| 6 |
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* 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 |
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* distribution. |
| 28 |
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* 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
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#include "selection/NameFinder.hpp" |
| 43 |
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#include "utils/wildcards.hpp" |
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#include "utils/StringTokenizer.hpp" |
| 45 |
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#include "primitives/Molecule.hpp" |
| 46 |
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#include "utils/StringUtils.hpp" |
| 47 |
< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
| 49 |
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TreeNode::~TreeNode(){ |
| 50 |
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std::map<std::string, TreeNode*>::iterator i; |
| 54 |
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children.clear(); |
| 55 |
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} |
| 56 |
|
|
| 56 |
– |
|
| 57 |
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NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){ |
| 58 |
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nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); |
| 59 |
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loadNames(); |
| 60 |
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} |
| 61 |
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|
| 62 |
– |
|
| 62 |
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NameFinder::~NameFinder(){ |
| 63 |
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delete root_; |
| 64 |
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} |
| 65 |
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|
| 66 |
|
void NameFinder::loadNames() { |
| 67 |
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|
| 69 |
– |
std::map<std::string, TreeNode*>::iterator foundIter; |
| 68 |
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SimInfo::MoleculeIterator mi; |
| 69 |
|
Molecule* mol; |
| 70 |
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Molecule::AtomIterator ai; |
| 76 |
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root_->bs.resize(nStuntDouble_); |
| 77 |
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root_->bs.setAll(); // |
| 78 |
|
|
| 79 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 79 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 80 |
> |
mol = info_->nextMolecule(mi)) { |
| 81 |
|
|
| 82 |
|
std::string molName = mol->getMoleculeName(); |
| 83 |
|
TreeNode* currentMolNode = createNode(root_, molName); |
| 90 |
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currentAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
| 91 |
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} |
| 92 |
|
|
| 93 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 93 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 94 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 95 |
|
std::string rbName = rb->getType(); |
| 96 |
|
TreeNode* currentRbNode = createNode(currentMolNode, rbName); |
| 97 |
|
|
| 105 |
|
|
| 106 |
|
currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex()); |
| 107 |
|
} |
| 108 |
– |
|
| 108 |
|
} |
| 109 |
< |
|
| 111 |
< |
} |
| 112 |
< |
|
| 109 |
> |
} |
| 110 |
|
} |
| 111 |
|
|
| 112 |
|
TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) { |
| 124 |
|
return node; |
| 125 |
|
} |
| 126 |
|
|
| 127 |
< |
BitSet NameFinder::match(const std::string& name){ |
| 128 |
< |
BitSet bs(nStuntDouble_); |
| 127 |
> |
OpenMDBitSet NameFinder::match(const std::string& name){ |
| 128 |
> |
OpenMDBitSet bs(nStuntDouble_); |
| 129 |
|
|
| 130 |
|
StringTokenizer tokenizer(name, "."); |
| 131 |
|
|
| 170 |
|
return bs; |
| 171 |
|
} |
| 172 |
|
|
| 173 |
< |
void NameFinder::matchMolecule(const std::string& molName, BitSet& bs) { |
| 173 |
> |
void NameFinder::matchMolecule(const std::string& molName, OpenMDBitSet& bs) { |
| 174 |
|
std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
| 175 |
|
std::vector<TreeNode*>::iterator i; |
| 176 |
|
for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
| 178 |
|
} |
| 179 |
|
} |
| 180 |
|
|
| 181 |
< |
void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, BitSet& bs){ |
| 181 |
> |
void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OpenMDBitSet& bs){ |
| 182 |
|
std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
| 183 |
|
std::vector<TreeNode*>::iterator i; |
| 184 |
|
for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
| 191 |
|
|
| 192 |
|
} |
| 193 |
|
|
| 194 |
< |
void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, BitSet& bs){ |
| 194 |
> |
void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& bs){ |
| 195 |
|
std::vector<TreeNode*> molNodes = getMatchedChildren(root_, molName); |
| 196 |
|
std::vector<TreeNode*>::iterator i; |
| 197 |
|
for( i = molNodes.begin(); i != molNodes.end(); ++i ) { |
| 222 |
|
} |
| 223 |
|
|
| 224 |
|
bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) { |
| 225 |
< |
return Wildcard::wildcardfit (wildcard.c_str(), str.c_str()); |
| 225 |
> |
return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false; |
| 226 |
|
} |
| 227 |
|
|
| 228 |
|
|
| 229 |
< |
void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, BitSet& bs){ |
| 229 |
> |
void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs){ |
| 230 |
|
|
| 234 |
– |
std::map<std::string, TreeNode*>::iterator foundIter; |
| 231 |
|
SimInfo::MoleculeIterator mi; |
| 232 |
|
Molecule* mol; |
| 233 |
|
|
| 234 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 234 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 235 |
> |
mol = info_->nextMolecule(mi)) { |
| 236 |
|
|
| 237 |
|
if (isMatched(mol->getMoleculeName(), name) ) { |
| 238 |
|
int natoms = mol->getNAtoms(); |
| 246 |
|
bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex()); |
| 247 |
|
} |
| 248 |
|
} |
| 249 |
< |
|
| 253 |
< |
} |
| 254 |
< |
|
| 249 |
> |
} |
| 250 |
|
} |
| 251 |
|
|
| 252 |
< |
bool NameFinder::isInteger(const std::string str) { |
| 253 |
< |
for(int i =0; i < str.size(); ++i){ |
| 252 |
> |
bool NameFinder::isInteger(const std::string &str) { |
| 253 |
> |
for(unsigned int i = 0; i < str.size(); ++i){ |
| 254 |
|
if (!std::isdigit(str[i])) { |
| 255 |
|
return false; |
| 256 |
|
} |
| 257 |
|
} |
| 263 |
– |
|
| 258 |
|
return true; |
| 259 |
|
} |
| 266 |
– |
|
| 260 |
|
} |
