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root/OpenMD/branches/development/src/selection/NameFinder.cpp

Comparing:
trunk/src/selection/NameFinder.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/selection/NameFinder.cpp (file contents), Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 UTC

#	Line 36 | Line 36
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).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "selection/NameFinder.hpp"
43		#include "utils/wildcards.hpp"
#	Line 53 | Line 54 | namespace OpenMD {
54		children.clear();
55		}
56
56	–
57		NameFinder::NameFinder(SimInfo* info) : info_(info), root_(NULL){
58		nStuntDouble_ = info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies();
59		loadNames();
60		}
61
62	–
62		NameFinder::~NameFinder(){
63		delete root_;
64		}
#	Line 78 | Line 77 | namespace OpenMD {
77		root_->bs.resize(nStuntDouble_);
78		root_->bs.setAll(); //
79
80	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
80	>	for (mol = info_->beginMolecule(mi); mol != NULL;
81	>	mol = info_->nextMolecule(mi)) {
82
83		std::string molName = mol->getMoleculeName();
84		TreeNode* currentMolNode = createNode(root_, molName);
#	Line 91 | Line 91 | namespace OpenMD {
91		currentAtomNode->bs.setBitOn(atom->getGlobalIndex());
92		}
93
94	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
94	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
95	>	rb = mol->nextRigidBody(rbIter)) {
96		std::string rbName = rb->getType();
97		TreeNode* currentRbNode = createNode(currentMolNode, rbName);
98
#	Line 105 | Line 106 | namespace OpenMD {
106
107		currentRbAtomNode->bs.setBitOn(atom->getGlobalIndex());
108		}
108	–
109		}
110	<
111	<	}
112	<
110	>	}
111		}
112
113		TreeNode* NameFinder::createNode(TreeNode* parent, const std::string& name) {
#	Line 225 | Line 223 | namespace OpenMD {
223		}
224
225		bool NameFinder::isMatched(const std::string& str, const std::string& wildcard) {
226	<	return Wildcard::wildcardfit (wildcard.c_str(), str.c_str());
226	>	return Wildcard::wildcardfit(wildcard.c_str(), str.c_str()) > 0 ? true : false;
227		}
228
229
#	Line 235 | Line 233 | namespace OpenMD {
233		SimInfo::MoleculeIterator mi;
234		Molecule* mol;
235
236	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
236	>	for (mol = info_->beginMolecule(mi); mol != NULL;
237	>	mol = info_->nextMolecule(mi)) {
238
239		if (isMatched(mol->getMoleculeName(), name) ) {
240		int natoms = mol->getNAtoms();
#	Line 249 | Line 248 | namespace OpenMD {
248		bs.setBitOn(mol->getRigidBodyAt(internalIndex - natoms)->getGlobalIndex());
249		}
250		}
251	<
253	<	}
254	<
251	>	}
252		}
253
254		bool NameFinder::isInteger(const std::string str) {
255	<	for(int i =0; i < str.size(); ++i){
255	>	for(unsigned int i = 0; i < str.size(); ++i){
256		if (!std::isdigit(str[i])) {
257		return false;
258		}
259		}
263	–
260		return true;
261		}
266	–
262		}

Comparing:
trunk/src/selection/NameFinder.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/selection/NameFinder.cpp (property svn:keywords), Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 UTC

#	Line 0 | Line 1
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