--- trunk/src/selection/NameFinder.cpp 2005/12/02 15:38:03 770 +++ trunk/src/selection/NameFinder.cpp 2013/06/16 15:15:42 1879 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 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. @@ -37,13 +28,23 @@ * 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, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include "selection/NameFinder.hpp" #include "utils/wildcards.hpp" #include "utils/StringTokenizer.hpp" #include "primitives/Molecule.hpp" #include "utils/StringUtils.hpp" -namespace oopse { +namespace OpenMD { TreeNode::~TreeNode(){ std::map::iterator i; @@ -53,20 +54,17 @@ namespace oopse { children.clear(); } - NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){ nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(); loadNames(); } - NameFinder::~NameFinder(){ delete root_; } void NameFinder::loadNames() { - std::map::iterator foundIter; SimInfo::MoleculeIterator mi; Molecule* mol; Molecule::AtomIterator ai; @@ -78,7 +76,8 @@ namespace oopse { root_->bs.resize(nStuntDouble_); root_->bs.setAll(); // - for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { + for (mol = info_->beginMolecule(mi); mol != NULL; + mol = info_->nextMolecule(mi)) { std::string molName = mol->getMoleculeName(); TreeNode* currentMolNode = createNode(root_, molName); @@ -91,7 +90,8 @@ namespace oopse { currentAtomNode->bs.setBitOn(atom->getGlobalIndex()); } - for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { + for (rb = mol->beginRigidBody(rbIter); rb != NULL; + rb = mol->nextRigidBody(rbIter)) { std::string rbName = rb->getType(); TreeNode* currentRbNode = createNode(currentMolNode, rbName); @@ -105,11 +105,8 @@ namespace oopse { currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex()); } - } - - } - + } } TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) { @@ -127,8 +124,8 @@ namespace oopse { return node; } - OOPSEBitSet NameFinder::match(const std::string& name){ - OOPSEBitSet bs(nStuntDouble_); + OpenMDBitSet NameFinder::match(const std::string& name){ + OpenMDBitSet bs(nStuntDouble_); StringTokenizer tokenizer(name, "."); @@ -173,7 +170,7 @@ namespace oopse { return bs; } - void NameFinder::matchMolecule(const std::string& molName, OOPSEBitSet& bs) { + void NameFinder::matchMolecule(const std::string& molName, OpenMDBitSet& bs) { std::vector molNodes = getMatchedChildren(root_, molName); std::vector::iterator i; for( i = molNodes.begin(); i != molNodes.end(); ++i ) { @@ -181,7 +178,7 @@ namespace oopse { } } - void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OOPSEBitSet& bs){ + void NameFinder::matchStuntDouble(const std::string& molName, const std::string& sdName, OpenMDBitSet& bs){ std::vector molNodes = getMatchedChildren(root_, molName); std::vector::iterator i; for( i = molNodes.begin(); i != molNodes.end(); ++i ) { @@ -194,7 +191,7 @@ namespace oopse { } - void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OOPSEBitSet& bs){ + void NameFinder::matchRigidAtoms(const std::string& molName, const std::string& rbName, const std::string& rbAtomName, OpenMDBitSet& bs){ std::vector molNodes = getMatchedChildren(root_, molName); std::vector::iterator i; for( i = molNodes.begin(); i != molNodes.end(); ++i ) { @@ -225,17 +222,17 @@ namespace oopse { } bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) { - return Wildcard::wildcardfit (wildcard.c_str(), str.c_str()); + return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false; } - void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OOPSEBitSet& bs){ + void NameFinder::matchInternalIndex(const std::string& name, int internalIndex, OpenMDBitSet& bs){ - std::map::iterator foundIter; SimInfo::MoleculeIterator mi; Molecule* mol; - for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { + for (mol = info_->beginMolecule(mi); mol != NULL; + mol = info_->nextMolecule(mi)) { if (isMatched(mol->getMoleculeName(), name) ) { int natoms = mol->getNAtoms(); @@ -249,19 +246,15 @@ namespace oopse { bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex()); } } - - } - + } } - bool NameFinder::isInteger(const std::string str) { - for(int i =0; i < str.size(); ++i){ + bool NameFinder::isInteger(const std::string &str) { + for(unsigned int i = 0; i < str.size(); ++i){ if (!std::isdigit(str[i])) { return false; } } - return true; } - }