 |
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|
| 234 |
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std::map<std::string, TreeNode*>::iterator foundIter; |
| 235 |
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SimInfo::MoleculeIterator mi; |
